Pioneer Award Program Publications

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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title	Author	Journal Name	PubMedID	Journal Abbreviation	Publication Date	PubMedLink
Glycolysis-Independent Glucose Metabolism Distinguishes TE from ICM Fate during Mammalian Embryogenesis.	Chi F, Sharpley MS, Nagaraj R, Roy SS, Banerjee U	Developmental cell	32197068	Dev Cell	2020 Apr 6	https://www.ncbi.nlm.nih.gov/pubmed/32197068
Metabolic plasticity drives development during mammalian embryogenesis.	Sharpley MS, Chi F, Hoeve JT, Banerjee U	Developmental cell	34428399	Dev Cell	2021 Aug 23	https://www.ncbi.nlm.nih.gov/pubmed/34428399
Regulated noise in the epigenetic landscape of development and disease.	Pujadas E, Feinberg AP	Cell	22424224	Cell	2012 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/22424224
Reversible switching between epigenetic states in honeybee behavioral subcastes.	Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP	Nature neuroscience	22983211	Nat Neurosci	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22983211
Minimal requirements for inhibition of MraY by lysis protein E from bacteriophage ΦX174.	Tanaka S, Clemons WM Jr	Molecular microbiology	22742425	Mol Microbiol	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22742425
The glove-like structure of the conserved membrane protein TatC provides insight into signal sequence recognition in twin-arginine translocation.	Ramasamy S, Abrol R, Suloway CJ, Clemons WM Jr	Structure (London, England : 1993)	23583035	Structure	2013 May 7	https://www.ncbi.nlm.nih.gov/pubmed/23583035
The evolution of bacterial mechanosensitive channels.	Booth IR, Miller S, Müller A, Lehtovirta-Morley L	Cell calcium	25591932	Cell Calcium	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25591932
Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq.	Cadwell CR, Scala F, Li S, Livrizzi G, Shen S, Sandberg R, Jiang X, Tolias AS	Nature protocols	29189773	Nat Protoc	2017 Dec	https://www.ncbi.nlm.nih.gov/pubmed/29189773
On the Structure of Neuronal Population Activity under Fluctuations in Attentional State.	Ecker AS, Denfield GH, Bethge M, Tolias AS	The Journal of neuroscience : the official journal of the Society for Neuroscience	26843656	J Neurosci	2016 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/26843656
Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex.	Cadwell CR, Scala F, Fahey PG, Kobak D, Mulherkar S, Sinz FH, Papadopoulos S, Tan ZH, Johnsson P, Hartmanis L, Li S, Cotton RJ, Tolias KF, Sandberg R, Berens P, Jiang X, Tolias AS	eLife	32134385	Elife	2020 Mar 5	https://www.ncbi.nlm.nih.gov/pubmed/32134385
Deep convolutional models improve predictions of macaque V1 responses to natural images.	Cadena SA, Denfield GH, Walker EY, Gatys LA, Tolias AS, Bethge M, Ecker AS	PLoS computational biology	31013278	PLoS Comput Biol	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/31013278
Attentional fluctuations induce shared variability in macaque primary visual cortex.	Denfield GH, Ecker AS, Shinn TJ, Bethge M, Tolias AS	Nature communications	29985411	Nat Commun	2018 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/29985411
Benchmarking Spike Rate Inference in Population Calcium Imaging.	Theis L, Berens P, Froudarakis E, Reimer J, Román Rosón M, Baden T, Euler T, Tolias AS, Bethge M	Neuron	27151639	Neuron	2016 May 4	https://www.ncbi.nlm.nih.gov/pubmed/27151639
Pupil fluctuations track fast switching of cortical states during quiet wakefulness.	Reimer J, Froudarakis E, Cadwell CR, Yatsenko D, Denfield GH, Tolias AS	Neuron	25374359	Neuron	2014 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/25374359
Population code in mouse V1 facilitates readout of natural scenes through increased sparseness.	Froudarakis E, Berens P, Ecker AS, Cotton RJ, Sinz FH, Yatsenko D, Saggau P, Bethge M, Tolias AS	Nature neuroscience	24747577	Nat Neurosci	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24747577
Principles of connectivity among morphologically defined cell types in adult neocortex.	Jiang X, Shen S, Cadwell CR, Berens P, Sinz F, Ecker AS, Patel S, Tolias AS	Science (New York, N.Y.)	26612957	Science	2015 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/26612957
Pupil fluctuations track rapid changes in adrenergic and cholinergic activity in cortex.	Reimer J, McGinley MJ, Liu Y, Rodenkirch C, Wang Q, McCormick DA, Tolias AS	Nature communications	27824036	Nat Commun	2016 Nov 8	https://www.ncbi.nlm.nih.gov/pubmed/27824036
Waking State: Rapid Variations Modulate Neural and Behavioral Responses.	McGinley MJ, Vinck M, Reimer J, Batista-Brito R, Zagha E, Cadwell CR, Tolias AS, Cardin JA, McCormick DA	Neuron	26402600	Neuron	2015 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/26402600
Improved estimation and interpretation of correlations in neural circuits.	Yatsenko D, Josić K, Ecker AS, Froudarakis E, Cotton RJ, Tolias AS	PLoS computational biology	25826696	PLoS Comput Biol	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25826696
Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq.	Cadwell CR, Palasantza A, Jiang X, Berens P, Deng Q, Yilmaz M, Reimer J, Shen S, Bethge M, Tolias KF, Sandberg R, Tolias AS	Nature biotechnology	26689543	Nat Biotechnol	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/26689543
Learning divisive normalization in primary visual cortex.	Burg MF, Cadena SA, Denfield GH, Walker EY, Tolias AS, Bethge M, Ecker AS	PLoS computational biology	34097695	PLoS Comput Biol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/34097695
Retinal gene therapy coming of age.	Cepko CL, Vandenberghe LH	Human gene therapy	23458444	Hum Gene Ther	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23458444
The Assembly-Activating Protein Promotes Stability and Interactions between AAV's Viral Proteins to Nucleate Capsid Assembly.	Maurer AC, Pacouret S, Cepeda Diaz AK, Blake J, Andres-Mateos E, Vandenberghe LH	Cell reports	29742436	Cell Rep	2018 May 8	https://www.ncbi.nlm.nih.gov/pubmed/29742436
In vitro and in vivo rescue of aberrant splicing in CEP290-associated LCA by antisense oligonucleotide delivery.	Garanto A, Chung DC, Duijkers L, Corral-Serrano JC, Messchaert M, Xiao R, Bennett J, Vandenberghe LH, Collin RW	Human molecular genetics	27106101	Hum Mol Genet	2016 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/27106101
Promising and delivering gene therapies for vision loss.	Carvalho LS, Vandenberghe LH	Vision research	25094052	Vision Res	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25094052
AAV9 targets cone photoreceptors in the nonhuman primate retina.	Vandenberghe LH, Bell P, Maguire AM, Xiao R, Hopkins TB, Grant R, Bennett J, Wilson JM	PloS one	23382846	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23382846
What Is Next for Retinal Gene Therapy?	Vandenberghe LH	Cold Spring Harbor perspectives in medicine	25877395	Cold Spring Harb Perspect Med	2015 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/25877395
Controlling AAV Tropism in the Nervous System with Natural and Engineered Capsids.	Castle MJ, Turunen HT, Vandenberghe LH, Wolfe JH	Methods in molecular biology (Clifton, N.J.)	26611584	Methods Mol Biol	2016	https://www.ncbi.nlm.nih.gov/pubmed/26611584
Perspectives on best practices for gene therapy programs.	Cheever TR, Berkley D, Braun S, Brown RH, Byrne BJ, Chamberlain JS, Cwik V, Duan D, Federoff HJ, High KA, Kaspar BK, Klinger KW, Larkindale J, Lincecum J, Mavilio F, McDonald CL, McLaughlin J, Weiss McLeod B, Mendell JR, Nuckolls G, Stedman HH, Tagle DA, Vandenberghe LH, Wang H, Wernett PJ, Wilson JM, Porter JD, Gubitz AK	Human gene therapy	25654329	Hum Gene Ther	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25654329
Basal exon skipping and genetic pleiotropy: A predictive model of disease pathogenesis.	Drivas TG, Wojno AP, Tucker BA, Stone EM, Bennett J	Science translational medicine	26062849	Sci Transl Med	2015 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/26062849
Efficient transduction and optogenetic stimulation of retinal bipolar cells by a synthetic adeno-associated virus capsid and promoter.	Cronin T, Vandenberghe LH, Hantz P, Juttner J, Reimann A, Kacsó AE, Huckfeldt RM, Busskamp V, Kohler H, Lagali PS, Roska B, Bennett J	EMBO molecular medicine	25092770	EMBO Mol Med	2014 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25092770
A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear.	Landegger LD, Pan B, Askew C, Wassmer SJ, Gluck SD, Galvin A, Taylor R, Forge A, Stankovic KM, Holt JR, Vandenberghe LH	Nature biotechnology	28165475	Nat Biotechnol	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28165475
Gene delivery to the retina: from mouse to man.	Bennett J, Chung DC, Maguire A	Methods in enzymology	22365778	Methods Enzymol	2012	https://www.ncbi.nlm.nih.gov/pubmed/22365778
In Silico Reconstruction of the Viral Evolutionary Lineage Yields a Potent Gene Therapy Vector.	Zinn E, Pacouret S, Khaychuk V, Turunen HT, Carvalho LS, Andres-Mateos E, Shah S, Shelke R, Maurer AC, Plovie E, Xiao R, Vandenberghe LH	Cell reports	26235624	Cell Rep	2015 Aug 11	https://www.ncbi.nlm.nih.gov/pubmed/26235624
Adeno-associated virus: fit to serve.	Zinn E, Vandenberghe LH	Current opinion in virology	25128609	Curr Opin Virol	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25128609
Restoration of Vision and Retinal Responses After Adeno-Associated Virus-Mediated Optogenetic Therapy in Blind Dogs.	Nikonov S, Aravand P, Lyubarsky A, Nikonov R, Luo AJ, Wei Z, Maguire AM, Phelps NT, Shpylchak I, Willett K, Aleman TS, Huckfeldt RM, Ramachandran PS, Bennett J	Translational vision science & technology	35604672	Transl Vis Sci Technol	2022 May 2	https://www.ncbi.nlm.nih.gov/pubmed/35604672
Membrane Potential Dynamics of CA1 Pyramidal Neurons during Hippocampal Ripples in Awake Mice.	Hulse BK, Moreaux LC, Lubenov EV, Siapas AG	Neuron	26889811	Neuron	2016 Feb 17	https://www.ncbi.nlm.nih.gov/pubmed/26889811
Spatial tuning and brain state account for dorsal hippocampal CA1 activity in a non-spatial learning task.	Shan KQ, Lubenov EV, Papadopoulou M, Siapas AG	eLife	27487561	Elife	2016 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/27487561
Structured Variability in Purkinje Cell Activity during Locomotion.	Sauerbrei BA, Lubenov EV, Siapas AG	Neuron	26291165	Neuron	2015 Aug 19	https://www.ncbi.nlm.nih.gov/pubmed/26291165
Nanofabricated Neural Probes for Dense 3-D Recordings of Brain Activity.	Rios G, Lubenov EV, Chi D, Roukes ML, Siapas AG	Nano letters	27766885	Nano Lett	2016 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/27766885
Model-based spike sorting with a mixture of drifting t-distributions.	Shan KQ, Lubenov EV, Siapas AG	Journal of neuroscience methods	28652008	J Neurosci Methods	2017 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/28652008
Brain State Dependence of Hippocampal Subthreshold Activity in Awake Mice.	Hulse BK, Lubenov EV, Siapas AG	Cell reports	28052244	Cell Rep	2017 Jan 3	https://www.ncbi.nlm.nih.gov/pubmed/28052244
Endogenous Retroviral Envelope Syncytin Induces HIV-1 Spreading and Establishes HIV Reservoirs in Placenta.	Tang Y, Woodward BO, Pastor L, George AM, Petrechko O, Nouvet FJ, Haas DW, Jiang G, Hildreth JEK	Cell reports	32234485	Cell Rep	2020 Mar 31	https://www.ncbi.nlm.nih.gov/pubmed/32234485
Spinal projection neurons control turning behaviors in zebrafish.	Huang KH, Ahrens MB, Dunn TW, Engert F	Current biology : CB	23910662	Curr Biol	2013 Aug 19	https://www.ncbi.nlm.nih.gov/pubmed/23910662
Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina.	Li YN, Tsujimura T, Kawamura S, Dowling JE	The Journal of comparative neurology	22907678	J Comp Neurol	2012 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/22907678
Large-scale imaging in small brains.	Ahrens MB, Engert F	Current opinion in neurobiology	25636154	Curr Opin Neurobiol	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25636154
Navigational strategies underlying phototaxis in larval zebrafish.	Chen X, Engert F	Frontiers in systems neuroscience	24723859	Front Syst Neurosci	2014	https://www.ncbi.nlm.nih.gov/pubmed/24723859
Neural Circuits Underlying Visually Evoked Escapes in Larval Zebrafish.	Dunn TW, Gebhardt C, Naumann EA, Riegler C, Ahrens MB, Engert F, Del Bene F	Neuron	26804997	Neuron	2016 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/26804997
A compressed sensing framework for efficient dissection of neural circuits.	Lee JB, Yonar A, Hallacy T, Shen CH, Milloz J, Srinivasan J, Kocabas A, Ramanathan S	Nature methods	30573831	Nat Methods	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30573831
Pluripotency factors in embryonic stem cells regulate differentiation into germ layers.	Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S	Cell	21663792	Cell	2011 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/21663792
Identification of the long, edited dsRNAome of LPS-stimulated immune cells.	Blango MG, Bass BL	Genome research	27197207	Genome Res	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27197207
Drosophila dicer-2 cleavage is mediated by helicase- and dsRNA termini-dependent states that are modulated by Loquacious-PD.	Sinha NK, Trettin KD, Aruscavage PJ, Bass BL	Molecular cell	25891075	Mol Cell	2015 May 7	https://www.ncbi.nlm.nih.gov/pubmed/25891075
Genome-wide profiling of the C. elegans dsRNAome.	Whipple JM, Youssef OA, Aruscavage PJ, Nix DA, Hong C, Johnson WE, Bass BL	RNA (New York, N.Y.)	25805852	RNA	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25805852
Potential role for snoRNAs in PKR activation during metabolic stress.	Youssef OA, Safran SA, Nakamura T, Nix DA, Hotamisligil GS, Bass BL	Proceedings of the National Academy of Sciences of the United States of America	25848059	Proc Natl Acad Sci U S A	2015 Apr 21	https://www.ncbi.nlm.nih.gov/pubmed/25848059
Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress.	Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M	The Journal of biological chemistry	23086926	J Biol Chem	2012 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/23086926
Tolerance of infections.	Ayres JS, Schneider DS	Annual review of immunology	22224770	Annu Rev Immunol	2012	https://www.ncbi.nlm.nih.gov/pubmed/22224770
Tracing personalized health curves during infections.	Schneider DS	PLoS biology	21957398	PLoS Biol	2011 Sep	https://www.ncbi.nlm.nih.gov/pubmed/21957398
Disease tolerance as a defense strategy.	Medzhitov R, Schneider DS, Soares MP	Science (New York, N.Y.)	22363001	Science	2012 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/22363001
How the fly balances its ability to combat different pathogens.	Chambers MC, Lightfield KL, Schneider DS	PLoS pathogens	23271964	PLoS Pathog	2012	https://www.ncbi.nlm.nih.gov/pubmed/23271964
Guided Homing of Cells in Multi-Photon Microfabricated Bioscaffolds.	Skylar-Scott MA, Liu MC, Wu Y, Dixit A, Yanik MF	Advanced healthcare materials	27059425	Adv Healthc Mater	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/27059425
Cholinergic Signaling Controls Conditioned Fear Behaviors and Enhances Plasticity of Cortical-Amygdala Circuits.	Jiang L, Kundu S, Lederman JD, López-Hernández GY, Ballinger EC, Wang S, Talmage DA, Role LW	Neuron	27161525	Neuron	2016 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/27161525
Electrophysiological properties of basal forebrain cholinergic neurons identified by genetic and optogenetic tagging.	López-Hernández GY, Ananth M, Jiang L, Ballinger EC, Talmage DA, Role LW	Journal of neurochemistry	28791701	J Neurochem	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28791701
Targeted gene knockout by direct delivery of zinc-finger nuclease proteins.	Gaj T, Guo J, Kato Y, Sirk SJ, Barbas CF 3rd	Nature methods	22751204	Nat Methods	2012 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/22751204
Intra-spike crosslinking overcomes antibody evasion by HIV-1.	Galimidi RP, Klein JS, Politzer MS, Bai S, Seaman MS, Nussenzweig MC, West AP Jr, Bjorkman PJ	Cell	25635457	Cell	2015 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/25635457
Antibody engineering for increased potency, breadth and half-life.	Sievers SA, Scharf L, West AP Jr, Bjorkman PJ	Current opinion in HIV and AIDS	25760931	Curr Opin HIV AIDS	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25760931
Structural characterization of anti-inflammatory immunoglobulin G Fc proteins.	Ahmed AA, Giddens J, Pincetic A, Lomino JV, Ravetch JV, Wang LX, Bjorkman PJ	Journal of molecular biology	25036289	J Mol Biol	2014 Sep 9	https://www.ncbi.nlm.nih.gov/pubmed/25036289
Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues.	West AP Jr, Scharf L, Horwitz J, Klein F, Nussenzweig MC, Bjorkman PJ	Proceedings of the National Academy of Sciences of the United States of America	23754383	Proc Natl Acad Sci U S A	2013 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/23754383
Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120.	West AP Jr, Diskin R, Nussenzweig MC, Bjorkman PJ	Proceedings of the National Academy of Sciences of the United States of America	22745174	Proc Natl Acad Sci U S A	2012 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/22745174
Design and characterization of structured protein linkers with differing flexibilities.	Klein JS, Jiang S, Galimidi RP, Keeffe JR, Bjorkman PJ	Protein engineering, design & selection : PEDS	25301959	Protein Eng Des Sel	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25301959
Structural insights on the role of antibodies in HIV-1 vaccine and therapy.	West AP Jr, Scharf L, Scheid JF, Klein F, Bjorkman PJ, Nussenzweig MC	Cell	24529371	Cell	2014 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/24529371
Surface reengineering of RPA70N enables cocrystallization with an inhibitor of the replication protein A interaction motif of ATR interacting protein.	Feldkamp MD, Frank AO, Kennedy JP, Patrone JD, Vangamudi B, Waterson AG, Fesik SW, Chazin WJ	Biochemistry	23962067	Biochemistry	2013 Sep 17	https://www.ncbi.nlm.nih.gov/pubmed/23962067
Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on RAS Using Fragment-Based Methods.	Sarkar D, Olejniczak ET, Phan J, Coker JA, Sai J, Arnold A, Beesetty Y, Waterson AG, Fesik SW	Journal of medicinal chemistry	32673492	J Med Chem	2020 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/32673492
Fragment-based screening of the bromodomain of ATAD2.	Harner MJ, Chauder BA, Phan J, Fesik SW	Journal of medicinal chemistry	25314628	J Med Chem	2014 Nov 26	https://www.ncbi.nlm.nih.gov/pubmed/25314628
Drugging the undruggable RAS: Mission possible?	Cox AD, Fesik SW, Kimmelman AC, Luo J, Der CJ	Nature reviews. Drug discovery	25323927	Nat Rev Drug Discov	2014 Nov	https://www.ncbi.nlm.nih.gov/pubmed/25323927
Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach.	Frank AO, Feldkamp MD, Kennedy JP, Waterson AG, Pelz NF, Patrone JD, Vangamudi B, Camper DV, Rossanese OW, Chazin WJ, Fesik SW	Journal of medicinal chemistry	24147804	J Med Chem	2013 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/24147804
Fragment-based drug discovery using NMR spectroscopy.	Harner MJ, Frank AO, Fesik SW	Journal of biomolecular NMR	23686385	J Biomol NMR	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23686385
Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC.	Thomas LR, Wang Q, Grieb BC, Phan J, Foshage AM, Sun Q, Olejniczak ET, Clark T, Dey S, Lorey S, Alicie B, Howard GC, Cawthon B, Ess KC, Eischen CM, Zhao Z, Fesik SW, Tansey WP	Molecular cell	25818646	Mol Cell	2015 May 7	https://www.ncbi.nlm.nih.gov/pubmed/25818646
Discovery of tricyclic indoles that potently inhibit Mcl-1 using fragment-based methods and structure-based design.	Burke JP, Bian Z, Shaw S, Zhao B, Goodwin CM, Belmar J, Browning CF, Vigil D, Friberg A, Camper DV, Rossanese OW, Lee T, Olejniczak ET, Fesik SW	Journal of medicinal chemistry	25844895	J Med Chem	2015 May 14	https://www.ncbi.nlm.nih.gov/pubmed/25844895
Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.	Hodges TR, Abbott JR, Little AJ, Sarkar D, Salovich JM, Howes JE, Akan DT, Sai J, Arnold AL, Browning C, Burns MC, Sobolik T, Sun Q, Beesetty Y, Coker JA, Scharn D, Stadtmueller H, Rossanese OW, Phan J, Waterson AG, McConnell DB, Fesik SW	Journal of medicinal chemistry	30205005	J Med Chem	2018 Oct 11	https://www.ncbi.nlm.nih.gov/pubmed/30205005
Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS.	Abbott JR, Patel PA, Howes JE, Akan DT, Kennedy JP, Burns MC, Browning CF, Sun Q, Rossanese OW, Phan J, Waterson AG, Fesik SW	ACS medicinal chemistry letters	30258545	ACS Med Chem Lett	2018 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/30258545
Discovery of small molecules that bind to K-Ras and inhibit Sos-mediated activation.	Sun Q, Burke JP, Phan J, Burns MC, Olejniczak ET, Waterson AG, Lee T, Rossanese OW, Fesik SW	Angewandte Chemie (International ed. in English)	22566140	Angew Chem Int Ed Engl	2012 Jun 18	https://www.ncbi.nlm.nih.gov/pubmed/22566140
Discovery and biological characterization of potent myeloid cell leukemia-1 inhibitors.	Lee T, Bian Z, Zhao B, Hogdal LJ, Sensintaffar JL, Goodwin CM, Belmar J, Shaw S, Tarr JC, Veerasamy N, Matulis SM, Koss B, Fischer MA, Arnold AL, Camper DV, Browning CF, Rossanese OW, Budhraja A, Opferman J, Boise LH, Savona MR, Letai A, Olejniczak ET, Fesik SW	FEBS letters	27878989	FEBS Lett	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27878989
A high-throughput fluorescence polarization anisotropy assay for the 70N domain of replication protein A.	Souza-Fagundes EM, Frank AO, Feldkamp MD, Dorset DC, Chazin WJ, Rossanese OW, Olejniczak ET, Fesik SW	Analytical biochemistry	22197419	Anal Biochem	2012 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/22197419
A method for the second-site screening of K-Ras in the presence of a covalently attached first-site ligand.	Sun Q, Phan J, Friberg AR, Camper DV, Olejniczak ET, Fesik SW	Journal of biomolecular NMR	25087006	J Biomol NMR	2014 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25087006
Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A.	Patrone JD, Kennedy JP, Frank AO, Feldkamp MD, Vangamudi B, Pelz NF, Rossanese OW, Waterson AG, Chazin WJ, Fesik SW	ACS medicinal chemistry letters	23914285	ACS Med Chem Lett	2013 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/23914285
Identification and Optimization of Anthranilic Acid Based Inhibitors of Replication Protein A.	Patrone JD, Pelz NF, Bates BS, Souza-Fagundes EM, Vangamudi B, Camper DV, Kuznetsov AG, Browning CF, Feldkamp MD, Frank AO, Gilston BA, Olejniczak ET, Rossanese OW, Waterson AG, Chazin WJ, Fesik SW	ChemMedChem	26748787	ChemMedChem	2016 Apr 19	https://www.ncbi.nlm.nih.gov/pubmed/26748787
Discovery of 2-Indole-acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods.	Pelz NF, Bian Z, Zhao B, Shaw S, Tarr JC, Belmar J, Gregg C, Camper DV, Goodwin CM, Arnold AL, Sensintaffar JL, Friberg A, Rossanese OW, Lee T, Olejniczak ET, Fesik SW	Journal of medicinal chemistry	26878343	J Med Chem	2016 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/26878343
Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design.	Friberg A, Vigil D, Zhao B, Daniels RN, Burke JP, Garcia-Barrantes PM, Camper D, Chauder BA, Lee T, Olejniczak ET, Fesik SW	Journal of medicinal chemistry	23244564	J Med Chem	2013 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/23244564
Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.	Burns MC, Sun Q, Daniels RN, Camper D, Kennedy JP, Phan J, Olejniczak ET, Lee T, Waterson AG, Rossanese OW, Fesik SW	Proceedings of the National Academy of Sciences of the United States of America	24550516	Proc Natl Acad Sci U S A	2014 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/24550516
Fragment Optimization of Reversible Binding to the Switch II Pocket on KRAS Leads to a Potent, In Vivo Active KRAS(G12C) Inhibitor.	Bröker J, Waterson AG, Smethurst C, Kessler D, Böttcher J, Mayer M, Gmaschitz G, Phan J, Little A, Abbott JR, Sun Q, Gmachl M, Rudolph D, Arnhof H, Rumpel K, Savarese F, Gerstberger T, Mischerikow N, Treu M, Herdeis L, Wunberg T, Gollner A, Weinstabl H, Mantoulidis A, Krämer O, McConnell DB, W Fesik S	Journal of medicinal chemistry	36300829	J Med Chem	2022 Nov 10	https://www.ncbi.nlm.nih.gov/pubmed/36300829
MYC and MCL1 Cooperatively Promote Chemotherapy-Resistant Breast Cancer Stem Cells via Regulation of Mitochondrial Oxidative Phosphorylation.	Lee KM, Giltnane JM, Balko JM, Schwarz LJ, Guerrero-Zotano AL, Hutchinson KE, Nixon MJ, Estrada MV, Sánchez V, Sanders ME, Lee T, Gómez H, Lluch A, Pérez-Fidalgo JA, Wolf MM, Andrejeva G, Rathmell JC, Fesik SW, Arteaga CL	Cell metabolism	28978427	Cell Metab	2017 Oct 3	https://www.ncbi.nlm.nih.gov/pubmed/28978427
Dynamic states of population activity in prefrontal cortical networks of freely-moving macaque.	Milton R, Shahidi N, Dragoi V	Nature communications	32327660	Nat Commun	2020 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/32327660
Surpassing fundamental limits of oscillators using nonlinear resonators.	Villanueva LG, Kenig E, Karabalin RB, Matheny MH, Lifshitz R, Cross MC, Roukes ML	Physical review letters	23679770	Phys Rev Lett	2013 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/23679770
Optimal operating points of oscillators using nonlinear resonators.	Kenig E, Cross MC, Villanueva LG, Karabalin RB, Matheny MH, Lifshitz R, Roukes ML	Physical review. E, Statistical, nonlinear, and soft matter physics	23214857	Phys Rev E Stat Nonlin Soft Matter Phys	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23214857
Nonlinear mode-coupling in nanomechanical systems.	Matheny MH, Villanueva LG, Karabalin RB, Sader JE, Roukes ML	Nano letters	23496001	Nano Lett	2013 Apr 10	https://www.ncbi.nlm.nih.gov/pubmed/23496001
Nanoelectromechanical resonator arrays for ultrafast, gas-phase chromatographic chemical analysis.	Li M, Myers EB, Tang HX, Aldridge SJ, McCaig HC, Whiting JJ, Simonson RJ, Lewis NS, Roukes ML	Nano letters	20795729	Nano Lett	2010 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/20795729
Surface adsorbate fluctuations and noise in nanoelectromechanical systems.	Yang YT, Callegari C, Feng XL, Roukes ML	Nano letters	21388120	Nano Lett	2011 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/21388120
Stress-induced variations in the stiffness of micro- and nanocantilever beams.	Karabalin RB, Villanueva LG, Matheny MH, Sader JE, Roukes ML	Physical review letters	23003973	Phys Rev Lett	2012 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/23003973
Passive phase noise cancellation scheme.	Kenig E, Cross MC, Lifshitz R, Karabalin RB, Villanueva LG, Matheny MH, Roukes ML	Physical review letters	23004985	Phys Rev Lett	2012 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/23004985
Large-scale integration of nanoelectromechanical systems for gas sensing applications.	Bargatin I, Myers EB, Aldridge JS, Marcoux C, Brianceau P, Duraffourg L, Colinet E, Hentz S, Andreucci P, Roukes ML	Nano letters	22280452	Nano Lett	2012 Mar 14	https://www.ncbi.nlm.nih.gov/pubmed/22280452
Comparative advantages of mechanical biosensors.	Arlett JL, Myers EB, Roukes ML	Nature nanotechnology	21441911	Nat Nanotechnol	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21441911
Transgenerational epigenetic effects of the Apobec1 cytidine deaminase deficiency on testicular germ cell tumor susceptibility and embryonic viability.	Nelson VR, Heaney JD, Tesar PJ, Davidson NO, Nadeau JH	Proceedings of the National Academy of Sciences of the United States of America	22923694	Proc Natl Acad Sci U S A	2012 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/22923694
CMV infection, TLR-2 and -4 expression, and cytokine profiles in early-onset preeclampsia with HELLP syndrome.	Xie F, von Dadelszen P, Nadeau J	American journal of reproductive immunology (New York, N.Y. : 1989)	24612145	Am J Reprod Immunol	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24612145
Maternal nutrition induces pervasive gene expression changes but no detectable DNA methylation differences in the liver of adult offspring.	Cannon MV, Buchner DA, Hester J, Miller H, Sehayek E, Nadeau JH, Serre D	PloS one	24594983	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24594983
Report of the National Heart, Lung, and Blood Institute Working Group on epigenetics and hypertension.	Cowley AW Jr, Nadeau JH, Baccarelli A, Berecek K, Fornage M, Gibbons GH, Harrison DG, Liang M, Nathanielsz PW, O'Connor DT, Ordovas J, Peng W, Soares MB, Szyf M, Tolunay HE, Wood KC, Zhao K, Galis ZS	Hypertension (Dallas, Tex. : 1979)	22431584	Hypertension	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22431584
Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver.	Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Ben Hamidane H, Graumann J, Mortazavi A, Nadeau JH, Davidson NO	Genome biology	24946870	Genome Biol	2014 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/24946870
Transgenerational genetic effects of the paternal Y chromosome on daughters' phenotypes.	Nelson VR, Spiezio SH, Nadeau JH	Epigenomics	22121971	Epigenomics	2010 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22121971
Transgenerational genetic effects.	Nelson VR, Nadeau JH	Epigenomics	22122083	Epigenomics	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/22122083
A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions.	Joung JK, Ramm EI, Pabo CO	Proceedings of the National Academy of Sciences of the United States of America	10852947	Proc Natl Acad Sci U S A	2000 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/10852947
Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA).	Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK	Nature methods	21151135	Nat Methods	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21151135
Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers.	Giesecke AV, Fang R, Joung JK	Molecular systems biology	16732192	Mol Syst Biol	2006	https://www.ncbi.nlm.nih.gov/pubmed/16732192
Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.	Thibodeau-Beganny S, Joung JK	Methods in molecular biology (Clifton, N.J.)	18314590	Methods Mol Biol	2007	https://www.ncbi.nlm.nih.gov/pubmed/18314590
Engineering designer nucleases with customized cleavage specificities.	Sander JD, Maeder ML, Joung JK	Current protocols in molecular biology	21987054	Curr Protoc Mol Biol	2011 Oct	https://www.ncbi.nlm.nih.gov/pubmed/21987054
Repression of phase-variable cup gene expression by H-NS-like proteins in Pseudomonas aeruginosa.	Vallet-Gely I, Donovan KE, Fang R, Joung JK, Dove SL	Proceedings of the National Academy of Sciences of the United States of America	16043713	Proc Natl Acad Sci U S A	2005 Aug 2	https://www.ncbi.nlm.nih.gov/pubmed/16043713
DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases.	Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Cathomen T	Molecular therapy : the journal of the American Society of Gene Therapy	18026168	Mol Ther	2008 Feb	https://www.ncbi.nlm.nih.gov/pubmed/18026168
Plant science. DNA binding made easy.	Voytas DF, Joung JK	Science (New York, N.Y.)	20007890	Science	2009 Dec 11	https://www.ncbi.nlm.nih.gov/pubmed/20007890
Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays.	Maeder ML, Thibodeau-Beganny S, Sander JD, Voytas DF, Joung JK	Nature protocols	19798082	Nat Protoc	2009	https://www.ncbi.nlm.nih.gov/pubmed/19798082
Robust, synergistic regulation of human gene expression using TALE activators.	Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK	Nature methods	23396285	Nat Methods	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23396285
TALEN-based gene correction for epidermolysis bullosa.	Osborn MJ, Starker CG, McElroy AN, Webber BR, Riddle MJ, Xia L, DeFeo AP, Gabriel R, Schmidt M, von Kalle C, Carlson DF, Maeder ML, Joung JK, Wagner JE, Voytas DF, Blazar BR, Tolar J	Molecular therapy : the journal of the American Society of Gene Therapy	23546300	Mol Ther	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23546300
Multidimensional control of therapeutic human cell function with synthetic gene circuits.	Li HS, Israni DV, Gagnon KA, Gan KA, Raymond MH, Sander JD, Roybal KT, Joung JK, Wong WW, Khalil AS	Science (New York, N.Y.)	36520914	Science	2022 Dec 16	https://www.ncbi.nlm.nih.gov/pubmed/36520914
Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein.	Joung JK, Koepp DM, Hochschild A	Science (New York, N.Y.)	8091212	Science	1994 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/8091212
Structural and functional characterization of human immunodeficiency virus tat protein.	Ruben S, Perkins A, Purcell R, Joung K, Sia R, Burghoff R, Haseltine WA, Rosen CA	Journal of virology	2535718	J Virol	1989 Jan	https://www.ncbi.nlm.nih.gov/pubmed/2535718
Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases.	Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ, Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM	Plant physiology	21464476	Plant Physiol	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/21464476
Engineering designer transcription activator-like effector nucleases (TALENs) by REAL or REAL-Fast assembly.	Reyon D, Khayter C, Regan MR, Joung JK, Sander JD	Current protocols in molecular biology	23026907	Curr Protoc Mol Biol	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23026907
Targeted gene disruption in somatic zebrafish cells using engineered TALENs.	Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK, Yeh JR	Nature biotechnology	21822241	Nat Biotechnol	2011 Aug 5	https://www.ncbi.nlm.nih.gov/pubmed/21822241
Targeted mutagenesis in zebrafish using customized zinc-finger nucleases.	Foley JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR	Nature protocols	20010934	Nat Protoc	2009	https://www.ncbi.nlm.nih.gov/pubmed/20010934
Engineering customized TALE nucleases (TALENs) and TALE transcription factors by fast ligation-based automatable solid-phase high-throughput (FLASH) assembly.	Reyon D, Maeder ML, Khayter C, Tsai SQ, Foley JE, Sander JD, Joung JK	Current protocols in molecular biology	23821439	Curr Protoc Mol Biol	2013 Jul	https://www.ncbi.nlm.nih.gov/pubmed/23821439
Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.	Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB Jr, Cathomen T, Voytas DF, Joung JK	Molecular cell	18657511	Mol Cell	2008 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/18657511
Engineering single Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.	Thibodeau-Beganny S, Maeder ML, Joung JK	Methods in molecular biology (Clifton, N.J.)	20680826	Methods Mol Biol	2010	https://www.ncbi.nlm.nih.gov/pubmed/20680826
An improved strategy for constructing "designer" Cys2His2 zinc finger proteins.	Thibodeau SA, Joung JK	Discovery medicine	20705034	Discov Med	2003 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20705034
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences.	Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D	BMC bioinformatics	21044337	BMC Bioinformatics	2010 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/21044337
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays.	Fu F, Sander JD, Maeder M, Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF	Nucleic acids research	18812396	Nucleic Acids Res	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/18812396
Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection.	Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK	Proceedings of the National Academy of Sciences of the United States of America	14527993	Proc Natl Acad Sci U S A	2003 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/14527993
Heritable and precise zebrafish genome editing using a CRISPR-Cas system.	Hwang WY, Fu Y, Reyon D, Maeder ML, Kaini P, Sander JD, Joung JK, Peterson RT, Yeh JR	PloS one	23874735	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23874735
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method.	Meng X, Thibodeau-Beganny S, Jiang T, Joung JK, Wolfe SA	Nucleic acids research	17537811	Nucleic Acids Res	2007	https://www.ncbi.nlm.nih.gov/pubmed/17537811
CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.	Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N, GAME-ON/ELLIPSE Consortium, Gayther SA, Joung JK, Freedman ML	Nature medicine	26398868	Nat Med	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26398868
Chromatin regulation at the frontier of synthetic biology.	Keung AJ, Joung JK, Khalil AS, Collins JJ	Nature reviews. Genetics	25668787	Nat Rev Genet	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25668787
A combined yeast/bacteria two-hybrid system: development and evaluation.	Serebriiskii IG, Fang R, Latypova E, Hopkins R, Vinson C, Joung JK, Golemis EA	Molecular & cellular proteomics : MCP	15781424	Mol Cell Proteomics	2005 Jun	https://www.ncbi.nlm.nih.gov/pubmed/15781424
Counter-selectable marker for bacterial-based interaction trap systems.	Meng X, Smith RM, Giesecke AV, Joung JK, Wolfe SA	BioTechniques	16526407	Biotechniques	2006 Feb	https://www.ncbi.nlm.nih.gov/pubmed/16526407
High-throughput beta-galactosidase assay for bacterial cell-based reporter systems.	Thibodeau SA, Fang R, Joung JK	BioTechniques	15038156	Biotechniques	2004 Mar	https://www.ncbi.nlm.nih.gov/pubmed/15038156
Genetic strategy for analyzing specificity of dimer formation: Escherichia coli cyclic AMP receptor protein mutant altered in its dimerization specificity.	Joung JK, Chung EH, King G, Yu C, Hirsh AS, Hochschild A	Genes & development	7498794	Genes Dev	1995 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/7498794
Activation of prokaryotic transcription through arbitrary protein-protein contacts.	Dove SL, Joung JK, Hochschild A	Nature	9121589	Nature	1997 Apr 10	https://www.ncbi.nlm.nih.gov/pubmed/9121589
Improved somatic mutagenesis in zebrafish using transcription activator-like effector nucleases (TALENs).	Moore FE, Reyon D, Sander JD, Martinez SA, Blackburn JS, Khayter C, Ramirez CL, Joung JK, Langenau DM	PloS one	22655075	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22655075
Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects.	Ramirez CL, Certo MT, Mussolino C, Goodwin MJ, Cradick TJ, McCaffrey AP, Cathomen T, Scharenberg AM, Joung JK	Nucleic acids research	22373919	Nucleic Acids Res	2012 Jul	https://www.ncbi.nlm.nih.gov/pubmed/22373919
Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs.	Cade L, Reyon D, Hwang WY, Tsai SQ, Patel S, Khayter C, Joung JK, Sander JD, Peterson RT, Yeh JR	Nucleic acids research	22684503	Nucleic Acids Res	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22684503
ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms.	Reyon D, Kirkpatrick JR, Sander JD, Zhang F, Voytas DF, Joung JK, Dobbs D, Coffman CR	BMC genomics	21276248	BMC Genomics	2011 Jan 28	https://www.ncbi.nlm.nih.gov/pubmed/21276248
Unexpected failure rates for modular assembly of engineered zinc fingers.	Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK	Nature methods	18446154	Nat Methods	2008 May	https://www.ncbi.nlm.nih.gov/pubmed/18446154
Comparison of zinc finger nucleases for use in gene targeting in mammalian cells.	Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH	Molecular therapy : the journal of the American Society of Gene Therapy	18334988	Mol Ther	2008 Apr	https://www.ncbi.nlm.nih.gov/pubmed/18334988
Zinc-finger nucleases: the next generation emerges.	Cathomen T, Joung JK	Molecular therapy : the journal of the American Society of Gene Therapy	18545224	Mol Ther	2008 Jul	https://www.ncbi.nlm.nih.gov/pubmed/18545224
Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly.	Wright DA, Thibodeau-Beganny S, Sander JD, Winfrey RJ, Hirsh AS, Eichtinger M, Fu F, Porteus MH, Dobbs D, Voytas DF, Joung JK	Nature protocols	17406455	Nat Protoc	2006	https://www.ncbi.nlm.nih.gov/pubmed/17406455
Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1.	Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K	Cell stem cell	24704492	Cell Stem Cell	2014 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/24704492
FLASH assembly of TALENs for high-throughput genome editing.	Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK	Nature biotechnology	22484455	Nat Biotechnol	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22484455
An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.	Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D	Nucleic acids research	19056825	Nucleic Acids Res	2009 Feb	https://www.ncbi.nlm.nih.gov/pubmed/19056825
High-frequency modification of plant genes using engineered zinc-finger nucleases.	Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF	Nature	19404258	Nature	2009 May 21	https://www.ncbi.nlm.nih.gov/pubmed/19404258
Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system.	Joung JK	Journal of cellular biochemistry. Supplement	11842428	J Cell Biochem Suppl	2001	https://www.ncbi.nlm.nih.gov/pubmed/11842428
Allosteric inhibition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands.	Nguyen-Hackley DH, Ramm E, Taylor CM, Joung JK, Dervan PB, Pabo CO	Biochemistry	15049695	Biochemistry	2004 Apr 6	https://www.ncbi.nlm.nih.gov/pubmed/15049695
Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN).	Foley JE, Yeh JR, Maeder ML, Reyon D, Sander JD, Peterson RT, Joung JK	PloS one	19198653	PLoS One	2009	https://www.ncbi.nlm.nih.gov/pubmed/19198653
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.	Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D	Nucleic acids research	17526515	Nucleic Acids Res	2007 Jul	https://www.ncbi.nlm.nih.gov/pubmed/17526515
A synthetic biology framework for programming eukaryotic transcription functions.	Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ	Cell	22863014	Cell	2012 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/22863014
Genome editing with modularly assembled zinc-finger nucleases.	Kim JS, Lee HJ, Carroll D	Nature methods	20111032	Nat Methods	2010 Feb	https://www.ncbi.nlm.nih.gov/pubmed/20111032
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.	Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D	Nucleic acids research	20435679	Nucleic Acids Res	2010 Jul	https://www.ncbi.nlm.nih.gov/pubmed/20435679
Synergistic activation of transcription by Escherichia coli cAMP receptor protein.	Joung JK, Le LU, Hochschild A	Proceedings of the National Academy of Sciences of the United States of America	7681995	Proc Natl Acad Sci U S A	1993 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/7681995
Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells.	Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou BK, Chen G, Ye Z, Park IH, Daley GQ, Porteus MH, Joung JK, Cheng L	Cell stem cell	19540188	Cell Stem Cell	2009 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/19540188
Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion.	Söllü C, Pars K, Cornu TI, Thibodeau-Beganny S, Maeder ML, Joung JK, Heilbronn R, Cathomen T	Nucleic acids research	20716517	Nucleic Acids Res	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20716517
Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection.	Pattanayak V, Ramirez CL, Joung JK, Liu DR	Nature methods	21822273	Nat Methods	2011 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/21822273
Engineering zinc finger nucleases for targeted mutagenesis of zebrafish.	Sander JD, Yeh JR, Peterson RT, Joung JK	Methods in cell biology	21924156	Methods Cell Biol	2011	https://www.ncbi.nlm.nih.gov/pubmed/21924156
In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases.	Sebastiano V, Maeder ML, Angstman JF, Haddad B, Khayter C, Yeo DT, Goodwin MJ, Hawkins JS, Ramirez CL, Batista LF, Artandi SE, Wernig M, Joung JK	Stem cells (Dayton, Ohio)	21898685	Stem Cells	2011 Nov	https://www.ncbi.nlm.nih.gov/pubmed/21898685
The bacterial two-hybrid system as a reporter system for analyzing protein-protein interactions.	Giesecke AV, Joung JK	CSH protocols	21357036	CSH Protoc	2007 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/21357036
Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors.	Tak YE, Boulay G, Lee L, Iyer S, Perry NT, Schultz HT, Garcia SP, Broye L, Horng JE, Rengarajan S, Naigles B, Volorio A, Sander JD, Gong J, Riggi N, Joung JK, Rivera MN	Cell genomics	35967079	Cell Genom	2022 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/35967079
Peroxisome proliferation-associated control of reactive oxygen species sets melanocortin tone and feeding in diet-induced obesity.	Diano S, Liu ZW, Jeong JK, Dietrich MO, Ruan HB, Kim E, Suyama S, Kelly K, Gyengesi E, Arbiser JL, Belsham DD, Sarruf DA, Schwartz MW, Bennett AM, Shanabrough M, Mobbs CV, Yang X, Gao XB, Horvath TL	Nature medicine	21873987	Nat Med	2011 Aug 28	https://www.ncbi.nlm.nih.gov/pubmed/21873987
In vivo veritas, in vitro artificia.	Matarese G, La Cava A, Horvath TL	Trends in molecular medicine	22682514	Trends Mol Med	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22682514
UCP2 induced by natural birth regulates neuronal differentiation of the hippocampus and related adult behavior.	Simon-Areces J, Dietrich MO, Hermes G, Garcia-Segura LM, Arevalo MA, Horvath TL	PloS one	22905184	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22905184
Mitofusin 2 in POMC neurons connects ER stress with leptin resistance and energy imbalance.	Schneeberger M, Dietrich MO, Sebastián D, Imbernón M, Castaño C, Garcia A, Esteban Y, Gonzalez-Franquesa A, Rodríguez IC, Bortolozzi A, Garcia-Roves PM, Gomis R, Nogueiras R, Horvath TL, Zorzano A, Claret M	Cell	24074867	Cell	2013 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/24074867
Prolonged oxaliplatin exposure alters intracellular calcium signaling: a new mechanism to explain oxaliplatin-associated peripheral neuropathy.	Schulze C, McGowan M, Jordt SE, Ehrlich BE	Clinical colorectal cancer	21859566	Clin Colorectal Cancer	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/21859566
CPG15 regulates synapse stability in the developing and adult brain.	Fujino T, Leslie JH, Eavri R, Chen JL, Lin WC, Flanders GH, Borok E, Horvath TL, Nedivi E	Genes & development	22190461	Genes Dev	2011 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/22190461
An oscillatory switch in mTOR kinase activity sets regulatory T cell responsiveness.	Procaccini C, De Rosa V, Galgani M, Abanni L, Calì G, Porcellini A, Carbone F, Fontana S, Horvath TL, La Cava A, Matarese G	Immunity	21145759	Immunity	2010 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/21145759
Role of breast cancer resistance protein in the adaptive response to cholestasis.	Mennone A, Soroka CJ, Harry KM, Boyer JL	Drug metabolism and disposition: the biological fate of chemicals	20601550	Drug Metab Dispos	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20601550
Hypothalamic Agrp neurons drive stereotypic behaviors beyond feeding.	Dietrich MO, Zimmer MR, Bober J, Horvath TL	Cell	25748653	Cell	2015 Mar 12	https://www.ncbi.nlm.nih.gov/pubmed/25748653
High-fat feeding promotes obesity via insulin receptor/PI3K-dependent inhibition of SF-1 VMH neurons.	Klöckener T, Hess S, Belgardt BF, Paeger L, Verhagen LA, Husch A, Sohn JW, Hampel B, Dhillon H, Zigman JM, Lowell BB, Williams KW, Elmquist JK, Horvath TL, Kloppenburg P, Brüning JC	Nature neuroscience	21642975	Nat Neurosci	2011 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/21642975
Nicotine decreases food intake through activation of POMC neurons.	Mineur YS, Abizaid A, Rao Y, Salas R, DiLeone RJ, Gündisch D, Diano S, De Biasi M, Horvath TL, Gao XB, Picciotto MR	Science (New York, N.Y.)	21659607	Science	2011 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/21659607
Oligodendrocyte regeneration after neonatal hypoxia requires FoxO1-mediated p27Kip1 expression.	Jablonska B, Scafidi J, Aguirre A, Vaccarino F, Nguyen V, Borok E, Horvath TL, Rowitch DH, Gallo V	The Journal of neuroscience : the official journal of the Society for Neuroscience	23077062	J Neurosci	2012 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/23077062
FoxO1 target Gpr17 activates AgRP neurons to regulate food intake.	Ren H, Orozco IJ, Su Y, Suyama S, Gutiérrez-Juárez R, Horvath TL, Wardlaw SL, Plum L, Arancio O, Accili D	Cell	22682251	Cell	2012 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/22682251
Mitofusin 2 in Mature Adipocytes Controls Adiposity and Body Weight.	Mancini G, Pirruccio K, Yang X, Blüher M, Rodeheffer M, Horvath TL	Cell reports	30865877	Cell Rep	2019 Mar 12	https://www.ncbi.nlm.nih.gov/pubmed/30865877
GPA protects the nigrostriatal dopamine system by enhancing mitochondrial function.	Horvath TL, Erion DM, Elsworth JD, Roth RH, Shulman GI, Andrews ZB	Neurobiology of disease	21406233	Neurobiol Dis	2011 Jul	https://www.ncbi.nlm.nih.gov/pubmed/21406233
Ghrelin-immunopositive hypothalamic neurons tie the circadian clock and visual system to the lateral hypothalamic arousal center.	Horvath TL, Abizaid A, Dietrich MO, Li Y, Takahashi JS, Bass J	Molecular metabolism	24024121	Mol Metab	2012	https://www.ncbi.nlm.nih.gov/pubmed/24024121
Intranasal epidermal growth factor treatment rescues neonatal brain injury.	Scafidi J, Hammond TR, Scafidi S, Ritter J, Jablonska B, Roncal M, Szigeti-Buck K, Coman D, Huang Y, McCarter RJ Jr, Hyder F, Horvath TL, Gallo V	Nature	24390343	Nature	2014 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/24390343
Physiology: Inflammation links ageing to the brain.	Gabuzda D, Yankner BA	Nature	23636321	Nature	2013 May 9	https://www.ncbi.nlm.nih.gov/pubmed/23636321
Alzheimer's Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci.	Karch CM, Ezerskiy LA, Bertelsen S, Alzheimer’s Disease Genetics Consortium (ADGC), Goate AM	PloS one	26919393	PLoS One	2016	https://www.ncbi.nlm.nih.gov/pubmed/26919393
REST and Neural Gene Network Dysregulation in iPSC Models of Alzheimer's Disease.	Meyer K, Feldman HM, Lu T, Drake D, Lim ET, Ling KH, Bishop NA, Pan Y, Seo J, Lin YT, Su SC, Church GM, Tsai LH, Yankner BA	Cell reports	30699343	Cell Rep	2019 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/30699343
REST and stress resistance in ageing and Alzheimer's disease.	Lu T, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang TH, Kim HM, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA	Nature	24670762	Nature	2014 Mar 27	https://www.ncbi.nlm.nih.gov/pubmed/24670762
Polygenic hazard score: an enrichment marker for Alzheimer's associated amyloid and tau deposition.	Tan CH, Fan CC, Mormino EC, Sugrue LP, Broce IJ, Hess CP, Dillon WP, Bonham LW, Yokoyama JS, Karch CM, Brewer JB, Rabinovici GD, Miller BL, Schellenberg GD, Kauppi K, Feldman HA, Holland D, McEvoy LK, Hyman BT, Bennett DA, Andreassen OA, Dale AM, Desikan RS, Alzheimer’s Disease Neuroimaging Initiative	Acta neuropathologica	29177679	Acta Neuropathol	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29177679
Common variants in DRD2 are associated with sleep duration: the CARe consortium.	Cade BE, Gottlieb DJ, Lauderdale DS, Bennett DA, Buchman AS, Buxbaum SG, De Jager PL, Evans DS, Fülöp T, Gharib SA, Johnson WC, Kim H, Larkin EK, Lee SK, Lim AS, Punjabi NM, Shin C, Stone KL, Tranah GJ, Weng J, Yaffe K, Zee PC, Patel SR, Zhu X, Redline S, Saxena R	Human molecular genetics	26464489	Hum Mol Genet	2016 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/26464489
The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4.	Kang C, Xu Q, Martin TD, Li MZ, Demaria M, Aron L, Lu T, Yankner BA, Campisi J, Elledge SJ	Science (New York, N.Y.)	26404840	Science	2015 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/26404840
The aging stress response.	Haigis MC, Yankner BA	Molecular cell	20965426	Mol Cell	2010 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/20965426
Neurodegenerative disorders: Neural synchronization in Alzheimer's disease.	Aron L, Yankner BA	Nature	27929001	Nature	2016 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/27929001
Regulation of lifespan by neural excitation and REST.	Zullo JM, Drake D, Aron L, O'Hern P, Dhamne SC, Davidsohn N, Mao CA, Klein WH, Rotenberg A, Bennett DA, Church GM, Colaiácovo MP, Yankner BA	Nature	31619788	Nature	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31619788
A neurodegeneration checkpoint mediated by REST protects against the onset of Alzheimer's disease.	Aron L, Qiu C, Ngian ZK, Liang M, Drake D, Choi J, Fernandez MA, Roche P, Bunting EL, Lacey EK, Hamplova SE, Yuan M, Wolfe MS, Bennett DA, Lee EA, Yankner BA	Nature communications	37919281	Nat Commun	2023 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/37919281
All-optical osteotomy to create windows for transcranial imaging in mice.	Jeong DC, Tsai PS, Kleinfeld D	Optics express	24104230	Opt Express	2013 Oct 7	https://www.ncbi.nlm.nih.gov/pubmed/24104230
ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation.	Lin JY, Knutsen PM, Muller A, Kleinfeld D, Tsien RY	Nature neuroscience	23995068	Nat Neurosci	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23995068
Two-photon microscopy as a tool to study blood flow and neurovascular coupling in the rodent brain.	Shih AY, Driscoll JD, Drew PJ, Nishimura N, Schaffer CB, Kleinfeld D	Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism	22293983	J Cereb Blood Flow Metab	2012 Jul	https://www.ncbi.nlm.nih.gov/pubmed/22293983
The cortical angiome: an interconnected vascular network with noncolumnar patterns of blood flow.	Blinder P, Tsai PS, Kaufhold JP, Knutsen PM, Suhl H, Kleinfeld D	Nature neuroscience	23749145	Nat Neurosci	2013 Jul	https://www.ncbi.nlm.nih.gov/pubmed/23749145
Differential Multiphoton Laser Scanning Microscopy.	Field JJ, Sheetz KE, Chandler EV, Hoover EE, Young MD, Ding SY, Sylvester AW, Kleinfeld D, Squier JA	IEEE journal of selected topics in quantum electronics : a publication of the IEEE Lasers and Electro-optics Society	27390511	IEEE J Sel Top Quantum Electron	2012 Jan-Feb	https://www.ncbi.nlm.nih.gov/pubmed/27390511
A guide to delineate the logic of neurovascular signaling in the brain.	Kleinfeld D, Blinder P, Drew PJ, Driscoll JD, Muller A, Tsai PS, Shih AY	Frontiers in neuroenergetics	21559095	Front Neuroenergetics	2011	https://www.ncbi.nlm.nih.gov/pubmed/21559095
Photon counting, censor corrections, and lifetime imaging for improved detection in two-photon microscopy.	Driscoll JD, Shih AY, Iyengar S, Field JJ, White GA, Squier JA, Cauwenberghs G, Kleinfeld D	Journal of neurophysiology	21471395	J Neurophysiol	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/21471395
Prospect for feedback guided surgery with ultra-short pulsed laser light.	Jeong DC, Tsai PS, Kleinfeld D	Current opinion in neurobiology	22088392	Curr Opin Neurobiol	2012 Feb	https://www.ncbi.nlm.nih.gov/pubmed/22088392
Quality metrics to accompany spike sorting of extracellular signals.	Hill DN, Mehta SB, Kleinfeld D	The Journal of neuroscience : the official journal of the Society for Neuroscience	21677152	J Neurosci	2011 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/21677152
Cell-based reporters reveal in vivo dynamics of dopamine and norepinephrine release in murine cortex.	Muller A, Joseph V, Slesinger PA, Kleinfeld D	Nature methods	25344639	Nat Methods	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25344639
Large-scale automated histology in the pursuit of connectomes.	Kleinfeld D, Bharioke A, Blinder P, Bock DD, Briggman KL, Chklovskii DB, Denk W, Helmstaedter M, Kaufhold JP, Lee WC, Meyer HS, Micheva KD, Oberlaender M, Prohaska S, Reid RC, Smith SJ, Takemura S, Tsai PS, Sakmann B	The Journal of neuroscience : the official journal of the Society for Neuroscience	22072665	J Neurosci	2011 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/22072665
The roadmap for estimation of cell-type-specific neuronal activity from non-invasive measurements.	Uhlirova H, Kılıç K, Tian P, Sakadžić S, Gagnon L, Thunemann M, Desjardins M, Saisan PA, Nizar K, Yaseen MA, Hagler DJ Jr, Vandenberghe M, Djurovic S, Andreassen OA, Silva GA, Masliah E, Kleinfeld D, Vinogradov S, Buxton RB, Einevoll GT, Boas DA, Dale AM, Devor A	Philosophical transactions of the Royal Society of London. Series B, Biological sciences	27574309	Philos Trans R Soc Lond B Biol Sci	2016 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/27574309
Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture.	Shih AY, Rühlmann C, Blinder P, Devor A, Drew PJ, Friedman B, Knutsen PM, Lyden PD, Mateo C, Mellander L, Nishimura N, Schaffer CB, Tsai PS, Kleinfeld D	Microcirculation (New York, N.Y. : 1994)	25705966	Microcirculation	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25705966
Ultra-large field-of-view two-photon microscopy.	Tsai PS, Mateo C, Field JJ, Schaffer CB, Anderson ME, Kleinfeld D	Optics express	26072755	Opt Express	2015 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/26072755
Fluctuating and sensory-induced vasodynamics in rodent cortex extend arteriole capacity.	Drew PJ, Shih AY, Kleinfeld D	Proceedings of the National Academy of Sciences of the United States of America	21536897	Proc Natl Acad Sci U S A	2011 May 17	https://www.ncbi.nlm.nih.gov/pubmed/21536897
The smallest stroke: occlusion of one penetrating vessel leads to infarction and a cognitive deficit.	Shih AY, Blinder P, Tsai PS, Friedman B, Stanley G, Lyden PD, Kleinfeld D	Nature neuroscience	23242312	Nat Neurosci	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23242312
Vectorization of optically sectioned brain microvasculature: learning aids completion of vascular graphs by connecting gaps and deleting open-ended segments.	Kaufhold JP, Tsai PS, Blinder P, Kleinfeld D	Medical image analysis	22854035	Med Image Anal	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22854035
The challenge of connecting the dots in the B.R.A.I.N.	Devor A, Bandettini PA, Boas DA, Bower JM, Buxton RB, Cohen LB, Dale AM, Einevoll GT, Fox PT, Franceschini MA, Friston KJ, Fujimoto JG, Geyer MA, Greenberg JH, Halgren E, Hämäläinen MS, Helmchen F, Hyman BT, Jasanoff A, Jernigan TL, Judd LL, Kim SG, Kleinfeld D, Kopell NJ, Kutas M, Kwong KK, Larkum ME, Lo EH, Magistretti PJ, Mandeville JB, Masliah E, Mitra PP, Mobley WC, Moskowitz MA, Nimmerjahn A, Reynolds JH, Rosen BR, Salzberg BM, Schaffer CB, Silva GA, So PT, Spitzer NC, Tootell RB, Van Essen DC, Vanduffel W, Vinogradov SA, Wald LL, Wang LV, Weber B, Yodh AG	Neuron	24139032	Neuron	2013 Oct 16	https://www.ncbi.nlm.nih.gov/pubmed/24139032
A polished and reinforced thinned-skull window for long-term imaging of the mouse brain.	Shih AY, Mateo C, Drew PJ, Tsai PS, Kleinfeld D	Journal of visualized experiments : JoVE	22433225	J Vis Exp	2012 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/22433225
Characterizing ligand-gated ion channel receptors with genetically encoded Ca2++ sensors.	Yamauchi JG, Nemecz Á, Nguyen QT, Muller A, Schroeder LF, Talley TT, Lindstrom J, Kleinfeld D, Taylor P	PloS one	21305050	PLoS One	2011 Jan 28	https://www.ncbi.nlm.nih.gov/pubmed/21305050
Chronic optical access through a polished and reinforced thinned skull.	Drew PJ, Shih AY, Driscoll JD, Knutsen PM, Blinder P, Davalos D, Akassoglou K, Tsai PS, Kleinfeld D	Nature methods	20966916	Nat Methods	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20966916
The capillary bed offers the largest hemodynamic resistance to the cortical blood supply.	Gould IG, Tsai P, Kleinfeld D, Linninger A	Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism	27780904	J Cereb Blood Flow Metab	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27780904
Construction of Cell-based Neurotransmitter Fluorescent Engineered Reporters (CNiFERs) for Optical Detection of Neurotransmitters In Vivo.	Lacin E, Muller A, Fernando M, Kleinfeld D, Slesinger PA	Journal of visualized experiments : JoVE	27214050	J Vis Exp	2016 May 12	https://www.ncbi.nlm.nih.gov/pubmed/27214050
Precision mapping of the vibrissa representation within murine primary somatosensory cortex.	Knutsen PM, Mateo C, Kleinfeld D	Philosophical transactions of the Royal Society of London. Series B, Biological sciences	27574305	Philos Trans R Soc Lond B Biol Sci	2016 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/27574305
Automatic identification of fluorescently labeled brain cells for rapid functional imaging.	Valmianski I, Shih AY, Driscoll JD, Matthews DW, Freund Y, Kleinfeld D	Journal of neurophysiology	20610792	J Neurophysiol	2010 Sep	https://www.ncbi.nlm.nih.gov/pubmed/20610792
The miRNA Regulation of Stem Cells.	Huang XA, Lin H	Wiley interdisciplinary reviews. Membrane transport and signaling	23024929	Wiley Interdiscip Rev Membr Transp Signal	2012 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/23024929
A major epigenetic programming mechanism guided by piRNAs.	Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H	Developmental cell	23434410	Dev Cell	2013 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/23434410
Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis.	Gonzalez J, Qi H, Liu N, Lin H	Cell reports	26119740	Cell Rep	2015 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/26119740
The microRNA regulation of stem cells.	Huang XA, Lin H	Wiley interdisciplinary reviews. Developmental biology	23801669	Wiley Interdiscip Rev Dev Biol	2012 Jan-Feb	https://www.ncbi.nlm.nih.gov/pubmed/23801669
PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition.	Liu L, Qi H, Wang J, Lin H	Development (Cambridge, England)	21447556	Development	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21447556
The Yb body, a major site for Piwi-associated RNA biogenesis and a gateway for Piwi expression and transport to the nucleus in somatic cells.	Qi H, Watanabe T, Ku HY, Liu N, Zhong M, Lin H	The Journal of biological chemistry	21106531	J Biol Chem	2011 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/21106531
A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster.	Yin H, Sweeney S, Raha D, Snyder M, Lin H	PLoS genetics	22194694	PLoS Genet	2011 Dec	https://www.ncbi.nlm.nih.gov/pubmed/22194694
Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.	Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M	Developmental cell	25805139	Dev Cell	2015 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/25805139
Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms.	Juliano C, Wang J, Lin H	Annual review of genetics	21942366	Annu Rev Genet	2011	https://www.ncbi.nlm.nih.gov/pubmed/21942366
Creating a neuroprosthesis for active tactile exploration of textures.	O'Doherty JE, Shokur S, Medina LE, Lebedev MA, Nicolelis MAL	Proceedings of the National Academy of Sciences of the United States of America	31591224	Proc Natl Acad Sci U S A	2019 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/31591224
Active tactile exploration using a brain-machine-brain interface.	O'Doherty JE, Lebedev MA, Ifft PJ, Zhuang KZ, Shokur S, Bleuler H, Nicolelis MA	Nature	21976021	Nature	2011 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/21976021
Chronic, wireless recordings of large-scale brain activity in freely moving rhesus monkeys.	Schwarz DA, Lebedev MA, Hanson TL, Dimitrov DF, Lehew G, Meloy J, Rajangam S, Subramanian V, Ifft PJ, Li Z, Ramakrishnan A, Tate A, Zhuang KZ, Nicolelis MA	Nature methods	24776634	Nat Methods	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24776634
Chronic spinal cord electrical stimulation protects against 6-hydroxydopamine lesions.	Yadav AP, Fuentes R, Zhang H, Vinholo T, Wang CH, Freire MA, Nicolelis MA	Scientific reports	24452435	Sci Rep	2014 Jan 23	https://www.ncbi.nlm.nih.gov/pubmed/24452435
Adaptive decoding for brain-machine interfaces through Bayesian parameter updates.	Li Z, O'Doherty JE, Lebedev MA, Nicolelis MA	Neural computation	21919788	Neural Comput	2011 Dec	https://www.ncbi.nlm.nih.gov/pubmed/21919788
Reprogramming movements: extraction of motor intentions from cortical ensemble activity when movement goals change.	Ifft PJ, Lebedev MA, Nicolelis MA	Frontiers in neuroengineering	22826698	Front Neuroeng	2012	https://www.ncbi.nlm.nih.gov/pubmed/22826698
A Brain to Spine Interface for Transferring Artificial Sensory Information.	Yadav AP, Li D, Nicolelis MAL	Scientific reports	31964948	Sci Rep	2020 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/31964948
Analysis of neuronal ensemble activity reveals the pitfalls and shortcomings of rotation dynamics.	Lebedev MA, Ossadtchi A, Mill NA, Urpí NA, Cervera MR, Nicolelis MAL	Scientific reports	31831758	Sci Rep	2019 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/31831758
Virtual active touch using randomly patterned intracortical microstimulation.	O'Doherty JE, Lebedev MA, Li Z, Nicolelis MA	IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society	22207642	IEEE Trans Neural Syst Rehabil Eng	2012 Jan	https://www.ncbi.nlm.nih.gov/pubmed/22207642
Stochastic facilitation of artificial tactile sensation in primates.	Medina LE, Lebedev MA, O'Doherty JE, Nicolelis MA	The Journal of neuroscience : the official journal of the Society for Neuroscience	23055496	J Neurosci	2012 Oct 10	https://www.ncbi.nlm.nih.gov/pubmed/23055496
Cortical correlates of fitts' law.	Ifft PJ, Lebedev MA, Nicolelis MA	Frontiers in integrative neuroscience	22275888	Front Integr Neurosci	2011	https://www.ncbi.nlm.nih.gov/pubmed/22275888
High-side digitally current controlled biphasic bipolar microstimulator.	Hanson TL, Ómarsson B, O'Doherty JE, Peikon ID, Lebedev MA, Nicolelis MA	IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society	22328184	IEEE Trans Neural Syst Rehabil Eng	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22328184
Subcortical neuronal ensembles: an analysis of motor task association, tremor, oscillations, and synchrony in human patients.	Hanson TL, Fuller AM, Lebedev MA, Turner DA, Nicolelis MA	The Journal of neuroscience : the official journal of the Society for Neuroscience	22723703	J Neurosci	2012 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/22723703
A simple and efficient route to the FKBP-binding domain from rapamycin.	Li W, Bhat S, Liu JO	Tetrahedron letters	21894238	Tetrahedron Lett	2011 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/21894238
Rapamycin-inspired macrocycles with new target specificity.	Guo Z, Hong SY, Wang J, Rehan S, Liu W, Peng H, Das M, Li W, Bhat S, Peiffer B, Ullman BR, Tse CM, Tarmakova Z, Schiene-Fischer C, Fischer G, Coe I, Paavilainen VO, Sun Z, Liu JO	Nature chemistry	30532015	Nat Chem	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30532015
Evaluation of the pathogenesis and treatment of Mycobacterium marinum infection in zebrafish.	Takaki K, Davis JM, Winglee K, Ramakrishnan L	Nature protocols	23680983	Nat Protoc	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23680983
Computer-Assisted Transgenesis of Caenorhabditis elegans for Deep Phenotyping.	Gilleland CL, Falls AT, Noraky J, Heiman MG, Yanik MF	Genetics	26163188	Genetics	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/26163188
Mycobacteria manipulate macrophage recruitment through coordinated use of membrane lipids.	Cambier CJ, Takaki KK, Larson RP, Hernandez RE, Tobin DM, Urdahl KB, Cosma CL, Ramakrishnan L	Nature	24336213	Nature	2014 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/24336213
Combinatorial programming of human neuronal progenitors using magnetically-guided stoichiometric mRNA delivery.	Azimi SM, Sheridan SD, Ghannad-Rezaie M, Eimon PM, Yanik MF	eLife	29714688	Elife	2018 May 1	https://www.ncbi.nlm.nih.gov/pubmed/29714688
Verapamil, and its metabolite norverapamil, inhibit macrophage-induced, bacterial efflux pump-mediated tolerance to multiple anti-tubercular drugs.	Adams KN, Szumowski JD, Ramakrishnan L	The Journal of infectious diseases	24532601	J Infect Dis	2014 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/24532601
TNF dually mediates resistance and susceptibility to mycobacteria via mitochondrial reactive oxygen species.	Roca FJ, Ramakrishnan L	Cell	23582643	Cell	2013 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/23582643
Strategic protein target analysis for developing drugs to stop dental caries.	Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD	Advances in dental research	22899687	Adv Dent Res	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22899687
Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications.	Fine J, Lackner R, Samudrala R, Chopra G	Scientific reports	31511563	Sci Rep	2019 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/31511563
Shotgun drug repurposing biotechnology to tackle epidemics and pandemics.	Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R	Drug discovery today	32405249	Drug Discov Today	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32405249
Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing.	Schuler J, Samudrala R	ACS omega	31656912	ACS Omega	2019 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/31656912
Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK.	Falls Z, Fine J, Chopra G, Samudrala R	Frontiers in chemistry	35111726	Front Chem	2021	https://www.ncbi.nlm.nih.gov/pubmed/35111726
Optimal COVID-19 therapeutic candidate discovery using the CANDO platform.	Mangione W, Falls Z, Samudrala R	Frontiers in pharmacology	36091793	Front Pharmacol	2022	https://www.ncbi.nlm.nih.gov/pubmed/36091793
Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform.	Chopra G, Samudrala R	Current pharmaceutical design	27013226	Curr Pharm Des	2016	https://www.ncbi.nlm.nih.gov/pubmed/27013226
Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils.	Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S	Biomacromolecules	22974364	Biomacromolecules	2012 Nov 12	https://www.ncbi.nlm.nih.gov/pubmed/22974364
Computational Grafting of Epitopes.	Manish M, Mishra S, Pahuja M, Anand A, Subbarao N, Samudrala R	Methods in molecular biology (Clifton, N.J.)	37258909	Methods Mol Biol	2023	https://www.ncbi.nlm.nih.gov/pubmed/37258909
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms.	Van Norden M, Mangione W, Falls Z, Samudrala R	bioRxiv : the preprint server for biology	39764006	bioRxiv	2024 Dec 16	https://www.ncbi.nlm.nih.gov/pubmed/39764006
The enzymatic and metabolic capabilities of early life.	Goldman AD, Baross JA, Samudrala R	PloS one	22970111	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22970111
CANDO and the infinite drug discovery frontier.	Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R	Drug discovery today	24980786	Drug Discov Today	2014 Sep	https://www.ncbi.nlm.nih.gov/pubmed/24980786
Structure prediction of partial-length protein sequences.	Laurenzi A, Hung LH, Samudrala R	International journal of molecular sciences	23867606	Int J Mol Sci	2013 Jul 17	https://www.ncbi.nlm.nih.gov/pubmed/23867606
A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment.	Schuler J, Hudson ML, Schwartz D, Samudrala R	Molecules (Basel, Switzerland)	29053626	Molecules	2017 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/29053626
Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform.	Sethi G, Chopra G, Samudrala R	Mini reviews in medicinal chemistry	25694071	Mini Rev Med Chem	2015	https://www.ncbi.nlm.nih.gov/pubmed/25694071
Combating Ebola with Repurposed Therapeutics Using the CANDO Platform.	Chopra G, Kaushik S, Elkin PL, Samudrala R	Molecules (Basel, Switzerland)	27898018	Molecules	2016 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/27898018
Shotgun drug repurposing biotechnology to tackle epidemics and pandemics.	Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R	ChemRxiv : the preprint server for chemistry	32511286	ChemRxiv	2020 May 4	https://www.ncbi.nlm.nih.gov/pubmed/32511286
Association of C>U RNA Editing with Human Disease Variants.	Mandloi S, Falls Z, Deng R, Samudrala R, Elkin PL	Studies in health technology and informatics	32570581	Stud Health Technol Inform	2020 Jun 16	https://www.ncbi.nlm.nih.gov/pubmed/32570581
Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function.	Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M, Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T, Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M	Nature communications	34172723	Nat Commun	2021 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/34172723
Evaluating the performance of drug-repurposing technologies.	Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R	Drug discovery today	34400352	Drug Discov Today	2022 Jan	https://www.ncbi.nlm.nih.gov/pubmed/34400352
The impact of nucleosome structure on CRISPR/Cas9 fidelity.	Handelmann CR, Tsompana M, Samudrala R, Buck MJ	Nucleic acids research	36727449	Nucleic Acids Res	2023 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/36727449
Exploration of interaction scoring criteria in the CANDO platform.	Falls Z, Mangione W, Schuler J, Samudrala R	BMC research notes	31174591	BMC Res Notes	2019 Jun 7	https://www.ncbi.nlm.nih.gov/pubmed/31174591
The Promise and Challenge of Digital Biology.	Minie ME, Samudrala R	Journal of bioengineering & biomedical science	30338132	J Bioeng Biomed Sci	2013	https://www.ncbi.nlm.nih.gov/pubmed/30338132
A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex.	Chatrikhi R, Feeney CF, Pulvino MJ, Alachouzos G, MacRae AJ, Falls Z, Rai S, Brennessel WW, Jenkins JL, Walter MJ, Graubert TA, Samudrala R, Jurica MS, Frontier AJ, Kielkopf CL	Cell chemical biology	33689684	Cell Chem Biol	2021 Aug 19	https://www.ncbi.nlm.nih.gov/pubmed/33689684
Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Corrigendum.	Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Dementiev A, Abad-Zapatero C, Movahedzadeh F	Acta crystallographica. Section F, Structural biology communications	32254053	Acta Crystallogr F Struct Biol Commun	2020 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/32254053
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates.	Moughon SE, Samudrala R	BMC bioinformatics	21920038	BMC Bioinformatics	2011 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/21920038
Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions.	Bruggemann L, Hawthorne C, Samudrala R, Lopez-Campos GH	Studies in health technology and informatics	32570644	Stud Health Technol Inform	2020 Jun 16	https://www.ncbi.nlm.nih.gov/pubmed/32570644
Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease.	Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R	Pharmaceuticals (Basel, Switzerland)	35631392	Pharmaceuticals (Basel)	2022 May 1	https://www.ncbi.nlm.nih.gov/pubmed/35631392
A Deep-Learning Proteomic-Scale Approach for Drug Design.	Overhoff B, Falls Z, Mangione W, Samudrala R	Pharmaceuticals (Basel, Switzerland)	34959678	Pharmaceuticals (Basel)	2021 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/34959678
Accelerated protein structure comparison using TM-score-GPU.	Hung LH, Samudrala R	Bioinformatics (Oxford, England)	22718788	Bioinformatics	2012 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/22718788
Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform.	Hudson ML, Samudrala R	Molecules (Basel, Switzerland)	33925237	Molecules	2021 Apr 28	https://www.ncbi.nlm.nih.gov/pubmed/33925237
A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition.	Dey-Rao R, Smith GR, Timilsina U, Falls Z, Samudrala R, Stavrou S, Melendy T	Antiviral research	34626674	Antiviral Res	2021 Nov	https://www.ncbi.nlm.nih.gov/pubmed/34626674
Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization.	Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Movahedzadeh F	Acta crystallographica. Section F, Structural biology communications	31584013	Acta Crystallogr F Struct Biol Commun	2019 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/31584013
Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens.	Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA	BMC plant biology	23497186	BMC Plant Biol	2013 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/23497186
Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology.	Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao M, Samudrala R	Molecules (Basel, Switzerland)	35566372	Molecules	2022 May 8	https://www.ncbi.nlm.nih.gov/pubmed/35566372
Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using the CANDO Platform: Implications for Drug Design.	Mangione W, Samudrala R	Molecules (Basel, Switzerland)	30621144	Molecules	2019 Jan 4	https://www.ncbi.nlm.nih.gov/pubmed/30621144
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials.	Fine J, Konc J, Samudrala R, Chopra G	Journal of chemical information and modeling	32069042	J Chem Inf Model	2020 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/32069042
cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data.	Mangione W, Falls Z, Chopra G, Samudrala R	Journal of chemical information and modeling	32515949	J Chem Inf Model	2020 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/32515949
Antiviral Approaches against Influenza Virus.	Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls Z, Samudrala R, Pohl J, Knight PR, Sambhara S	Clinical microbiology reviews	36645300	Clin Microbiol Rev	2023 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/36645300
Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer.	Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S, Aalinkeel R, Mahajan SD, Samudrala R	International journal of molecular sciences	36674513	Int J Mol Sci	2023 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/36674513
A founder mutation in LEPRE1 carried by 1.5% of West Africans and 0.4% of African Americans causes lethal recessive osteogenesis imperfecta.	Cabral WA, Barnes AM, Adeyemo A, Cushing K, Chitayat D, Porter FD, Panny SR, Gulamali-Majid F, Tishkoff SA, Rebbeck TR, Gueye SM, Bailey-Wilson JE, Brody LC, Rotimi CN, Marini JC	Genetics in medicine : official journal of the American College of Medical Genetics	22281939	Genet Med	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22281939
Living the high life: high-altitude adaptation.	Scheinfeldt LB, Tishkoff SA	Genome biology	20979669	Genome Biol	2010	https://www.ncbi.nlm.nih.gov/pubmed/20979669
Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations.	Ko WY, Kaercher KA, Giombini E, Marcatili P, Froment A, Ibrahim M, Lema G, Nyambo TB, Omar SA, Wambebe C, Ranciaro A, Hirbo JB, Tishkoff SA	American journal of human genetics	21664997	Am J Hum Genet	2011 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/21664997
Haplotype variation and genotype imputation in African populations.	Huang L, Jakobsson M, Pemberton TJ, Ibrahim M, Nyambo T, Omar S, Pritchard JK, Tishkoff SA, Rosenberg NA	Genetic epidemiology	22125220	Genet Epidemiol	2011 Dec	https://www.ncbi.nlm.nih.gov/pubmed/22125220
Recent human adaptation: genomic approaches, interpretation and insights.	Scheinfeldt LB, Tishkoff SA	Nature reviews. Genetics	24052086	Nat Rev Genet	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24052086
Evolution of functionally diverse alleles associated with PTC bitter taste sensitivity in Africa.	Campbell MC, Ranciaro A, Froment A, Hirbo J, Omar S, Bodo JM, Nyambo T, Lema G, Zinshteyn D, Drayna D, Breslin PA, Tishkoff SA	Molecular biology and evolution	22130969	Mol Biol Evol	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22130969
Obesity-susceptibility loci and the tails of the pediatric BMI distribution.	Mitchell JA, Hakonarson H, Rebbeck TR, Grant SF	Obesity (Silver Spring, Md.)	23408508	Obesity (Silver Spring)	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23408508
The evolution of human genetic and phenotypic variation in Africa.	Campbell MC, Tishkoff SA	Current biology : CB	20178763	Curr Biol	2010 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/20178763
Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies.	Jarvis JP, Scheinfeldt LB, Soi S, Lambert C, Omberg L, Ferwerda B, Froment A, Bodo JM, Beggs W, Hoffman G, Mezey J, Tishkoff SA	PLoS genetics	22570615	PLoS Genet	2012	https://www.ncbi.nlm.nih.gov/pubmed/22570615
Genetic structure in African populations: implications for human demographic history.	Lambert CA, Tishkoff SA	Cold Spring Harbor symposia on quantitative biology	20453204	Cold Spring Harb Symp Quant Biol	2009	https://www.ncbi.nlm.nih.gov/pubmed/20453204
Evidence from Cameroon reveals differences in the genetic structure and histories of chimpanzee populations.	Gonder MK, Locatelli S, Ghobrial L, Mitchell MW, Kujawski JT, Lankester FJ, Stewart CB, Tishkoff SA	Proceedings of the National Academy of Sciences of the United States of America	21368170	Proc Natl Acad Sci U S A	2011 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/21368170
Colloquium paper: working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history.	Scheinfeldt LB, Soi S, Tishkoff SA	Proceedings of the National Academy of Sciences of the United States of America	20445100	Proc Natl Acad Sci U S A	2010 May 11	https://www.ncbi.nlm.nih.gov/pubmed/20445100
Characterization of genetic variation and natural selection at the arylamine N-acetyltransferase genes in global human populations.	Mortensen HM, Froment A, Lema G, Bodo JM, Ibrahim M, Nyambo TB, Omar SA, Tishkoff SA	Pharmacogenomics	21995608	Pharmacogenomics	2011 Nov	https://www.ncbi.nlm.nih.gov/pubmed/21995608
Patterns of nucleotide and haplotype diversity at ICAM-1 across global human populations with varying levels of malaria exposure.	Gomez F, Tomas G, Ko WY, Ranciaro A, Froment A, Ibrahim M, Lema G, Nyambo TB, Omar SA, Wambebe C, Hirbo JB, Rocha J, Tishkoff SA	Human genetics	23609612	Hum Genet	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23609612
Patient-derived xenografts of low-grade B-cell lymphomas demonstrate roles of the tumor microenvironment.	Burack WR, Spence JM, Spence JP, Spence SA, Rock PJ, Shenoy GN, Shultz LD, Bankert RB, Bernstein SH	Blood advances	29296768	Blood Adv	2017 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/29296768
Small heat shock proteins in redox metabolism: implications for cardiovascular diseases.	Christians ES, Ishiwata T, Benjamin IJ	The international journal of biochemistry & cell biology	22710345	Int J Biochem Cell Biol	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22710345
Targeting endoglin, an auxiliary transforming growth factor β coreceptor, to prevent fibrosis and heart failure.	Benjamin IJ	Circulation	22592899	Circulation	2012 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/22592899
Human alpha B-crystallin mutation causes oxido-reductive stress and protein aggregation cardiomyopathy in mice.	Rajasekaran NS, Connell P, Christians ES, Yan LJ, Taylor RP, Orosz A, Zhang XQ, Stevenson TJ, Peshock RM, Leopold JA, Barry WH, Loscalzo J, Odelberg SJ, Benjamin IJ	Cell	17693254	Cell	2007 Aug 10	https://www.ncbi.nlm.nih.gov/pubmed/17693254
Profibrotic COVID-19 subphenotype exhibits enhanced localized ER-dependent HSP47(+) expression in cardiac myofibroblasts in situ.	Jacobs ER, Ross GR, Padilla N, Pan AY, Liegl M, Puzyrenko A, Lai S, Dai Q, Uche N, Rubenstein JC, North PE, Ibrahim EH, Sun Y, Felix JC, Rui H, Benjamin IJ	Journal of molecular and cellular cardiology	37839656	J Mol Cell Cardiol	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37839656
HSPB2 is dispensable for the cardiac hypertrophic response but reduces mitochondrial energetics following pressure overload in mice.	Ishiwata T, Orosz A, Wang X, Mustafi SB, Pratt GW, Christians ES, Boudina S, Abel ED, Benjamin IJ	PloS one	22870288	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22870288
Glutathione-dependent reductive stress triggers mitochondrial oxidation and cytotoxicity.	Zhang H, Limphong P, Pieper J, Liu Q, Rodesch CK, Christians E, Benjamin IJ	FASEB journal : official publication of the Federation of American Societies for Experimental Biology	22202674	FASEB J	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22202674
Sustained activation of nuclear erythroid 2-related factor 2/antioxidant response element signaling promotes reductive stress in the human mutant protein aggregation cardiomyopathy in mice.	Rajasekaran NS, Varadharaj S, Khanderao GD, Davidson CJ, Kannan S, Firpo MA, Zweier JL, Benjamin IJ	Antioxidants & redox signaling	21126175	Antioxid Redox Signal	2011 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/21126175
Rescue of αB Crystallin (HSPB5) Mutants Associated Protein Aggregation by Co-Expression of HSPB5 Partners.	Hussein RM, Benjamin IJ, Kampinga HH	PloS one	25961584	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/25961584
Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome.	Grose JH, Langston K, Wang X, Squires S, Mustafi SB, Hayes W, Neubert J, Fischer SK, Fasano M, Saunders GM, Dai Q, Christians E, Lewandowski ED, Ping P, Benjamin IJ	PloS one	26465331	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26465331
Selective degradation of aggregate-prone CryAB mutants by HSPB1 is mediated by ubiquitin-proteasome pathways.	Zhang H, Rajasekaran NS, Orosz A, Xiao X, Rechsteiner M, Benjamin IJ	Journal of molecular and cellular cardiology	20863832	J Mol Cell Cardiol	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20863832
Chaperones and cardiac misfolding protein diseases.	Christians ES, Mustafi SB, Benjamin IJ	Current protein & peptide science	24694370	Curr Protein Pept Sci	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24694370
Aggregate-prone R120GCRYAB triggers multifaceted modifications of the thioredoxin system.	Banerjee Mustafi S, Grose JH, Zhang H, Pratt GW, Sadoshima J, Christians ES, Benjamin IJ	Antioxidants & redox signaling	24180415	Antioxid Redox Signal	2014 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/24180415
Reductive stress linked to small HSPs, G6PD, and Nrf2 pathways in heart disease.	Brewer AC, Mustafi SB, Murray TV, Rajasekaran NS, Benjamin IJ	Antioxidants & redox signaling	22938199	Antioxid Redox Signal	2013 Mar 20	https://www.ncbi.nlm.nih.gov/pubmed/22938199
Effects of redox state on the efficient uptake of cell permeable Peptide in Mammalian cells.	Squires S, Christians E, Riedel M, Timothy D, Rodesch CK, Marvin J, Benjamin I	The open biochemistry journal	23919090	Open Biochem J	2013	https://www.ncbi.nlm.nih.gov/pubmed/23919090
The NADPH metabolic network regulates human αB-crystallin cardiomyopathy and reductive stress in Drosophila melanogaster.	Xie HB, Cammarato A, Rajasekaran NS, Zhang H, Suggs JA, Lin HC, Bernstein SI, Benjamin IJ, Golic KG	PLoS genetics	23818860	PLoS Genet	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23818860
HSF1 critically attunes proteotoxic stress sensing by mTORC1 to combat stress and promote growth.	Su KH, Cao J, Tang Z, Dai S, He Y, Sampson SB, Benjamin IJ, Dai C	Nature cell biology	27043084	Nat Cell Biol	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/27043084
Proteostasis and REDOX state in the heart.	Christians ES, Benjamin IJ	American journal of physiology. Heart and circulatory physiology	22003057	Am J Physiol Heart Circ Physiol	2012 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/22003057
Knockout of Lysosomal Enzyme-Targeting Gene Causes Abnormalities in Mouse Pup Isolation Calls.	Barnes TD, Holy TE	Frontiers in behavioral neuroscience	28101008	Front Behav Neurosci	2016	https://www.ncbi.nlm.nih.gov/pubmed/28101008
Vasoactive intestinal polypeptide mediates circadian rhythms in mammalian olfactory bulb and olfaction.	Miller JE, Granados-Fuentes D, Wang T, Marpegan L, Holy TE, Herzog ED	The Journal of neuroscience : the official journal of the Society for Neuroscience	24760863	J Neurosci	2014 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/24760863
Organization of vomeronasal sensory coding revealed by fast volumetric calcium imaging.	Turaga D, Holy TE	The Journal of neuroscience : the official journal of the Society for Neuroscience	22302803	J Neurosci	2012 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/22302803
Experience-Dependent Plasticity Drives Individual Differences in Pheromone-Sensing Neurons.	Xu PS, Lee D, Holy TE	Neuron	27537487	Neuron	2016 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/27537487
A Mutation Associated with Stuttering Alters Mouse Pup Ultrasonic Vocalizations.	Barnes TD, Wozniak DF, Gutierrez J, Han TU, Drayna D, Holy TE	Current biology : CB	27151663	Curr Biol	2016 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/27151663
mir-181a-1/b-1 Modulates Tolerance through Opposing Activities in Selection and Peripheral T Cell Function.	Schaffert SA, Loh C, Wang S, Arnold CP, Axtell RC, Newell EW, Nolan G, Ansel KM, Davis MM, Steinman L, Chen CZ	Journal of immunology (Baltimore, Md. : 1950)	26163591	J Immunol	2015 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/26163591
The Mir181ab1 cluster promotes KRAS-driven oncogenesis and progression in lung and pancreas.	Valencia K, Erice O, Kostyrko K, Hausmann S, Guruceaga E, Tathireddy A, Flores NM, Sayles LC, Lee AG, Fragoso R, Sun TQ, Vallejo A, Roman M, Entrialgo-Cadierno R, Migueliz I, Razquin N, Fortes P, Lecanda F, Lu J, Ponz-Sarvise M, Chen CZ, Mazur PK, Sweet-Cordero EA, Vicent S	The Journal of clinical investigation	31874105	J Clin Invest	2020 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/31874105
MicroRNAs regulate B-cell receptor signaling-induced apoptosis.	Kluiver JL, Chen CZ	Genes and immunity	22357493	Genes Immun	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22357493
Modulating the strength and threshold of NOTCH oncogenic signals by mir-181a-1/b-1.	Fragoso R, Mao T, Wang S, Schaffert S, Gong X, Yue S, Luong R, Min H, Yashiro-Ohtani Y, Davis M, Pear W, Chen CZ	PLoS genetics	22916024	PLoS Genet	2012	https://www.ncbi.nlm.nih.gov/pubmed/22916024
The miR-17-92 microRNA polycistron regulates MLL leukemia stem cell potential by modulating p21 expression.	Wong P, Iwasaki M, Somervaille TC, Ficara F, Carico C, Arnold C, Chen CZ, Cleary ML	Cancer research	20406979	Cancer Res	2010 May 1	https://www.ncbi.nlm.nih.gov/pubmed/20406979
Loop nucleotides control primary and mature miRNA function in target recognition and repression.	Yue SB, Trujillo RD, Tang Y, O'Gorman WE, Chen CZ	RNA biology	22142974	RNA Biol	2011 Nov-Dec	https://www.ncbi.nlm.nih.gov/pubmed/22142974
An unsolved mystery: the target-recognizing RNA species of microRNA genes.	Chen CZ	Biochimie	23685275	Biochimie	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23685275
The potential functions of primary microRNAs in target recognition and repression.	Trujillo RD, Yue SB, Tang Y, O'Gorman WE, Chen CZ	The EMBO journal	20808284	EMBO J	2010 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/20808284
Regulation of immune responses and tolerance: the microRNA perspective.	Chen CZ, Schaffert S, Fragoso R, Loh C	Immunological reviews	23550642	Immunol Rev	2013 May	https://www.ncbi.nlm.nih.gov/pubmed/23550642
Pre-miRNA loop nucleotides control the distinct activities of mir-181a-1 and mir-181c in early T cell development.	Liu G, Min H, Yue S, Chen CZ	PloS one	18974849	PLoS One	2008	https://www.ncbi.nlm.nih.gov/pubmed/18974849
MicroRNA programs in normal and aberrant stem and progenitor cells.	Arnold CP, Tan R, Zhou B, Yue SB, Schaffert S, Biggs JR, Doyonnas R, Lo MC, Perry JM, Renault VM, Sacco A, Somervaille T, Viatour P, Brunet A, Cleary ML, Li L, Sage J, Zhang DE, Blau HM, Chen C, Chen CZ	Genome research	21451113	Genome Res	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21451113
Transcriptional reprogramming of mature CD4⁺ helper T cells generates distinct MHC class II-restricted cytotoxic T lymphocytes.	Mucida D, Husain MM, Muroi S, van Wijk F, Shinnakasu R, Naoe Y, Reis BS, Huang Y, Lambolez F, Docherty M, Attinger A, Shui JW, Kim G, Lena CJ, Sakaguchi S, Miyamoto C, Wang P, Atarashi K, Park Y, Nakayama T, Honda K, Ellmeier W, Kronenberg M, Taniuchi I, Cheroutre H	Nature immunology	23334788	Nat Immunol	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23334788
Themis sets the signal threshold for positive and negative selection in T-cell development.	Fu G, Casas J, Rigaud S, Rybakin V, Lambolez F, Brzostek J, Hoerter JA, Paster W, Acuto O, Cheroutre H, Sauer K, Gascoigne NR	Nature	24226767	Nature	2013 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/24226767
The importance of being earnestly selfish.	Cheroutre H, Mucida D, Lambolez F	Nature immunology	19767722	Nat Immunol	2009 Oct	https://www.ncbi.nlm.nih.gov/pubmed/19767722
Unique lamina propria stromal cells imprint the functional phenotype of mucosal dendritic cells.	Vicente-Suarez I, Larange A, Reardon C, Matho M, Feau S, Chodaczek G, Park Y, Obata Y, Gold R, Wang-Zhu Y, Lena C, Zajonc DM, Schoenberger SP, Kronenberg M, Cheroutre H	Mucosal immunology	24938743	Mucosal Immunol	2015 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24938743
αβT cell receptors expressed by CD4(-)CD8αβ(-) intraepithelial T cells drive their fate into a unique lineage with unusual MHC reactivities.	Mayans S, Stepniak D, Palida S, Larange A, Dreux J, Arlian B, Shinnakasu R, Kronenberg M, Cheroutre H, Lambolez F	Immunity	25131531	Immunity	2014 Aug 21	https://www.ncbi.nlm.nih.gov/pubmed/25131531
Protein kinase C η is required for T cell activation and homeostatic proliferation.	Fu G, Hu J, Niederberger-Magnenat N, Rybakin V, Casas J, Yachi PP, Feldstein S, Ma B, Hoerter JA, Ampudia J, Rigaud S, Lambolez F, Gavin AL, Sauer K, Cheroutre H, Gascoigne NR	Science signaling	22155788	Sci Signal	2011 Dec 6	https://www.ncbi.nlm.nih.gov/pubmed/22155788
CD4 CTL: living up to the challenge.	Cheroutre H, Husain MM	Seminars in immunology	24246226	Semin Immunol	2013 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/24246226
More effective nanomedicines through particle design.	Wang J, Byrne JD, Napier ME, DeSimone JM	Small (Weinheim an der Bergstrasse, Germany)	21695781	Small	2011 Jul 18	https://www.ncbi.nlm.nih.gov/pubmed/21695781
Using mechanobiological mimicry of red blood cells to extend circulation times of hydrogel microparticles.	Merkel TJ, Jones SW, Herlihy KP, Kersey FR, Shields AR, Napier M, Luft JC, Wu H, Zamboni WC, Wang AZ, Bear JE, DeSimone JM	Proceedings of the National Academy of Sciences of the United States of America	21220299	Proc Natl Acad Sci U S A	2011 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/21220299
Rendering protein-based particles transiently insoluble for therapeutic applications.	Xu J, Wang J, Luft JC, Tian S, Owens G Jr, Pandya AA, Berglund P, Pohlhaus P, Maynor BW, Smith J, Hubby B, Napier ME, DeSimone JM	Journal of the American Chemical Society	22568387	J Am Chem Soc	2012 May 30	https://www.ncbi.nlm.nih.gov/pubmed/22568387
Engineering nanomedicines using stimuli-responsive biomaterials.	Wang Y, Byrne JD, Napier ME, DeSimone JM	Advanced drug delivery reviews	22266128	Adv Drug Deliv Rev	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22266128
Dodging drug-resistant cancer with diamonds.	Merkel TJ, DeSimone JM	Science translational medicine	21389261	Sci Transl Med	2011 Mar 9	https://www.ncbi.nlm.nih.gov/pubmed/21389261
RNA replicon delivery via lipid-complexed PRINT protein particles.	Xu J, Luft JC, Yi X, Tian S, Owens G, Wang J, Johnson A, Berglund P, Smith J, Napier ME, DeSimone JM	Molecular pharmaceutics	23924216	Mol Pharm	2013 Sep 3	https://www.ncbi.nlm.nih.gov/pubmed/23924216
Effect of aspect ratio and deformability on nanoparticle extravasation through nanopores.	Kersey FR, Merkel TJ, Perry JL, Napier ME, DeSimone JM	Langmuir : the ACS journal of surfaces and colloids	22612428	Langmuir	2012 Jun 12	https://www.ncbi.nlm.nih.gov/pubmed/22612428
Tunable bifunctional silyl ether cross-linkers for the design of acid-sensitive biomaterials.	Parrott MC, Luft JC, Byrne JD, Fain JH, Napier ME, Desimone JM	Journal of the American Chemical Society	21105720	J Am Chem Soc	2010 Dec 22	https://www.ncbi.nlm.nih.gov/pubmed/21105720
Subtumoral analysis of PRINT nanoparticle distribution reveals targeting variation based on cellular and particle properties.	Roode LE, Brighton H, Bo T, Perry JL, Parrott MC, Kersey F, Luft JC, Bear JE, DeSimone JM, Davis IJ	Nanomedicine : nanotechnology, biology, and medicine	26772430	Nanomedicine	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/26772430
Local iontophoretic administration of cytotoxic therapies to solid tumors.	Byrne JD, Jajja MR, O'Neill AT, Bickford LR, Keeler AW, Hyder N, Wagner K, Deal A, Little RE, Moffitt RA, Stack C, Nelson M, Brooks CR, Lee W, Luft JC, Napier ME, Darr D, Anders CK, Stack R, Tepper JE, Wang AZ, Zamboni WC, Yeh JJ, DeSimone JM	Science translational medicine	25653220	Sci Transl Med	2015 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/25653220
New insights into immunomodulation via overexpressing lipoic acid synthase as a therapeutic potential to reduce atherosclerosis.	Tian S, Nakamura J, Hiller S, Simington S, Holley DW, Mota R, Willis MS, Bultman SJ, Luft JC, DeSimone JM, Jia Z, Maeda N, Yi X	Vascular pharmacology	32750408	Vascul Pharmacol	2020 Oct-Nov	https://www.ncbi.nlm.nih.gov/pubmed/32750408
Nanoparticle surface charge impacts distribution, uptake and lymph node trafficking by pulmonary antigen-presenting cells.	Fromen CA, Rahhal TB, Robbins GR, Kai MP, Shen TW, Luft JC, DeSimone JM	Nanomedicine : nanotechnology, biology, and medicine	26656533	Nanomedicine	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/26656533
Organic Polymer Chemistry in the Context of Novel Processes.	DeSimone JM, Mecham SJ, Farrell CL	ACS central science	27725955	ACS Cent Sci	2016 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/27725955
Rapidly-dissolvable microneedle patches via a highly scalable and reproducible soft lithography approach.	Moga KA, Bickford LR, Geil RD, Dunn SS, Pandya AA, Wang Y, Fain JH, Archuleta CF, O'Neill AT, Desimone JM	Advanced materials (Deerfield Beach, Fla.)	23893866	Adv Mater	2013 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/23893866
Future of the particle replication in nonwetting templates (PRINT) technology.	Xu J, Wong DH, Byrne JD, Chen K, Bowerman C, DeSimone JM	Angewandte Chemie (International ed. in English)	23670869	Angew Chem Int Ed Engl	2013 Jun 24	https://www.ncbi.nlm.nih.gov/pubmed/23670869
Reductively responsive siRNA-conjugated hydrogel nanoparticles for gene silencing.	Dunn SS, Tian S, Blake S, Wang J, Galloway AL, Murphy A, Pohlhaus PD, Rolland JP, Napier ME, DeSimone JM	Journal of the American Chemical Society	22475061	J Am Chem Soc	2012 May 2	https://www.ncbi.nlm.nih.gov/pubmed/22475061
Controlled analysis of nanoparticle charge on mucosal and systemic antibody responses following pulmonary immunization.	Fromen CA, Robbins GR, Shen TW, Kai MP, Ting JP, DeSimone JM	Proceedings of the National Academy of Sciences of the United States of America	25548169	Proc Natl Acad Sci U S A	2015 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/25548169
Tumor Presence Induces Global Immune Changes and Enhances Nanoparticle Clearance.	Kai MP, Brighton HE, Fromen CA, Shen TW, Luft JC, Luft YE, Keeler AW, Robbins GR, Ting JP, Zamboni WC, Bear JE, DeSimone JM	ACS nano	26592524	ACS Nano	2016 Jan 26	https://www.ncbi.nlm.nih.gov/pubmed/26592524
Distribution and Cellular Uptake of PEGylated Polymeric Particles in the Lung Towards Cell-Specific Targeted Delivery.	Shen TW, Fromen CA, Kai MP, Luft JC, Rahhal TB, Robbins GR, DeSimone JM	Pharmaceutical research	26002743	Pharm Res	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26002743
Retinoic Acid-Loaded Poly(lactic-co-glycolic acid) Nanoparticle Formulation of ApoB-100-Derived Peptide 210 Attenuates Atherosclerosis.	Yi X, Wang Y, Jia Z, Hiller S, Nakamura J, Luft JC, Tian S, DeSimone JM	Journal of biomedical nanotechnology	32970979	J Biomed Nanotechnol	2020 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/32970979
Generating Better Medicines for Cancer.	Dunn SS, Byrne JD, Perry JL, Chen K, Desimone JM	ACS macro letters	23772351	ACS Macro Lett	2013 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/23772351
Anti-Müllerian Hormone in the Domestic Dog during the Anestrus to Oestrous Transition.	Nagashima JB, Hansen BS, Songsasen N, Travis AJ, Place NJ	Reproduction in domestic animals = Zuchthygiene	26708613	Reprod Domest Anim	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/26708613
Characterization of the proteomes associating with three distinct membrane raft sub-types in murine sperm.	Asano A, Nelson JL, Zhang S, Travis AJ	Proteomics	20815087	Proteomics	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20815087
Activation of actin-cardiac myosin subfragment 1 MgATPase rate by Ca2+ shows cooperativity intrinsic to the thin filament.	Tobacman LS	Biochemistry	2950924	Biochemistry	1987 Jan 27	https://www.ncbi.nlm.nih.gov/pubmed/2950924
Lipid modulation of calcium flux through CaV2.3 regulates acrosome exocytosis and fertilization.	Cohen R, Buttke DE, Asano A, Mukai C, Nelson JL, Ren D, Miller RJ, Cohen-Kutner M, Atlas D, Travis AJ	Developmental cell	24525187	Dev Cell	2014 Feb 10	https://www.ncbi.nlm.nih.gov/pubmed/24525187
Use of Tethered Enzymes as a Platform Technology for Rapid Analyte Detection.	Cohen R, Lata JP, Lee Y, Hernández JC, Nishimura N, Schaffer CB, Mukai C, Nelson JL, Brangman SA, Agrawal Y, Travis AJ	PloS one	26605916	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26605916
What sperm can teach us about energy production.	Mukai C, Travis AJ	Reproduction in domestic animals = Zuchthygiene	22827366	Reprod Domest Anim	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22827366
Cysteine dioxygenase is essential for mouse sperm osmoadaptation and male fertility.	Asano A, Roman HB, Hirschberger LL, Ushiyama A, Nelson JL, Hinchman MM, Stipanuk MH, Travis AJ	The FEBS journal	29604178	FEBS J	2018 May	https://www.ncbi.nlm.nih.gov/pubmed/29604178
Phospholipase B is activated in response to sterol removal and stimulates acrosome exocytosis in murine sperm.	Asano A, Nelson-Harrington JL, Travis AJ	The Journal of biological chemistry	23943622	J Biol Chem	2013 Sep 27	https://www.ncbi.nlm.nih.gov/pubmed/23943622
Stem cells in veterinary medicine.	Fortier LA, Travis AJ	Stem cell research & therapy	21371354	Stem Cell Res Ther	2011 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/21371354
Ubiquitin-conjugating enzyme Ubc13 controls breast cancer metastasis through a TAK1-p38 MAP kinase cascade.	Wu X, Zhang W, Font-Burgada J, Palmer T, Hamil AS, Biswas SK, Poidinger M, Borcherding N, Xie Q, Ellies LG, Lytle NK, Wu LW, Fox RG, Yang J, Dowdy SF, Reya T, Karin M	Proceedings of the National Academy of Sciences of the United States of America	25189770	Proc Natl Acad Sci U S A	2014 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/25189770
Lis1 regulates asymmetric division in hematopoietic stem cells and in leukemia.	Zimdahl B, Ito T, Blevins A, Bajaj J, Konuma T, Weeks J, Koechlein CS, Kwon HY, Arami O, Rizzieri D, Broome HE, Chuah C, Oehler VG, Sasik R, Hardiman G, Reya T	Nature genetics	24487275	Nat Genet	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24487275
High-resolution imaging and computational analysis of haematopoietic cell dynamics in vivo.	Koechlein CS, Harris JR, Lee TK, Weeks J, Fox RG, Zimdahl B, Ito T, Blevins A, Jung SH, Chute JP, Chourasia A, Covert MW, Reya T	Nature communications	27425143	Nat Commun	2016 Jul 18	https://www.ncbi.nlm.nih.gov/pubmed/27425143
Tetraspanin 3 Is Required for the Development and Propagation of Acute Myelogenous Leukemia.	Kwon HY, Bajaj J, Ito T, Blevins A, Konuma T, Weeks J, Lytle NK, Koechlein CS, Rizzieri D, Chuah C, Oehler VG, Sasik R, Hardiman G, Reya T	Cell stem cell	26212080	Cell Stem Cell	2015 Aug 6	https://www.ncbi.nlm.nih.gov/pubmed/26212080
Regulation of myeloid leukaemia by the cell-fate determinant Musashi.	Ito T, Kwon HY, Zimdahl B, Congdon KL, Blum J, Lento WE, Zhao C, Lagoo A, Gerrard G, Foroni L, Goldman J, Goh H, Kim SH, Kim DW, Chuah C, Oehler VG, Radich JP, Jordan CT, Reya T	Nature	20639863	Nature	2010 Aug 5	https://www.ncbi.nlm.nih.gov/pubmed/20639863
Loss of β-catenin triggers oxidative stress and impairs hematopoietic regeneration.	Lento W, Ito T, Zhao C, Harris JR, Huang W, Jiang C, Owzar K, Piryani S, Racioppi L, Chao N, Reya T	Genes & development	24788518	Genes Dev	2014 May 1	https://www.ncbi.nlm.nih.gov/pubmed/24788518
Microbiology. Antibiotic resistance, not shaken or stirred.	Frisch RL, Rosenberg SM	Science (New York, N.Y.)	21940884	Science	2011 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/21940884
Isl1 identifies a cardiac progenitor population that proliferates prior to differentiation and contributes a majority of cells to the heart.	Cai CL, Liang X, Shi Y, Chu PH, Pfaff SL, Chen J, Evans S	Developmental cell	14667410	Dev Cell	2003 Dec	https://www.ncbi.nlm.nih.gov/pubmed/14667410
HCN4 dynamically marks the first heart field and conduction system precursors.	Liang X, Wang G, Lin L, Lowe J, Zhang Q, Bu L, Chen Y, Chen J, Sun Y, Evans SM	Circulation research	23743334	Circ Res	2013 Aug 2	https://www.ncbi.nlm.nih.gov/pubmed/23743334
Revisiting Preadolescent Cardiomyocyte Proliferation in Mice.	Hirai M, Cattaneo P, Chen J, Evans SM	Circulation research	26987912	Circ Res	2016 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/26987912
Pericytes of Multiple Organs Do Not Behave as Mesenchymal Stem Cells In Vivo.	Guimarães-Camboa N, Cattaneo P, Sun Y, Moore-Morris T, Gu Y, Dalton ND, Rockenstein E, Masliah E, Peterson KL, Stallcup WB, Chen J, Evans SM	Cell stem cell	28111199	Cell Stem Cell	2017 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/28111199
Are Perivascular Adipocyte Progenitors Mural Cells or Adventitial Fibroblasts?	Guimarães-Camboa N, Evans SM	Cell stem cell	28475883	Cell Stem Cell	2017 May 4	https://www.ncbi.nlm.nih.gov/pubmed/28475883
Infarct Fibroblasts Do Not Derive From Bone Marrow Lineages.	Moore-Morris T, Cattaneo P, Guimarães-Camboa N, Bogomolovas J, Cedenilla M, Banerjee I, Ricote M, Kisseleva T, Zhang L, Gu Y, Dalton ND, Peterson KL, Chen J, Pucéat M, Evans SM	Circulation research	29269349	Circ Res	2018 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/29269349
Cardiac fibroblasts: from development to heart failure.	Moore-Morris T, Guimarães-Camboa N, Yutzey KE, Pucéat M, Evans SM	Journal of molecular medicine (Berlin, Germany)	26169532	J Mol Med (Berl)	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26169532
Development of the cardiac pacemaker.	Liang X, Evans SM, Sun Y	Cellular and molecular life sciences : CMLS	27770149	Cell Mol Life Sci	2017 Apr	https://www.ncbi.nlm.nih.gov/pubmed/27770149
Myocardial lineage development.	Evans SM, Yelon D, Conlon FL, Kirby ML	Circulation research	21148449	Circ Res	2010 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/21148449
A myocardial lineage derives from Tbx18 epicardial cells.	Cai CL, Martin JC, Sun Y, Cui L, Wang L, Ouyang K, Yang L, Bu L, Liang X, Zhang X, Stallcup WB, Denton CP, McCulloch A, Chen J, Evans SM	Nature	18480752	Nature	2008 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/18480752
Localization of Islet-1-positive cells in the healthy and infarcted adult murine heart.	Weinberger F, Mehrkens D, Friedrich FW, Stubbendorff M, Hua X, Müller JC, Schrepfer S, Evans SM, Carrier L, Eschenhagen T	Circulation research	22427341	Circ Res	2012 May 11	https://www.ncbi.nlm.nih.gov/pubmed/22427341
Islet1 regulates establishment of the posterior hindlimb field upstream of the Hand2-Shh morphoregulatory gene network in mouse embryos.	Itou J, Kawakami H, Quach T, Osterwalder M, Evans SM, Zeller R, Kawakami Y	Development (Cambridge, England)	22438573	Development	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22438573
The contribution of Islet1-expressing splanchnic mesoderm cells to distinct branchiomeric muscles reveals significant heterogeneity in head muscle development.	Nathan E, Monovich A, Tirosh-Finkel L, Harrelson Z, Rousso T, Rinon A, Harel I, Evans SM, Tzahor E	Development (Cambridge, England)	18184728	Development	2008 Feb	https://www.ncbi.nlm.nih.gov/pubmed/18184728
Pitx2 regulates cardiac left-right asymmetry by patterning second cardiac lineage-derived myocardium.	Ai D, Liu W, Ma L, Dong F, Lu MF, Wang D, Verzi MP, Cai C, Gage PJ, Evans S, Black BL, Brown NA, Martin JF	Developmental biology	16836994	Dev Biol	2006 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/16836994
HIF1α Represses Cell Stress Pathways to Allow Proliferation of Hypoxic Fetal Cardiomyocytes.	Guimarães-Camboa N, Stowe J, Aneas I, Sakabe N, Cattaneo P, Henderson L, Kilberg MS, Johnson RS, Chen J, McCulloch AD, Nobrega MA, Evans SM, Zambon AC	Developmental cell	26028220	Dev Cell	2015 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/26028220
IL-11 is a crucial determinant of cardiovascular fibrosis.	Schafer S, Viswanathan S, Widjaja AA, Lim WW, Moreno-Moral A, DeLaughter DM, Ng B, Patone G, Chow K, Khin E, Tan J, Chothani SP, Ye L, Rackham OJL, Ko NSJ, Sahib NE, Pua CJ, Zhen NTG, Xie C, Wang M, Maatz H, Lim S, Saar K, Blachut S, Petretto E, Schmidt S, Putoczki T, Guimarães-Camboa N, Wakimoto H, van Heesch S, Sigmundsson K, Lim SL, Soon JL, Chao VTT, Chua YL, Tan TE, Evans SM, Loh YJ, Jamal MH, Ong KK, Chua KC, Ong BH, Chakaramakkil MJ, Seidman JG, Seidman CE, Hubner N, Sin KYK, Cook SA	Nature	29160304	Nature	2017 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/29160304
Smooth muscle origin of postnatal 2nd CVP is pre-determined in early embryo.	Liu Q, Zhang H, Tian X, He L, Huang X, Tan Z, Yan Y, Evans SM, Wythe JD, Zhou B	Biochemical and biophysical research communications	26902114	Biochem Biophys Res Commun	2016 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/26902114
Tissue specific requirements for WNT11 in developing outflow tract and dorsal mesenchymal protrusion.	van Vliet PP, Lin L, Boogerd CJ, Martin JF, Andelfinger G, Grossfeld PD, Evans SM	Developmental biology	28669819	Dev Biol	2017 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/28669819
Postnatal isl1+ cardioblasts enter fully differentiated cardiomyocyte lineages.	Laugwitz KL, Moretti A, Lam J, Gruber P, Chen Y, Woodard S, Lin LZ, Cai CL, Lu MM, Reth M, Platoshyn O, Yuan JX, Evans S, Chien KR	Nature	15703750	Nature	2005 Feb 10	https://www.ncbi.nlm.nih.gov/pubmed/15703750
T-Box transcription factor Tbx20 regulates a genetic program for cranial motor neuron cell body migration.	Song MR, Shirasaki R, Cai CL, Ruiz EC, Evans SM, Lee SK, Pfaff SL	Development (Cambridge, England)	17119020	Development	2006 Dec	https://www.ncbi.nlm.nih.gov/pubmed/17119020
Isl1Cre reveals a common Bmp pathway in heart and limb development.	Yang L, Cai CL, Lin L, Qyang Y, Chung C, Monteiro RM, Mummery CL, Fishman GI, Cogen A, Evans S	Development (Cambridge, England)	16556916	Development	2006 Apr	https://www.ncbi.nlm.nih.gov/pubmed/16556916
Muscle acetylcholine receptor biosynthesis. Regulation by transcript availability.	Evans S, Goldman D, Heinemann S, Patrick J	The Journal of biological chemistry	2435720	J Biol Chem	1987 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/2435720
Expression of Isl1 during mouse development.	Zhuang S, Zhang Q, Zhuang T, Evans SM, Liang X, Sun Y	Gene expression patterns : GEP	23906961	Gene Expr Patterns	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23906961
Retinoic acid signaling regulates sonic hedgehog and bone morphogenetic protein signalings during genital tubercle development.	Liu L, Suzuki K, Nakagata N, Mihara K, Matsumaru D, Ogino Y, Yashiro K, Hamada H, Liu Z, Evans SM, Mendelsohn C, Yamada G	Birth defects research. Part B, Developmental and reproductive toxicology	22127979	Birth Defects Res B Dev Reprod Toxicol	2012 Feb	https://www.ncbi.nlm.nih.gov/pubmed/22127979
MicroRNAs in a cardiac loop: progenitor or myocyte?	Evans SM, Moretti A, Laugwitz KL	Developmental cell	21145492	Dev Cell	2010 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/21145492
Modulation of morphogenesis by noncanonical Wnt signaling requires ATF/CREB family-mediated transcriptional activation of TGFbeta2.	Zhou W, Lin L, Majumdar A, Li X, Zhang X, Liu W, Etheridge L, Shi Y, Martin J, Van de Ven W, Kaartinen V, Wynshaw-Boris A, McMahon AP, Rosenfeld MG, Evans SM	Nature genetics	17767158	Nat Genet	2007 Oct	https://www.ncbi.nlm.nih.gov/pubmed/17767158
Pinch1 is required for normal development of cranial and cardiac neural crest-derived structures.	Liang X, Sun Y, Schneider J, Ding JH, Cheng H, Ye M, Bhattacharya S, Rearden A, Evans S, Chen J	Circulation research	17272814	Circ Res	2007 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/17272814
Promoter activity and transcript mapping in the regulatory region for genes encoding ribosomal protein S15 and polynucleotide phosphorylase of Escherichia coli.	Evans S, Dennis PP	Gene	3005122	Gene	1985	https://www.ncbi.nlm.nih.gov/pubmed/3005122
Expression of the hyperpolarization-activated cyclic nucleotide-gated cation channel HCN4 during mouse heart development.	Garcia-Frigola C, Shi Y, Evans SM	Gene expression patterns : GEP	14643687	Gene Expr Patterns	2003 Dec	https://www.ncbi.nlm.nih.gov/pubmed/14643687
T-box genes coordinate regional rates of proliferation and regional specification during cardiogenesis.	Cai CL, Zhou W, Yang L, Bu L, Qyang Y, Zhang X, Li X, Rosenfeld MG, Chen J, Evans S	Development (Cambridge, England)	15843407	Development	2005 May	https://www.ncbi.nlm.nih.gov/pubmed/15843407
Insights into cardiac conduction system formation provided by HCN4 expression.	Liang X, Evans SM, Sun Y	Trends in cardiovascular medicine	25442735	Trends Cardiovasc Med	2015 Jan	https://www.ncbi.nlm.nih.gov/pubmed/25442735
Tissue-Specific Cell Cycle Indicator Reveals Unexpected Findings for Cardiac Myocyte Proliferation.	Hirai M, Chen J, Evans SM	Circulation research	26472817	Circ Res	2016 Jan 8	https://www.ncbi.nlm.nih.gov/pubmed/26472817
Redox Paradox: Can Hypoxia Heal Ischemic Hearts?	Guimarães-Camboa N, Evans SM	Developmental cell	27875683	Dev Cell	2016 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/27875683
To activate or not to activate: the existential dilemma of an enhancer.	Boogerd CJ, Evans SM	Circulation research	23538274	Circ Res	2013 Mar 29	https://www.ncbi.nlm.nih.gov/pubmed/23538274
A custody battle for the mind: evidence for extensive imprinting in the brain.	Tollkuhn J, Xu X, Shah NM	Neuron	20696374	Neuron	2010 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/20696374
Restriction of transient receptor potential vanilloid-1 to the peptidergic subset of primary afferent neurons follows its developmental downregulation in nonpeptidergic neurons.	Cavanaugh DJ, Chesler AT, Bráz JM, Shah NM, Julius D, Basbaum AI	The Journal of neuroscience : the official journal of the Society for Neuroscience	21752988	J Neurosci	2011 Jul 13	https://www.ncbi.nlm.nih.gov/pubmed/21752988
Generation of induced pluripotent stem cells from the prairie vole.	Manoli DS, Subramanyam D, Carey C, Sudin E, Van Westerhuyzen JA, Bales KL, Blelloch R, Shah NM	PloS one	22675440	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22675440
Control of masculinization of the brain and behavior.	Wu MV, Shah NM	Current opinion in neurobiology	20970320	Curr Opin Neurobiol	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/20970320
Modular genetic control of sexually dimorphic behaviors.	Xu X, Coats JK, Yang CF, Wang A, Ahmed OM, Alvarado M, Izumi T, Shah NM	Cell	22304924	Cell	2012 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/22304924
The androgen receptor governs the execution, but not programming, of male sexual and territorial behaviors.	Juntti SA, Tollkuhn J, Wu MV, Fraser EJ, Soderborg T, Tan S, Honda S, Harada N, Shah NM	Neuron	20435002	Neuron	2010 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/20435002
Trpv1 reporter mice reveal highly restricted brain distribution and functional expression in arteriolar smooth muscle cells.	Cavanaugh DJ, Chesler AT, Jackson AC, Sigal YM, Yamanaka H, Grant R, O'Donnell D, Nicoll RA, Shah NM, Julius D, Basbaum AI	The Journal of neuroscience : the official journal of the Society for Neuroscience	21451044	J Neurosci	2011 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/21451044
Balancing repair and tolerance of DNA damage caused by alkylating agents.	Fu D, Calvo JA, Samson LD	Nature reviews. Cancer	22237395	Nat Rev Cancer	2012 Jan 12	https://www.ncbi.nlm.nih.gov/pubmed/22237395
Luminescent kinase activity biosensors based on a versatile bimolecular switch.	Herbst KJ, Allen MD, Zhang J	Journal of the American Chemical Society	21438554	J Am Chem Soc	2011 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/21438554
Global analysis of phosphorylation networks in humans.	Hu J, Rho HS, Newman RH, Hwang W, Neiswinger J, Zhu H, Zhang J, Qian J	Biochimica et biophysica acta	23524292	Biochim Biophys Acta	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23524292
Genetically encodable fluorescent biosensors for tracking signaling dynamics in living cells.	Newman RH, Fosbrink MD, Zhang J	Chemical reviews	21456512	Chem Rev	2011 May 11	https://www.ncbi.nlm.nih.gov/pubmed/21456512
How cells process information: quantification of spatiotemporal signaling dynamics.	Ganesan A, Zhang J	Protein science : a publication of the Protein Society	22573643	Protein Sci	2012 Jul	https://www.ncbi.nlm.nih.gov/pubmed/22573643
Galphas-biased beta2-adrenergic receptor signaling from restoring synchronous contraction in the failing heart.	Chakir K, Depry C, Dimaano VL, Zhu WZ, Vanderheyden M, Bartunek J, Abraham TP, Tomaselli GF, Liu SB, Xiang YK, Zhang M, Takimoto E, Dulin N, Xiao RP, Zhang J, Kass DA	Science translational medicine	21918105	Sci Transl Med	2011 Sep 14	https://www.ncbi.nlm.nih.gov/pubmed/21918105
Reporting from the field: genetically encoded fluorescent reporters uncover signaling dynamics in living biological systems.	Mehta S, Zhang J	Annual review of biochemistry	21495849	Annu Rev Biochem	2011	https://www.ncbi.nlm.nih.gov/pubmed/21495849
Widely accessible method for superresolution fluorescence imaging of living systems.	Dedecker P, Mo GC, Dertinger T, Zhang J	Proceedings of the National Academy of Sciences of the United States of America	22711840	Proc Natl Acad Sci U S A	2012 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/22711840
Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor.	Fosbrink M, Aye-Han NN, Cheong R, Levchenko A, Zhang J	Proceedings of the National Academy of Sciences of the United States of America	20212108	Proc Natl Acad Sci U S A	2010 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/20212108
Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy.	Dedecker P, Duwé S, Neely RK, Zhang J	Journal of biomedical optics	23208219	J Biomed Opt	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23208219
Regulation of nuclear PKA revealed by spatiotemporal manipulation of cyclic AMP.	Sample V, DiPilato LM, Yang JH, Ni Q, Saucerman JJ, Zhang J	Nature chemical biology	22366721	Nat Chem Biol	2012 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/22366721
Signaling diversity of PKA achieved via a Ca2+-cAMP-PKA oscillatory circuit.	Ni Q, Ganesan A, Aye-Han NN, Gao X, Allen MD, Levchenko A, Zhang J	Nature chemical biology	21102470	Nat Chem Biol	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21102470
Direct activation of Epac by sulfonylurea is isoform selective.	Herbst KJ, Coltharp C, Amzel LM, Zhang J	Chemistry & biology	21338921	Chem Biol	2011 Feb 25	https://www.ncbi.nlm.nih.gov/pubmed/21338921
RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee.	Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, Jacobsen SE, Ma J, Robinson GE	Proceedings of the National Academy of Sciences of the United States of America	23852726	Proc Natl Acad Sci U S A	2013 Jul 30	https://www.ncbi.nlm.nih.gov/pubmed/23852726
Physiology of reproductive worker honey bees (Apis mellifera): insights for the development of the worker caste.	Peso M, Even N, Søvik E, Naeger NL, Robinson GE, Barron AB	Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology	26715114	J Comp Physiol A Neuroethol Sens Neural Behav Physiol	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/26715114
The genomes of two key bumblebee species with primitive eusocial organization.	Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MM, Blaxter ML, Bourke AF, Brown MJ, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FC, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HM, Leask M, Lockett GA, Mallon EB, Antonio DS, Marxer M, Meeus I, Moritz RF, Nair A, Näpflin K, Nissen I, Niu J, Nunes FM, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZL, Soares MP, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KK, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC	Genome biology	25908251	Genome Biol	2015 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/25908251
Caste-specific differences in hindgut microbial communities of honey bees (Apis mellifera).	Kapheim KM, Rao VD, Yeoman CJ, Wilson BA, White BA, Goldenfeld N, Robinson GE	PloS one	25874551	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/25874551
Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states.	Chandrasekaran S, Ament SA, Eddy JA, Rodriguez-Zas SL, Schatz BR, Price ND, Robinson GE	Proceedings of the National Academy of Sciences of the United States of America	21960440	Proc Natl Acad Sci U S A	2011 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/21960440
New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior.	Ament SA, Blatti CA, Alaux C, Wheeler MM, Toth AL, Le Conte Y, Hunt GJ, Guzmán-Novoa E, Degrandi-Hoffman G, Uribe-Rubio JL, Amdam GV, Page RE Jr, Rodriguez-Zas SL, Robinson GE, Sinha S	Proceedings of the National Academy of Sciences of the United States of America	22691501	Proc Natl Acad Sci U S A	2012 Jun 26	https://www.ncbi.nlm.nih.gov/pubmed/22691501
Comparative brain transcriptomic analyses of scouting across distinct behavioural and ecological contexts in honeybees.	Liang ZS, Mattila HR, Rodriguez-Zas SL, Southey BR, Seeley TD, Robinson GE	Proceedings. Biological sciences	25355476	Proc Biol Sci	2014 Dec 22	https://www.ncbi.nlm.nih.gov/pubmed/25355476
Genomic features of a bumble bee symbiont reflect its host environment.	Martinson VG, Magoc T, Koch H, Salzberg SL, Moran NA	Applied and environmental microbiology	24747890	Appl Environ Microbiol	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24747890
Activity-dependent gene expression in honey bee mushroom bodies in response to orientation flight.	Lutz CC, Robinson GE	The Journal of experimental biology	23678099	J Exp Biol	2013 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/23678099
Brain regions and molecular pathways responding to food reward type and value in honey bees.	McNeill MS, Kapheim KM, Brockmann A, McGill TA, Robinson GE	Genes, brain, and behavior	26566901	Genes Brain Behav	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26566901
Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.	Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ÉD, Simões ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G	Science (New York, N.Y.)	25977371	Science	2015 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/25977371
Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation.	Traniello IM, Bukhari SA, Kevill J, Ahmed AC, Hamilton AR, Naeger NL, Schroeder DC, Robinson GE	Scientific reports	32080242	Sci Rep	2020 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/32080242
Transcriptomic analysis of instinctive and learned reward-related behaviors in honey bees.	Naeger NL, Robinson GE	The Journal of experimental biology	27852762	J Exp Biol	2016 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/27852762
Aggression is associated with aerobic glycolysis in the honey bee brain(1).	Chandrasekaran S, Rittschof CC, Djukovic D, Gu H, Raftery D, Price ND, Robinson GE	Genes, brain, and behavior	25640316	Genes Brain Behav	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25640316
Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera.	Khamis AM, Hamilton AR, Medvedeva YA, Alam T, Alam I, Essack M, Umylny B, Jankovic BR, Naeger NL, Suzuki M, Harbers M, Robinson GE, Bajic VB	Scientific reports	26073445	Sci Rep	2015 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/26073445
Molecular determinants of scouting behavior in honey bees.	Liang ZS, Nguyen T, Mattila HR, Rodriguez-Zas SL, Seeley TD, Robinson GE	Science (New York, N.Y.)	22403390	Science	2012 Mar 9	https://www.ncbi.nlm.nih.gov/pubmed/22403390
DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.	Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R	Proceedings of the National Academy of Sciences of the United States of America	22416128	Proc Natl Acad Sci U S A	2012 Mar 27	https://www.ncbi.nlm.nih.gov/pubmed/22416128
Understanding the relationship between brain gene expression and social behavior: lessons from the honey bee.	Zayed A, Robinson GE	Annual review of genetics	22994354	Annu Rev Genet	2012	https://www.ncbi.nlm.nih.gov/pubmed/22994354
Manipulation of colony environment modulates honey bee aggression and brain gene expression.	Rittschof CC, Robinson GE	Genes, brain, and behavior	24034579	Genes Brain Behav	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24034579
Laboratory Assay of Brood Care for Quantitative Analyses of Individual Differences in Honey Bee (Apis mellifera) Affiliative Behavior.	Shpigler HY, Robinson GE	PloS one	26569402	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26569402
Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees.	Liu H, Robinson GE, Jakobsson E	PLoS computational biology	27359102	PLoS Comput Biol	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27359102
Neuropeptide Y-like signalling and nutritionally mediated gene expression and behaviour in the honey bee.	Ament SA, Velarde RA, Kolodkin MH, Moyse D, Robinson GE	Insect molecular biology	21349120	Insect Mol Biol	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/21349120
Genomics: moving behavioural ecology beyond the phenotypic gambit.	Rittschof CC, Robinson GE	Animal behaviour	24954950	Anim Behav	2014 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/24954950
Socially responsive effects of brain oxidative metabolism on aggression.	Li-Byarlay H, Rittschof CC, Massey JH, Pittendrigh BR, Robinson GE	Proceedings of the National Academy of Sciences of the United States of America	25092297	Proc Natl Acad Sci U S A	2014 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/25092297
Cross-linking in the silks of bees, ants and hornets.	Campbell PM, Trueman HE, Zhang Q, Kojima K, Kameda T, Sutherland TD	Insect biochemistry and molecular biology	24607851	Insect Biochem Mol Biol	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24607851
Insulin Signaling in a Bit of a Jam.	Kutyavin VI, Chawla A	Cell	27058657	Cell	2016 Apr 7	https://www.ncbi.nlm.nih.gov/pubmed/27058657
Eosinophils sustain adipose alternatively activated macrophages associated with glucose homeostasis.	Wu D, Molofsky AB, Liang HE, Ricardo-Gonzalez RR, Jouihan HA, Bando JK, Chawla A, Locksley RM	Science (New York, N.Y.)	21436399	Science	2011 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/21436399
Macrophage-mediated inflammation in metabolic disease.	Chawla A, Nguyen KD, Goh YP	Nature reviews. Immunology	21984069	Nat Rev Immunol	2011 Oct 10	https://www.ncbi.nlm.nih.gov/pubmed/21984069
Alternative macrophage activation and metabolism.	Odegaard JI, Chawla A	Annual review of pathology	21034223	Annu Rev Pathol	2011	https://www.ncbi.nlm.nih.gov/pubmed/21034223
Control of macrophage activation and function by PPARs.	Chawla A	Circulation research	20508200	Circ Res	2010 May 28	https://www.ncbi.nlm.nih.gov/pubmed/20508200
Connecting type 1 and type 2 diabetes through innate immunity.	Odegaard JI, Chawla A	Cold Spring Harbor perspectives in medicine	22393536	Cold Spring Harb Perspect Med	2012 Mar	https://www.ncbi.nlm.nih.gov/pubmed/22393536
In obesity and weight loss, all roads lead to the mighty macrophage.	Red Eagle A, Chawla A	The Journal of clinical investigation	20877005	J Clin Invest	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20877005
Type 2 innate signals stimulate fibro/adipogenic progenitors to facilitate muscle regeneration.	Heredia JE, Mukundan L, Chen FM, Mueller AA, Deo RC, Locksley RM, Rando TA, Chawla A	Cell	23582327	Cell	2013 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/23582327
Leukocyte set points in metabolic disease.	Odegaard JI, Chawla A	F1000 biology reports	22802874	F1000 Biol Rep	2012	https://www.ncbi.nlm.nih.gov/pubmed/22802874
Alternatively activated macrophages produce catecholamines to sustain adaptive thermogenesis.	Nguyen KD, Qiu Y, Cui X, Goh YP, Mwangi J, David T, Mukundan L, Brombacher F, Locksley RM, Chawla A	Nature	22101429	Nature	2011 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/22101429
IL-4/STAT6 immune axis regulates peripheral nutrient metabolism and insulin sensitivity.	Ricardo-Gonzalez RR, Red Eagle A, Odegaard JI, Jouihan H, Morel CR, Heredia JE, Mukundan L, Wu D, Locksley RM, Chawla A	Proceedings of the National Academy of Sciences of the United States of America	21149710	Proc Natl Acad Sci U S A	2010 Dec 28	https://www.ncbi.nlm.nih.gov/pubmed/21149710
Eosinophils and type 2 cytokine signaling in macrophages orchestrate development of functional beige fat.	Qiu Y, Nguyen KD, Odegaard JI, Cui X, Tian X, Locksley RM, Palmiter RD, Chawla A	Cell	24906148	Cell	2014 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/24906148
Pleiotropic actions of insulin resistance and inflammation in metabolic homeostasis.	Odegaard JI, Chawla A	Science (New York, N.Y.)	23307735	Science	2013 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/23307735
Involvement of adenosine A2A receptors in engulfment-dependent apoptotic cell suppression of inflammation.	Köröskényi K, Duró E, Pallai A, Sarang Z, Kloor D, Ucker DS, Beceiro S, Castrillo A, Chawla A, Ledent CA, Fésüs L, Szondy Z	Journal of immunology (Baltimore, Md. : 1950)	21593381	J Immunol	2011 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/21593381
The immune system as a sensor of the metabolic state.	Odegaard JI, Chawla A	Immunity	23601683	Immunity	2013 Apr 18	https://www.ncbi.nlm.nih.gov/pubmed/23601683
Macrophage biology in development, homeostasis and disease.	Wynn TA, Chawla A, Pollard JW	Nature	23619691	Nature	2013 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/23619691
Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting.	Maynard ND, Macklin DN, Kirkegaard K, Covert MW	Molecular systems biology	22294093	Mol Syst Biol	2012 Jan 31	https://www.ncbi.nlm.nih.gov/pubmed/22294093
WholeCellViz: data visualization for whole-cell models.	Lee R, Karr JR, Covert MW	BMC bioinformatics	23964998	BMC Bioinformatics	2013 Aug 21	https://www.ncbi.nlm.nih.gov/pubmed/23964998
Accelerated discovery via a whole-cell model.	Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B Jr, Covert MW	Nature methods	24185838	Nat Methods	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24185838
A forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy.	Maynard ND, Birch EW, Sanghvi JC, Chen L, Gutschow MV, Covert MW	PLoS genetics	20628568	PLoS Genet	2010 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/20628568
The virus as metabolic engineer.	Maynard ND, Gutschow MV, Birch EW, Covert MW	Biotechnology journal	20665642	Biotechnol J	2010 Jul	https://www.ncbi.nlm.nih.gov/pubmed/20665642
A whole-cell computational model predicts phenotype from genotype.	Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW	Cell	22817898	Cell	2012 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/22817898
Single-cell and population NF-κB dynamic responses depend on lipopolysaccharide preparation.	Gutschow MV, Hughey JJ, Ruggero NA, Bajar BT, Valle SD, Covert MW	PloS one	23301045	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23301045
The future of whole-cell modeling.	Macklin DN, Ruggero NA, Covert MW	Current opinion in biotechnology	24556244	Curr Opin Biotechnol	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/24556244
Towards a whole-cell modeling approach for synthetic biology.	Purcell O, Jain B, Karr JR, Covert MW, Lu TK	Chaos (Woodbury, N.Y.)	23822510	Chaos	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23822510
High-sensitivity measurements of multiple kinase activities in live single cells.	Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW	Cell	24949979	Cell	2014 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/24949979
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.	Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P	PLoS computational biology	26020786	PLoS Comput Biol	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/26020786
Why Build Whole-Cell Models?	Carrera J, Covert MW	Trends in cell biology	26471224	Trends Cell Biol	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26471224
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.	Macklin DN, Ahn-Horst TA, Choi H, Ruggero NA, Carrera J, Mason JC, Sun G, Agmon E, DeFelice MM, Maayan I, Lane K, Spangler RK, Gillies TE, Paull ML, Akhter S, Bray SR, Weaver DS, Keseler IM, Karp PD, Morrison JH, Covert MW	Science (New York, N.Y.)	32703847	Science	2020 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/32703847
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.	Karr JR, Phillips NC, Covert MW	Database : the journal of biological databases and curation	25231498	Database (Oxford)	2014	https://www.ncbi.nlm.nih.gov/pubmed/25231498
WholeCellKB: model organism databases for comprehensive whole-cell models.	Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW	Nucleic acids research	23175606	Nucleic Acids Res	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23175606
Homeostatic regulation of dendritic dynamics in a motor map in vivo.	Kishore S, Fetcho JR	Nature communications	23803587	Nat Commun	2013	https://www.ncbi.nlm.nih.gov/pubmed/23803587
A procedure for implanting a spinal chamber for longitudinal in vivo imaging of the mouse spinal cord.	Farrar MJ, Schaffer CB	Journal of visualized experiments : JoVE	25548864	J Vis Exp	2014 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/25548864
Chronic in vivo imaging in the mouse spinal cord using an implanted chamber.	Farrar MJ, Bernstein IM, Schlafer DH, Cleland TA, Fetcho JR, Schaffer CB	Nature methods	22266542	Nat Methods	2012 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/22266542
A circuit motif in the zebrafish hindbrain for a two alternative behavioral choice to turn left or right.	Koyama M, Minale F, Shum J, Nishimura N, Schaffer CB, Fetcho JR	eLife	27502742	Elife	2016 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/27502742
In Vivo Measurement of Glycine Receptor Turnover and Synaptic Size Reveals Differences between Functional Classes of Motoneurons in Zebrafish.	Chow DM, Zuchowski KA, Fetcho JR	Current biology : CB	28416115	Curr Biol	2017 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/28416115
Movement, technology and discovery in the zebrafish.	McLean DL, Fetcho JR	Current opinion in neurobiology	20970321	Curr Opin Neurobiol	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/20970321
In vivo imaging of myelin in the vertebrate central nervous system using third harmonic generation microscopy.	Farrar MJ, Wise FW, Fetcho JR, Schaffer CB	Biophysical journal	21354410	Biophys J	2011 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/21354410
TRP channel mediated neuronal activation and ablation in freely behaving zebrafish.	Chen S, Chiu CN, McArthur KL, Fetcho JR, Prober DA	Nature methods	26657556	Nat Methods	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/26657556
Monkey models for brain-machine interfaces: the need for maintaining diversity.	Nuyujukian P, Fan JM, Gilja V, Kalanithi PS, Chestek CA, Shenoy KV	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22254555	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22254555
Stimulus onset quenches neural variability: a widespread cortical phenomenon.	Churchland MM, Yu BM, Cunningham JP, Sugrue LP, Cohen MR, Corrado GS, Newsome WT, Clark AM, Hosseini P, Scott BB, Bradley DC, Smith MA, Kohn A, Movshon JA, Armstrong KM, Moore T, Chang SW, Snyder LH, Lisberger SG, Priebe NJ, Finn IM, Ferster D, Ryu SI, Santhanam G, Sahani M, Shenoy KV	Nature neuroscience	20173745	Nat Neurosci	2010 Mar	https://www.ncbi.nlm.nih.gov/pubmed/20173745
Neural correlates of attention and distractibility in the lateral intraparietal area.	Bisley JW, Goldberg ME	Journal of neurophysiology	16339000	J Neurophysiol	2006 Mar	https://www.ncbi.nlm.nih.gov/pubmed/16339000
Re-valuing the amygdala.	Morrison SE, Salzman CD	Current opinion in neurobiology	20299204	Curr Opin Neurobiol	2010 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20299204
Design and validation of a real-time spiking-neural-network decoder for brain-machine interfaces.	Dethier J, Nuyujukian P, Ryu SI, Shenoy KV, Boahen K	Journal of neural engineering	23574919	J Neural Eng	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23574919
A coaxial optrode as multifunction write-read probe for optogenetic studies in non-human primates.	Ozden I, Wang J, Lu Y, May T, Lee J, Goo W, O'Shea DJ, Kalanithi P, Diester I, Diagne M, Deisseroth K, Shenoy KV, Nurmikko AV	Journal of neuroscience methods	23867081	J Neurosci Methods	2013 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/23867081
Cortical control of arm movements: a dynamical systems perspective.	Shenoy KV, Sahani M, Churchland MM	Annual review of neuroscience	23725001	Annu Rev Neurosci	2013 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/23725001
A freely-moving monkey treadmill model.	Foster JD, Nuyujukian P, Freifeld O, Gao H, Walker R, I Ryu S, H Meng T, Murmann B, J Black M, Shenoy KV	Journal of neural engineering	24995476	J Neural Eng	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/24995476
Combining Wireless Neural Recording and Video Capture for the Analysis of Natural Gait.	Foster JD, Freifeld O, Nuyujukian P, Ryu SI, Black MJ, Shenoy KV	International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering	26019730	Int IEEE EMBS Conf Neural Eng	2011 Apr-May	https://www.ncbi.nlm.nih.gov/pubmed/26019730
Neural circuits as computational dynamical systems.	Sussillo D	Current opinion in neurobiology	24509098	Curr Opin Neurobiol	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24509098
The Largest Response Component in the Motor Cortex Reflects Movement Timing but Not Movement Type.	Kaufman MT, Seely JS, Sussillo D, Ryu SI, Shenoy KV, Churchland MM	eNeuro	27761519	eNeuro	2016 Jul-Aug	https://www.ncbi.nlm.nih.gov/pubmed/27761519
Development of an optogenetic toolkit for neural circuit dissection in squirrel monkeys.	O'Shea DJ, Kalanithi P, Ferenczi EA, Hsueh B, Chandrasekaran C, Goo W, Diester I, Ramakrishnan C, Kaufman MT, Ryu SI, Yeom KW, Deisseroth K, Shenoy KV	Scientific reports	29712920	Sci Rep	2018 Apr 30	https://www.ncbi.nlm.nih.gov/pubmed/29712920
A Non-Human Primate Brain-Computer Typing Interface.	Nuyujukian P, Kao JC, Ryu SI, Shenoy KV	Proceedings of the IEEE. Institute of Electrical and Electronics Engineers	33746239	Proc IEEE Inst Electr Electron Eng	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/33746239
Low-dimensional neural features predict muscle EMG signals.	Rivera-Alvidrez Z, Kalmar RS, Ryu SI, Shenoy KV	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	21097116	Annu Int Conf IEEE Eng Med Biol Soc	2010	https://www.ncbi.nlm.nih.gov/pubmed/21097116
Self-recalibrating classifiers for intracortical brain-computer interfaces.	Bishop W, Chestek CC, Gilja V, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV, Yu BM	Journal of neural engineering	24503597	J Neural Eng	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24503597
The roles of monkey M1 neuron classes in movement preparation and execution.	Kaufman MT, Churchland MM, Shenoy KV	Journal of neurophysiology	23699057	J Neurophysiol	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23699057
A high-performance neural prosthesis enabled by control algorithm design.	Gilja V, Nuyujukian P, Chestek CA, Cunningham JP, Yu BM, Fan JM, Churchland MM, Kaufman MT, Kao JC, Ryu SI, Shenoy KV	Nature neuroscience	23160043	Nat Neurosci	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23160043
An optogenetic toolbox designed for primates.	Diester I, Kaufman MT, Mogri M, Pashaie R, Goo W, Yizhar O, Ramakrishnan C, Deisseroth K, Shenoy KV	Nature neuroscience	21278729	Nat Neurosci	2011 Mar	https://www.ncbi.nlm.nih.gov/pubmed/21278729
Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex.	Chestek CA, Gilja V, Nuyujukian P, Foster JD, Fan JM, Kaufman MT, Churchland MM, Rivera-Alvidrez Z, Cunningham JP, Ryu SI, Shenoy KV	Journal of neural engineering	21775782	J Neural Eng	2011 Aug	https://www.ncbi.nlm.nih.gov/pubmed/21775782
Accurate Estimation of Neural Population Dynamics without Spike Sorting.	Trautmann EM, Stavisky SD, Lahiri S, Ames KC, Kaufman MT, O'Shea DJ, Vyas S, Sun X, Ryu SI, Ganguli S, Shenoy KV	Neuron	31171448	Neuron	2019 Jul 17	https://www.ncbi.nlm.nih.gov/pubmed/31171448
ERAASR: an algorithm for removing electrical stimulation artifacts from multielectrode array recordings.	O'Shea DJ, Shenoy KV	Journal of neural engineering	29265009	J Neural Eng	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29265009
Challenges and opportunities for next-generation intracortically based neural prostheses.	Gilja V, Chestek CA, Diester I, Henderson JM, Deisseroth K, Shenoy KV	IEEE transactions on bio-medical engineering	21257365	IEEE Trans Biomed Eng	2011 Jul	https://www.ncbi.nlm.nih.gov/pubmed/21257365
A closed-loop human simulator for investigating the role of feedback control in brain-machine interfaces.	Cunningham JP, Nuyujukian P, Gilja V, Chestek CA, Ryu SI, Shenoy KV	Journal of neurophysiology	20943945	J Neurophysiol	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20943945
Neural population dynamics during reaching.	Churchland MM, Cunningham JP, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV	Nature	22722855	Nature	2012 Jul 5	https://www.ncbi.nlm.nih.gov/pubmed/22722855
Context-dependent computation by recurrent dynamics in prefrontal cortex.	Mante V, Sussillo D, Shenoy KV, Newsome WT	Nature	24201281	Nature	2013 Nov 7	https://www.ncbi.nlm.nih.gov/pubmed/24201281
A brain machine interface control algorithm designed from a feedback control perspective.	Gilja V, Nuyujukian P, Chestek CA, Cunningham JP, Yu BM, Fan JM, Ryu SI, Shenoy KV	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	23366141	Annu Int Conf IEEE Eng Med Biol Soc	2012	https://www.ncbi.nlm.nih.gov/pubmed/23366141
A dynamical systems view of motor preparation: implications for neural prosthetic system design.	Shenoy KV, Kaufman MT, Sahani M, Churchland MM	Progress in brain research	21763517	Prog Brain Res	2011	https://www.ncbi.nlm.nih.gov/pubmed/21763517
Autonomous head-mounted electrophysiology systems for freely behaving primates.	Gilja V, Chestek CA, Nuyujukian P, Foster J, Shenoy KV	Current opinion in neurobiology	20655733	Curr Opin Neurobiol	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20655733
Cortical activity in the null space: permitting preparation without movement.	Kaufman MT, Churchland MM, Ryu SI, Shenoy KV	Nature neuroscience	24487233	Nat Neurosci	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24487233
Combining decoder design and neural adaptation in brain-machine interfaces.	Shenoy KV, Carmena JM	Neuron	25459407	Neuron	2014 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/25459407
A high-performance keyboard neural prosthesis enabled by task optimization.	Nuyujukian P, Fan JM, Kao JC, Ryu SI, Shenoy KV	IEEE transactions on bio-medical engineering	25203982	IEEE Trans Biomed Eng	2015 Jan	https://www.ncbi.nlm.nih.gov/pubmed/25203982
A framework for relating neural activity to freely moving behavior.	Foster JD, Nuyujukian P, Freifeld O, Ryu SI, Black MJ, Shenoy KV	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	23366491	Annu Int Conf IEEE Eng Med Biol Soc	2012	https://www.ncbi.nlm.nih.gov/pubmed/23366491
Intention estimation in brain-machine interfaces.	Fan JM, Nuyujukian P, Kao JC, Chestek CA, Ryu SI, Shenoy KV	Journal of neural engineering	24654266	J Neural Eng	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24654266
DataHigh: graphical user interface for visualizing and interacting with high-dimensional neural activity.	Cowley BR, Kaufman MT, Butler ZS, Churchland MM, Ryu SI, Shenoy KV, Yu BM	Journal of neural engineering	24216250	J Neural Eng	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24216250
Neural dynamics of reaching following incorrect or absent motor preparation.	Ames KC, Ryu SI, Shenoy KV	Neuron	24462104	Neuron	2014 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/24462104
Spiking Neural Network Decoder for Brain-Machine Interfaces.	Dethier J, Gilja V, Nuyujukian P, Elassaad SA, Shenoy KV, Boahen K	International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering	24352611	Int IEEE EMBS Conf Neural Eng	2011	https://www.ncbi.nlm.nih.gov/pubmed/24352611
A recurrent neural network for closed-loop intracortical brain-machine interface decoders.	Sussillo D, Nuyujukian P, Fan JM, Kao JC, Stavisky SD, Ryu S, Shenoy K	Journal of neural engineering	22427488	J Neural Eng	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22427488
Cortical preparatory activity: representation of movement or first cog in a dynamical machine?	Churchland MM, Cunningham JP, Kaufman MT, Ryu SI, Shenoy KV	Neuron	21040842	Neuron	2010 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/21040842
Roles of monkey premotor neuron classes in movement preparation and execution.	Kaufman MT, Churchland MM, Santhanam G, Yu BM, Afshar A, Ryu SI, Shenoy KV	Journal of neurophysiology	20538784	J Neurophysiol	2010 Aug	https://www.ncbi.nlm.nih.gov/pubmed/20538784
Investigating the role of firing-rate normalization and dimensionality reduction in brain-machine interface robustness.	Kao JC, Nuyujukian P, Stavisky S, Ryu SI, Ganguli S, Shenoy KV	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	24109682	Annu Int Conf IEEE Eng Med Biol Soc	2013	https://www.ncbi.nlm.nih.gov/pubmed/24109682
Perspectives on cell reprogramming with RNA.	Sul JY, Kim TK, Lee JH, Eberwine J	Trends in biotechnology	22459515	Trends Biotechnol	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22459515
Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis.	Buckley PT, Khaladkar M, Kim J, Eberwine J	Wiley interdisciplinary reviews. RNA	24190870	Wiley Interdiscip Rev RNA	2014 Mar-Apr	https://www.ncbi.nlm.nih.gov/pubmed/24190870
Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.	Spaethling JM, Piel D, Dueck H, Buckley PT, Morris JF, Fisher SA, Lee J, Sul JY, Kim J, Bartfai T, Beck SG, Eberwine JH	FASEB journal : official publication of the Federation of American Societies for Experimental Biology	24192459	FASEB J	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24192459
Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.	Lovatt D, Ruble BK, Lee J, Dueck H, Kim TK, Fisher S, Francis C, Spaethling JM, Wolf JA, Grady MS, Ulyanova AV, Yeldell SB, Griepenburg JC, Buckley PT, Kim J, Sul JY, Dmochowski IJ, Eberwine J	Nature methods	24412976	Nat Methods	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24412976
Towards A Fully Automated High-Throughput Phototransfection System.	Cappelleri DJ, Halasz A, Sul JY, Kim TK, Eberwine J, Kumar V	JALA (Charlottesville, Va.)	20706617	JALA Charlottesv Va	2010 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/20706617
RNA: state memory and mediator of cellular phenotype.	Kim J, Eberwine J	Trends in cell biology	20382532	Trends Cell Biol	2010 Jun	https://www.ncbi.nlm.nih.gov/pubmed/20382532
Insulin causes hyperthermia by direct inhibition of warm-sensitive neurons.	Sanchez-Alavez M, Tabarean IV, Osborn O, Mitsukawa K, Schaefer J, Dubins J, Holmberg KH, Klein I, Klaus J, Gomez LF, Kolb H, Secrest J, Jochems J, Myashiro K, Buckley P, Hadcock JR, Eberwine J, Conti B, Bartfai T	Diabetes	19846801	Diabetes	2010 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19846801
Insulin-like growth factor 1-mediated hyperthermia involves anterior hypothalamic insulin receptors.	Sanchez-Alavez M, Osborn O, Tabarean IV, Holmberg KH, Eberwine J, Kahn CR, Bartfai T	The Journal of biological chemistry	21330367	J Biol Chem	2011 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/21330367
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.	Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher SA, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J	Genome biology	26056000	Genome Biol	2015 Jun 9	https://www.ncbi.nlm.nih.gov/pubmed/26056000
Cytoplasmic intron sequence-retaining transcripts can be dendritically targeted via ID element retrotransposons.	Buckley PT, Lee MT, Sul JY, Miyashiro KY, Bell TJ, Fisher SA, Kim J, Eberwine J	Neuron	21382548	Neuron	2011 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/21382548
Transcriptome transfer produces a predictable cellular phenotype.	Sul JY, Wu CW, Zeng F, Jochems J, Lee MT, Kim TK, Peritz T, Buckley P, Cappelleri DJ, Maronski M, Kim M, Kumar V, Meaney D, Kim J, Eberwine J	Proceedings of the National Academy of Sciences of the United States of America	19380745	Proc Natl Acad Sci U S A	2009 May 5	https://www.ncbi.nlm.nih.gov/pubmed/19380745
Navigational decision making in Drosophila thermotaxis.	Luo L, Gershow M, Rosenzweig M, Kang K, Fang-Yen C, Garrity PA, Samuel AD	The Journal of neuroscience : the official journal of the Society for Neuroscience	20335462	J Neurosci	2010 Mar 24	https://www.ncbi.nlm.nih.gov/pubmed/20335462
Sensory determinants of behavioral dynamics in Drosophila thermotaxis.	Klein M, Afonso B, Vonner AJ, Hernandez-Nunez L, Berck M, Tabone CJ, Kane EA, Pieribone VA, Nitabach MN, Cardona A, Zlatic M, Sprecher SG, Gershow M, Garrity PA, Samuel AD	Proceedings of the National Academy of Sciences of the United States of America	25550513	Proc Natl Acad Sci U S A	2015 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/25550513
Multimodal stimulus coding by a gustatory sensory neuron in Drosophila larvae.	van Giesen L, Hernandez-Nunez L, Delasoie-Baranek S, Colombo M, Renaud P, Bruggmann R, Benton R, Samuel ADT, Sprecher SG	Nature communications	26864722	Nat Commun	2016 Feb 11	https://www.ncbi.nlm.nih.gov/pubmed/26864722
Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans.	Leifer AM, Fang-Yen C, Gershow M, Alkema MJ, Samuel AD	Nature methods	21240279	Nat Methods	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21240279
Proprioceptive coupling within motor neurons drives C. elegans forward locomotion.	Wen Q, Po MD, Hulme E, Chen S, Liu X, Kwok SW, Gershow M, Leifer AM, Butler V, Fang-Yen C, Kawano T, Schafer WR, Whitesides G, Wyart M, Chklovskii DB, Zhen M, Samuel AD	Neuron	23177960	Neuron	2012 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/23177960
Caenorhabditis elegans: a model system for systems neuroscience.	Sengupta P, Samuel AD	Current opinion in neurobiology	19896359	Curr Opin Neurobiol	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19896359
Running hot and cold: behavioral strategies, neural circuits, and the molecular machinery for thermotaxis in C. elegans and Drosophila.	Garrity PA, Goodman MB, Samuel AD, Sengupta P	Genes & development	21041406	Genes Dev	2010 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/21041406
Imaging trans-cellular neurexin-neuroligin interactions by enzymatic probe ligation.	Liu DS, Loh KH, Lam SS, White KA, Ting AY	PloS one	23457442	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23457442
Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.	Hung V, Zou P, Rhee HW, Udeshi ND, Cracan V, Svinkina T, Carr SA, Mootha VK, Ting AY	Molecular cell	25002142	Mol Cell	2014 Jul 17	https://www.ncbi.nlm.nih.gov/pubmed/25002142
Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy.	Martell JD, Deerinck TJ, Sancak Y, Poulos TL, Mootha VK, Sosinsky GE, Ellisman MH, Ting AY	Nature biotechnology	23086203	Nat Biotechnol	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23086203
Imaging activity-dependent regulation of neurexin-neuroligin interactions using trans-synaptic enzymatic biotinylation.	Thyagarajan A, Ting AY	Cell	20933261	Cell	2010 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/20933261
Antibiotics induce redox-related physiological alterations as part of their lethality.	Dwyer DJ, Belenky PA, Yang JH, MacDonald IC, Martell JD, Takahashi N, Chan CT, Lobritz MA, Braff D, Schwarz EG, Ye JD, Pati M, Vercruysse M, Ralifo PS, Allison KR, Khalil AS, Ting AY, Walker GC, Collins JJ	Proceedings of the National Academy of Sciences of the United States of America	24803433	Proc Natl Acad Sci U S A	2014 May 20	https://www.ncbi.nlm.nih.gov/pubmed/24803433
Computational design of a red fluorophore ligase for site-specific protein labeling in living cells.	Liu DS, Nivón LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS, Ye AZ, Ellisman MH, Drennan CL, Baker D, Ting AY	Proceedings of the National Academy of Sciences of the United States of America	25313043	Proc Natl Acad Sci U S A	2014 Oct 28	https://www.ncbi.nlm.nih.gov/pubmed/25313043
Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.	Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY	Science (New York, N.Y.)	23371551	Science	2013 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/23371551
Digital transcriptome profiling from attomole-level RNA samples.	Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM	Genome research	20133332	Genome Res	2010 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20133332
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.	Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A	Proceedings of the National Academy of Sciences of the United States of America	19208812	Proc Natl Acad Sci U S A	2009 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/19208812
Dynamic single-cell imaging of direct reprogramming reveals an early specifying event.	Smith ZD, Nachman I, Regev A, Meissner A	Nature biotechnology	20436460	Nat Biotechnol	2010 May	https://www.ncbi.nlm.nih.gov/pubmed/20436460
Comprehensive comparative analysis of strand-specific RNA sequencing methods.	Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A	Nature methods	20711195	Nat Methods	2010 Sep	https://www.ncbi.nlm.nih.gov/pubmed/20711195
In vivo profiles in malaria are consistent with a novel physiological state.	Wirth D, Daily J, Winzeler E, Mesirov JP, Regev A	Proceedings of the National Academy of Sciences of the United States of America	19570993	Proc Natl Acad Sci U S A	2009 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/19570993
Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations.	Anderson JB, Funt J, Thompson DA, Prabhu S, Socha A, Sirjusingh C, Dettman JR, Parreiras L, Guttman DS, Regev A, Kohn LM	Current biology : CB	20637622	Curr Biol	2010 Aug 10	https://www.ncbi.nlm.nih.gov/pubmed/20637622
SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.	Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, Wardwell L, Tamayo P, Gat-Viks I, Ramos AH, Woo MS, Weir BA, Getz G, Beroukhim R, O'Kelly M, Dutt A, Rozenblatt-Rosen O, Dziunycz P, Komisarof J, Chirieac LR, Lafargue CJ, Scheble V, Wilbertz T, Ma C, Rao S, Nakagawa H, Stairs DB, Lin L, Giordano TJ, Wagner P, Minna JD, Gazdar AF, Zhu CQ, Brose MS, Cecconello I, Ribeiro U Jr, Marie SK, Dahl O, Shivdasani RA, Tsao MS, Rubin MA, Wong KK, Regev A, Hahn WC, Beer DG, Rustgi AK, Meyerson M	Nature genetics	19801978	Nat Genet	2009 Nov	https://www.ncbi.nlm.nih.gov/pubmed/19801978
Induction and molecular signature of pathogenic TH17 cells.	Lee Y, Awasthi A, Yosef N, Quintana FJ, Xiao S, Peters A, Wu C, Kleinewietfeld M, Kunder S, Hafler DA, Sobel RA, Regev A, Kuchroo VK	Nature immunology	22961052	Nat Immunol	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22961052
A unique regulatory phase of DNA methylation in the early mammalian embryo.	Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A	Nature	22456710	Nature	2012 Mar 28	https://www.ncbi.nlm.nih.gov/pubmed/22456710
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.	Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE	Nature methods	19946276	Nat Methods	2010 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19946276
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.	Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M	Nature	20237561	Nature	2010 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/20237561
Comparative analysis of RNA sequencing methods for degraded or low-input samples.	Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ	Nature methods	23685885	Nat Methods	2013 Jul	https://www.ncbi.nlm.nih.gov/pubmed/23685885
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses.	Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A	Science (New York, N.Y.)	19729616	Science	2009 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/19729616
Transcriptional regulatory circuits: predicting numbers from alphabets.	Kim HD, Shay T, O'Shea EK, Regev A	Science (New York, N.Y.)	19628860	Science	2009 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/19628860
The role of nucleosome positioning in the evolution of gene regulation.	Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ	PLoS biology	20625544	PLoS Biol	2010 Jul 6	https://www.ncbi.nlm.nih.gov/pubmed/20625544
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.	Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A, Hacohen N	Cell	20064372	Cell	2009 Dec 24	https://www.ncbi.nlm.nih.gov/pubmed/20064372
Mouse ooplasm confers context-specific reprogramming capacity.	Chan MM, Smith ZD, Egli D, Regev A, Meissner A	Nature genetics	22902786	Nat Genet	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22902786
Densely interconnected transcriptional circuits control cell states in human hematopoiesis.	Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N, Yosef N, Chang CY, Shay T, Frampton GM, Drake AC, Leskov I, Nilsson B, Preffer F, Dombkowski D, Evans JW, Liefeld T, Smutko JS, Chen J, Friedman N, Young RA, Golub TR, Regev A, Ebert BL	Cell	21241896	Cell	2011 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/21241896
Physical Module Networks: an integrative approach for reconstructing transcription regulation.	Novershtern N, Regev A, Friedman N	Bioinformatics (Oxford, England)	21685068	Bioinformatics	2011 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/21685068
Deconstructing transcriptional heterogeneity in pluripotent stem cells.	Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser A, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ	Nature	25471879	Nature	2014 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/25471879
DNA methylation dynamics of the human preimplantation embryo.	Smith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev A, Eggan K, Meissner A	Nature	25079558	Nature	2014 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/25079558
Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies.	Koch C, Konieczka J, Delorey T, Lyons A, Socha A, Davis K, Knaack SA, Thompson D, O'Shea EK, Regev A, Roy S	Cell systems	28544882	Cell Syst	2017 May 24	https://www.ncbi.nlm.nih.gov/pubmed/28544882
Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms.	Xiao S, Yosef N, Yang J, Wang Y, Zhou L, Zhu C, Wu C, Baloglu E, Schmidt D, Ramesh R, Lobera M, Sundrud MS, Tsai PY, Xiang Z, Wang J, Xu Y, Lin X, Kretschmer K, Rahl PB, Young RA, Zhong Z, Hafler DA, Regev A, Ghosh S, Marson A, Kuchroo VK	Immunity	24745332	Immunity	2014 Apr 17	https://www.ncbi.nlm.nih.gov/pubmed/24745332
Gene duplication and the evolution of ribosomal protein gene regulation in yeast.	Wapinski I, Pfiffner J, French C, Socha A, Thompson DA, Regev A	Proceedings of the National Academy of Sciences of the United States of America	20212107	Proc Natl Acad Sci U S A	2010 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/20212107
Reconstructing gene histories in Ascomycota fungi.	Wapinski I, Regev A	Methods in enzymology	20946821	Methods Enzymol	2010	https://www.ncbi.nlm.nih.gov/pubmed/20946821
Comparative functional genomics of the fission yeasts.	Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C	Science (New York, N.Y.)	21511999	Science	2011 May 20	https://www.ncbi.nlm.nih.gov/pubmed/21511999
Impulse control: temporal dynamics in gene transcription.	Yosef N, Regev A	Cell	21414481	Cell	2011 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/21414481
Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1.	Wu C, Yosef N, Thalhamer T, Zhu C, Xiao S, Kishi Y, Regev A, Kuchroo VK	Nature	23467085	Nature	2013 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/23467085
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.	Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A	Nature biotechnology	20436462	Nat Biotechnol	2010 May	https://www.ncbi.nlm.nih.gov/pubmed/20436462
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.	Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A	Nature	24919153	Nature	2014 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/24919153
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.	Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL	Cell	20673990	Cell	2010 Aug 6	https://www.ncbi.nlm.nih.gov/pubmed/20673990
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.	Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A	Nature	23685454	Nature	2013 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/23685454
Venetoclax combined with decitabine or azacitidine in treatment-naive, elderly patients with acute myeloid leukemia.	DiNardo CD, Pratz K, Pullarkat V, Jonas BA, Arellano M, Becker PS, Frankfurt O, Konopleva M, Wei AH, Kantarjian HM, Xu T, Hong WJ, Chyla B, Potluri J, Pollyea DA, Letai A	Blood	30361262	Blood	2019 Jan 3	https://www.ncbi.nlm.nih.gov/pubmed/30361262
High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.	Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Pauli A, Hacohen N, Schier AF, Blackshear PJ, Friedman N, Amit I, Regev A	Cell	25497548	Cell	2014 Dec 18	https://www.ncbi.nlm.nih.gov/pubmed/25497548
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.	Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A	Genome biology	25630241	Genome Biol	2015 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/25630241
Dynamic regulatory network controlling TH17 cell differentiation.	Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, Park H, Kuchroo VK, Regev A	Nature	23467089	Nature	2013 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/23467089
BRNI: Modular analysis of transcriptional regulatory programs.	Nachman I, Regev A	BMC bioinformatics	19457258	BMC Bioinformatics	2009 May 20	https://www.ncbi.nlm.nih.gov/pubmed/19457258
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.	Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A	Genome biology	20796282	Genome Biol	2010	https://www.ncbi.nlm.nih.gov/pubmed/20796282
Full-length transcriptome assembly from RNA-Seq data without a reference genome.	Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A	Nature biotechnology	21572440	Nat Biotechnol	2011 May 15	https://www.ncbi.nlm.nih.gov/pubmed/21572440
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing.	Trombetta JJ, Gennert D, Lu D, Satija R, Shalek AK, Regev A	Current protocols in molecular biology	24984854	Curr Protoc Mol Biol	2014 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/24984854
Fungal regulatory evolution: cis and trans in the balance.	Thompson DA, Regev A	FEBS letters	19914250	FEBS Lett	2009 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/19914250
From elements to modules: regulatory evolution in Ascomycota fungi.	Wohlbach DJ, Thompson DA, Gasch AP, Regev A	Current opinion in genetics & development	19879128	Curr Opin Genet Dev	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19879128
Chromatin signature of embryonic pluripotency is established during genome activation.	Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, Liu XS, Rinn J, Schier AF	Nature	20336069	Nature	2010 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/20336069
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.	Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL	Proceedings of the National Academy of Sciences of the United States of America	19571010	Proc Natl Acad Sci U S A	2009 Jul 14	https://www.ncbi.nlm.nih.gov/pubmed/19571010
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.	Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES	Nature	19182780	Nature	2009 Mar 12	https://www.ncbi.nlm.nih.gov/pubmed/19182780
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.	Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, Amit I, Regev A	Nature biotechnology	21516085	Nat Biotechnol	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21516085
Semiconductor-based DNA sequencing of histone modification states.	Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Macbeth A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon N, Nusbaum C, Chin L, Regev A, Amit I	Nature communications	24157732	Nat Commun	2013	https://www.ncbi.nlm.nih.gov/pubmed/24157732
Synthetic biology: understanding biological design from synthetic circuits.	Mukherji S, van Oudenaarden A	Nature reviews. Genetics	19898500	Nat Rev Genet	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19898500
Growth landscape formed by perception and import of glucose in yeast.	Youk H, van Oudenaarden A	Nature	20016593	Nature	2009 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/20016593
Cellular decision making and biological noise: from microbes to mammals.	Balázsi G, van Oudenaarden A, Collins JJ	Cell	21414483	Cell	2011 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/21414483
Validating transcripts with probes and imaging technology.	Itzkovitz S, van Oudenaarden A	Nature methods	21451512	Nat Methods	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21451512
Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase.	Buganim Y, Faddah DA, Cheng AW, Itskovich E, Markoulaki S, Ganz K, Klemm SL, van Oudenaarden A, Jaenisch R	Cell	22980981	Cell	2012 Sep 14	https://www.ncbi.nlm.nih.gov/pubmed/22980981
Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment.	Bumgarner SL, Neuert G, Voight BF, Symbor-Nagrabska A, Grisafi P, van Oudenaarden A, Fink GR	Molecular cell	22264825	Mol Cell	2012 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/22264825
Using gene expression noise to understand gene regulation.	Munsky B, Neuert G, van Oudenaarden A	Science (New York, N.Y.)	22499939	Science	2012 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/22499939
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.	Bienko M, Crosetto N, Teytelman L, Klemm S, Itzkovitz S, van Oudenaarden A	Nature methods	23263692	Nat Methods	2013 Feb	https://www.ncbi.nlm.nih.gov/pubmed/23263692
Variability in gene expression underlies incomplete penetrance.	Raj A, Rifkin SA, Andersen E, van Oudenaarden A	Nature	20164922	Nature	2010 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/20164922
Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures.	Tsang JS, Ebert MS, van Oudenaarden A	Molecular cell	20385095	Mol Cell	2010 Apr 9	https://www.ncbi.nlm.nih.gov/pubmed/20385095
Systematic identification of signal-activated stochastic gene regulation.	Neuert G, Munsky B, Tan RZ, Teytelman L, Khammash M, van Oudenaarden A	Science (New York, N.Y.)	23372015	Science	2013 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/23372015
Deconvolving the roles of Wnt ligands and receptors in sensing and amplification.	Tan RZ, Ji N, Mentink RA, Korswagen HC, van Oudenaarden A	Molecular systems biology	23295860	Mol Syst Biol	2013	https://www.ncbi.nlm.nih.gov/pubmed/23295860
Optimality in the development of intestinal crypts.	Itzkovitz S, Blat IC, Jacks T, Clevers H, van Oudenaarden A	Cell	22304925	Cell	2012 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/22304925
Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression.	Topalidou I, van Oudenaarden A, Chalfie M	Proceedings of the National Academy of Sciences of the United States of America	21368126	Proc Natl Acad Sci U S A	2011 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/21368126
Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis.	Slavov N, Budnik BA, Schwab D, Airoldi EM, van Oudenaarden A	Cell reports	24767987	Cell Rep	2014 May 8	https://www.ncbi.nlm.nih.gov/pubmed/24767987
The Caenorhabditis elegans synthetic multivulva genes prevent ras pathway activation by tightly repressing global ectopic expression of lin-3 EGF.	Saffer AM, Kim DH, van Oudenaarden A, Horvitz HR	PLoS genetics	22242000	PLoS Genet	2011 Dec	https://www.ncbi.nlm.nih.gov/pubmed/22242000
MicroRNAs can generate thresholds in target gene expression.	Mukherji S, Ebert MS, Zheng GX, Tsang JS, Sharp PA, van Oudenaarden A	Nature genetics	21857679	Nat Genet	2011 Aug 21	https://www.ncbi.nlm.nih.gov/pubmed/21857679
Single-molecule transcript counting of stem-cell markers in the mouse intestine.	Itzkovitz S, Lyubimova A, Blat IC, Maynard M, van Es J, Lees J, Jacks T, Clevers H, van Oudenaarden A	Nature cell biology	22119784	Nat Cell Biol	2011 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/22119784
Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer.	Steine EJ, Ehrich M, Bell GW, Raj A, Reddy S, van Oudenaarden A, Jaenisch R, Linhart HG	The Journal of clinical investigation	21490393	J Clin Invest	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21490393
A general mechanism for network-dosage compensation in gene circuits.	Acar M, Pando BF, Arnold FH, Elowitz MB, van Oudenaarden A	Science (New York, N.Y.)	20929850	Science	2010 Sep 24	https://www.ncbi.nlm.nih.gov/pubmed/20929850
Neuroblast migration along the anteroposterior axis of C. elegans is controlled by opposing gradients of Wnts and a secreted Frizzled-related protein.	Harterink M, Kim DH, Middelkoop TC, Doan TD, van Oudenaarden A, Korswagen HC	Development (Cambridge, England)	21653614	Development	2011 Jul	https://www.ncbi.nlm.nih.gov/pubmed/21653614
A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes.	Slavov N, Airoldi EM, van Oudenaarden A, Botstein D	Molecular biology of the cell	22456505	Mol Biol Cell	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22456505
Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies.	Ramanan V, Trehan K, Ong ML, Luna JM, Hoffmann HH, Espiritu C, Sheahan TP, Chandrasekar H, Schwartz RE, Christine KS, Rice CM, van Oudenaarden A, Bhatia SN	Virology	27128351	Virology	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/27128351
A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model.	Chiu IM, Morimoto ET, Goodarzi H, Liao JT, O'Keeffe S, Phatnani HP, Muratet M, Carroll MC, Levy S, Tavazoie S, Myers RM, Maniatis T	Cell reports	23850290	Cell Rep	2013 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/23850290
Distinct roles for motor neuron autophagy early and late in the SOD1(G93A) mouse model of ALS.	Rudnick ND, Griffey CJ, Guarnieri P, Gerbino V, Wang X, Piersaint JA, Tapia JC, Rich MM, Maniatis T	Proceedings of the National Academy of Sciences of the United States of America	28904095	Proc Natl Acad Sci U S A	2017 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/28904095
The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation.	Wallrapp A, Riesenfeld SJ, Burkett PR, Abdulnour RE, Nyman J, Dionne D, Hofree M, Cuoco MS, Rodman C, Farouq D, Haas BJ, Tickle TL, Trombetta JJ, Baral P, Klose CSN, Mahlakõiv T, Artis D, Rozenblatt-Rosen O, Chiu IM, Levy BD, Kowalczyk MS, Regev A, Kuchroo VK	Nature	28902842	Nature	2017 Sep 21	https://www.ncbi.nlm.nih.gov/pubmed/28902842
FUS-SMN protein interactions link the motor neuron diseases ALS and SMA.	Yamazaki T, Chen S, Yu Y, Yan B, Haertlein TC, Carrasco MA, Tapia JC, Zhai B, Das R, Lalancette-Hebert M, Sharma A, Chandran S, Sullivan G, Nishimura AL, Shaw CE, Gygi SP, Shneider NA, Maniatis T, Reed R	Cell reports	23022481	Cell Rep	2012 Oct 25	https://www.ncbi.nlm.nih.gov/pubmed/23022481
Single-molecule imaging of transcription factor binding to DNA in live mammalian cells.	Gebhardt JC, Suter DM, Roy R, Zhao ZW, Chapman AR, Basu S, Maniatis T, Xie XS	Nature methods	23524394	Nat Methods	2013 May	https://www.ncbi.nlm.nih.gov/pubmed/23524394
Accelerated high-yield generation of limb-innervating motor neurons from human stem cells.	Amoroso MW, Croft GF, Williams DJ, O'Keeffe S, Carrasco MA, Davis AR, Roybon L, Oakley DH, Maniatis T, Henderson CE, Wichterle H	The Journal of neuroscience : the official journal of the Society for Neuroscience	23303937	J Neurosci	2013 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/23303937
Electrical recording from hearts with flexible nanowire device arrays.	Timko BP, Cohen-Karni T, Yu G, Qing Q, Tian B, Lieber CM	Nano letters	19170614	Nano Lett	2009 Feb	https://www.ncbi.nlm.nih.gov/pubmed/19170614
Frequency domain detection of biomolecules using silicon nanowire biosensors.	Zheng G, Gao XP, Lieber CM	Nano letters	20698634	Nano Lett	2010 Aug 11	https://www.ncbi.nlm.nih.gov/pubmed/20698634
Kinked p-n junction nanowire probes for high spatial resolution sensing and intracellular recording.	Jiang Z, Qing Q, Xie P, Gao R, Lieber CM	Nano letters	22309132	Nano Lett	2012 Mar 14	https://www.ncbi.nlm.nih.gov/pubmed/22309132
Synthetically encoded ultrashort-channel nanowire transistors for fast, pointlike cellular signal detection.	Cohen-Karni T, Casanova D, Cahoon JF, Qing Q, Bell DC, Lieber CM	Nano letters	22468846	Nano Lett	2012 May 9	https://www.ncbi.nlm.nih.gov/pubmed/22468846
Semiconductor nanowires: A platform for nanoscience and nanotechnology.	Lieber CM	MRS bulletin	22707850	MRS Bull	2011 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/22707850
Synthesis of monolithic graphene-graphite integrated electronics.	Park JU, Nam S, Lee MS, Lieber CM	Nature materials	22101813	Nat Mater	2011 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/22101813
Graphene and nanowire transistors for cellular interfaces and electrical recording.	Cohen-Karni T, Qing Q, Li Q, Fang Y, Lieber CM	Nano letters	20136098	Nano Lett	2010 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/20136098
Outside looking in: nanotube transistor intracellular sensors.	Gao R, Strehle S, Tian B, Cohen-Karni T, Xie P, Duan X, Qing Q, Lieber CM	Nano letters	22583370	Nano Lett	2012 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/22583370
Nanoelectronics meets biology: from new nanoscale devices for live-cell recording to 3D innervated tissues.	Duan X, Lieber CM	Chemistry, an Asian journal	23946279	Chem Asian J	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23946279
Nanoelectronics-biology frontier: From nanoscopic probes for action potential recording in live cells to three-dimensional cyborg tissues.	Duan X, Fu TM, Liu J, Lieber CM	Nano today	24073014	Nano Today	2013 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/24073014
Design and synthesis of diverse functional kinked nanowire structures for nanoelectronic bioprobes.	Xu L, Jiang Z, Qing Q, Mai L, Zhang Q, Lieber CM	Nano letters	23273386	Nano Lett	2013 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/23273386
Macroporous nanowire nanoelectronic scaffolds for synthetic tissues.	Tian B, Liu J, Dvir T, Jin L, Tsui JH, Qing Q, Suo Z, Langer R, Kohane DS, Lieber CM	Nature materials	22922448	Nat Mater	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/22922448
Nanowire biosensors for label-free, real-time, ultrasensitive protein detection.	Zheng G, Lieber CM	Methods in molecular biology (Clifton, N.J.)	21948419	Methods Mol Biol	2011	https://www.ncbi.nlm.nih.gov/pubmed/21948419
Three-dimensional, flexible nanoscale field-effect transistors as localized bioprobes.	Tian B, Cohen-Karni T, Qing Q, Duan X, Xie P, Lieber CM	Science (New York, N.Y.)	20705858	Science	2010 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/20705858
Intracellular recordings of action potentials by an extracellular nanoscale field-effect transistor.	Duan X, Gao R, Xie P, Cohen-Karni T, Qing Q, Choe HS, Tian B, Jiang X, Lieber CM	Nature nanotechnology	22179566	Nat Nanotechnol	2011 Dec 18	https://www.ncbi.nlm.nih.gov/pubmed/22179566
Single-crystalline kinked semiconductor nanowire superstructures.	Tian B, Xie P, Kempa TJ, Bell DC, Lieber CM	Nature nanotechnology	19893521	Nat Nanotechnol	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19893521
Local electrical potential detection of DNA by nanowire-nanopore sensors.	Xie P, Xiong Q, Fang Y, Qing Q, Lieber CM	Nature nanotechnology	22157724	Nat Nanotechnol	2011 Dec 11	https://www.ncbi.nlm.nih.gov/pubmed/22157724
Synthetic nanoelectronic probes for biological cells and tissues.	Tian B, Lieber CM	Annual review of analytical chemistry (Palo Alto, Calif.)	23451719	Annu Rev Anal Chem (Palo Alto Calif)	2013	https://www.ncbi.nlm.nih.gov/pubmed/23451719
Design and Implementation of Functional Nanoelectronic Interfaces With Biomolecules, Cells, and Tissue Using Nanowire Device Arrays.	Timko BP, Cohen-Karni T, Qing Q, Tian B, Lieber CM	IEEE transactions on nanotechnology	21785576	IEEE Trans Nanotechnol	2010 May	https://www.ncbi.nlm.nih.gov/pubmed/21785576
Nanowire transistor arrays for mapping neural circuits in acute brain slices.	Qing Q, Pal SK, Tian B, Duan X, Timko BP, Cohen-Karni T, Murthy VN, Lieber CM	Proceedings of the National Academy of Sciences of the United States of America	20133836	Proc Natl Acad Sci U S A	2010 Feb 2	https://www.ncbi.nlm.nih.gov/pubmed/20133836
Subthreshold regime has the optimal sensitivity for nanowire FET biosensors.	Gao XP, Zheng G, Lieber CM	Nano letters	19908823	Nano Lett	2010 Feb 10	https://www.ncbi.nlm.nih.gov/pubmed/19908823
Design, synthesis, and characterization of novel nanowire structures for photovoltaics and intracellular probes.	Tian B, Lieber CM	Pure and applied chemistry. Chimie pure et appliquee	22707797	Pure Appl Chem	2011 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/22707797
Free-standing kinked nanowire transistor probes for targeted intracellular recording in three dimensions.	Qing Q, Jiang Z, Xu L, Gao R, Mai L, Lieber CM	Nature nanotechnology	24336402	Nat Nanotechnol	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24336402
Gold Nanopyramids Assembled into High-Order Stacks Exhibit Increased SERS Response.	Stoerzinger KA, Hasan W, Lin JY, Robles A, Odom TW	The journal of physical chemistry letters	21666758	J Phys Chem Lett	2010 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/21666758
A Three-Channel Spectrometer for Wide-Field Imaging of Anisotropic Plasmonic Nanoparticles.	Sweeney CM, Nehl CL, Hasan W, Liang T, Eckermann A, Meade TJ, Odom TW	The journal of physical chemistry. C, Nanomaterials and interfaces	21927639	J Phys Chem C Nanomater Interfaces	2011 Aug 18	https://www.ncbi.nlm.nih.gov/pubmed/21927639
Direct observation of nanoparticle-cancer cell nucleus interactions.	Dam DH, Lee JH, Sisco PN, Co DT, Zhang M, Wasielewski MR, Odom TW	ACS nano	22424173	ACS Nano	2012 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/22424173
Optical properties of anisotropic core-shell pyramidal particles.	Sweeney CM, Hasan W, Nehl CL, Odom TW	The journal of physical chemistry. A	19290590	J Phys Chem A	2009 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/19290590
High relaxivity Gd(III)-DNA gold nanostars: investigation of shape effects on proton relaxation.	Rotz MW, Culver KS, Parigi G, MacRenaris KW, Luchinat C, Odom TW, Meade TJ	ACS nano	25723190	ACS Nano	2015 Mar 24	https://www.ncbi.nlm.nih.gov/pubmed/25723190
Grafting aptamers onto gold nanostars increases in vitro efficacy in a wide range of cancer cell types.	Dam DH, Culver KS, Odom TW	Molecular pharmaceutics	24422969	Mol Pharm	2014 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/24422969
Talbot effect beyond the paraxial limit at optical frequencies.	Hua Y, Suh JY, Zhou W, Huntington MD, Odom TW	Optics express	22714490	Opt Express	2012 Jun 18	https://www.ncbi.nlm.nih.gov/pubmed/22714490
Tuning the Thickness and Orientation of Single Au Pyramids for Improved Refractive Index Sensitivities.	Lee J, Hasan W, Odom TW	The journal of physical chemistry. C, Nanomaterials and interfaces	20157343	J Phys Chem C Nanomater Interfaces	2009 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/20157343
Shining light on nuclear-targeted therapy using gold nanostar constructs.	Dam DH, Culver KS, Sisco PN, Odom TW	Therapeutic delivery	23259247	Ther Deliv	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23259247
A Markedly Improved Synthetic Approach for the Preparation of Multifunctional Au-DNA Nanoparticle Conjugates Modified with Optical and MR Imaging Probes.	Rotz MW, Holbrook RJ, MacRenaris KW, Meade TJ	Bioconjugate chemistry	30193061	Bioconjug Chem	2018 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/30193061
Improved in vitro efficacy of gold nanoconstructs by increased loading of G-quadruplex aptamer.	Dam DH, Lee RC, Odom TW	Nano letters	24689438	Nano Lett	2014 May 14	https://www.ncbi.nlm.nih.gov/pubmed/24689438
Broadband plasmonic microlenses based on patches of nanoholes.	Gao H, Hyun JK, Lee MH, Yang JC, Lauhon LJ, Odom TW	Nano letters	20839781	Nano Lett	2010 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/20839781
Optical Properties of Nested Pyramidal Nanoshells.	Lin JY, Hasan W, Yang JC, Odom TW	The journal of physical chemistry. C, Nanomaterials and interfaces	20431688	J Phys Chem C Nanomater Interfaces	2010 Jan 8	https://www.ncbi.nlm.nih.gov/pubmed/20431688
Extraordinary nonlinear absorption in 3D bowtie nanoantennas.	Suh JY, Huntington MD, Kim CH, Zhou W, Wasielewski MR, Odom TW	Nano letters	22149352	Nano Lett	2012 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/22149352
Nanoparticle SERS substrates with 3D Raman-active volumes.	Stoerzinger KA, Lin JY, Odom TW	Chemical science	23997929	Chem Sci	2011 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/23997929
Tailoring the structure of nanopyramids for optimal heat generation.	Hasan W, Stender CL, Lee MH, Nehl CL, Lee J	Nano letters	19271715	Nano Lett	2009 Apr	https://www.ncbi.nlm.nih.gov/pubmed/19271715
Enhanced optical transmission mediated by localized plasmons in anisotropic, three-dimensional nanohole arrays.	Yang JC, Gao H, Suh JY, Zhou W, Lee MH, Odom TW	Nano letters	20698633	Nano Lett	2010 Aug 11	https://www.ncbi.nlm.nih.gov/pubmed/20698633
Biodistribution and in vivo toxicity of aptamer-loaded gold nanostars.	Dam DH, Culver KS, Kandela I, Lee RC, Chandra K, Lee H, Mantis C, Ugolkov A, Mazar AP, Odom TW	Nanomedicine : nanotechnology, biology, and medicine	25461281	Nanomedicine	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25461281
Nanometre-scale thermometry in a living cell.	Kucsko G, Maurer PC, Yao NY, Kubo M, Noh HJ, Lo PK, Park H, Lukin MD	Nature	23903748	Nature	2013 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/23903748
A nanoelectrode array for obtaining intracellular recordings from thousands of connected neurons.	Abbott J, Ye T, Krenek K, Gertner RS, Ban S, Kim Y, Qin L, Wu W, Park H, Ham D	Nature biomedical engineering	31548592	Nat Biomed Eng	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/31548592
Nanowire electrodes for high-density stimulation and measurement of neural circuits.	Robinson JT, Jorgolli M, Park H	Frontiers in neural circuits	23486552	Front Neural Circuits	2013	https://www.ncbi.nlm.nih.gov/pubmed/23486552
Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits.	Robinson JT, Jorgolli M, Shalek AK, Yoon MH, Gertner RS, Park H	Nature nanotechnology	22231664	Nat Nanotechnol	2012 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/22231664
Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL.	Wang L, Shalek AK, Lawrence M, Ding R, Gaublomme JT, Pochet N, Stojanov P, Sougnez C, Shukla SA, Stevenson KE, Zhang W, Wong J, Sievers QL, MacDonald BT, Vartanov AR, Goldstein NR, Neuberg D, He X, Lander E, Hacohen N, Regev A, Getz G, Brown JR, Park H, Wu CJ	Blood	24778153	Blood	2014 Aug 14	https://www.ncbi.nlm.nih.gov/pubmed/24778153
Probing enzymatic activity inside living cells using a nanowire-cell "sandwich" assay.	Na YR, Kim SY, Gaublomme JT, Shalek AK, Jorgolli M, Park H, Yang EG	Nano letters	23244056	Nano Lett	2013 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/23244056
Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia.	Shalek AK, Gaublomme JT, Wang L, Yosef N, Chevrier N, Andersen MS, Robinson JT, Pochet N, Neuberg D, Gertner RS, Amit I, Brown JR, Hacohen N, Regev A, Wu CJ, Park H	Nano letters	23190424	Nano Lett	2012 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/23190424
The CRAC channel activator STIM1 binds and inhibits L-type voltage-gated calcium channels.	Park CY, Shcheglovitov A, Dolmetsch R	Science (New York, N.Y.)	20929812	Science	2010 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/20929812
In vitro human corticogenesis.	Wang Y, Dolmetsch R	Neuron	23395367	Neuron	2013 Feb 6	https://www.ncbi.nlm.nih.gov/pubmed/23395367
STIM1 and calmodulin interact with Orai1 to induce Ca2+-dependent inactivation of CRAC channels.	Mullins FM, Park CY, Dolmetsch RE, Lewis RS	Proceedings of the National Academy of Sciences of the United States of America	19706428	Proc Natl Acad Sci U S A	2009 Sep 8	https://www.ncbi.nlm.nih.gov/pubmed/19706428
Using light to control signaling cascades in live neurons.	Rana A, Dolmetsch RE	Current opinion in neurobiology	20850295	Curr Opin Neurobiol	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20850295
Using induced pluripotent stem cells to investigate cardiac phenotypes in Timothy syndrome.	Yazawa M, Hsueh B, Jia X, Pasca AM, Bernstein JA, Hallmayer J, Dolmetsch RE	Nature	21307850	Nature	2011 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/21307850
Modeling Timothy syndrome with iPS cells.	Yazawa M, Dolmetsch RE	Journal of cardiovascular translational research	23299782	J Cardiovasc Transl Res	2013 Feb	https://www.ncbi.nlm.nih.gov/pubmed/23299782
Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome.	Paşca SP, Portmann T, Voineagu I, Yazawa M, Shcheglovitov A, Paşca AM, Cord B, Palmer TD, Chikahisa S, Nishino S, Bernstein JA, Hallmayer J, Geschwind DH, Dolmetsch RE	Nature medicine	22120178	Nat Med	2011 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/22120178
Aberrant calcium channel splicing drives defects in cortical differentiation in Timothy syndrome.	Panagiotakos G, Haveles C, Arjun A, Petrova R, Rana A, Portmann T, Paşca SP, Palmer TD, Dolmetsch RE	eLife	31868578	Elife	2019 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/31868578
16p11.2 Deletion Syndrome Mice Display Sensory and Ultrasonic Vocalization Deficits During Social Interactions.	Yang M, Mahrt EJ, Lewis F, Foley G, Portmann T, Dolmetsch RE, Portfors CV, Crawley JN	Autism research : official journal of the International Society for Autism Research	25663600	Autism Res	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25663600
PIKfyve mediates the motility of late endosomes and lysosomes in neuronal dendrites.	Tsuruta F, Dolmetsch RE	Neuroscience letters	26232680	Neurosci Lett	2015 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/26232680
Identification of Orai1 channel inhibitors by using minimal functional domains to screen small molecule microarrays.	Sadaghiani AM, Lee SM, Odegaard JI, Leveson-Gower DB, McPherson OM, Novick P, Kim MR, Koehler AN, Negrin R, Dolmetsch RE, Park CY	Chemistry & biology	25308275	Chem Biol	2014 Oct 23	https://www.ncbi.nlm.nih.gov/pubmed/25308275
Timothy syndrome is associated with activity-dependent dendritic retraction in rodent and human neurons.	Krey JF, Paşca SP, Shcheglovitov A, Yazawa M, Schwemberger R, Rasmusson R, Dolmetsch RE	Nature neuroscience	23313911	Nat Neurosci	2013 Feb	https://www.ncbi.nlm.nih.gov/pubmed/23313911
Induction of protein-protein interactions in live cells using light.	Yazawa M, Sadaghiani AM, Hsueh B, Dolmetsch RE	Nature biotechnology	19801976	Nat Biotechnol	2009 Oct	https://www.ncbi.nlm.nih.gov/pubmed/19801976
Generating human neurons in vitro and using them to understand neuropsychiatric disease.	Paşca SP, Panagiotakos G, Dolmetsch RE	Annual review of neuroscience	25002278	Annu Rev Neurosci	2014	https://www.ncbi.nlm.nih.gov/pubmed/25002278
Direct in vivo assessment of human stem cell graft-host neural circuits.	Byers B, Lee HJ, Liu J, Weitz AJ, Lin P, Zhang P, Shcheglovitov A, Dolmetsch R, Pera RR, Lee JH	NeuroImage	25936696	Neuroimage	2015 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/25936696
SHANK3 and IGF1 restore synaptic deficits in neurons from 22q13 deletion syndrome patients.	Shcheglovitov A, Shcheglovitova O, Yazawa M, Portmann T, Shu R, Sebastiano V, Krawisz A, Froehlich W, Bernstein JA, Hallmayer JF, Dolmetsch RE	Nature	24132240	Nature	2013 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/24132240
Engineering the genomes of wild insect populations: challenges, and opportunities provided by synthetic Medea selfish genetic elements.	Hay BA, Chen CH, Ward CM, Huang H, Su JT, Guo M	Journal of insect physiology	20570677	J Insect Physiol	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20570677
Medea selfish genetic elements as tools for altering traits of wild populations: a theoretical analysis.	Ward CM, Su JT, Huang Y, Lloyd AL, Gould F, Hay BA	Evolution; international journal of organic evolution	21062278	Evolution	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21062278
General principles of single-construct chromosomal gene drive.	Marshall JM, Hay BA	Evolution; international journal of organic evolution	22759292	Evolution	2012 Jul	https://www.ncbi.nlm.nih.gov/pubmed/22759292
Identification of germline transcriptional regulatory elements in Aedes aegypti.	Akbari OS, Papathanos PA, Sandler JE, Kennedy K, Hay BA	Scientific reports	24492376	Sci Rep	2014 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/24492376
A drug-inducible sex-separation technique for insects.	Kandul NP, Liu J, Hsu AD, Hay BA, Akbari OS	Nature communications	32355156	Nat Commun	2020 Apr 30	https://www.ncbi.nlm.nih.gov/pubmed/32355156
Semele: a killer-male, rescue-female system for suppression and replacement of insect disease vector populations.	Marshall JM, Pittman GW, Buchman AB, Hay BA	Genetics	21078687	Genetics	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21078687
The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector.	Akbari OS, Antoshechkin I, Amrhein H, Williams B, Diloreto R, Sandler J, Hay BA	G3 (Bethesda, Md.)	23833213	G3 (Bethesda)	2013 Sep 4	https://www.ncbi.nlm.nih.gov/pubmed/23833213
A synthetic gene drive system for local, reversible modification and suppression of insect populations.	Akbari OS, Matzen KD, Marshall JM, Huang H, Ward CM, Hay BA	Current biology : CB	23541732	Curr Biol	2013 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/23541732
Inverse Medea as a novel gene drive system for local population replacement: a theoretical analysis.	Marshall JM, Hay BA	The Journal of heredity	21493596	J Hered	2011 May-Jun	https://www.ncbi.nlm.nih.gov/pubmed/21493596
Confinement of gene drive systems to local populations: a comparative analysis.	Marshall JM, Hay BA	Journal of theoretical biology	22094363	J Theor Biol	2012 Feb 7	https://www.ncbi.nlm.nih.gov/pubmed/22094363
The toxin and antidote puzzle: new ways to control insect pest populations through manipulating inheritance.	Marshall JM	Bioengineered bugs	21876382	Bioeng Bugs	2011 Sep-Oct	https://www.ncbi.nlm.nih.gov/pubmed/21876382
The impact of heterogeneous transmission on the establishment and spread of antimalarial drug resistance.	Klein EY	Journal of theoretical biology	24076451	J Theor Biol	2014 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/24076451
On the problem of boundaries and scaling for urban street networks.	Masucci AP, Arcaute E, Hatna E, Stanilov K, Batty M	Journal of the Royal Society, Interface	26468071	J R Soc Interface	2015 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/26468071
Constructing cities, deconstructing scaling laws.	Arcaute E, Hatna E, Ferguson P, Youn H, Johansson A, Batty M	Journal of the Royal Society, Interface	25411405	J R Soc Interface	2015 Jan 6	https://www.ncbi.nlm.nih.gov/pubmed/25411405
National and local influenza surveillance through Twitter: an analysis of the 2012-2013 influenza epidemic.	Broniatowski DA, Paul MJ, Dredze M	PloS one	24349542	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24349542
A formal model of fuzzy-trace theory: Variations on framing effects and the Allais paradox.	Broniatowski DA, Reyna VF	Decision (Washington, D.C.)	30320145	Decision (Wash D C )	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30320145
The Emergence and Collapse of Knowledge Boundaries.	Broniatowski DA, Magee CL	IEEE transactions on engineering management	29255326	IEEE Trans Eng Manag	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29255326
An agent-based model of centralized institutions, social network technology, and revolution.	Makowsky MD, Rubin J	PloS one	24278280	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24278280
Coupled contagion dynamics of fear and disease: mathematical and computational explorations.	Epstein JM, Parker J, Cummings D, Hammond RA	PloS one	19079607	PLoS One	2008	https://www.ncbi.nlm.nih.gov/pubmed/19079607
The Determinants of Federal and State Enforcement of Workplace Safety Regulations: OSHA Inspections 1990-2010.	Jung J, Makowsky MD	Journal of regulatory economics	24659856	J Regul Econ	2014 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/24659856
Endogenous Group Formation via Unproductive Costs.	Aimone JA, Iannaccone LR, Makowsky MD, Rubin J	The Review of economic studies	24808623	Rev Econ Stud	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24808623
Twitter: big data opportunities.	Broniatowski DA, Paul MJ, Dredze M	Science (New York, N.Y.)	25013052	Science	2014 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/25013052
Influenza A H1N1 pandemic strain evolution--divergence and the potential for antigenic drift variants.	Klein EY, Serohijos AW, Choi JM, Shakhnovich EI, Pekosz A	PloS one	24699432	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24699432
The cultural evolution of emergent group-level traits.	Smaldino PE	The Behavioral and brain sciences	24970399	Behav Brain Sci	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24970399
Germs are germs, and why not take a risk? Patients' expectations for prescribing antibiotics in an inner-city emergency department.	Broniatowski DA, Klein EY, Reyna VF	Medical decision making : an international journal of the Society for Medical Decision Making	25331913	Med Decis Making	2015 Jan	https://www.ncbi.nlm.nih.gov/pubmed/25331913
Simulating the evolution of the human family: cooperative breeding increases in harsh environments.	Smaldino PE, Newson L, Schank JC, Richerson PJ	PloS one	24278318	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24278318
Modelling to contain pandemics.	Epstein JM	Nature	19661897	Nature	2009 Aug 6	https://www.ncbi.nlm.nih.gov/pubmed/19661897
Recasting the theory of mosquito-borne pathogen transmission dynamics and control.	Smith DL, Perkins TA, Reiner RC Jr, Barker CM, Niu T, Chaves LF, Ellis AM, George DB, Le Menach A, Pulliam JR, Bisanzio D, Buckee C, Chiyaka C, Cummings DA, Garcia AJ, Gatton ML, Gething PW, Hartley DM, Johnston G, Klein EY, Michael E, Lloyd AL, Pigott DM, Reisen WK, Ruktanonchai N, Singh BK, Stoller J, Tatem AJ, Kitron U, Godfray HC, Cohen JM, Hay SI, Scott TW	Transactions of the Royal Society of Tropical Medicine and Hygiene	24591453	Trans R Soc Trop Med Hyg	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24591453
Combining Computational Fluid Dynamics and Agent-Based Modeling: a new approach to evacuation planning.	Epstein JM, Pankajakshan R, Hammond RA	PloS one	21687788	PLoS One	2011	https://www.ncbi.nlm.nih.gov/pubmed/21687788
A Distributed Platform for Global-Scale Agent-Based Models of Disease Transmission.	Parker J, Epstein JM	ACM transactions on modeling and computer simulation : a publication of the Association for Computing Machinery	24465120	ACM Trans Model Comput Simul	2011 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24465120
Institutions and cooperation in an ecology of games.	Smaldino PE, Lubell M	Artificial life	24494613	Artif Life	2014 Spring	https://www.ncbi.nlm.nih.gov/pubmed/24494613
Trends in antibiotic resistance in coagulase-negative staphylococci in the United States, 1999 to 2012.	May L, Klein EY, Rothman RE, Laxminarayan R	Antimicrobial agents and chemotherapy	24342646	Antimicrob Agents Chemother	2014	https://www.ncbi.nlm.nih.gov/pubmed/24342646
Cross-reactive immune responses as primary drivers of malaria chronicity.	Klein EY, Graham AL, Llinás M, Levin S	Infection and immunity	24126530	Infect Immun	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24126530
Cooperation in Harsh Environments and the Emergence of Spatial Patterns.	Smaldino PE	Chaos, solitons, and fractals	24277977	Chaos Solitons Fractals	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24277977
Targeting device therapy: genomics of sudden death.	Frangiskakis JM, London B	Heart failure clinics	19945065	Heart Fail Clin	2010 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19945065
The many faces of repolarization instability: which one is prognostic?	Shusterman V, Lampert R, London B	Journal of electrocardiology	19717165	J Electrocardiol	2009 Nov-Dec	https://www.ncbi.nlm.nih.gov/pubmed/19717165
High-energy external defibrillation and transcutaneous pacing during MRI: feasibility and safety.	Shusterman V, Hodgson-Zingman D, Thedens D, Zhu X, Hoffman S, Sieren JC, Morgan GM, Faranesh A, London B	Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance	31378203	J Cardiovasc Magn Reson	2019 Aug 5	https://www.ncbi.nlm.nih.gov/pubmed/31378203
Mechanism of automaticity in cardiomyocytes derived from human induced pluripotent stem cells.	Kim JJ, Yang L, Lin B, Zhu X, Sun B, Kaplan AD, Bett GC, Rasmusson RL, London B, Salama G	Journal of molecular and cellular cardiology	25644533	J Mol Cell Cardiol	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25644533
Acoustic radiation force for vascular cell therapy: in vitro validation.	Kaya M, Toma C, Wang J, Grata M, Fu H, Villanueva FS, Chen X	Ultrasound in medicine & biology	22975034	Ultrasound Med Biol	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/22975034
Homozygous missense N629D hERG (KCNH2) potassium channel mutation causes developmental defects in the right ventricle and its outflow tract and embryonic lethality.	Teng GQ, Zhao X, Lees-Miller JP, Quinn FR, Li P, Rancourt DE, London B, Cross JC, Duff HJ	Circulation research	18948620	Circ Res	2008 Dec 5	https://www.ncbi.nlm.nih.gov/pubmed/18948620
Magnetic Resonance Imaging of Contracting Ultrathin Cardiac Tissue.	Shusterman V, Nagpal P, Thedens D, Zhu X, Matasic DS, Yoon JY, Morgan G, Hoffman S, London B	Biomedical physics & engineering express	32733693	Biomed Phys Eng Express	2019 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32733693
Genetic reporter system for positioning of proteins at the bacterial pole.	Fixen KR, Janakiraman A, Garrity S, Slade DJ, Gray AN, Karahan N, Hochschild A, Goldberg MB	mBio	22375072	mBio	2012	https://www.ncbi.nlm.nih.gov/pubmed/22375072
Conversion of a yeast prion protein to an infectious form in bacteria.	Garrity SJ, Sivanathan V, Dong J, Lindquist S, Hochschild A	Proceedings of the National Academy of Sciences of the United States of America	20484678	Proc Natl Acad Sci U S A	2010 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/20484678
Prion propagation can occur in a prokaryote and requires the ClpB chaperone.	Yuan AH, Garrity SJ, Nako E, Hochschild A	eLife	25122461	Elife	2014 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/25122461
A bacterial global regulator forms a prion.	Yuan AH, Hochschild A	Science (New York, N.Y.)	28082594	Science	2017 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/28082594
Atomic insights into the genesis of cellular filaments by globular proteins.	McPartland L, Heller DM, Eisenberg DS, Hochschild A, Sawaya MR	Nature structural & molecular biology	30076408	Nat Struct Mol Biol	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/30076408
CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB.	Heller DM, Tavag M, Hochschild A	PLoS genetics	28931012	PLoS Genet	2017 Sep	https://www.ncbi.nlm.nih.gov/pubmed/28931012
Generating extracellular amyloid aggregates using E. coli cells.	Sivanathan V, Hochschild A	Genes & development	23166018	Genes Dev	2012 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/23166018
A bacterial export system for generating extracellular amyloid aggregates.	Sivanathan V, Hochschild A	Nature protocols	23787895	Nat Protoc	2013	https://www.ncbi.nlm.nih.gov/pubmed/23787895
Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development.	Shestopalov IA, Pitt CL, Chen JK	Nature chemical biology	22286130	Nat Chem Biol	2012 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/22286130
Oligonucleotide-based tools for studying zebrafish development.	Shestopalov IA, Chen JK	Zebrafish	20392138	Zebrafish	2010 Mar	https://www.ncbi.nlm.nih.gov/pubmed/20392138
Cyclic caged morpholinos: conformationally gated probes of embryonic gene function.	Yamazoe S, Shestopalov IA, Provost E, Leach SD, Chen JK	Angewandte Chemie (International ed. in English)	22689470	Angew Chem Int Ed Engl	2012 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/22689470
Synthetic strategies for studying embryonic development.	Ouyang X, Chen JK	Chemistry & biology	20609409	Chem Biol	2010 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/20609409
Spatiotemporal control of embryonic gene expression using caged morpholinos.	Shestopalov IA, Chen JK	Methods in cell biology	21924162	Methods Cell Biol	2011	https://www.ncbi.nlm.nih.gov/pubmed/21924162
Controlling destiny through chemistry: small-molecule regulators of cell fate.	Firestone AJ, Chen JK	ACS chemical biology	20000447	ACS Chem Biol	2010 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/20000447
The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome.	Kuo AJ, Song J, Cheung P, Ishibe-Murakami S, Yamazoe S, Chen JK, Patel DJ, Gozani O	Nature	22398447	Nature	2012 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/22398447
Protein occupancy landscape of a bacterial genome.	Vora T, Hottes AK, Tavazoie S	Molecular cell	19647521	Mol Cell	2009 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/19647521
Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms.	Amini S, Hottes AK, Smith LE, Tavazoie S	PLoS pathogens	22028649	PLoS Pathog	2011 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22028649
Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli.	Amini S, Goodarzi H, Tavazoie S	PLoS pathogens	19436718	PLoS Pathog	2009 May	https://www.ncbi.nlm.nih.gov/pubmed/19436718
Genetic architecture of intrinsic antibiotic susceptibility.	Girgis HS, Hottes AK, Tavazoie S	PloS one	19462005	PLoS One	2009 May 20	https://www.ncbi.nlm.nih.gov/pubmed/19462005
Predictive behavior within microbial genetic networks.	Tagkopoulos I, Liu YC, Tavazoie S	Science (New York, N.Y.)	18467556	Science	2008 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/18467556
Systematic discovery of structural elements governing stability of mammalian messenger RNAs.	Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S	Nature	22495308	Nature	2012 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/22495308
Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli.	Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S	Molecular systems biology	20531407	Mol Syst Biol	2010 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/20531407
Revealing global regulatory perturbations across human cancers.	Goodarzi H, Elemento O, Tavazoie S	Molecular cell	20005852	Mol Cell	2009 Dec 11	https://www.ncbi.nlm.nih.gov/pubmed/20005852
Global discovery of adaptive mutations.	Goodarzi H, Hottes AK, Tavazoie S	Nature methods	19597501	Nat Methods	2009 Aug	https://www.ncbi.nlm.nih.gov/pubmed/19597501
Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior.	Freddolino PL, Tavazoie S	Annual review of cell and developmental biology	22559263	Annu Rev Cell Dev Biol	2012	https://www.ncbi.nlm.nih.gov/pubmed/22559263
Synaptic state matching: a dynamical architecture for predictive internal representation and feature detection.	Tavazoie S	PloS one	23991161	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23991161
Otx2 binding to perineuronal nets persistently regulates plasticity in the mature visual cortex.	Beurdeley M, Spatazza J, Lee HH, Sugiyama S, Bernard C, Di Nardo AA, Hensch TK, Prochiantz A	The Journal of neuroscience : the official journal of the Society for Neuroscience	22764251	J Neurosci	2012 Jul 4	https://www.ncbi.nlm.nih.gov/pubmed/22764251
Choroid-plexus-derived Otx2 homeoprotein constrains adult cortical plasticity.	Spatazza J, Lee HH, Di Nardo AA, Tibaldi L, Joliot A, Hensch TK, Prochiantz A	Cell reports	23770240	Cell Rep	2013 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/23770240
NMDA receptor regulation prevents regression of visual cortical function in the absence of Mecp2.	Durand S, Patrizi A, Quast KB, Hachigian L, Pavlyuk R, Saxena A, Carninci P, Hensch TK, Fagiolini M	Neuron	23259945	Neuron	2012 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/23259945
Sensory integration in mouse insular cortex reflects GABA circuit maturation.	Gogolla N, Takesian AE, Feng G, Fagiolini M, Hensch TK	Neuron	25088363	Neuron	2014 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/25088363
Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells.	Dougherty JD, Schmidt EF, Nakajima M, Heintz N	Nucleic acids research	20308160	Nucleic Acids Res	2010 Jul	https://www.ncbi.nlm.nih.gov/pubmed/20308160
Excitatory projection neuron subtypes control the distribution of local inhibitory interneurons in the cerebral cortex.	Lodato S, Rouaux C, Quast KB, Jantrachotechatchawan C, Studer M, Hensch TK, Arlotta P	Neuron	21338885	Neuron	2011 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/21338885
From brain formation to plasticity: insights on Otx2 homeoprotein.	Sugiyama S, Prochiantz A, Hensch TK	Development, growth & differentiation	19298552	Dev Growth Differ	2009 Apr	https://www.ncbi.nlm.nih.gov/pubmed/19298552
Lynx1, a cholinergic brake, limits plasticity in adult visual cortex.	Morishita H, Miwa JM, Heintz N, Hensch TK	Science (New York, N.Y.)	21071629	Science	2010 Nov 26	https://www.ncbi.nlm.nih.gov/pubmed/21071629
Calculation of electrostatic effects at the amino terminus of an alpha helix.	Sitkoff D, Lockhart DJ, Sharp KA, Honig B	Biophysical journal	7696466	Biophys J	1994 Dec	https://www.ncbi.nlm.nih.gov/pubmed/7696466
Early Seizures Prematurely Unsilence Auditory Synapses to Disrupt Thalamocortical Critical Period Plasticity.	Sun H, Takesian AE, Wang TT, Lippman-Bell JJ, Hensch TK, Jensen FE	Cell reports	29847785	Cell Rep	2018 May 29	https://www.ncbi.nlm.nih.gov/pubmed/29847785
Prolonged Period of Cortical Plasticity upon Redox Dysregulation in Fast-Spiking Interneurons.	Morishita H, Cabungcal JH, Chen Y, Do KQ, Hensch TK	Biological psychiatry	25758057	Biol Psychiatry	2015 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/25758057
A probabilistic framework for learning robust common spatial patterns.	Wu W, Chen Z, Gao S, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	19963618	Annu Int Conf IEEE Eng Med Biol Soc	2009	https://www.ncbi.nlm.nih.gov/pubmed/19963618
A state-space model of the burst suppression ratio.	Chemali JJ, Wong KF, Solt K, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22254587	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22254587
Modeling two-photon calcium fluorescence of episodic V1 recordings using multifrequency analysis.	Zheng HW, Malik WQ, Runyan CA, Sur M, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22254975	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22254975
Assessing neuronal interactions of cell assemblies during general anesthesia.	Chen Z, Vijayan S, Ching S, Hale G, Flores FJ, Wilson MA, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22255259	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22255259
Methylphenidate actively induces emergence from general anesthesia.	Solt K, Cotten JF, Cimenser A, Wong KF, Chemali JJ, Brown EN	Anesthesiology	21934407	Anesthesiology	2011 Oct	https://www.ncbi.nlm.nih.gov/pubmed/21934407
STATE-SPACE SOLUTIONS TO THE DYNAMIC MAGNETOENCEPHALOGRAPHY INVERSE PROBLEM USING HIGH PERFORMANCE COMPUTING.	Long CJ, Purdon PL, Temereanca S, Desai NU, Hämäläinen MS, Brown EN	The annals of applied statistics	22081780	Ann Appl Stat	2011 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/22081780
Dynamic Cardiovagal Response to Motion Sickness: A Point-Process Heart Rate Variability Study.	Lacount L, Napadow V, Kuo B, Park K, Kim J, Brown E, Barbieri R	Computers in cardiology	20445767	Comput Cardiol	2009 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/20445767
Interaction between Heart Rate Variability and Respiration in Preterm Infants.	Indic P, Salisbury E, Paydarfar D, Brown E, Barbieri R	Computers in cardiology	20333264	Comput Cardiol	2008 Sep	https://www.ncbi.nlm.nih.gov/pubmed/20333264
Using point process models to compare neural spiking activity in the subthalamic nucleus of Parkinson's patients and a healthy primate.	Sarma SV, Eden UT, Cheng ML, Williams ZM, Hu R, Eskandar E, Brown EN	IEEE transactions on bio-medical engineering	20172804	IEEE Trans Biomed Eng	2010 Jun	https://www.ncbi.nlm.nih.gov/pubmed/20172804
Efficient decoding with steady-state Kalman filter in neural interface systems.	Malik WQ, Truccolo W, Brown EN, Hochberg LR	IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society	21078582	IEEE Trans Neural Syst Rehabil Eng	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21078582
Delayed orexin signaling consolidates wakefulness and sleep: physiology and modeling.	Diniz Behn CG, Kopell N, Brown EN, Mochizuki T, Scammell TE	Journal of neurophysiology	18417630	J Neurophysiol	2008 Jun	https://www.ncbi.nlm.nih.gov/pubmed/18417630
Potential network mechanisms mediating electroencephalographic beta rhythm changes during propofol-induced paradoxical excitation.	McCarthy MM, Brown EN, Kopell N	The Journal of neuroscience : the official journal of the Society for Neuroscience	19074022	J Neurosci	2008 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/19074022
Inferring evoked brain connectivity through adaptive perturbation.	Lepage KQ, Ching S, Kramer MA	Journal of computational neuroscience	22990598	J Comput Neurosci	2013 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22990598
A neurophysiological-metabolic model for burst suppression.	Ching S, Purdon PL, Vijayan S, Kopell NJ, Brown EN	Proceedings of the National Academy of Sciences of the United States of America	22323592	Proc Natl Acad Sci U S A	2012 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/22323592
Point process time-frequency analysis of dynamic respiratory patterns during meditation practice.	Kodituwakku S, Lazar SW, Indic P, Chen Z, Brown EN, Barbieri R	Medical & biological engineering & computing	22350435	Med Biol Eng Comput	2012 Mar	https://www.ncbi.nlm.nih.gov/pubmed/22350435
Assessment of autonomic control and respiratory sinus arrhythmia using point process models of human heart beat dynamics.	Chen Z, Brown EN, Barbieri R	IEEE transactions on bio-medical engineering	19272971	IEEE Trans Biomed Eng	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19272971
Convergence and Stability of a Class of Iteratively Re-weighted Least Squares Algorithms for Sparse Signal Recovery in the Presence of Noise.	Babadi B, Ba D, Purdon PL, Brown EN	IEEE transactions on signal processing : a publication of the IEEE Signal Processing Society	26549965	IEEE Trans Signal Process	2013 Oct 30	https://www.ncbi.nlm.nih.gov/pubmed/26549965
Biophysical Modeling of Alpha Rhythms During Halothane-Induced Unconsciousness.	Vijayan S, Ching S, Purdon PL, Brown EN, Kopell NJ	International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering	25284633	Int IEEE EMBS Conf Neural Eng	2013	https://www.ncbi.nlm.nih.gov/pubmed/25284633
Disruption of thalamic functional connectivity is a neural correlate of dexmedetomidine-induced unconsciousness.	Akeju O, Loggia ML, Catana C, Pavone KJ, Vazquez R, Rhee J, Contreras Ramirez V, Chonde DB, Izquierdo-Garcia D, Arabasz G, Hsu S, Habeeb K, Hooker JM, Napadow V, Brown EN, Purdon PL	eLife	25432022	Elife	2014 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/25432022
The human burst suppression electroencephalogram of deep hypothermia.	Westover MB, Ching S, Kumaraswamy VM, Akeju SO, Pierce E, Cash SS, Kilbride R, Brown EN, Purdon PL	Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology	25649968	Clin Neurophysiol	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25649968
Beamforming approach to phase-amplitude modulation analysis of multi-channel EEG.	Sampson AL, Babadi B, Prerau MJ, Mukamel EA, Brown EN, Purdon PL	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	23367474	Annu Int Conf IEEE Eng Med Biol Soc	2012	https://www.ncbi.nlm.nih.gov/pubmed/23367474
Encoding through patterns: regression tree-based neuronal population models.	Haslinger R, Pipa G, Lewis LD, Nikolić D, Williams Z, Brown E	Neural computation	23607564	Neural Comput	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23607564
Mapping of visual receptive fields by tomographic reconstruction.	Pipa G, Chen Z, Neuenschwander S, Lima B, Brown EN	Neural computation	22734491	Neural Comput	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22734491
Rapid fragmentation of neuronal networks at the onset of propofol-induced unconsciousness.	Lewis LD, Weiner VS, Mukamel EA, Donoghue JA, Eskandar EN, Madsen JR, Anderson WS, Hochberg LR, Cash SS, Brown EN, Purdon PL	Proceedings of the National Academy of Sciences of the United States of America	23129622	Proc Natl Acad Sci U S A	2012 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/23129622
Neural population partitioning and a concurrent brain-machine interface for sequential motor function.	Shanechi MM, Hu RC, Powers M, Wornell GW, Brown EN, Williams ZM	Nature neuroscience	23143511	Nat Neurosci	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23143511
Ageing delays emergence from general anaesthesia in rats by increasing anaesthetic sensitivity in the brain.	Chemali JJ, Kenny JD, Olutola O, Taylor NE, Kimchi EY, Purdon PL, Brown EN, Solt K	British journal of anaesthesia	26174302	Br J Anaesth	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26174302
Robust control of burst suppression for medical coma.	Westover MB, Kim SE, Ching S, Purdon PL, Brown EN	Journal of neural engineering	26020243	J Neural Eng	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26020243
GABAA circuit mechanisms are associated with ether anesthesia-induced unconsciousness.	Akeju O, Hamilos AE, Song AH, Pavone KJ, Purdon PL, Brown EN	Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology	27178867	Clin Neurophysiol	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27178867
A point process model for auditory neurons considering both their intrinsic dynamics and the spectrotemporal properties of an extrinsic signal.	Plourde E, Delgutte B, Brown EN	IEEE transactions on bio-medical engineering	21317068	IEEE Trans Biomed Eng	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/21317068
Single-neuron dynamics in human focal epilepsy.	Truccolo W, Donoghue JA, Hochberg LR, Eskandar EN, Madsen JR, Anderson WS, Brown EN, Halgren E, Cash SS	Nature neuroscience	21441925	Nat Neurosci	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21441925
Point-process analysis of neural spiking activity of muscle spindles recorded from thin-film longitudinal intrafascicular electrodes.	Citi L, Djilas M, Azevedo-Coste C, Yoshida K, Brown EN, Barbieri R	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22254803	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22254803
Heart Rate Variability and Respiratory Sinus Arrhythmia Assessment of Affective States by Bivariate Autoregressive Spectral Analysis.	Magagnin V, Mauri M, Cipresso P, Mainardi L, Brown E, Cerutti S, Villamira M, Barbieri R	Computing in cardiology	22158520	Comput Cardiol (2010)	2010	https://www.ncbi.nlm.nih.gov/pubmed/22158520
A real-time automated point-process method for the detection and correction of erroneous and ectopic heartbeats.	Citi L, Brown EN, Barbieri R	IEEE transactions on bio-medical engineering	22875239	IEEE Trans Biomed Eng	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22875239
A Bayesian statistical analysis of behavioral facilitation associated with deep brain stimulation.	Smith AC, Shah SA, Hudson AE, Purpura KP, Victor JD, Brown EN, Schiff ND	Journal of neuroscience methods	19576932	J Neurosci Methods	2009 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/19576932
Discrete time rescaling theorem: determining goodness of fit for discrete time statistical models of neural spiking.	Haslinger R, Pipa G, Brown E	Neural computation	20608868	Neural Comput	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20608868
Assessment of Baroreflex Control of Heart Rate During General Anesthesia Using a Point Process Method.	Chen Z, Purdon P, Pierce E, Harrell G, Brown E, Barbieri R	Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP (Conference)	20473342	Proc IEEE Int Conf Acoust Speech Signal Process	2009 May 26	https://www.ncbi.nlm.nih.gov/pubmed/20473342
Analysis of between-trial and within-trial neural spiking dynamics.	Czanner G, Eden UT, Wirth S, Yanike M, Suzuki WA, Brown EN	Journal of neurophysiology	18216233	J Neurophysiol	2008 May	https://www.ncbi.nlm.nih.gov/pubmed/18216233
Local cortical dynamics of burst suppression in the anaesthetized brain.	Lewis LD, Ching S, Weiner VS, Peterfreund RA, Eskandar EN, Cash SS, Brown EN, Purdon PL	Brain : a journal of neurology	23887187	Brain	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23887187
Real-time closed-loop control in a rodent model of medically induced coma using burst suppression.	Ching S, Liberman MY, Chemali JJ, Westover MB, Kenny JD, Solt K, Purdon PL, Brown EN	Anesthesiology	23770601	Anesthesiology	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23770601
Reference-free harmonic regression technique to remove EEG-fMRI ballistocardiogram artifacts.	Krishnaswamy P, Bonmassar G, Purdon PL, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	24110963	Annu Int Conf IEEE Eng Med Biol Soc	2013	https://www.ncbi.nlm.nih.gov/pubmed/24110963
Real-time segmentation and tracking of brain metabolic state in ICU EEG recordings of burst suppression.	Westover MB, Ching S, Shafi MM, Cash SS, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	24111383	Annu Int Conf IEEE Eng Med Biol Soc	2013	https://www.ncbi.nlm.nih.gov/pubmed/24111383
Likelihood methods for point processes with refractoriness.	Citi L, Ba D, Brown EN, Barbieri R	Neural computation	24206384	Neural Comput	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24206384
A Granger causality measure for point process models of ensemble neural spiking activity.	Kim S, Putrino D, Ghosh S, Brown EN	PLoS computational biology	21455283	PLoS Comput Biol	2011 Mar	https://www.ncbi.nlm.nih.gov/pubmed/21455283
Linear and nonlinear quantification of respiratory sinus arrhythmia during propofol general anesthesia.	Chen Z, Purdon PL, Pierce ET, Harrell G, Walsh J, Salazar AF, Tavares CL, Brown EN, Barbieri R	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	19963899	Annu Int Conf IEEE Eng Med Biol Soc	2009	https://www.ncbi.nlm.nih.gov/pubmed/19963899
A regularized point process generalized linear model for assessing the functional connectivity in the cat motor cortex.	Chen Z, Putrino DF, Ba DE, Ghosh S, Barbieri R, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	19965032	Annu Int Conf IEEE Eng Med Biol Soc	2009	https://www.ncbi.nlm.nih.gov/pubmed/19965032
Instantaneous frequency and amplitude modulation of EEG in the hippocampus reveals state dependent temporal structure.	Nguyen DP, Barbieri R, Wilson MA, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	19163009	Annu Int Conf IEEE Eng Med Biol Soc	2008	https://www.ncbi.nlm.nih.gov/pubmed/19163009
A fast iterative greedy algorithm for MEG source localization.	Obregon-Henao G, Babadi B, Lamus C, Brown EN, Purdon PL	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	23367478	Annu Int Conf IEEE Eng Med Biol Soc	2012	https://www.ncbi.nlm.nih.gov/pubmed/23367478
State-space analysis of time-varying higher-order spike correlation for multiple neural spike train data.	Shimazaki H, Amari S, Brown EN, Grün S	PLoS computational biology	22412358	PLoS Comput Biol	2012	https://www.ncbi.nlm.nih.gov/pubmed/22412358
Assessment of cardio-respiratory interactions in preterm infants by bivariate autoregressive modeling and surrogate data analysis.	Indic P, Bloch-Salisbury E, Bednarek F, Brown EN, Paydarfar D, Barbieri R	Early human development	21511413	Early Hum Dev	2011 Jul	https://www.ncbi.nlm.nih.gov/pubmed/21511413
General anesthesia and altered states of arousal: a systems neuroscience analysis.	Brown EN, Purdon PL, Van Dort CJ	Annual review of neuroscience	21513454	Annu Rev Neurosci	2011	https://www.ncbi.nlm.nih.gov/pubmed/21513454
Denoising two-photon calcium imaging data.	Malik WQ, Schummers J, Sur M, Brown EN	PloS one	21687727	PLoS One	2011	https://www.ncbi.nlm.nih.gov/pubmed/21687727
Instantaneous assessment of autonomic cardiovascular control during general anesthesia.	Chen Z, Citi L, Purdon PL, Brown EN, Barbieri R	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22256307	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22256307
Brain correlates of autonomic modulation: combining heart rate variability with fMRI.	Napadow V, Dhond R, Conti G, Makris N, Brown EN, Barbieri R	NeuroImage	18524629	Neuroimage	2008 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/18524629
Active emergence from propofol general anesthesia is induced by methylphenidate.	Chemali JJ, Van Dort CJ, Brown EN, Solt K	Anesthesiology	22446983	Anesthesiology	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22446983
Physostigmine and Methylphenidate Induce Distinct Arousal States During Isoflurane General Anesthesia in Rats.	Kenny JD, Chemali JJ, Cotten JF, Van Dort CJ, Kim SE, Ba D, Taylor NE, Brown EN, Solt K	Anesthesia and analgesia	26991753	Anesth Analg	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26991753
A Neurologic Examination for Anesthesiologists: Assessing Arousal Level during Induction, Maintenance, and Emergence.	Reshef ER, Schiff ND, Brown EN	Anesthesiology	30664547	Anesthesiology	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30664547
Effects of sevoflurane and propofol on frontal electroencephalogram power and coherence.	Akeju O, Westover MB, Pavone KJ, Sampson AL, Hartnack KE, Brown EN, Purdon PL	Anesthesiology	25233374	Anesthesiology	2014 Nov	https://www.ncbi.nlm.nih.gov/pubmed/25233374
Measuring the signal-to-noise ratio of a neuron.	Czanner G, Sarma SV, Ba D, Eden UT, Wu W, Eskandar E, Lim HH, Temereanca S, Suzuki WA, Brown EN	Proceedings of the National Academy of Sciences of the United States of America	25995363	Proc Natl Acad Sci U S A	2015 Jun 9	https://www.ncbi.nlm.nih.gov/pubmed/25995363
Optogenetic activation of cholinergic neurons in the PPT or LDT induces REM sleep.	Van Dort CJ, Zachs DP, Kenny JD, Zheng S, Goldblum RR, Gelwan NA, Ramos DM, Nolan MA, Wang K, Weng FJ, Lin Y, Wilson MA, Brown EN	Proceedings of the National Academy of Sciences of the United States of America	25548191	Proc Natl Acad Sci U S A	2015 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/25548191
Electroencephalographic markers of brain development during sevoflurane anaesthesia in children up to 3 years old.	Cornelissen L, Kim SE, Lee JM, Brown EN, Purdon PL, Berde CB	British journal of anaesthesia	29793594	Br J Anaesth	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29793594
Probabilistic Common Spatial Patterns for Multichannel EEG Analysis.	Wu W, Chen Z, Gao X, Li Y, Brown EN, Gao S	IEEE transactions on pattern analysis and machine intelligence	26005228	IEEE Trans Pattern Anal Mach Intell	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26005228
Clinical Electroencephalography for Anesthesiologists: Part I: Background and Basic Signatures.	Purdon PL, Sampson A, Pavone KJ, Brown EN	Anesthesiology	26275092	Anesthesiology	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26275092
Statistical inference for assessing functional connectivity of neuronal ensembles with sparse spiking data.	Chen Z, Putrino DF, Ghosh S, Barbieri R, Brown EN	IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society	20937583	IEEE Trans Neural Syst Rehabil Eng	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20937583
Tracking brain states under general anesthesia by using global coherence analysis.	Cimenser A, Purdon PL, Pierce ET, Walsh JL, Salazar-Gomez AF, Harrell PG, Tavares-Stoeckel C, Habeeb K, Brown EN	Proceedings of the National Academy of Sciences of the United States of America	21555565	Proc Natl Acad Sci U S A	2011 May 24	https://www.ncbi.nlm.nih.gov/pubmed/21555565
Static and dynamic autonomic response with increasing nausea perception.	LaCount LT, Barbieri R, Park K, Kim J, Brown EN, Kuo B, Napadow V	Aviation, space, and environmental medicine	21485400	Aviat Space Environ Med	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21485400
Human leg model predicts ankle muscle-tendon morphology, state, roles and energetics in walking.	Krishnaswamy P, Brown EN, Herr HM	PLoS computational biology	21445231	PLoS Comput Biol	2011 Mar	https://www.ncbi.nlm.nih.gov/pubmed/21445231
Assessing the effects of pharmacological agents on respiratory dynamics using time-series modeling.	Wong KF, Gong JJ, Cotten JF, Solt K, Brown EN	IEEE transactions on bio-medical engineering	23193230	IEEE Trans Biomed Eng	2013 Apr	https://www.ncbi.nlm.nih.gov/pubmed/23193230
Distributed control in a mean-field cortical network model: implications for seizure suppression.	Ching S, Brown EN, Kramer MA	Physical review. E, Statistical, nonlinear, and soft matter physics	23005798	Phys Rev E Stat Nonlin Soft Matter Phys	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23005798
Context matters: the illusive simplicity of macaque V1 receptive fields.	Haslinger R, Pipa G, Lima B, Singer W, Brown EN, Neuenschwander S	PloS one	22802940	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22802940
A spatiotemporal dynamic distributed solution to the MEG inverse problem.	Lamus C, Hämäläinen MS, Temereanca S, Brown EN, Purdon PL	NeuroImage	22155043	Neuroimage	2012 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/22155043
Electroencephalogram signatures of loss and recovery of consciousness from propofol.	Purdon PL, Pierce ET, Mukamel EA, Prerau MJ, Walsh JL, Wong KF, Salazar-Gomez AF, Harrell PG, Sampson AL, Cimenser A, Ching S, Kopell NJ, Tavares-Stoeckel C, Habeeb K, Merhar R, Brown EN	Proceedings of the National Academy of Sciences of the United States of America	23487781	Proc Natl Acad Sci U S A	2013 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/23487781
A real-time brain-machine interface combining motor target and trajectory intent using an optimal feedback control design.	Shanechi MM, Williams ZM, Wornell GW, Hu RC, Powers M, Brown EN	PloS one	23593130	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23593130
Thalamocortical mechanisms for the anteriorization of α rhythms during propofol-induced unconsciousness.	Vijayan S, Ching S, Purdon PL, Brown EN, Kopell NJ	The Journal of neuroscience : the official journal of the Society for Neuroscience	23825412	J Neurosci	2013 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/23825412
A brain-machine interface for control of medically-induced coma.	Shanechi MM, Chemali JJ, Liberman M, Solt K, Brown EN	PLoS computational biology	24204231	PLoS Comput Biol	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24204231
Understanding the TXA seizure connection.	Schwinn DA, Mackensen GB, Brown EN	The Journal of clinical investigation	23187134	J Clin Invest	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23187134
A closed-loop anesthetic delivery system for real-time control of burst suppression.	Liberman MY, Ching S, Chemali J, Brown EN	Journal of neural engineering	23744607	J Neural Eng	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23744607
Quantification of the benefit from integrating MEG and EEG data in minimum l2-norm estimation.	Molins A, Stufflebeam SM, Brown EN, Hämäläinen MS	NeuroImage	18602485	Neuroimage	2008 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/18602485
Activity in the barrel cortex during active behavior and sleep.	Vijayan S, Hale GJ, Moore CI, Brown EN, Wilson M	Journal of neurophysiology	20164403	J Neurophysiol	2010 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20164403
Motor cortical networks for skilled movements have dynamic properties that are related to accurate reaching.	Putrino DF, Chen Z, Ghosh S, Brown EN	Neural plasticity	22007332	Neural Plast	2011	https://www.ncbi.nlm.nih.gov/pubmed/22007332
Correcting for serial dependence in studies of respiratory dynamics.	Gong JJ, Wong KF, Cotten JF, Solt K, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22254658	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22254658
A Prospective Study of Age-dependent Changes in Propofol-induced Electroencephalogram Oscillations in Children.	Lee JM, Akeju O, Terzakis K, Pavone KJ, Deng H, Houle TT, Firth PG, Shank ES, Brown EN, Purdon PL	Anesthesiology	28657957	Anesthesiology	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28657957
Differential involvement of excitatory and inhibitory neurons of cat motor cortex in coincident spike activity related to behavioral context.	Putrino D, Brown EN, Mastaglia FL, Ghosh S	The Journal of neuroscience : the official journal of the Society for Neuroscience	20534853	J Neurosci	2010 Jun 9	https://www.ncbi.nlm.nih.gov/pubmed/20534853
Deconvolution of serum cortisol levels by using compressed sensing.	Faghih RT, Dahleh MA, Adler GK, Klerman EB, Brown EN	PloS one	24489656	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24489656
Statistical modeling of behavioral dynamics during propofol-induced loss of consciousness.	Wong KF, Smith AC, Pierce ET, Harrell PG, Walsh JL, Salazar-Gómez AF, Tavares CL, Purdon PL, Brown EN	Journal of neuroscience methods	24530701	J Neurosci Methods	2014 Apr 30	https://www.ncbi.nlm.nih.gov/pubmed/24530701
Functional biases in visual cortex neurons with identified projections to higher cortical targets.	Jarosiewicz B, Schummers J, Malik WQ, Brown EN, Sur M	Current biology : CB	22305753	Curr Biol	2012 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/22305753
Uncovering spatial topology represented by rat hippocampal population neuronal codes.	Chen Z, Kloosterman F, Brown EN, Wilson MA	Journal of computational neuroscience	22307459	J Comput Neurosci	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22307459
A unified point process probabilistic framework to assess heartbeat dynamics and autonomic cardiovascular control.	Chen Z, Purdon PL, Brown EN, Barbieri R	Frontiers in physiology	22375120	Front Physiol	2012	https://www.ncbi.nlm.nih.gov/pubmed/22375120
Broad range of neural dynamics from a time-varying FitzHugh-Nagumo model and its spiking threshold estimation.	Faghih RT, Savla K, Dahleh MA, Brown EN	IEEE transactions on bio-medical engineering	22186931	IEEE Trans Biomed Eng	2012 Mar	https://www.ncbi.nlm.nih.gov/pubmed/22186931
Phase-based measures of cross-frequency coupling in brain electrical dynamics under general anesthesia.	Mukamel EA, Wong KF, Prerau MJ, Brown EN, Purdon PL	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22254722	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22254722
Bayesian analysis of trinomial data in behavioral experiments and its application to human studies of general anesthesia.	Wong KF, Smith AC, Pierce ET, Harrell PG, Walsh JL, Salazar AF, Tavares CL, Cimenser A, Prerau MJ, Mukamel EA, Sampson A, Purdon PL, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22255388	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22255388
Robust time-varying multivariate coherence estimation: application to electroencephalogram recordings during general anesthesia.	Wong KF, Mukamel EA, Salazar AF, Pierce ET, Harrell PG, Walsh JL, Sampson A, Brown EN, Purdon PL	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	22255393	Annu Int Conf IEEE Eng Med Biol Soc	2011	https://www.ncbi.nlm.nih.gov/pubmed/22255393
Simultaneous electroencephalography and functional magnetic resonance imaging of general anesthesia.	Purdon PL, Pierce ET, Bonmassar G, Walsh J, Harrell PG, Kwo J, Deschler D, Barlow M, Merhar RC, Lamus C, Mullaly CM, Sullivan M, Maginnis S, Skoniecki D, Higgins HA, Brown EN	Annals of the New York Academy of Sciences	19351356	Ann N Y Acad Sci	2009 Mar	https://www.ncbi.nlm.nih.gov/pubmed/19351356
Left-Lateralized Contributions of Saccades to Cortical Activity During a One-Back Word Recognition Task.	Chang YC, Khan S, Taulu S, Kuperberg G, Brown EN, Hämäläinen MS, Temereanca S	Frontiers in neural circuits	29867372	Front Neural Circuits	2018	https://www.ncbi.nlm.nih.gov/pubmed/29867372
Corticoamygdala Transfer of Socially Derived Information Gates Observational Learning.	Allsop SA, Wichmann R, Mills F, Burgos-Robles A, Chang CJ, Felix-Ortiz AC, Vienne A, Beyeler A, Izadmehr EM, Glober G, Cum MI, Stergiadou J, Anandalingam KK, Farris K, Namburi P, Leppla CA, Weddington JC, Nieh EH, Smith AC, Ba D, Brown EN, Tye KM	Cell	29731170	Cell	2018 May 31	https://www.ncbi.nlm.nih.gov/pubmed/29731170
Quantifying Pituitary-Adrenal Dynamics and Deconvolution of Concurrent Cortisol and Adrenocorticotropic Hormone Data by Compressed Sensing.	Faghih RT, Dahleh MA, Adler GK, Klerman EB, Brown EN	IEEE transactions on bio-medical engineering	25935025	IEEE Trans Biomed Eng	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25935025
Nitrous oxide-induced slow and delta oscillations.	Pavone KJ, Akeju O, Sampson AL, Ling K, Purdon PL, Brown EN	Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology	26118489	Clin Neurophysiol	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26118489
A PK-PD model of ketamine-induced high-frequency oscillations.	Flores FJ, Ching S, Hartnack K, Fath AB, Purdon PL, Wilson MA, Brown EN	Journal of neural engineering	26268223	J Neural Eng	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26268223
A spatially-regularized dynamic source localization algorithm for EEG.	Pirondini E, Babadi B, Lamus C, Brown EN, Purdon PL	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	23367479	Annu Int Conf IEEE Eng Med Biol Soc	2012	https://www.ncbi.nlm.nih.gov/pubmed/23367479
Activation of D1 dopamine receptors induces emergence from isoflurane general anesthesia.	Taylor NE, Chemali JJ, Brown EN, Solt K	Anesthesiology	23221866	Anesthesiology	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23221866
Transductive neural decoding for unsorted neuronal spikes of rat hippocampus.	Chen Z, Kloosterman F, Layton S, Wilson MA	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	23366139	Annu Int Conf IEEE Eng Med Biol Soc	2012	https://www.ncbi.nlm.nih.gov/pubmed/23366139
A hierarchical Bayesian approach for learning sparse spatio-temporal decompositions of multichannel EEG.	Wu W, Chen Z, Gao S, Brown EN	NeuroImage	21420499	Neuroimage	2011 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/21420499
General anesthesia, sleep, and coma.	Brown EN, Lydic R, Schiff ND	The New England journal of medicine	21190458	N Engl J Med	2010 Dec 30	https://www.ncbi.nlm.nih.gov/pubmed/21190458
Point process time-frequency analysis of respiratory sinus arrhythmia under altered respiration dynamics.	Kodituwakku S, Lazar SW, Indic P, Brown EN, Barbieri R	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	21096135	Annu Int Conf IEEE Eng Med Biol Soc	2010	https://www.ncbi.nlm.nih.gov/pubmed/21096135
The Fitzhugh-Nagumo model: Firing modes with time-varying parameters & parameter estimation.	Faghih RT, Savla K, Dahleh MA, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	21096631	Annu Int Conf IEEE Eng Med Biol Soc	2010	https://www.ncbi.nlm.nih.gov/pubmed/21096631
Psychophysiological signals associated with affective states.	Mauri M, Magagnin V, Cipresso P, Mainardi L, Brown EN, Cerutti S, Villamira M, Barbieri R	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	21096828	Annu Int Conf IEEE Eng Med Biol Soc	2010	https://www.ncbi.nlm.nih.gov/pubmed/21096828
A differential autoregressive modeling approach within a point process framework for non-stationary heartbeat intervals analysis.	Chen Z, Purdon PL, Brown EN, Barbieri R	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	21096829	Annu Int Conf IEEE Eng Med Biol Soc	2010	https://www.ncbi.nlm.nih.gov/pubmed/21096829
Thalamocortical model for a propofol-induced alpha-rhythm associated with loss of consciousness.	Ching S, Cimenser A, Purdon PL, Brown EN, Kopell NJ	Proceedings of the National Academy of Sciences of the United States of America	21149695	Proc Natl Acad Sci U S A	2010 Dec 28	https://www.ncbi.nlm.nih.gov/pubmed/21149695
Modulation depth estimation and variable selection in state-space models for neural interfaces.	Malik WQ, Hochberg LR, Donoghue JP, Brown EN	IEEE transactions on bio-medical engineering	25265627	IEEE Trans Biomed Eng	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25265627
A comparison of propofol- and dexmedetomidine-induced electroencephalogram dynamics using spectral and coherence analysis.	Akeju O, Pavone KJ, Westover MB, Vazquez R, Prerau MJ, Harrell PG, Hartnack KE, Rhee J, Sampson AL, Habeeb K, Gao L, Pierce ET, Walsh JL, Brown EN, Purdon PL	Anesthesiology	25187999	Anesthesiology	2014 Nov	https://www.ncbi.nlm.nih.gov/pubmed/25187999
Characterizing nonlinear heartbeat dynamics within a point process framework.	Chen Z, Brown EN, Barbieri R	IEEE transactions on bio-medical engineering	20172783	IEEE Trans Biomed Eng	2010 Jun	https://www.ncbi.nlm.nih.gov/pubmed/20172783
A statistical model for multiphoton calcium imaging of the brain.	Malik WQ, Schummers J, Sur M, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	19964727	Annu Int Conf IEEE Eng Med Biol Soc	2009	https://www.ncbi.nlm.nih.gov/pubmed/19964727
State-space algorithms for estimating spike rate functions.	Smith AC, Scalon JD, Wirth S, Yanike M, Suzuki WA, Brown EN	Computational intelligence and neuroscience	19911062	Comput Intell Neurosci	2010	https://www.ncbi.nlm.nih.gov/pubmed/19911062
Discrete- and continuous-time probabilistic models and algorithms for inferring neuronal UP and DOWN states.	Chen Z, Vijayan S, Barbieri R, Wilson MA, Brown EN	Neural computation	19323637	Neural Comput	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19323637
Trial outcome and associative learning signals in the monkey hippocampus.	Wirth S, Avsar E, Chiu CC, Sharma V, Smith AC, Brown E, Suzuki WA	Neuron	19324001	Neuron	2009 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/19324001
Characterizing nonlinear heartbeat dynamics within a point process framework.	Chen Z, Brown EN, Barbieri R	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	19163282	Annu Int Conf IEEE Eng Med Biol Soc	2008	https://www.ncbi.nlm.nih.gov/pubmed/19163282
Assessment of hippocampal and autonomic neural activity by point process models.	Barbieri R, Chen Z, Brown EN	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	19163509	Annu Int Conf IEEE Eng Med Biol Soc	2008	https://www.ncbi.nlm.nih.gov/pubmed/19163509
Application of dynamic point process models to cardiovascular control.	Barbieri R, Brown EN	Bio Systems	18515000	Biosystems	2008 Jul-Aug	https://www.ncbi.nlm.nih.gov/pubmed/18515000
Dynamic assessment of baroreflex control of heart rate during induction of propofol anesthesia using a point process method.	Chen Z, Purdon PL, Harrell G, Pierce ET, Walsh J, Brown EN, Barbieri R	Annals of biomedical engineering	20945159	Ann Biomed Eng	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/20945159
Electrical stimulation of the ventral tegmental area induces reanimation from general anesthesia.	Solt K, Van Dort CJ, Chemali JJ, Taylor NE, Kenny JD, Brown EN	Anesthesiology	24398816	Anesthesiology	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/24398816
Modeling the dynamical effects of anesthesia on brain circuits.	Ching S, Brown EN	Current opinion in neurobiology	24457211	Curr Opin Neurobiol	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24457211
Optogenetics and Chemogenetics.	Vlasov K, Van Dort CJ, Solt K	Methods in enzymology	29673525	Methods Enzymol	2018	https://www.ncbi.nlm.nih.gov/pubmed/29673525
Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition.	Martorell AJ, Paulson AL, Suk HJ, Abdurrob F, Drummond GT, Guan W, Young JZ, Kim DN, Kritskiy O, Barker SJ, Mangena V, Prince SM, Brown EN, Chung K, Boyden ES, Singer AC, Tsai LH	Cell	30879788	Cell	2019 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/30879788
Burst suppression probability algorithms: state-space methods for tracking EEG burst suppression.	Chemali J, Ching S, Purdon PL, Solt K, Brown EN	Journal of neural engineering	24018288	J Neural Eng	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24018288
A transition in brain state during propofol-induced unconsciousness.	Mukamel EA, Pirondini E, Babadi B, Wong KF, Pierce ET, Harrell PG, Walsh JL, Salazar-Gomez AF, Cash SS, Eskandar EN, Weiner VS, Brown EN, Purdon PL	The Journal of neuroscience : the official journal of the Society for Neuroscience	24431442	J Neurosci	2014 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/24431442
Eye movements modulate the spatiotemporal dynamics of word processing.	Temereanca S, Hämäläinen MS, Kuperberg GR, Stufflebeam SM, Halgren E, Brown EN	The Journal of neuroscience : the official journal of the Society for Neuroscience	22457496	J Neurosci	2012 Mar 28	https://www.ncbi.nlm.nih.gov/pubmed/22457496
Point Process Heart Rate Variability Assessment during Sleep Deprivation.	Citi L, Klerman E, Brown E, Barbieri R	Computing in cardiology	22517071	Comput Cardiol (2010)	2010 Dec 31	https://www.ncbi.nlm.nih.gov/pubmed/22517071
The aging brain and anesthesia.	Brown EN, Purdon PL	Current opinion in anaesthesiology	23820102	Curr Opin Anaesthesiol	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23820102
Real-time segmentation of burst suppression patterns in critical care EEG monitoring.	Brandon Westover M, Shafi MM, Ching S, Chemali JJ, Purdon PL, Cash SS, Brown EN	Journal of neuroscience methods	23891828	J Neurosci Methods	2013 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/23891828
Age-dependency of sevoflurane-induced electroencephalogram dynamics in children.	Akeju O, Pavone KJ, Thum JA, Firth PG, Westover MB, Puglia M, Shank ES, Brown EN, Purdon PL	British journal of anaesthesia	26174303	Br J Anaesth	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26174303
Reference-free removal of EEG-fMRI ballistocardiogram artifacts with harmonic regression.	Krishnaswamy P, Bonmassar G, Poulsen C, Pierce ET, Purdon PL, Brown EN	NeuroImage	26151100	Neuroimage	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26151100
In reply.	Purdon PL, Zhou DW, Akeju O, Brown EN	Anesthesiology	26284863	Anesthesiology	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/26284863
The Role of Glutamatergic and Dopaminergic Neurons in the Periaqueductal Gray/Dorsal Raphe: Separating Analgesia and Anxiety.	Taylor NE, Pei J, Zhang J, Vlasov KY, Davis T, Taylor E, Weng FJ, Van Dort CJ, Solt K, Brown EN	eNeuro	31058210	eNeuro	2019 Jan-Feb	https://www.ncbi.nlm.nih.gov/pubmed/31058210
Adaptation to elastic loads and BMI robot controls during rat locomotion examined with point-process GLMs.	Song W, Cajigas I, Brown EN, Giszter SF	Frontiers in systems neuroscience	25972789	Front Syst Neurosci	2015	https://www.ncbi.nlm.nih.gov/pubmed/25972789
Cognitive Impairment Is Associated with Absolute Intraoperative Frontal α-Band Power but Not with Baseline α-Band Power: A Pilot Study.	Koch S, Feinkohl I, Chakravarty S, Windmann V, Lichtner G, Pischon T, Brown EN, Spies C, BioCog Study Group	Dementia and geriatric cognitive disorders	31578031	Dement Geriatr Cogn Disord	2019	https://www.ncbi.nlm.nih.gov/pubmed/31578031
Electroencephalogram signatures of ketamine anesthesia-induced unconsciousness.	Akeju O, Song AH, Hamilos AE, Pavone KJ, Flores FJ, Brown EN, Purdon PL	Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology	27178861	Clin Neurophysiol	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27178861
Metabolite-enabled eradication of bacterial persisters by aminoglycosides.	Allison KR, Brynildsen MP, Collins JJ	Nature	21562562	Nature	2011 May 12	https://www.ncbi.nlm.nih.gov/pubmed/21562562
A network biology approach to aging in yeast.	Lorenz DR, Cantor CR, Collins JJ	Proceedings of the National Academy of Sciences of the United States of America	19164565	Proc Natl Acad Sci U S A	2009 Jan 27	https://www.ncbi.nlm.nih.gov/pubmed/19164565
Bacteria as control engineers.	Allison KR, Collins JJ	Molecular cell	21211717	Mol Cell	2011 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/21211717
Wisdom of crowds for robust gene network inference.	Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G	Nature methods	22796662	Nat Methods	2012 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/22796662
Role of reactive oxygen species in antibiotic action and resistance.	Dwyer DJ, Kohanski MA, Collins JJ	Current opinion in microbiology	19647477	Curr Opin Microbiol	2009 Oct	https://www.ncbi.nlm.nih.gov/pubmed/19647477
A role for the bacterial GATC methylome in antibiotic stress survival.	Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, Collins JJ	Nature genetics	26998690	Nat Genet	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/26998690
Fungicidal drugs induce a common oxidative-damage cellular death pathway.	Belenky P, Camacho D, Collins JJ	Cell reports	23416050	Cell Rep	2013 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/23416050
Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria.	Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ, Walker GC	BMC genomics	24511998	BMC Genomics	2014 Feb 11	https://www.ncbi.nlm.nih.gov/pubmed/24511998
Genetic switchboard for synthetic biology applications.	Callura JM, Cantor CR, Collins JJ	Proceedings of the National Academy of Sciences of the United States of America	22454498	Proc Natl Acad Sci U S A	2012 Apr 10	https://www.ncbi.nlm.nih.gov/pubmed/22454498
Tunable signal processing in synthetic MAP kinase cascades.	O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA	Cell	21215374	Cell	2011 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/21215374
Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis.	Kohanski MA, DePristo MA, Collins JJ	Molecular cell	20159551	Mol Cell	2010 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/20159551
Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli.	Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ, Walker GC	Molecular cell	20005847	Mol Cell	2009 Dec 11	https://www.ncbi.nlm.nih.gov/pubmed/20005847
Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death.	Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G, Collins JJ	Cell	19013277	Cell	2008 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/19013277
Diversity-based, model-guided construction of synthetic gene networks with predicted functions.	Ellis T, Wang X, Collins JJ	Nature biotechnology	19377462	Nat Biotechnol	2009 May	https://www.ncbi.nlm.nih.gov/pubmed/19377462
Heterogeneous bacterial persisters and engineering approaches to eliminate them.	Allison KR, Brynildsen MP, Collins JJ	Current opinion in microbiology	21937262	Curr Opin Microbiol	2011 Oct	https://www.ncbi.nlm.nih.gov/pubmed/21937262
Synthetic biology: applications come of age.	Khalil AS, Collins JJ	Nature reviews. Genetics	20395970	Nat Rev Genet	2010 May	https://www.ncbi.nlm.nih.gov/pubmed/20395970
Iterative plug-and-play methodology for constructing and modifying synthetic gene networks.	Litcofsky KD, Afeyan RB, Krom RJ, Khalil AS, Collins JJ	Nature methods	23042452	Nat Methods	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23042452
Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis.	Dwyer DJ, Camacho DM, Kohanski MA, Callura JM, Collins JJ	Molecular cell	22633370	Mol Cell	2012 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/22633370
Microbial environments confound antibiotic efficacy.	Lee HH, Collins JJ	Nature chemical biology	22173343	Nat Chem Biol	2011 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/22173343
Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production.	Brynildsen MP, Winkler JA, Spina CS, MacDonald IC, Collins JJ	Nature biotechnology	23292609	Nat Biotechnol	2013 Feb	https://www.ncbi.nlm.nih.gov/pubmed/23292609
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome.	Modi SR, Lee HH, Spina CS, Collins JJ	Nature	23748443	Nature	2013 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/23748443
Microbial persistence and the road to drug resistance.	Cohen NR, Lobritz MA, Collins JJ	Cell host & microbe	23768488	Cell Host Microbe	2013 Jun 12	https://www.ncbi.nlm.nih.gov/pubmed/23768488
How antibiotics kill bacteria: from targets to networks.	Kohanski MA, Dwyer DJ, Collins JJ	Nature reviews. Microbiology	20440275	Nat Rev Microbiol	2010 Jun	https://www.ncbi.nlm.nih.gov/pubmed/20440275
Functional characterization of bacterial sRNAs using a network biology approach.	Modi SR, Camacho DM, Kohanski MA, Walker GC, Collins JJ	Proceedings of the National Academy of Sciences of the United States of America	21876160	Proc Natl Acad Sci U S A	2011 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/21876160
Networking opportunities for bacteria.	Dwyer DJ, Kohanski MA, Collins JJ	Cell	19109881	Cell	2008 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/19109881
Next-generation synthetic gene networks.	Lu TK, Khalil AS, Collins JJ	Nature biotechnology	20010597	Nat Biotechnol	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20010597
Antibiotic efficacy is linked to bacterial cellular respiration.	Lobritz MA, Belenky P, Porter CB, Gutierrez A, Yang JH, Schwarz EG, Dwyer DJ, Khalil AS, Collins JJ	Proceedings of the National Academy of Sciences of the United States of America	26100898	Proc Natl Acad Sci U S A	2015 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/26100898
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators.	Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ	Proceedings of the National Academy of Sciences of the United States of America	20713708	Proc Natl Acad Sci U S A	2010 Sep 7	https://www.ncbi.nlm.nih.gov/pubmed/20713708
Bacterial charity work leads to population-wide resistance.	Lee HH, Molla MN, Cantor CR, Collins JJ	Nature	20811456	Nature	2010 Sep 2	https://www.ncbi.nlm.nih.gov/pubmed/20811456
Tunable protein degradation in bacteria.	Cameron DE, Collins JJ	Nature biotechnology	25402616	Nat Biotechnol	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25402616
Synthetic gene networks that count.	Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ	Science (New York, N.Y.)	19478183	Science	2009 May 29	https://www.ncbi.nlm.nih.gov/pubmed/19478183
Signaling-mediated bacterial persister formation.	Vega NM, Allison KR, Khalil AS, Collins JJ	Nature chemical biology	22426114	Nat Chem Biol	2012 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/22426114
Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics.	Foti JJ, Devadoss B, Winkler JA, Collins JJ, Walker GC	Science (New York, N.Y.)	22517853	Science	2012 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/22517853
Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage.	Belenky P, Ye JD, Porter CB, Cohen NR, Lobritz MA, Ferrante T, Jain S, Korry BJ, Schwarz EG, Walker GC, Collins JJ	Cell reports	26565910	Cell Rep	2015 Nov 3	https://www.ncbi.nlm.nih.gov/pubmed/26565910
Socioeconomic Status and the Increased Prevalence of Autism in California.	King MD, Bearman PS	American sociological review	21547238	Am Sociol Rev	2011 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/21547238
The spatial structure of autism in California, 1993-2001.	Mazumdar S, King M, Liu KY, Zerubavel N, Bearman P	Health & place	20097113	Health Place	2010 May	https://www.ncbi.nlm.nih.gov/pubmed/20097113
The Temporal Structure of Scientific Consensus Formation.	Shwed U, Bearman PS	American sociological review	21886269	Am Sociol Rev	2010 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/21886269
Just-so Stories: Vaccines, Autism, and the Single-bullet Disorder.	Bearman P	Social psychology quarterly	20721312	Soc Psychol Q	2009 Jun	https://www.ncbi.nlm.nih.gov/pubmed/20721312
Social influence and the autism epidemic.	Liu KY, King M, Bearman PS	AJS; American journal of sociology	20503647	AJS	2010 Mar	https://www.ncbi.nlm.nih.gov/pubmed/20503647
Does Autism Diagnosis Age or Symptom Severity Differ Among Children According to Whether Assisted Reproductive Technology was Used to Achieve Pregnancy?	Schieve LA, Fountain C, Boulet SL, Yeargin-Allsopp M, Kissin DM, Jamieson DJ, Rice C, Bearman P	Journal of autism and developmental disorders	25997596	J Autism Dev Disord	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25997596
The disappearing seasonality of autism conceptions in California.	Mazumdar S, Liu KY, Susser E, Bearman P	PloS one	22859972	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22859972
Estimated autism risk and older reproductive age.	King MD, Fountain C, Dakhlallah D, Bearman PS	American journal of public health	19608957	Am J Public Health	2009 Sep	https://www.ncbi.nlm.nih.gov/pubmed/19608957
Estimated autism risk, older reproductive age, and parameterization.	Durkin MS, Maenner MJ, Newschaffer CJ	American journal of public health	20075308	Am J Public Health	2010 Mar	https://www.ncbi.nlm.nih.gov/pubmed/20075308
Closely spaced pregnancies are associated with increased odds of autism in California sibling births.	Cheslack-Postava K, Liu K, Bearman PS	Pediatrics	21220394	Pediatrics	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21220394
Association of assisted reproductive technology (ART) treatment and parental infertility diagnosis with autism in ART-conceived children.	Kissin DM, Zhang Y, Boulet SL, Fountain C, Bearman P, Schieve L, Yeargin-Allsopp M, Jamieson DJ	Human reproduction (Oxford, England)	25518976	Hum Reprod	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25518976
Can Sibling Sex Ratios Be Used as a Valid Test for the Prenatal Androgen Hypothesis of Autism Spectrum Disorders?	Cheslack-Postava K, Susser E, Liu K, Bearman PS	PloS one	26495967	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26495967
Risk as Social Context: Immigration Policy and Autism in California.	Fountain C, Bearman P	Sociological forum (Randolph, N.J.)	21643443	Sociol Forum (Randolph N J)	2011 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/21643443
Six developmental trajectories characterize children with autism.	Fountain C, Winter AS, Bearman PS	Pediatrics	22473372	Pediatrics	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22473372
Age of diagnosis for autism: individual and community factors across 10 birth cohorts.	Fountain C, King MD, Bearman PS	Journal of epidemiology and community health	20974836	J Epidemiol Community Health	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/20974836
Social demographic change and autism.	Liu K, Zerubavel N, Bearman P	Demography	20608100	Demography	2010 May	https://www.ncbi.nlm.nih.gov/pubmed/20608100
Association between assisted reproductive technology conception and autism in California, 1997-2007.	Fountain C, Zhang Y, Kissin DM, Schieve LA, Jamieson DJ, Rice C, Bearman P	American journal of public health	25790396	Am J Public Health	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25790396
Gifts and influence: Conflict of interest policies and prescribing of psychotropic medications in the United States.	King M, Bearman PS	Social science & medicine (1982)	27856120	Soc Sci Med	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27856120
Authors' response to: cohort effects explain the increase in autism diagnosis: an identifiability problem of the age-period-cohort model.	Keyes KM, Susser E, Cheslack-Postava K, Fountain C, Liu K, Bearman PS	International journal of epidemiology	25361588	Int J Epidemiol	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25361588
Spatial clusters of autism births and diagnoses point to contextual drivers of increased prevalence.	Mazumdar S, Winter A, Liu KY, Bearman P	Social science & medicine (1982)	23267775	Soc Sci Med	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23267775
Cohort effects explain the increase in autism diagnosis among children born from 1992 to 2003 in California.	Keyes KM, Susser E, Cheslack-Postava K, Fountain C, Liu K, Bearman PS	International journal of epidemiology	22253308	Int J Epidemiol	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22253308
Medical school gift restriction policies and physician prescribing of newly marketed psychotropic medications: difference-in-differences analysis.	King M, Essick C, Bearman P, Ross JS	BMJ (Clinical research ed.)	23372175	BMJ	2013 Jan 30	https://www.ncbi.nlm.nih.gov/pubmed/23372175
Diagnostic change and the increased prevalence of autism.	King M, Bearman P	International journal of epidemiology	19737791	Int J Epidemiol	2009 Oct	https://www.ncbi.nlm.nih.gov/pubmed/19737791
Focal Points, Endogenous Processes, and Exogenous Shocks in the Autism Epidemic.	Liu K, Bearman PS	Sociological methods & research	26166907	Sociol Methods Res	2015 May 1	https://www.ncbi.nlm.nih.gov/pubmed/26166907
Reply: CDC analysis of ICSI/autism: association is not causation.	Kissin DM, Zhang Y, Boulet SL, Fountain C, Bearman P, Schieve L, Yeargin-Allsopp M, Jamieson DJ	Human reproduction (Oxford, England)	25976658	Hum Reprod	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/25976658
Dead-end filling of SlipChip evaluated theoretically and experimentally as a function of the surface chemistry and the gap size between the plates for lubricated and dry SlipChips.	Li L, Karymov MA, Nichols KP, Ismagilov RF	Langmuir : the ACS journal of surfaces and colloids	20575548	Langmuir	2010 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/20575548
Microfluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability.	Boedicker JQ, Vincent ME, Ismagilov RF	Angewandte Chemie (International ed. in English)	19565587	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19565587
Defined spatial structure stabilizes a synthetic multispecies bacterial community.	Kim HJ, Boedicker JQ, Choi JW, Ismagilov RF	Proceedings of the National Academy of Sciences of the United States of America	19011107	Proc Natl Acad Sci U S A	2008 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/19011107
Measuring fate and rate of single-molecule competition of amplification and restriction digestion, and its use for rapid genotyping tested with hepatitis C viral RNA.	Sun B, Rodriguez-Manzano J, Selck DA, Khorosheva E, Karymov MA, Ismagilov RF	Angewandte Chemie (International ed. in English)	24889060	Angew Chem Int Ed Engl	2014 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/24889060
Mechanistic evaluation of the pros and cons of digital RT-LAMP for HIV-1 viral load quantification on a microfluidic device and improved efficiency via a two-step digital protocol.	Sun B, Shen F, McCalla SE, Kreutz JE, Karymov MA, Ismagilov RF	Analytical chemistry	23324061	Anal Chem	2013 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/23324061
SlipChip.	Du W, Li L, Nichols KP, Ismagilov RF	Lab on a chip	19636458	Lab Chip	2009 Aug 21	https://www.ncbi.nlm.nih.gov/pubmed/19636458
Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(ii).	Kim HJ, Du W, Ismagilov RF	Integrative biology : quantitative biosciences from nano to macro	20717565	Integr Biol (Camb)	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/20717565
Chemical stimulation of the Arabidopsis thaliana root using multi-laminar flow on a microfluidic chip.	Meier M, Lucchetta EM, Ismagilov RF	Lab on a chip	20544086	Lab Chip	2010 Aug 21	https://www.ncbi.nlm.nih.gov/pubmed/20544086
Microfluidic stochastic confinement enhances analysis of rare cells by isolating cells and creating high density environments for control of diffusible signals.	Vincent ME, Liu W, Haney EB, Ismagilov RF	Chemical Society reviews	20179819	Chem Soc Rev	2010 Mar	https://www.ncbi.nlm.nih.gov/pubmed/20179819
Increased robustness of single-molecule counting with microfluidics, digital isothermal amplification, and a mobile phone versus real-time kinetic measurements.	Selck DA, Karymov MA, Sun B, Ismagilov RF	Analytical chemistry	24199852	Anal Chem	2013 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/24199852
Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip.	Shen F, Davydova EK, Du W, Kreutz JE, Piepenburg O, Ismagilov RF	Analytical chemistry	21476587	Anal Chem	2011 May 1	https://www.ncbi.nlm.nih.gov/pubmed/21476587
Using TIRF microscopy to quantify and confirm efficient mass transfer at the substrate surface of the chemistrode.	Chen D, Du W, Ismagilov RF	New journal of physics	19809528	New J Phys	2009	https://www.ncbi.nlm.nih.gov/pubmed/19809528
Spatial localization of bacteria controls coagulation of human blood by 'quorum acting'.	Kastrup CJ, Boedicker JQ, Pomerantsev AP, Moayeri M, Bian Y, Pompano RR, Kline TR, Sylvestre P, Shen F, Leppla SH, Tang WJ, Ismagilov RF	Nature chemical biology	19031531	Nat Chem Biol	2008 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19031531
Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics.	Boedicker JQ, Li L, Kline TR, Ismagilov RF	Lab on a chip	18651067	Lab Chip	2008 Aug	https://www.ncbi.nlm.nih.gov/pubmed/18651067
Theoretical design and analysis of multivolume digital assays with wide dynamic range validated experimentally with microfluidic digital PCR.	Kreutz JE, Munson T, Huynh T, Shen F, Du W, Ismagilov RF	Analytical chemistry	21981344	Anal Chem	2011 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/21981344
SlipChip for immunoassays in nanoliter volumes.	Liu W, Chen D, Du W, Nichols KP, Ismagilov RF	Analytical chemistry	20334360	Anal Chem	2010 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/20334360
Microfluidics using spatially defined arrays of droplets in one, two, and three dimensions.	Pompano RR, Liu W, Du W, Ismagilov RF	Annual review of analytical chemistry (Palo Alto, Calif.)	21370983	Annu Rev Anal Chem (Palo Alto Calif)	2011	https://www.ncbi.nlm.nih.gov/pubmed/21370983
The chemistrode: a droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution.	Chen D, Du W, Liu Y, Liu W, Kuznetsov A, Mendez FE, Philipson LH, Ismagilov RF	Proceedings of the National Academy of Sciences of the United States of America	18974218	Proc Natl Acad Sci U S A	2008 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/18974218
Multiplexed quantification of nucleic acids with large dynamic range using multivolume digital RT-PCR on a rotational SlipChip tested with HIV and hepatitis C viral load.	Shen F, Sun B, Kreutz JE, Davydova EK, Du W, Reddy PL, Joseph LJ, Ismagilov RF	Journal of the American Chemical Society	21995644	J Am Chem Soc	2011 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/21995644
Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching.	Pompano RR, Chiang AH, Kastrup CJ, Ismagilov RF	Annual review of biochemistry	28654324	Annu Rev Biochem	2017 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/28654324
User-loaded SlipChip for equipment-free multiplexed nanoliter-scale experiments.	Li L, Du W, Ismagilov R	Journal of the American Chemical Society	20000708	J Am Chem Soc	2010 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/20000708
Multiparameter screening on SlipChip used for nanoliter protein crystallization combining free interface diffusion and microbatch methods.	Li L, Du W, Ismagilov RF	Journal of the American Chemical Society	20000709	J Am Chem Soc	2010 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/20000709
Isolation, incubation, and parallel functional testing and identification by FISH of rare microbial single-copy cells from multi-species mixtures using the combination of chemistrode and stochastic confinement.	Liu W, Kim HJ, Lucchetta EM, Du W, Ismagilov RF	Lab on a chip	19606291	Lab Chip	2009 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/19606291
Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP.	Khorosheva EM, Karymov MA, Selck DA, Ismagilov RF	Nucleic acids research	26358811	Nucleic Acids Res	2016 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/26358811
Digital PCR on a SlipChip.	Shen F, Du W, Kreutz JE, Fok A, Ismagilov RF	Lab on a chip	20596567	Lab Chip	2010 Oct 21	https://www.ncbi.nlm.nih.gov/pubmed/20596567
Nanoliter multiplex PCR arrays on a SlipChip.	Shen F, Du W, Davydova EK, Karymov MA, Pandey J, Ismagilov RF	Analytical chemistry	20446698	Anal Chem	2010 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/20446698
Plug-based microfluidics with defined surface chemistry to miniaturize and control aggregation of amyloidogenic peptides.	Meier M, Kennedy-Darling J, Choi SH, Norstrom EM, Sisodia SS, Ismagilov RF	Angewandte Chemie (International ed. in English)	19152390	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19152390
Chemical analog-to-digital signal conversion based on robust threshold chemistry and its evaluation in the context of microfluidics-based quantitative assays.	Huynh T, Sun B, Li L, Nichols KP, Koyner JL, Ismagilov RF	Journal of the American Chemical Society	24060606	J Am Chem Soc	2013 Oct 2	https://www.ncbi.nlm.nih.gov/pubmed/24060606
Dexterous robotic manipulation of alert adult Drosophila for high-content experimentation.	Savall J, Ho ETW, Huang C, Maxey JR, Schnitzer MJ	Nature methods	26005812	Nat Methods	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26005812
Advances in light microscopy for neuroscience.	Wilt BA, Burns LD, Wei Ho ET, Ghosh KK, Mukamel EA, Schnitzer MJ	Annual review of neuroscience	19555292	Annu Rev Neurosci	2009	https://www.ncbi.nlm.nih.gov/pubmed/19555292
Estimation theoretic measure of resolution for stochastic localization microscopy.	Fitzgerald JE, Lu J, Schnitzer MJ	Physical review letters	23006110	Phys Rev Lett	2012 Jul 27	https://www.ncbi.nlm.nih.gov/pubmed/23006110
Engineering approaches to illuminating brain structure and dynamics.	Deisseroth K, Schnitzer MJ	Neuron	24183010	Neuron	2013 Oct 30	https://www.ncbi.nlm.nih.gov/pubmed/24183010
Long-term dynamics of CA1 hippocampal place codes.	Ziv Y, Burns LD, Cocker ED, Hamel EO, Ghosh KK, Kitch LJ, El Gamal A, Schnitzer MJ	Nature neuroscience	23396101	Nat Neurosci	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23396101
Symmetries in stimulus statistics shape the form of visual motion estimators.	Fitzgerald JE, Katsov AY, Clandinin TR, Schnitzer MJ	Proceedings of the National Academy of Sciences of the United States of America	21768376	Proc Natl Acad Sci U S A	2011 Aug 2	https://www.ncbi.nlm.nih.gov/pubmed/21768376
Imaging neuronal populations in behaving rodents: paradigms for studying neural circuits underlying behavior in the mammalian cortex.	Chen JL, Andermann ML, Keck T, Xu NL, Ziv Y	The Journal of neuroscience : the official journal of the Society for Neuroscience	24198355	J Neurosci	2013 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/24198355
Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors.	Gong Y, Wagner MJ, Zhong Li J, Schnitzer MJ	Nature communications	24755708	Nat Commun	2014 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/24755708
The evolving capabilities of rhodopsin-based genetically encoded voltage indicators.	Gong Y	Current opinion in chemical biology	26143170	Curr Opin Chem Biol	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26143170
High-speed recording of neural spikes in awake mice and flies with a fluorescent voltage sensor.	Gong Y, Huang C, Li JZ, Grewe BF, Zhang Y, Eismann S, Schnitzer MJ	Science (New York, N.Y.)	26586188	Science	2015 Dec 11	https://www.ncbi.nlm.nih.gov/pubmed/26586188
Genetic dissection reveals two separate retinal substrates for polarization vision in Drosophila.	Wernet MF, Velez MM, Clark DA, Baumann-Klausener F, Brown JR, Klovstad M, Labhart T, Clandinin TR	Current biology : CB	22177904	Curr Biol	2012 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/22177904
Processing properties of ON and OFF pathways for Drosophila motion detection.	Behnia R, Clark DA, Carter AG, Clandinin TR, Desplan C	Nature	25043016	Nature	2014 Aug 28	https://www.ncbi.nlm.nih.gov/pubmed/25043016
A Drosophila toolkit for the visualization and quantification of viral replication launched from transgenic genomes.	Wernet MF, Klovstad M, Clandinin TR	PloS one	25386852	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/25386852
Dynamic structure of locomotor behavior in walking fruit flies.	Katsov AY, Freifeld L, Horowitz M, Kuehn S, Clandinin TR	eLife	28742018	Elife	2017 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/28742018
Loom-sensitive neurons link computation to action in the Drosophila visual system.	de Vries SE, Clandinin TR	Current biology : CB	22305754	Curr Biol	2012 Mar 6	https://www.ncbi.nlm.nih.gov/pubmed/22305754
Mapping and cracking sensorimotor circuits in genetic model organisms.	Clark DA, Freifeld L, Clandinin TR	Neuron	23719159	Neuron	2013 May 22	https://www.ncbi.nlm.nih.gov/pubmed/23719159
Differences in neural circuitry guiding behavioral responses to polarized light presented to either the dorsal or ventral retina in Drosophila.	Velez MM, Gohl D, Clandinin TR, Wernet MF	Journal of neurogenetics	24912584	J Neurogenet	2014 Sep-Dec	https://www.ncbi.nlm.nih.gov/pubmed/24912584
A versatile in vivo system for directed dissection of gene expression patterns.	Gohl DM, Silies MA, Gao XJ, Bhalerao S, Luongo FJ, Lin CC, Potter CJ, Clandinin TR	Nature methods	21473015	Nat Methods	2011 Mar	https://www.ncbi.nlm.nih.gov/pubmed/21473015
Modular use of peripheral input channels tunes motion-detecting circuitry.	Silies M, Gohl DM, Fisher YE, Freifeld L, Clark DA, Clandinin TR	Neuron	23849199	Neuron	2013 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/23849199
Defining the computational structure of the motion detector in Drosophila.	Clark DA, Bursztyn L, Horowitz MA, Schnitzer MJ, Clandinin TR	Neuron	21689602	Neuron	2011 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/21689602
Motion processing streams in Drosophila are behaviorally specialized.	Katsov AY, Clandinin TR	Neuron	18667159	Neuron	2008 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/18667159
Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.	Gohl DM, Freifeld L, Silies M, Hwa JJ, Horowitz M, Clandinin TR	Genetics	24374352	Genetics	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24374352
GABAergic lateral interactions tune the early stages of visual processing in Drosophila.	Freifeld L, Clark DA, Schnitzer MJ, Horowitz MA, Clandinin TR	Neuron	23791198	Neuron	2013 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/23791198
Specific kinematics and motor-related neurons for aversive chemotaxis in Drosophila.	Gao XJ, Potter CJ, Gohl DM, Silies M, Katsov AY, Clandinin TR, Luo L	Current biology : CB	23770185	Curr Biol	2013 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/23770185
Walking Drosophila align with the e-vector of linearly polarized light through directed modulation of angular acceleration.	Velez MM, Wernet MF, Clark DA, Clandinin TR	Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology	24810784	J Comp Physiol A Neuroethol Sens Neural Behav Physiol	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24810784
High-numerical-aperture cryogenic light microscopy for increased precision of superresolution reconstructions.	Nahmani M, Lanahan C, DeRosier D, Turrigiano GG	Proceedings of the National Academy of Sciences of the United States of America	28348224	Proc Natl Acad Sci U S A	2017 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/28348224
Dynamic and structural signatures of lamellar actomyosin force generation.	Aratyn-Schaus Y, Oakes PW, Gardel ML	Molecular biology of the cell	21307339	Mol Biol Cell	2011 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/21307339
Cell-substrate interactions.	Gardel M, Schwarz U	Journal of physics. Condensed matter : an Institute of Physics journal	21386358	J Phys Condens Matter	2010 May 19	https://www.ncbi.nlm.nih.gov/pubmed/21386358
Reconstitution of contractile actomyosin bundles.	Thoresen T, Lenz M, Gardel ML	Biophysical journal	21641315	Biophys J	2011 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/21641315
Regulation of cell motile behavior by crosstalk between cadherin- and integrin-mediated adhesions.	Borghi N, Lowndes M, Maruthamuthu V, Gardel ML, Nelson WJ	Proceedings of the National Academy of Sciences of the United States of America	20566866	Proc Natl Acad Sci U S A	2010 Jul 27	https://www.ncbi.nlm.nih.gov/pubmed/20566866
Mechanical integration of actin and adhesion dynamics in cell migration.	Gardel ML, Schneider IC, Aratyn-Schaus Y, Waterman CM	Annual review of cell and developmental biology	19575647	Annu Rev Cell Dev Biol	2010	https://www.ncbi.nlm.nih.gov/pubmed/19575647
Traction stress in focal adhesions correlates biphasically with actin retrograde flow speed.	Gardel ML, Sabass B, Ji L, Danuser G, Schwarz US, Waterman CM	The Journal of cell biology	19075110	J Cell Biol	2008 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/19075110
Local cortical tension by myosin II guides 3D endothelial cell branching.	Fischer RS, Gardel M, Ma X, Adelstein RS, Waterman CM	Current biology : CB	19185493	Curr Biol	2009 Feb 10	https://www.ncbi.nlm.nih.gov/pubmed/19185493
Biophysics. Clutch dynamics.	Aratyn-Schaus Y, Gardel ML	Science (New York, N.Y.)	19074337	Science	2008 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/19074337
Identification and characterization of a small molecule inhibitor of formin-mediated actin assembly.	Rizvi SA, Neidt EM, Cui J, Feiger Z, Skau CT, Gardel ML, Kozmin SA, Kovar DR	Chemistry & biology	19942139	Chem Biol	2009 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/19942139
Contractile units in disordered actomyosin bundles arise from F-actin buckling.	Lenz M, Thoresen T, Gardel ML, Dinner AR	Physical review letters	23003998	Phys Rev Lett	2012 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/23003998
Reconstitution of contractile actomyosin arrays.	Murrell M, Thoresen T, Gardel M	Methods in enzymology	24630112	Methods Enzymol	2014	https://www.ncbi.nlm.nih.gov/pubmed/24630112
Shear thickening of F-actin networks crosslinked with non-muscle myosin IIB.	Norstrom M, Gardel ML	Soft matter	21552431	Soft Matter	2011 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/21552431
Preparation of complaint matrices for quantifying cellular contraction.	Aratyn-Schaus Y, Oakes PW, Stricker J, Winter SP, Gardel ML	Journal of visualized experiments : JoVE	21178972	J Vis Exp	2010 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/21178972
Endothelial barrier disruption and recovery is controlled by substrate stiffness.	Birukova AA, Tian X, Cokic I, Beckham Y, Gardel ML, Birukov KG	Microvascular research	23296034	Microvasc Res	2013 May	https://www.ncbi.nlm.nih.gov/pubmed/23296034
Chapter 19: Mechanical response of cytoskeletal networks.	Gardel ML, Kasza KE, Brangwynne CP, Liu J, Weitz DA	Methods in cell biology	19118688	Methods Cell Biol	2008	https://www.ncbi.nlm.nih.gov/pubmed/19118688
High resolution traction force microscopy based on experimental and computational advances.	Sabass B, Gardel ML, Waterman CM, Schwarz US	Biophysical journal	17827246	Biophys J	2008 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/17827246
Stressing the limits of focal adhesion mechanosensitivity.	Oakes PW, Gardel ML	Current opinion in cell biology	24998185	Curr Opin Cell Biol	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24998185
Materials science: Synthetic polymers with biological rigidity.	Gardel ML	Nature	23354043	Nature	2013 Jan 31	https://www.ncbi.nlm.nih.gov/pubmed/23354043
Requirements for contractility in disordered cytoskeletal bundles.	Lenz M, Gardel ML, Dinner AR	New journal of physics	23155355	New J Phys	2012 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/23155355
Observation and characterization of the vestige of the jamming transition in a thermal three-dimensional system.	Caswell TA, Zhang Z, Gardel ML, Nagel SR	Physical review. E, Statistical, nonlinear, and soft matter physics	23410327	Phys Rev E Stat Nonlin Soft Matter Phys	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23410327
Optimization of traction force microscopy for micron-sized focal adhesions.	Stricker J, Sabass B, Schwarz US, Gardel ML	Journal of physics. Condensed matter : an Institute of Physics journal	20523913	J Phys Condens Matter	2010 May 19	https://www.ncbi.nlm.nih.gov/pubmed/20523913
Conserved F-actin dynamics and force transmission at cell adhesions.	Maruthamuthu V, Aratyn-Schaus Y, Gardel ML	Current opinion in cell biology	20728328	Curr Opin Cell Biol	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20728328
Cell-ECM traction force modulates endogenous tension at cell-cell contacts.	Maruthamuthu V, Sabass B, Schwarz US, Gardel ML	Proceedings of the National Academy of Sciences of the United States of America	21383129	Proc Natl Acad Sci U S A	2011 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/21383129
Transient frictional slip between integrin and the ECM in focal adhesions under myosin II tension.	Aratyn-Schaus Y, Gardel ML	Current biology : CB	20541412	Curr Biol	2010 Jul 13	https://www.ncbi.nlm.nih.gov/pubmed/20541412
Mechanics of the F-actin cytoskeleton.	Stricker J, Falzone T, Gardel ML	Journal of biomechanics	19913792	J Biomech	2010 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/19913792
A zyxin-mediated mechanism for actin stress fiber maintenance and repair.	Smith MA, Blankman E, Gardel ML, Luettjohann L, Waterman CM, Beckerle MC	Developmental cell	20833360	Dev Cell	2010 Sep 14	https://www.ncbi.nlm.nih.gov/pubmed/20833360
Benign rolandic epileptiform discharges are associated with mood and behavior problems.	Sarco DP, Boyer K, Lundy-Krigbaum SM, Takeoka M, Jensen F, Gregas M, Waber DP	Epilepsy & behavior : E&B	21862414	Epilepsy Behav	2011 Oct	https://www.ncbi.nlm.nih.gov/pubmed/21862414
The developing oligodendrocyte: key cellular target in brain injury in the premature infant.	Volpe JJ, Kinney HC, Jensen FE, Rosenberg PA	International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience	21382469	Int J Dev Neurosci	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/21382469
Finding a better drug for epilepsy: antiepileptogenesis targets.	Kobow K, Auvin S, Jensen F, Löscher W, Mody I, Potschka H, Prince D, Sierra A, Simonato M, Pitkänen A, Nehlig A, Rho JM	Epilepsia	23061663	Epilepsia	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23061663
Regional differences in susceptibility to hypoxic-ischemic injury in the preterm brain: exploring the spectrum from white matter loss to selective grey matter injury in a rat model.	Selip DB, Jantzie LL, Chang M, Jackson MC, Fitzgerald EC, Boll G, Murphy A, Jensen FE	Neurology research international	22530125	Neurol Res Int	2012	https://www.ncbi.nlm.nih.gov/pubmed/22530125
Early alterations of AMPA receptors mediate synaptic potentiation induced by neonatal seizures.	Rakhade SN, Zhou C, Aujla PK, Fishman R, Sucher NJ, Jensen FE	The Journal of neuroscience : the official journal of the Society for Neuroscience	18685023	J Neurosci	2008 Aug 6	https://www.ncbi.nlm.nih.gov/pubmed/18685023
The tower of Babel: survey on concepts and terminology in electrical status epilepticus in sleep and continuous spikes and waves during sleep in North America.	Fernández IS, Chapman KE, Peters JM, Kothare SV, Nordli DR Jr, Jensen FE, Berg AT, Loddenkemper T	Epilepsia	23163318	Epilepsia	2013 Apr	https://www.ncbi.nlm.nih.gov/pubmed/23163318
Bumetanide enhances phenobarbital efficacy in a rat model of hypoxic neonatal seizures.	Cleary RT, Sun H, Huynh T, Manning SM, Li Y, Rotenberg A, Talos DM, Kahle KT, Jackson M, Rakhade SN, Berry G, Jensen FE	PloS one	23536761	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23536761
Antiepileptic effects of levetiracetam in a rodent neonatal seizure model.	Talos DM, Chang M, Kosaras B, Fitzgerald E, Murphy A, Folkerth RD, Jensen FE	Pediatric research	23138400	Pediatr Res	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23138400
AMPA receptor antagonist NBQX attenuates later-life epileptic seizures and autistic-like social deficits following neonatal seizures.	Lippman-Bell JJ, Rakhade SN, Klein PM, Obeid M, Jackson MC, Joseph A, Jensen FE	Epilepsia	24117347	Epilepsia	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24117347
Models of hypoxia and ischemia-induced seizures.	Sun H, Juul HM, Jensen FE	Journal of neuroscience methods	26434705	J Neurosci Methods	2016 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/26434705
Regulation of seizure-induced MeCP2 Ser421 phosphorylation in the developing brain.	Rosenberg EC, Lippman-Bell JJ, Handy M, Soldan SS, Rakhade S, Hilario-Gomez C, Folweiler K, Jacobs L, Jensen FE	Neurobiology of disease	29738885	Neurobiol Dis	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29738885
Contribution of axonal orientation to pathway-dependent modulation of excitatory transmission by direct current stimulation in isolated rat hippocampus.	Kabakov AY, Muller PA, Pascual-Leone A, Jensen FE, Rotenberg A	Journal of neurophysiology	22219028	J Neurophysiol	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22219028
Developmental regulation of group I metabotropic glutamate receptors in the premature brain and their protective role in a rodent model of periventricular leukomalacia.	Jantzie LL, Talos DM, Selip DB, An L, Jackson MC, Folkerth RD, Deng W, Jensen FE	Neuron glia biology	22169210	Neuron Glia Biol	2010 Nov	https://www.ncbi.nlm.nih.gov/pubmed/22169210
Altered development of glutamatergic synapses in layer V pyramidal neurons in NR3A knockout mice.	Zhou C, Jensen FE, Sucher NJ	Molecular and cellular neurosciences	19782137	Mol Cell Neurosci	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19782137
Issues related to development of antiepileptogenic therapies.	Pitkänen A, Nehlig A, Brooks-Kayal AR, Dudek FE, Friedman D, Galanopoulou AS, Jensen FE, Kaminski RM, Kapur J, Klitgaard H, Löscher W, Mody I, Schmidt D	Epilepsia	23909852	Epilepsia	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23909852
Does acquired epileptogenesis in the immature brain require neuronal death.	Baram TZ, Jensen FE, Brooks-Kayal A	Epilepsy currents	21461261	Epilepsy Curr	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21461261
Strain-specific differences in perinatal rodent oligodendrocyte lineage progression and its correlation with human.	Dean JM, Moravec MD, Grafe M, Abend N, Ren J, Gong X, Volpe JJ, Jensen FE, Hohimer AR, Back SA	Developmental neuroscience	21865655	Dev Neurosci	2011	https://www.ncbi.nlm.nih.gov/pubmed/21865655
Epilepsy as a spectrum disorder: Implications from novel clinical and basic neuroscience.	Jensen FE	Epilepsia	21214533	Epilepsia	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21214533
Developmental expression of N-methyl-D-aspartate (NMDA) receptor subunits in human white and gray matter: potential mechanism of increased vulnerability in the immature brain.	Jantzie LL, Talos DM, Jackson MC, Park HK, Graham DA, Lechpammer M, Folkerth RD, Volpe JJ, Jensen FE	Cerebral cortex (New York, N.Y. : 1991)	24046081	Cereb Cortex	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24046081
Early-life seizures alter synaptic calcium-permeable AMPA receptor function and plasticity.	Lippman-Bell JJ, Zhou C, Sun H, Feske JS, Jensen FE	Molecular and cellular neurosciences	27521497	Mol Cell Neurosci	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27521497
Lestaurtinib (CEP-701) attenuates "second hit" kainic acid-induced seizures following early life hypoxic seizures.	Obeid M, Rosenberg EC, Klein PM, Jensen FE	Epilepsy research	24582454	Epilepsy Res	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24582454
Altered hippocampal dendritic spine maturation after hypoxia-induced seizures in neonatal rats.	Lippman-Bell JJ, Handy M, Nieder CG, Getzfread M, Jensen FE	Molecular and cellular neurosciences	34015497	Mol Cell Neurosci	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/34015497
Blinders, phenotype, and fashionable genetic analysis: a critical examination of the current state of epilepsy genetic studies.	Greenberg DA, Subaran R	Epilepsia	21219301	Epilepsia	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21219301
Glutamate receptor 1 phosphorylation at serine 831 and 845 modulates seizure susceptibility and hippocampal hyperexcitability after early life seizures.	Rakhade SN, Fitzgerald EF, Klein PM, Zhou C, Sun H, Huganir RL, Jensen FE	The Journal of neuroscience : the official journal of the Society for Neuroscience	23223299	J Neurosci	2012 Dec 5	https://www.ncbi.nlm.nih.gov/pubmed/23223299
Hypoxia-induced neonatal seizures diminish silent synapses and long-term potentiation in hippocampal CA1 neurons.	Zhou C, Lippman JJ, Sun H, Jensen FE	The Journal of neuroscience : the official journal of the Society for Neuroscience	22171027	J Neurosci	2011 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/22171027
Gene expression profiling of a hypoxic seizure model of epilepsy suggests a role for mTOR and Wnt signaling in epileptogenesis.	Theilhaber J, Rakhade SN, Sudhalter J, Kothari N, Klein P, Pollard J, Jensen FE	PloS one	24086344	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24086344
Altered inhibition in tuberous sclerosis and type IIb cortical dysplasia.	Talos DM, Sun H, Kosaras B, Joseph A, Folkerth RD, Poduri A, Madsen JR, Black PM, Jensen FE	Annals of neurology	22447678	Ann Neurol	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22447678
Epilepsy biomarkers.	Engel J Jr, Pitkänen A, Loeb JA, Dudek FE, Bertram EH 3rd, Cole AJ, Moshé SL, Wiebe S, Jensen FE, Mody I, Nehlig A, Vezzani A	Epilepsia	23909854	Epilepsia	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23909854
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.	Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM	Genome biology	24667040	Genome Biol	2014 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/24667040
Chloride cotransporter NKCC1 inhibitor bumetanide protects against white matter injury in a rodent model of periventricular leukomalacia.	Jantzie LL, Hu MY, Park HK, Jackson MC, Yu J, Maxwell JR, Jensen FE	Pediatric research	25585037	Pediatr Res	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25585037
Neonatal seizures alter NMDA glutamate receptor GluN2A and 3A subunit expression and function in hippocampal CA1 neurons.	Zhou C, Sun H, Klein PM, Jensen FE	Frontiers in cellular neuroscience	26441533	Front Cell Neurosci	2015	https://www.ncbi.nlm.nih.gov/pubmed/26441533
Dysregulation of FMRP/mTOR Signaling Cascade in Hypoxic-Ischemic Injury of Premature Human Brain.	Lechpammer M, Wintermark P, Merry KM, Jackson MC, Jantzie LL, Jensen FE	Journal of child neurology	26239490	J Child Neurol	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26239490
Cannabidiol attenuates seizure susceptibility and behavioural deficits in adult CDKL5(R59X) knock-in mice.	Li X, Yennawar M, Wiest A, O'Brien WT, Babrowicz B, White RS, Talos DM, Jensen FE	The European journal of neuroscience	38654472	Eur J Neurosci	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/38654472
Mammalian target of rapamycin complex 1 activation negatively regulates Polo-like kinase 2-mediated homeostatic compensation following neonatal seizures.	Sun H, Kosaras B, Klein PM, Jensen FE	Proceedings of the National Academy of Sciences of the United States of America	23479645	Proc Natl Acad Sci U S A	2013 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/23479645
The interaction between early life epilepsy and autistic-like behavioral consequences: a role for the mammalian target of rapamycin (mTOR) pathway.	Talos DM, Sun H, Zhou X, Fitzgerald EC, Jackson MC, Klein PM, Lan VJ, Joseph A, Jensen FE	PloS one	22567115	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22567115
Development of later life spontaneous seizures in a rodent model of hypoxia-induced neonatal seizures.	Rakhade SN, Klein PM, Huynh T, Hilario-Gomez C, Kosaras B, Rotenberg A, Jensen FE	Epilepsia	21366558	Epilepsia	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21366558
Association of the small GTPase Rheb with the NMDA receptor subunit NR3A.	Sucher NJ, Yu E, Chan SF, Miri M, Lee BJ, Xiao B, Worley PF, Jensen FE	Neuro-Signals	21135540	Neurosignals	2010	https://www.ncbi.nlm.nih.gov/pubmed/21135540
Subunit composition of glutamate and gamma-aminobutyric acid receptors in status epilepticus.	Loddenkemper T, Talos DM, Cleary RT, Joseph A, Sánchez Fernández I, Alexopoulos A, Kotagal P, Najm I, Jensen FE	Epilepsy research	24613745	Epilepsy Res	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24613745
Developmental factors in the pathogenesis of neonatal seizures.	Jensen FE	Journal of pediatric neurology : JPN	20191097	J Pediatr Neurol	2009 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/20191097
Neonatal seizures: an update on mechanisms and management.	Jensen FE	Clinics in perinatology	19944840	Clin Perinatol	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19944840
Epileptogenesis in the immature brain: emerging mechanisms.	Rakhade SN, Jensen FE	Nature reviews. Neurology	19578345	Nat Rev Neurol	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19578345
A mouse model of tuberous sclerosis: neuronal loss of Tsc1 causes dysplastic and ectopic neurons, reduced myelination, seizure activity, and limited survival.	Meikle L, Talos DM, Onda H, Pollizzi K, Rotenberg A, Sahin M, Jensen FE, Kwiatkowski DJ	The Journal of neuroscience : the official journal of the Society for Neuroscience	17522300	J Neurosci	2007 May 23	https://www.ncbi.nlm.nih.gov/pubmed/17522300
The clinically available NMDA receptor antagonist, memantine, exhibits relative safety in the developing rat brain.	Manning SM, Boll G, Fitzgerald E, Selip DB, Volpe JJ, Jensen FE	International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience	21624454	Int J Dev Neurosci	2011 Nov	https://www.ncbi.nlm.nih.gov/pubmed/21624454
AMPA Receptor Dysregulation and Therapeutic Interventions in a Mouse Model of CDKL5 Deficiency Disorder.	Yennawar M, White RS, Jensen FE	The Journal of neuroscience : the official journal of the Society for Neuroscience	30952813	J Neurosci	2019 Jun 12	https://www.ncbi.nlm.nih.gov/pubmed/30952813
Perfusion Imaging of Focal Cortical Dysplasia Using Arterial Spin Labeling: Correlation With Histopathological Vascular Density.	Wintermark P, Lechpammer M, Warfield SK, Kosaras B, Takeoka M, Poduri A, Madsen JR, Bergin AM, Whalen S, Jensen FE	Journal of child neurology	23696629	J Child Neurol	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23696629
Issues related to symptomatic and disease-modifying treatments affecting cognitive and neuropsychiatric comorbidities of epilepsy.	Brooks-Kayal AR, Bath KG, Berg AT, Galanopoulou AS, Holmes GL, Jensen FE, Kanner AM, O'Brien TJ, Whittemore VH, Winawer MR, Patel M, Scharfman HE	Epilepsia	23909853	Epilepsia	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23909853
Emotion Generation and Emotion Regulation: One or Two Depends on Your Point of View.	Gross JJ, Barrett LF	Emotion review : journal of the International Society for Research on Emotion	21479078	Emot Rev	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21479078
What You Feel Influences What You See: The Role of Affective Feelings in Resolving Binocular Rivalry.	Anderson E, Siegel EH, Barrett LF	Journal of experimental social psychology	21789027	J Exp Soc Psychol	2011 Jul	https://www.ncbi.nlm.nih.gov/pubmed/21789027
Variety is the spice of life: A psychological construction approach to understanding variability in emotion.	Barrett LF	Cognition & emotion	20221411	Cogn Emot	2009 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/20221411
Reconstructing the Past: A Century of Ideas About Emotion in Psychology.	Gendron M, Barrett LF	Emotion review : journal of the International Society for Research on Emotion	20221412	Emot Rev	2009 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/20221412
Understanding the Mind by Measuring the Brain: Lessons From Measuring Behavior (Commentary on Vul et al., 2009).	Barrett LF	Perspectives on psychological science : a journal of the Association for Psychological Science	19672318	Perspect Psychol Sci	2009 May	https://www.ncbi.nlm.nih.gov/pubmed/19672318
Grounding emotion in situated conceptualization.	Wilson-Mendenhall CD, Barrett LF, Simmons WK, Barsalou LW	Neuropsychologia	21192959	Neuropsychologia	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21192959
Amygdala and fusiform gyrus temporal dynamics: responses to negative facial expressions.	Britton JC, Shin LM, Barrett LF, Rauch SL, Wright CI	BMC neuroscience	18474111	BMC Neurosci	2008 May 12	https://www.ncbi.nlm.nih.gov/pubmed/18474111
She's emotional. He's having a bad day: attributional explanations for emotion stereotypes.	Barrett LF, Bliss-Moreau E	Emotion (Washington, D.C.)	19803587	Emotion	2009 Oct	https://www.ncbi.nlm.nih.gov/pubmed/19803587
Constructing emotion: the experience of fear as a conceptual act.	Lindquist KA, Barrett LF	Psychological science	18947355	Psychol Sci	2008 Sep	https://www.ncbi.nlm.nih.gov/pubmed/18947355
Differential hemodynamic response in affective circuitry with aging: an FMRI study of novelty, valence, and arousal.	Moriguchi Y, Negreira A, Weierich M, Dautoff R, Dickerson BC, Wright CI, Barrett LF	Journal of cognitive neuroscience	20521849	J Cogn Neurosci	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/20521849
Perceptions of emotion from facial expressions are not culturally universal: evidence from a remote culture.	Gendron M, Roberson D, van der Vyver JM, Barrett LF	Emotion (Washington, D.C.)	24708506	Emotion	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24708506
Intrinsic connectivity in the human brain does not reveal networks for 'basic' emotions.	Touroutoglou A, Lindquist KA, Dickerson BC, Barrett LF	Social cognitive and affective neuroscience	25680990	Soc Cogn Affect Neurosci	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25680990
Trends in ambulatory self-report: the role of momentary experience in psychosomatic medicine.	Conner TS, Barrett LF	Psychosomatic medicine	22582330	Psychosom Med	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22582330
Identification of discrete functional subregions of the human periaqueductal gray.	Satpute AB, Wager TD, Cohen-Adad J, Bianciardi M, Choi JK, Buhle JT, Wald LL, Barrett LF	Proceedings of the National Academy of Sciences of the United States of America	24082116	Proc Natl Acad Sci U S A	2013 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/24082116
Conceptualizing and experiencing compassion.	Condon P, Feldman Barrett L	Emotion (Washington, D.C.)	23914766	Emotion	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23914766
Emotion perception, but not affect perception, is impaired with semantic memory loss.	Lindquist KA, Gendron M, Barrett LF, Dickerson BC	Emotion (Washington, D.C.)	24512242	Emotion	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24512242
Emotion fingerprints or emotion populations? A meta-analytic investigation of autonomic features of emotion categories.	Siegel EH, Sands MK, Van den Noortgate W, Condon P, Chang Y, Dy J, Quigley KS, Barrett LF	Psychological bulletin	29389177	Psychol Bull	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29389177
Stronger Functional Connectivity in the Default Mode and Salience Networks Is Associated With Youthful Memory in Superaging.	Zhang J, Andreano JM, Dickerson BC, Touroutoglou A, Barrett LF	Cerebral cortex (New York, N.Y. : 1991)	31058917	Cereb Cortex	2020 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/31058917
Semantic Clustering during Verbal Episodic Memory Encoding and Retrieval in Older Adults: One Cognitive Mechanism of Superaging.	Shaffer C, Andreano JM, Touroutoglou A, Barrett LF, Dickerson BC, Wong B	Brain sciences	38391745	Brain Sci	2024 Feb 8	https://www.ncbi.nlm.nih.gov/pubmed/38391745
Amygdala volume and social network size in humans.	Bickart KC, Wright CI, Dautoff RJ, Dickerson BC, Barrett LF	Nature neuroscience	21186358	Nat Neurosci	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21186358
Affective value and associative processing share a cortical substrate.	Shenhav A, Barrett LF, Bar M	Cognitive, affective & behavioral neuroscience	23090717	Cogn Affect Behav Neurosci	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23090717
Novelty as a dimension in the affective brain.	Weierich MR, Wright CI, Negreira A, Dickerson BC, Barrett LF	NeuroImage	19796697	Neuroimage	2010 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/19796697
I Like the Sound of Your Voice: Affective Learning about Vocal Signals.	Bliss-Moreau E, Barrett LF, Owren MJ	Journal of experimental social psychology	20495619	J Exp Soc Psychol	2010 May 1	https://www.ncbi.nlm.nih.gov/pubmed/20495619
Situating emotional experience.	Wilson-Mendenhall CD, Barrett LF, Barsalou LW	Frontiers in human neuroscience	24324420	Front Hum Neurosci	2013	https://www.ncbi.nlm.nih.gov/pubmed/24324420
Visual predictions in the orbitofrontal cortex rely on associative content.	Chaumon M, Kveraga K, Barrett LF, Bar M	Cerebral cortex (New York, N.Y. : 1991)	23771980	Cereb Cortex	2014 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23771980
Affective learning enhances activity and functional connectivity in early visual cortex.	Damaraju E, Huang YM, Barrett LF, Pessoa L	Neuropsychologia	19410587	Neuropsychologia	2009 Oct	https://www.ncbi.nlm.nih.gov/pubmed/19410587
Experience Sampling Methods: A Modern Idiographic Approach to Personality Research.	Conner TS, Tennen H, Fleeson W, Barrett LF	Social and personality psychology compass	19898679	Soc Personal Psychol Compass	2009 May 1	https://www.ncbi.nlm.nih.gov/pubmed/19898679
Functional grouping and cortical-subcortical interactions in emotion: a meta-analysis of neuroimaging studies.	Kober H, Barrett LF, Joseph J, Bliss-Moreau E, Lindquist K, Wager TD	NeuroImage	18579414	Neuroimage	2008 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/18579414
Sex differences in the neural correlates of affective experience.	Moriguchi Y, Touroutoglou A, Dickerson BC, Barrett LF	Social cognitive and affective neuroscience	23596188	Soc Cogn Affect Neurosci	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/23596188
The role of affective experience in work motivation: Test of a conceptual model.	Seo MG, Bartunek JM, Barrett LF	Journal of organizational behavior	21785527	J Organ Behav	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/21785527
Individual differences in learning the affective value of others under minimal conditions.	Bliss-Moreau E, Barrett LF, Wright CI	Emotion (Washington, D.C.)	18729580	Emotion	2008 Aug	https://www.ncbi.nlm.nih.gov/pubmed/18729580
Emotion Words' Effect on Visual Awareness and Attention of Emotional Faces.	Fugate JMB, MacDonald C, O'Hare AJ	Frontiers in psychology	32010012	Front Psychol	2019	https://www.ncbi.nlm.nih.gov/pubmed/32010012
Gender moderates the effect of oxytocin on social judgments.	Hoge EA, Anderson E, Lawson EA, Bui E, Fischer LE, Khadge SD, Barrett LF, Simon NM	Human psychopharmacology	24911580	Hum Psychopharmacol	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24911580
Emotion words, emotion concepts, and emotional development in children: A constructionist hypothesis.	Hoemann K, Xu F, Barrett LF	Developmental psychology	31464489	Dev Psychol	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31464489
Novel response patterns during repeated presentation of affective and neutral stimuli.	Satpute AB, Hanington L, Barrett LF	Social cognitive and affective neuroscience	27928070	Soc Cogn Affect Neurosci	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27928070
Establishing the situated features associated with perceived stress.	Lebois LA, Hertzog C, Slavich GM, Barrett LF, Barsalou LW	Acta psychologica	27288834	Acta Psychol (Amst)	2016 Sep	https://www.ncbi.nlm.nih.gov/pubmed/27288834
Unseen Affective Faces Influence Person Perception Judgments in Schizophrenia.	Kring AM, Siegel EH, Barrett LF	Clinical psychological science : a journal of the Association for Psychological Science	25664225	Clin Psychol Sci	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/25664225
Cultural variation in emotion perception is real: a response to Sauter, Eisner, Ekman, and Scott (2015).	Gendron M, Roberson D, Barrett LF	Psychological science	25608863	Psychol Sci	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25608863
Variety in emotional life: within-category typicality of emotional experiences is associated with neural activity in large-scale brain networks.	Wilson-Mendenhall CD, Barrett LF, Barsalou LW	Social cognitive and affective neuroscience	24563528	Soc Cogn Affect Neurosci	2015 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24563528
The power of predictions: An emerging paradigm for psychological research.	Hutchinson JB, Barrett LF	Current directions in psychological science	31749520	Curr Dir Psychol Sci	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31749520
Emotional Granularity is Associated with Daily Experiential Diversity.	Hoemann K, Lee Y, Kuppens P, Gendron M, Boyd RL	Affective science	37304562	Affect Sci	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/37304562
Emotional granularity and borderline personality disorder.	Suvak MK, Litz BT, Sloan DM, Zanarini MC, Barrett LF, Hofmann SG	Journal of abnormal psychology	21171723	J Abnorm Psychol	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21171723
Considering PTSD from the perspective of brain processes: a psychological construction approach.	Suvak MK, Barrett LF	Journal of traumatic stress	21298725	J Trauma Stress	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21298725
The hundred-year emotion war: are emotions natural kinds or psychological constructions? Comment on Lench, Flores, and Bench (2011).	Lindquist KA, Siegel EH, Quigley KS, Barrett LF	Psychological bulletin	23294094	Psychol Bull	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23294094
States of mind: emotions, body feelings, and thoughts share distributed neural networks.	Oosterwijk S, Lindquist KA, Anderson E, Dautoff R, Moriguchi Y, Barrett LF	NeuroImage	22677148	Neuroimage	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22677148
The brain basis of emotion: a meta-analytic review.	Lindquist KA, Wager TD, Kober H, Bliss-Moreau E, Barrett LF	The Behavioral and brain sciences	22617651	Behav Brain Sci	2012 Jun	https://www.ncbi.nlm.nih.gov/pubmed/22617651
Amygdala atrophy is prominent in early Alzheimer's disease and relates to symptom severity.	Poulin SP, Dautoff R, Morris JC, Barrett LF, Dickerson BC, Alzheimer's Disease Neuroimaging Initiative	Psychiatry research	21920712	Psychiatry Res	2011 Oct 31	https://www.ncbi.nlm.nih.gov/pubmed/21920712
Emotion words: Adding face value.	Fugate JMB, Gendron M, Nakashima SF, Barrett LF	Emotion (Washington, D.C.)	28604040	Emotion	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28604040
Reading chimpanzee faces: evidence for the role of verbal labels in categorical perception of emotion.	Fugate JM, Gouzoules H, Barrett LF	Emotion (Washington, D.C.)	20677871	Emotion	2010 Aug	https://www.ncbi.nlm.nih.gov/pubmed/20677871
Emotion words shape emotion percepts.	Gendron M, Lindquist KA, Barsalou L, Barrett LF	Emotion (Washington, D.C.)	22309717	Emotion	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22309717
Bridging Token Identity Theory and Supervenience Theory Through Psychological Construction.	Barrett LF	Psychological inquiry	21785534	Psychol Inq	2011 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/21785534
Affective state influences perception by affecting decision parameters underlying bias and sensitivity.	Lynn SK, Zhang X, Barrett LF	Emotion (Washington, D.C.)	22251054	Emotion	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22251054
Words are a context for mental inference.	Betz N, Hoemann K, Barrett LF	Emotion (Washington, D.C.)	30628815	Emotion	2019 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30628815
Learning situated emotions.	Lebois LAM, Wilson-Mendenhall CD, Simmons WK, Barrett LF, Barsalou LW	Neuropsychologia	29330097	Neuropsychologia	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29330097
Does language do more than communicate emotion?	Lindquist KA, Satpute AB, Gendron M	Current directions in psychological science	25983400	Curr Dir Psychol Sci	2015 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/25983400
How does this make you feel? A comparison of four affect induction procedures.	Zhang X, Yu HW, Barrett LF	Frontiers in psychology	25071659	Front Psychol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25071659
"Utilizing" signal detection theory.	Lynn SK, Barrett LF	Psychological science	25097061	Psychol Sci	2014 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25097061
Methodological recommendations for a heartbeat detection-based measure of interoceptive sensitivity.	Kleckner IR, Wormwood JB, Simmons WK, Barrett LF, Quigley KS	Psychophysiology	26265009	Psychophysiology	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26265009
Gender differences in oxytocin-associated disruption of decision bias during emotion perception.	Lynn SK, Hoge EA, Fischer LE, Barrett LF, Simon NM	Psychiatry research	24814142	Psychiatry Res	2014 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/24814142
AFFECT AND THE FRAMING EFFECT WITHIN INDIVIDUALS OVER TIME: RISK TAKING IN A DYNAMIC INVESTMENT SIMULATION.	Seo MG, Goldfarb B, Barrett LF	Academy of Management journal. Academy of Management	26412860	Acad Manage J	2010 Apr	https://www.ncbi.nlm.nih.gov/pubmed/26412860
Brain network connectivity-behavioral relationships exhibit trait-like properties: Evidence from hippocampal connectivity and memory.	Touroutoglou A, Andreano JM, Barrett LF, Dickerson BC	Hippocampus	26105075	Hippocampus	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26105075
The neural representation of typical and atypical experiences of negative images: comparing fear, disgust and morbid fascination.	Oosterwijk S, Lindquist KA, Adebayo M, Barrett LF	Social cognitive and affective neuroscience	26180088	Soc Cogn Affect Neurosci	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26180088
The Brain Basis of Positive and Negative Affect: Evidence from a Meta-Analysis of the Human Neuroimaging Literature.	Lindquist KA, Satpute AB, Wager TD, Weber J, Barrett LF	Cerebral cortex (New York, N.Y. : 1991)	25631056	Cereb Cortex	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/25631056
The relation between valence and arousal in subjective experience.	Kuppens P, Tuerlinckx F, Russell JA, Barrett LF	Psychological bulletin	23231533	Psychol Bull	2013 Jul	https://www.ncbi.nlm.nih.gov/pubmed/23231533
A reliable protocol for the manual segmentation of the human amygdala and its subregions using ultra-high resolution MRI.	Entis JJ, Doerga P, Barrett LF, Dickerson BC	NeuroImage	22245260	Neuroimage	2012 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/22245260
Neural evidence that human emotions share core affective properties.	Wilson-Mendenhall CD, Barrett LF, Barsalou LW	Psychological science	23603916	Psychol Sci	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23603916
Authors’ response: what are emotions and how are they created in the brain?	Lindquist KA, Wager TD, Bliss-Moreau E, Kober H, Barret LF	The Behavioral and brain sciences	22783560	Behav Brain Sci	2012 Jun	https://www.ncbi.nlm.nih.gov/pubmed/22783560
Emotions are real.	Barrett LF	Emotion (Washington, D.C.)	22642358	Emotion	2012 Jun	https://www.ncbi.nlm.nih.gov/pubmed/22642358
Large-scale brain networks in affective and social neuroscience: towards an integrative functional architecture of the brain.	Barrett LF, Satpute AB	Current opinion in neurobiology	23352202	Curr Opin Neurobiol	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23352202
Valence focus and self-esteem lability: reacting to hedonic cues in the social environment.	Pietromonaco PR, Barrett LF	Emotion (Washington, D.C.)	19485618	Emotion	2009 Jun	https://www.ncbi.nlm.nih.gov/pubmed/19485618
See it with feeling: affective predictions during object perception.	Barrett LF, Bar M	Philosophical transactions of the Royal Society of London. Series B, Biological sciences	19528014	Philos Trans R Soc Lond B Biol Sci	2009 May 12	https://www.ncbi.nlm.nih.gov/pubmed/19528014
Older and wiser? An affective science perspective on age-related challenges in financial decision making.	Weierich MR, Kensinger EA, Munnell AH, Sass SA, Dickerson BC, Wright CI, Barrett LF	Social cognitive and affective neuroscience	20587596	Soc Cogn Affect Neurosci	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20587596
Affect as a Psychological Primitive.	Barrett LF, Bliss-Moreau E	Advances in experimental social psychology	20552040	Adv Exp Soc Psychol	2009	https://www.ncbi.nlm.nih.gov/pubmed/20552040
The visual impact of gossip.	Anderson E, Siegel EH, Bliss-Moreau E, Barrett LF	Science (New York, N.Y.)	21596956	Science	2011 Jun 17	https://www.ncbi.nlm.nih.gov/pubmed/21596956
Threat perception after the Boston Marathon bombings: The effects of personal relevance and conceptual framing.	Wormwood JB, Lynn SK, Feldman Barrett L, Quigley KS	Cognition & emotion	25707419	Cogn Emot	2016	https://www.ncbi.nlm.nih.gov/pubmed/25707419
Amygdala task-evoked activity and task-free connectivity independently contribute to feelings of arousal.	Touroutoglou A, Bickart KC, Barrett LF, Dickerson BC	Human brain mapping	24862171	Hum Brain Mapp	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24862171
The Future of Psychology: Connecting Mind to Brain.	Barrett LF	Perspectives on psychological science : a journal of the Association for Psychological Science	19844601	Perspect Psychol Sci	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19844601
Context is routinely encoded during emotion perception.	Barrett LF, Kensinger EA	Psychological science	20424107	Psychol Sci	2010 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20424107
Neural correlates of novelty and face-age effects in young and elderly adults.	Wright CI, Negreira A, Gold AL, Britton JC, Williams D, Barrett LF	NeuroImage	18586522	Neuroimage	2008 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/18586522
Primary Interoceptive Cortex Activity during Simulated Experiences of the Body.	Wilson-Mendenhall CD, Henriques A, Barsalou LW, Barrett LF	Journal of cognitive neuroscience	30277431	J Cogn Neurosci	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30277431
Introducing a Face Sort Paradigm to Evaluate Age Differences in Emotion Perception.	Hoemann K, Vicaria IM, Gendron M, Stanley JT	The journals of gerontology. Series B, Psychological sciences and social sciences	32211791	J Gerontol B Psychol Sci Soc Sci	2021 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/32211791
Cultural relativity in perceiving emotion from vocalizations.	Gendron M, Roberson D, van der Vyver JM, Barrett LF	Psychological science	24501109	Psychol Sci	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24501109
Dissociable large-scale networks anchored in the right anterior insula subserve affective experience and attention.	Touroutoglou A, Hollenbeck M, Dickerson BC, Feldman Barrett L	NeuroImage	22361166	Neuroimage	2012 May 1	https://www.ncbi.nlm.nih.gov/pubmed/22361166
Out of sight but not out of mind: unseen affective faces influence evaluations and social impressions.	Anderson E, Siegel E, White D, Barrett LF	Emotion (Washington, D.C.)	22506501	Emotion	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/22506501
Intrinsic amygdala-cortical functional connectivity predicts social network size in humans.	Bickart KC, Hollenbeck MC, Barrett LF, Dickerson BC	The Journal of neuroscience : the official journal of the Society for Neuroscience	23077058	J Neurosci	2012 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/23077058
A functional architecture of the human brain: emerging insights from the science of emotion.	Lindquist KA, Barrett LF	Trends in cognitive sciences	23036719	Trends Cogn Sci	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23036719
Atrophy in distinct corticolimbic networks in frontotemporal dementia relates to social impairments measured using the Social Impairment Rating Scale.	Bickart KC, Brickhouse M, Negreira A, Sapolsky D, Barrett LF, Dickerson BC	Journal of neurology, neurosurgery, and psychiatry	24133285	J Neurol Neurosurg Psychiatry	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24133285
Is there consistency and specificity of autonomic changes during emotional episodes? Guidance from the Conceptual Act Theory and psychophysiology.	Quigley KS, Barrett LF	Biological psychology	24388802	Biol Psychol	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24388802
Involvement of Sensory Regions in Affective Experience: A Meta-Analysis.	Satpute AB, Kang J, Bickart KC, Yardley H, Wager TD, Barrett LF	Frontiers in psychology	26696928	Front Psychol	2015	https://www.ncbi.nlm.nih.gov/pubmed/26696928
Decision making from economic and signal detection perspectives: development of an integrated framework.	Lynn SK, Wormwood JB, Barrett LF, Quigley KS	Frontiers in psychology	26217275	Front Psychol	2015	https://www.ncbi.nlm.nih.gov/pubmed/26217275
Functional connectivity dynamics during film viewing reveal common networks for different emotional experiences.	Raz G, Touroutoglou A, Wilson-Mendenhall C, Gilam G, Lin T, Gonen T, Jacob Y, Atzil S, Admon R, Bleich-Cohen M, Maron-Katz A, Hendler T, Barrett LF	Cognitive, affective & behavioral neuroscience	27142636	Cogn Affect Behav Neurosci	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27142636
A Bayesian model of category-specific emotional brain responses.	Wager TD, Kang J, Johnson TD, Nichols TE, Satpute AB, Barrett LF	PLoS computational biology	25853490	PLoS Comput Biol	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25853490
A shift in perspective: Decentering through mindful attention to imagined stressful events.	Lebois LA, Papies EK, Gopinath K, Cabanban R, Quigley KS, Krishnamurthy V, Barrett LF, Barsalou LW	Neuropsychologia	26111487	Neuropsychologia	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26111487
Conscious awareness is necessary for affective faces to influence social judgments.	Kleckner IR, Anderson EC, Betz NJ, Wormwood JB, Eskew RT Jr, Barrett LF	Journal of experimental social psychology	31097841	J Exp Soc Psychol	2018 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31097841
Risk Factors, Neuroanatomical Correlates, and Outcome of Neuropsychiatric Symptoms in Alzheimer's Disease.	Poulin SP, Bergeron D, Dickerson BC, Alzheimer’s Disease Neuroimaging Initiative	Journal of Alzheimer's disease : JAD	28869463	J Alzheimers Dis	2017	https://www.ncbi.nlm.nih.gov/pubmed/28869463
Internal valence modulates the speed of object recognition.	Panichello MF, Kveraga K, Chaumon M, Bar M, Barrett LF	Scientific reports	28336933	Sci Rep	2017 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/28336933
Heightened sensitivity to emotional expressions in generalised anxiety disorder, compared to social anxiety disorder, and controls.	Bui E, Anderson E, Goetter EM, Campbell AA, Fischer LE, Barrett LF, Simon NM	Cognition & emotion	26395075	Cogn Emot	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26395075
Working memory capacity is associated with optimal adaptation of response bias to perceptual sensitivity in emotion perception.	Lynn SK, Ibagon C, Bui E, Palitz SA, Simon NM, Barrett LF	Emotion (Washington, D.C.)	26461251	Emotion	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26461251
Clonal expansions in ulcerative colitis identify patients with neoplasia.	Salk JJ, Salipante SJ, Risques RA, Crispin DA, Li L, Bronner MP, Brentnall TA, Rabinovitch PS, Horwitz MS, Loeb LA	Proceedings of the National Academy of Sciences of the United States of America	19926851	Proc Natl Acad Sci U S A	2009 Dec 8	https://www.ncbi.nlm.nih.gov/pubmed/19926851
Phylogenetic analysis of developmental and postnatal mouse cell lineages.	Salipante SJ, Kas A, McMonagle E, Horwitz MS	Evolution & development	20156285	Evol Dev	2010 Jan-Feb	https://www.ncbi.nlm.nih.gov/pubmed/20156285
Use of somatic mutations to quantify random contributions to mouse development.	Zhou W, Tan Y, Anderson DJ, Crist EM, Ruohola-Baker H, Salipante SJ, Horwitz MS	BMC genomics	23327737	BMC Genomics	2013 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/23327737
Phylogenetic fate mapping: theoretical and experimental studies applied to the development of mouse fibroblasts.	Salipante SJ, Thompson JM, Horwitz MS	Genetics	18245843	Genetics	2008 Feb	https://www.ncbi.nlm.nih.gov/pubmed/18245843
Passenger mutations as a marker of clonal cell lineages in emerging neoplasia.	Salk JJ, Horwitz MS	Seminars in cancer biology	20951806	Semin Cancer Biol	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20951806
Decoding cell lineage from acquired mutations using arbitrary deep sequencing.	Carlson CA, Kas A, Kirkwood R, Hays LE, Preston BD, Salipante SJ, Horwitz MS	Nature methods	22120468	Nat Methods	2011 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/22120468
The membrane environment can promote or suppress bistability in cell signaling networks.	Abel SM, Roose JP, Groves JT, Weiss A, Chakraborty AK	The journal of physical chemistry. B	22332778	J Phys Chem B	2012 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/22332778
Empty class II major histocompatibility complex created by peptide photolysis establishes the role of DM in peptide association.	Grotenbreg GM, Nicholson MJ, Fowler KD, Wilbuer K, Octavio L, Yang M, Chakraborty AK, Ploegh HL, Wucherpfennig KW	The Journal of biological chemistry	17525157	J Biol Chem	2007 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/17525157
Interaction of streptavidin-based peptide-MHC oligomers (tetramers) with cell-surface TCRs.	Stone JD, Artyomov MN, Chervin AS, Chakraborty AK, Eisen HN, Kranz DM	Journal of immunology (Baltimore, Md. : 1950)	22102724	J Immunol	2011 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/22102724
The effect of mutations on the alloreactive T cell receptor/peptide-MHC interface structure: a molecular dynamics study.	Wolfson MY, Nam K, Chakraborty AK	The journal of physical chemistry. B	21651302	J Phys Chem B	2011 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/21651302
Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection.	Kosmrlj A, Read EL, Qi Y, Allen TM, Altfeld M, Deeks SG, Pereyra F, Carrington M, Walker BD, Chakraborty AK	Nature	20445539	Nature	2010 May 20	https://www.ncbi.nlm.nih.gov/pubmed/20445539
Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes.	Shekhar K, Ruberman CF, Ferguson AL, Barton JP, Kardar M, Chakraborty AK	Physical review. E, Statistical, nonlinear, and soft matter physics	24483484	Phys Rev E Stat Nonlin Soft Matter Phys	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24483484
Space coding by gamma oscillations in the barn owl optic tectum.	Sridharan D, Boahen K, Knudsen EI	Journal of neurophysiology	21325681	J Neurophysiol	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21325681
Neurotech for neuroscience: unifying concepts, organizing principles, and emerging tools.	Silver R, Boahen K, Grillner S, Kopell N, Olsen KL	The Journal of neuroscience : the official journal of the Society for Neuroscience	17978017	J Neurosci	2007 Oct 31	https://www.ncbi.nlm.nih.gov/pubmed/17978017
A superposable silicon synapse with programmable reversal potential.	Benjamin BV, Arthur JV, Gao P, Merolla P, Boahen K	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	23366006	Annu Int Conf IEEE Eng Med Biol Soc	2012	https://www.ncbi.nlm.nih.gov/pubmed/23366006
Silicon-Neuron Design: A Dynamical Systems Approach.	Arthur JV, Boahen K	IEEE transactions on circuits and systems. I, Regular papers : a publication of the IEEE Circuits and Systems Society	21617741	IEEE Trans Circuits Syst I Regul Pap	2011	https://www.ncbi.nlm.nih.gov/pubmed/21617741
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome.	Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA 3rd, Loomer P, Armitage GC, Relman DA	The ISME journal	22158393	ISME J	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22158393
Bacterial diversity in the oral cavity of 10 healthy individuals.	Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA	The ISME journal	20336157	ISME J	2010 Aug	https://www.ncbi.nlm.nih.gov/pubmed/20336157
SmashCell: a software framework for the analysis of single-cell amplified genome sequences.	Harrington ED, Arumugam M, Raes J, Bork P, Relman DA	Bioinformatics (Oxford, England)	20966005	Bioinformatics	2010 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/20966005
Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time.	Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA	Genome research	21149389	Genome Res	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21149389
Genetic technologies. Synthetic "life," ethics, national security, and public discourse.	Cho MK, Relman DA	Science (New York, N.Y.)	20595601	Science	2010 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/20595601
Microbial invasion of the amniotic cavity in pregnancies with small-for-gestational-age fetuses.	DiGiulio DB, Gervasi MT, Romero R, Vaisbuch E, Mazaki-Tovi S, Kusanovic JP, Seok KS, Gómez R, Mittal P, Gotsch F, Chaiworapongsa T, Oyarzún E, Kim CJ, Relman DA	Journal of perinatal medicine	20482466	J Perinat Med	2010 Sep	https://www.ncbi.nlm.nih.gov/pubmed/20482466
Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time.	Hoy YE, Bik EM, Lawley TD, Holmes SP, Monack DM, Theriot JA, Relman DA	PloS one	26565698	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26565698
Microbiology. Undernutrition--looking within for answers.	Relman DA	Science (New York, N.Y.)	23363770	Science	2013 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/23363770
Gut immune maturation depends on colonization with a host-specific microbiota.	Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, Reading NC, Villablanca EJ, Wang S, Mora JR, Umesaki Y, Mathis D, Benoist C, Relman DA, Kasper DL	Cell	22726443	Cell	2012 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/22726443
Microbiome assembly across multiple body sites in low-birthweight infants.	Costello EK, Carlisle EM, Bik EM, Morowitz MJ, Relman DA	mBio	24169577	mBio	2013 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/24169577
Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage.	Yan M, Pamp SJ, Fukuyama J, Hwang PH, Cho DY, Holmes S, Relman DA	Cell host & microbe	24331461	Cell Host Microbe	2013 Dec 11	https://www.ncbi.nlm.nih.gov/pubmed/24331461
The application of ecological theory toward an understanding of the human microbiome.	Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA	Science (New York, N.Y.)	22674335	Science	2012 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/22674335
Microbiota-targeted therapies: an ecological perspective.	Lemon KP, Armitage GC, Relman DA, Fischbach MA	Science translational medicine	22674555	Sci Transl Med	2012 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/22674555
Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses.	Pride DT, Salzman J, Relman DA	Environmental microbiology	22583485	Environ Microbiol	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22583485
Comparisons of distance methods for combining covariates and abundances in microbiome studies.	Fukuyama J, McMurdie PJ, Dethlefsen L, Relman DA, Holmes S	Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing	22174277	Pac Symp Biocomput	2012	https://www.ncbi.nlm.nih.gov/pubmed/22174277
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.	Dethlefsen L, Relman DA	Proceedings of the National Academy of Sciences of the United States of America	20847294	Proc Natl Acad Sci U S A	2011 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/20847294
Microbial invasion of the amniotic cavity in preeclampsia as assessed by cultivation and sequence-based methods.	DiGiulio DB, Gervasi M, Romero R, Mazaki-Tovi S, Vaisbuch E, Kusanovic JP, Seok KS, Gómez R, Mittal P, Gotsch F, Chaiworapongsa T, Oyarzún E, Kim CJ, Relman DA	Journal of perinatal medicine	20482470	J Perinat Med	2010 Sep	https://www.ncbi.nlm.nih.gov/pubmed/20482470
Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS.	Behrens S, Lösekann T, Pett-Ridge J, Weber PK, Ng WO, Stevenson BS, Hutcheon ID, Relman DA, Spormann AM	Applied and environmental microbiology	18359832	Appl Environ Microbiol	2008 May	https://www.ncbi.nlm.nih.gov/pubmed/18359832
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.	Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF	Genome research	22936250	Genome Res	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/22936250
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.	Dethlefsen L, Huse S, Sogin ML, Relman DA	PLoS biology	19018661	PLoS Biol	2008 Nov 18	https://www.ncbi.nlm.nih.gov/pubmed/19018661
Thinking about the microbiome as a causal factor in human health and disease: philosophical and experimental considerations.	Relman DA	Current opinion in microbiology	32114367	Curr Opin Microbiol	2020 Apr	https://www.ncbi.nlm.nih.gov/pubmed/32114367
A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow.	Proctor DM, Fukuyama JA, Loomer PM, Armitage GC, Lee SA, Davis NM, Ryder MI, Holmes SP, Relman DA	Nature communications	29445174	Nat Commun	2018 Feb 14	https://www.ncbi.nlm.nih.gov/pubmed/29445174
The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat.	Proctor DM, Relman DA	Cell host & microbe	28407480	Cell Host Microbe	2017 Apr 12	https://www.ncbi.nlm.nih.gov/pubmed/28407480
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant.	Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF	Proceedings of the National Academy of Sciences of the United States of America	21191099	Proc Natl Acad Sci U S A	2011 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/21191099
Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States.	Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, Singh U	PloS one	23349750	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23349750
Physics. Measuring mass in seconds.	Debs JE, Robins NP, Close JD	Science (New York, N.Y.)	23372004	Science	2013 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/23372004
The human microbiome: ecosystem resilience and health.	Relman DA	Nutrition reviews	22861804	Nutr Rev	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22861804
"Inconvenient truths" in the pursuit of scientific knowledge and public health.	Relman DA	The Journal of infectious diseases	24106297	J Infect Dis	2014 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/24106297
Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation.	DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, Kim CJ, Erez O, Edwin S, Relman DA	PloS one	18725970	PLoS One	2008 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/18725970
Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity.	Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP Jr, Rohwer F, Haynes M	Proceedings of the National Academy of Sciences of the United States of America	20547834	Proc Natl Acad Sci U S A	2011 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/20547834
Microbiota's 'little helpers': bacteriophages and antibiotic-associated responses in the gut microbiome.	Sun CL, Relman DA	Genome biology	23906048	Genome Biol	2013 Jul 30	https://www.ncbi.nlm.nih.gov/pubmed/23906048
'Til death do us part': coming to terms with symbiotic relationships. Forward.	Relman DA	Nature reviews. Microbiology	19086265	Nat Rev Microbiol	2008 Oct	https://www.ncbi.nlm.nih.gov/pubmed/19086265
Restoration of the gut microbial habitat as a disease therapy.	Relman DA	Nature biotechnology	23302933	Nat Biotechnol	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23302933
Prevalence and diversity of microbes in the amniotic fluid, the fetal inflammatory response, and pregnancy outcome in women with preterm pre-labor rupture of membranes.	DiGiulio DB, Romero R, Kusanovic JP, Gómez R, Kim CJ, Seok KS, Gotsch F, Mazaki-Tovi S, Vaisbuch E, Sanders K, Bik EM, Chaiworapongsa T, Oyarzún E, Relman DA	American journal of reproductive immunology (New York, N.Y. : 1989)	20331587	Am J Reprod Immunol	2010 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/20331587
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.	Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML	PLoS genetics	19023400	PLoS Genet	2008 Nov	https://www.ncbi.nlm.nih.gov/pubmed/19023400
Development of the human infant intestinal microbiota.	Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO	PLoS biology	17594176	PLoS Biol	2007 Jul	https://www.ncbi.nlm.nih.gov/pubmed/17594176
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).	Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC	Genome research	22434425	Genome Res	2012 Jun	https://www.ncbi.nlm.nih.gov/pubmed/22434425
Microbial genomics and infectious diseases.	Relman DA	The New England journal of medicine	21793746	N Engl J Med	2011 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/21793746
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota.	Kashyap PC, Marcobal A, Ursell LK, Smits SA, Sonnenburg ED, Costello EK, Higginbottom SK, Domino SE, Holmes SP, Relman DA, Knight R, Gordon JI, Sonnenburg JL	Proceedings of the National Academy of Sciences of the United States of America	24062455	Proc Natl Acad Sci U S A	2013 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/24062455
Characterizing the oral and distal gut microbiota of the threatened southern sea otter (Enhydra lutris nereis) to enhance conservation practice.	Dudek NK, Switzer AD, Costello EK, Murray MJ, Tomoleoni JA, Staedler MM, Tinker MT, Relman DA	Conservation science and practice	35382031	Conserv Sci Pract	2022 Apr	https://www.ncbi.nlm.nih.gov/pubmed/35382031
Exploring weak, transient protein--protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy.	Wang Q, Zhuravleva A, Gierasch LM	Biochemistry	21942871	Biochemistry	2011 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/21942871
How one bad protein spoils the barrel: structural details of β2-microglobulin amyloidogenicity.	Gierasch LM	Molecular cell	21255721	Mol Cell	2011 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/21255721
Sending signals dynamically.	Smock RG, Gierasch LM	Science (New York, N.Y.)	19359576	Science	2009 Apr 10	https://www.ncbi.nlm.nih.gov/pubmed/19359576
Protein folding in the cell: challenges and progress.	Gershenson A, Gierasch LM	Current opinion in structural biology	21112769	Curr Opin Struct Biol	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21112769
Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state.	Hong J, Gierasch LM	Journal of the American Chemical Society	20662522	J Am Chem Soc	2010 Aug 4	https://www.ncbi.nlm.nih.gov/pubmed/20662522
Rett syndrome-causing mutations in human MeCP2 result in diverse structural changes that impact folding and DNA interactions.	Ghosh RP, Horowitz-Scherer RA, Nikitina T, Gierasch LM, Woodcock CL	The Journal of biological chemistry	18499664	J Biol Chem	2008 Jul 18	https://www.ncbi.nlm.nih.gov/pubmed/18499664
From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein.	Ignatova Z, Krishnan B, Bombardier JP, Marcelino AM, Hong J, Gierasch LM	Biopolymers	17206628	Biopolymers	2007	https://www.ncbi.nlm.nih.gov/pubmed/17206628
Using a low denaturant model to explore the conformational features of translocation-active SecA.	Maki JL, Krishnan B, Gierasch LM	Biochemistry	22304380	Biochemistry	2012 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/22304380
How bacteria survive an acid trip.	Hingorani KS, Gierasch LM	Proceedings of the National Academy of Sciences of the United States of America	23530238	Proc Natl Acad Sci U S A	2013 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/23530238
Early folding events protect aggregation-prone regions of a β-rich protein.	Budyak IL, Krishnan B, Marcelino-Cruz AM, Ferrolino MC, Zhuravleva A, Gierasch LM	Structure (London, England : 1993)	23454187	Structure	2013 Mar 5	https://www.ncbi.nlm.nih.gov/pubmed/23454187
Its preferential interactions with biopolymers account for diverse observed effects of trehalose.	Hong J, Gierasch LM, Liu Z	Biophysical journal	26153711	Biophys J	2015 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/26153711
Nature's molecular sponges: small heat shock proteins grow into their chaperone roles.	Eyles SJ, Gierasch LM	Proceedings of the National Academy of Sciences of the United States of America	20133678	Proc Natl Acad Sci U S A	2010 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/20133678
Celebrating the scientific legacy of Elkan R. Blout.	Gierasch LM, Deber CM, Brodsky B	Biopolymers	18307218	Biopolymers	2008 May	https://www.ncbi.nlm.nih.gov/pubmed/18307218
Unique physical properties and interactions of the domains of methylated DNA binding protein 2.	Ghosh RP, Nikitina T, Horowitz-Scherer RA, Gierasch LM, Uversky VN, Hite K, Hansen JC, Woodcock CL	Biochemistry	20405910	Biochemistry	2010 May 25	https://www.ncbi.nlm.nih.gov/pubmed/20405910
Site-specific fluorescent labeling of poly-histidine sequences using a metal-chelating cysteine.	Krishnan B, Szymanska A, Gierasch LM	Chemical biology & drug design	17313455	Chem Biol Drug Des	2007 Jan	https://www.ncbi.nlm.nih.gov/pubmed/17313455
Roles of beta-turns in protein folding: from peptide models to protein engineering.	Marcelino AM, Gierasch LM	Biopolymers	18275088	Biopolymers	2008 May	https://www.ncbi.nlm.nih.gov/pubmed/18275088
The molecular dating game: an antibody heavy chain hangs loose with a chaperone while waiting for its life partner.	Hebert DN, Gierasch LM	Molecular cell	19560414	Mol Cell	2009 Jun 26	https://www.ncbi.nlm.nih.gov/pubmed/19560414
Cross-strand split tetra-Cys motifs as structure sensors in a beta-sheet protein.	Krishnan B, Gierasch LM	Chemistry & biology	18940670	Chem Biol	2008 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/18940670
Chapter 3: A fluorescent window into protein folding and aggregation in cells.	Ignatova Z, Gierasch LM	Methods in cell biology	19118672	Methods Cell Biol	2008	https://www.ncbi.nlm.nih.gov/pubmed/19118672
The Role of Aromatic-Aromatic Interactions in Strand-Strand Stabilization of β-Sheets.	Budyak IL, Zhuravleva A, Gierasch LM	Journal of molecular biology	23810905	J Mol Biol	2013 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/23810905
Delicate balance between functionally required flexibility and aggregation risk in a β-rich protein.	Ferrolino MC, Zhuravleva A, Budyak IL, Krishnan B, Gierasch LM	Biochemistry	24236614	Biochemistry	2013 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/24236614
In-cell aggregation of a polyglutamine-containing chimera is a multistep process initiated by the flanking sequence.	Ignatova Z, Thakur AK, Wetzel R, Gierasch LM	The Journal of biological chemistry	17942400	J Biol Chem	2007 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/17942400
Dynamic local unfolding in the serpin α-1 antitrypsin provides a mechanism for loop insertion and polymerization.	Krishnan B, Gierasch LM	Nature structural & molecular biology	21258324	Nat Struct Mol Biol	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21258324
Orthogonal cross-seeding: an approach to explore protein aggregates in living cells.	Hinz J, Gierasch LM, Ignatova Z	Biochemistry	18330996	Biochemistry	2008 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/18330996
Expression and Purification of Active Recombinant Human Alpha-1 Antitrypsin (AAT) from Escherichia coli.	Krishnan B, Hedstrom L, Hebert DN, Gierasch LM, Gershenson A	Methods in molecular biology (Clifton, N.J.)	28752459	Methods Mol Biol	2017	https://www.ncbi.nlm.nih.gov/pubmed/28752459
A career pathway in protein folding: from model peptides to postreductionist protein science.	Gierasch LM	Protein science : a publication of the Protein Society	21404361	Protein Sci	2011 May	https://www.ncbi.nlm.nih.gov/pubmed/21404361
Post-reductionist protein science, or putting Humpty Dumpty back together again.	Gierasch LM, Gershenson A	Nature chemical biology	19841622	Nat Chem Biol	2009 Nov	https://www.ncbi.nlm.nih.gov/pubmed/19841622
A method for direct measurement of protein stability in vivo.	Ignatova Z, Gierasch LM	Methods in molecular biology (Clifton, N.J.)	19157083	Methods Mol Biol	2009	https://www.ncbi.nlm.nih.gov/pubmed/19157083
Effects of osmolytes on protein folding and aggregation in cells.	Ignatova Z, Gierasch LM	Methods in enzymology	17875429	Methods Enzymol	2007	https://www.ncbi.nlm.nih.gov/pubmed/17875429
Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge.	Hingorani KS, Gierasch LM	Current opinion in structural biology	24434632	Curr Opin Struct Biol	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24434632
FoldEco: a model for proteostasis in E. coli.	Powers ET, Powers DL, Gierasch LM	Cell reports	22509487	Cell Rep	2012 Mar 29	https://www.ncbi.nlm.nih.gov/pubmed/22509487
A role of erythrocytes in adenosine monophosphate initiation of hypometabolism in mammals.	Daniels IS, Zhang J, O'Brien WG 3rd, Tao Z, Miki T, Zhao Z, Blackburn MR, Lee CC	The Journal of biological chemistry	20430891	J Biol Chem	2010 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/20430891
Hepatic gene expression profiling of 5'-AMP-induced hypometabolism in mice.	Zhao Z, Miki T, Van Oort-Jansen A, Matsumoto T, Loose DS, Lee CC	Physiological genomics	21224422	Physiol Genomics	2011 Apr 12	https://www.ncbi.nlm.nih.gov/pubmed/21224422
AMP deaminase 3 deficiency enhanced 5'-AMP induction of hypometabolism.	Daniels IS, O Brien WG 3rd, Nath V, Zhao Z, Lee CC	PloS one	24066180	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24066180
p53 regulates Period2 expression and the circadian clock.	Miki T, Matsumoto T, Zhao Z, Lee CC	Nature communications	24051492	Nat Commun	2013	https://www.ncbi.nlm.nih.gov/pubmed/24051492
New insights on the regulation of the adenine nucleotide pool of erythrocytes in mouse models.	O'Brien WG 3rd, Ling HS, Zhao Z, Lee CC	PloS one	28746349	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28746349
Metabolite Profiling of 5'-AMP-Induced Hypometabolism.	Zhao Z, Van Oort A, Tao Z, O'Brien WG 3rd, Lee CC	Metabolomics : Official journal of the Metabolomic Society	24511307	Metabolomics	2014 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/24511307
The Small Molecule Nobiletin Targets the Molecular Oscillator to Enhance Circadian Rhythms and Protect against Metabolic Syndrome.	He B, Nohara K, Park N, Park YS, Guillory B, Zhao Z, Garcia JM, Koike N, Lee CC, Takahashi JS, Yoo SH, Chen Z	Cell metabolism	27076076	Cell Metab	2016 Apr 12	https://www.ncbi.nlm.nih.gov/pubmed/27076076
Heparan sulfate proteoglycans containing a glypican 5 core and 2-O-sulfo-iduronic acid function as Sonic Hedgehog co-receptors to promote proliferation.	Witt RM, Hecht ML, Pazyra-Murphy MF, Cohen SM, Noti C, van Kuppevelt TH, Fuller M, Chan JA, Hopwood JJ, Seeberger PH, Segal RA	The Journal of biological chemistry	23867465	J Biol Chem	2013 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/23867465
Numb links extracellular cues to intracellular polarity machinery to promote chemotaxis.	Zhou P, Alfaro J, Chang EH, Zhao X, Porcionatto M, Segal RA	Developmental cell	21571219	Dev Cell	2011 May 17	https://www.ncbi.nlm.nih.gov/pubmed/21571219
Shh-proteoglycan interactions regulate maturation of olfactory glomerular circuitry.	Persson L, Witt RM, Galligan M, Greer PL, Eisner A, Pazyra-Murphy MF, Datta SR, Segal RA	Developmental neurobiology	24913191	Dev Neurobiol	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24913191
Olfactory behavioral testing in the adult mouse.	Witt RM, Galligan MM, Despinoy JR, Segal R	Journal of visualized experiments : JoVE	19229182	J Vis Exp	2009 Jan 28	https://www.ncbi.nlm.nih.gov/pubmed/19229182
Proteoglycan interactions with Sonic Hedgehog specify mitogenic responses.	Chan JA, Balasubramanian S, Witt RM, Nazemi KJ, Choi Y, Pazyra-Murphy MF, Walsh CO, Thompson M, Segal RA	Nature neuroscience	19287388	Nat Neurosci	2009 Apr	https://www.ncbi.nlm.nih.gov/pubmed/19287388
The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus.	Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, Chang HY, Brahic M, Kirkegaard K	Cell	23415224	Cell	2013 Feb 14	https://www.ncbi.nlm.nih.gov/pubmed/23415224
The ins and outs of viral infection: keystone meeting review.	Bird SW, Kirkegaard K, Agbandje-McKenna M, Freed EO	Viruses	25256395	Viruses	2014 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/25256395
Neuron-to-neuron transmission of α-synuclein fibrils through axonal transport.	Freundt EC, Maynard N, Clancy EK, Roy S, Bousset L, Sourigues Y, Covert M, Melki R, Kirkegaard K, Brahic M	Annals of neurology	23109146	Ann Neurol	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23109146
Nonlytic viral spread enhanced by autophagy components.	Bird SW, Maynard ND, Covert MW, Kirkegaard K	Proceedings of the National Academy of Sciences of the United States of America	25157142	Proc Natl Acad Sci U S A	2014 Sep 9	https://www.ncbi.nlm.nih.gov/pubmed/25157142
Dominant drug targets suppress the emergence of antiviral resistance.	Tanner EJ, Liu HM, Oberste MS, Pallansch M, Collett MS, Kirkegaard K	eLife	25365453	Elife	2014 Nov 3	https://www.ncbi.nlm.nih.gov/pubmed/25365453
Nonlytic spread of naked viruses.	Bird SW, Kirkegaard K	Autophagy	25680079	Autophagy	2015	https://www.ncbi.nlm.nih.gov/pubmed/25680079
Exploiting Genetic Interference for Antiviral Therapy.	Tanner EJ, Kirkegaard KA, Weinberger LS	PLoS genetics	27149616	PLoS Genet	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/27149616
Interstitial contacts in an RNA-dependent RNA polymerase lattice.	Tellez AB, Wang J, Tanner EJ, Spagnolo JF, Kirkegaard K, Bullitt E	Journal of molecular biology	21839092	J Mol Biol	2011 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/21839092
Detection and Differentiation of Multiple Viral RNAs Using Branched DNA FISH Coupled to Confocal Microscopy and Flow Cytometry.	van Buuren N, Kirkegaard K	Bio-protocol	30505886	Bio Protoc	2018 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/30505886
A computational model predicts Xenopus meiotic spindle organization.	Loughlin R, Heald R, Nédélec F	The Journal of cell biology	21173114	J Cell Biol	2010 Dec 27	https://www.ncbi.nlm.nih.gov/pubmed/21173114
Mitotic chromosome size scaling in Xenopus.	Kieserman EK, Heald R	Cell cycle (Georgetown, Tex.)	22071695	Cell Cycle	2011 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/22071695
Mechanisms of intracellular scaling.	Levy DL, Heald R	Annual review of cell and developmental biology	22804576	Annu Rev Cell Dev Biol	2012	https://www.ncbi.nlm.nih.gov/pubmed/22804576
Katanin contributes to interspecies spindle length scaling in Xenopus.	Loughlin R, Wilbur JD, McNally FJ, Nédélec FJ, Heald R	Cell	22153081	Cell	2011 Dec 9	https://www.ncbi.nlm.nih.gov/pubmed/22153081
Nuclear size is regulated by importin α and Ntf2 in Xenopus.	Levy DL, Heald R	Cell	20946986	Cell	2010 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/20946986
Mechanisms of mitotic spindle assembly and function.	Walczak CE, Heald R	International review of cytology	18275887	Int Rev Cytol	2008	https://www.ncbi.nlm.nih.gov/pubmed/18275887
Culture environment-induced pluripotency of SACK-expanded tissue stem cells.	Paré JF, Sherley JL	Journal of biomedicine & biotechnology	22523467	J Biomed Biotechnol	2011	https://www.ncbi.nlm.nih.gov/pubmed/22523467
Decreased H3K27 and H3K4 trimethylation on mortal chromosomes in distributed stem cells.	Huh YH, Sherley JL	Cell death & disease	25476902	Cell Death Dis	2014 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/25476902
Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells.	Huh YH, Cohen J, Sherley JL	Proceedings of the National Academy of Sciences of the United States of America	24082118	Proc Natl Acad Sci U S A	2013 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/24082118
CXCR6, a newly defined biomarker of tissue-specific stem cell asymmetric self-renewal, identifies more aggressive human melanoma cancer stem cells.	Taghizadeh R, Noh M, Huh YH, Ciusani E, Sigalotti L, Maio M, Arosio B, Nicotra MR, Natali P, Sherley JL, La Porta CA	PloS one	21203549	PLoS One	2010 Dec 22	https://www.ncbi.nlm.nih.gov/pubmed/21203549
A resource for discovering specific and universal biomarkers for distributed stem cells.	Noh M, Smith JL, Huh YH, Sherley JL	PloS one	21818293	PLoS One	2011	https://www.ncbi.nlm.nih.gov/pubmed/21818293
Sparse feature selection identifies H2A.Z as a novel, pattern-specific biomarker for asymmetrically self-renewing distributed stem cells.	Huh YH, Noh M, Burden FR, Chen JC, Winkler DA, Sherley JL	Stem cell research	25636161	Stem Cell Res	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25636161
A new mechanism for aging: chemical "age spots" in immortal DNA strands in distributed stem cells.	Sherley JL	Breast disease	19029623	Breast Dis	2008	https://www.ncbi.nlm.nih.gov/pubmed/19029623
Molecular cloaking of H2A.Z on mortal DNA chromosomes during nonrandom segregation.	Huh YH, Sherley JL	Stem cells (Dayton, Ohio)	21905168	Stem Cells	2011 Oct	https://www.ncbi.nlm.nih.gov/pubmed/21905168
Ex vivo Expansion of Human Adult Pancreatic Cells with Properties of Distributed Stem Cells by Suppression of Asymmetric Cell Kinetics.	Paré J, Sherley J	Journal of stem cell research & therapy	25197614	J Stem Cell Res Ther	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25197614
Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics.	Gusarov I, Shatalin K, Starodubtseva M, Nudler E	Science (New York, N.Y.)	19745150	Science	2009 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/19745150
Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages.	Shatalin K, Gusarov I, Avetissova E, Shatalina Y, McQuade LE, Lippard SJ, Nudler E	Proceedings of the National Academy of Sciences of the United States of America	18215992	Proc Natl Acad Sci U S A	2008 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/18215992
Bacterial nitric-oxide synthases operate without a dedicated redox partner.	Gusarov I, Starodubtseva M, Wang ZQ, McQuade L, Lippard SJ, Stuehr DJ, Nudler E	The Journal of biological chemistry	18316370	J Biol Chem	2008 May 9	https://www.ncbi.nlm.nih.gov/pubmed/18316370
Immuno gold nanocages with tailored optical properties for targeted photothermal destruction of cancer cells.	Chen J, Wang D, Xi J, Au L, Siekkinen A, Warsen A, Li ZY, Zhang H, Xia Y, Li X	Nano letters	17430005	Nano Lett	2007 May	https://www.ncbi.nlm.nih.gov/pubmed/17430005
Generation of hot spots with silver nanocubes for single-molecule detection by surface-enhanced Raman scattering.	Rycenga M, Xia X, Moran CH, Zhou F, Qin D, Li ZY, Xia Y	Angewandte Chemie (International ed. in English)	21542081	Angew Chem Int Ed Engl	2011 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/21542081
Fabrication of Density Gradients of Biodegradable Polymer Microparticles and Their Use in Guiding Neurite Outgrowth.	Li X, Macewan MR, Xie J Dr, Siewe D, Yuan X, Xia Y	Advanced functional materials	21687818	Adv Funct Mater	2010 May 25	https://www.ncbi.nlm.nih.gov/pubmed/21687818
Quantifying the cellular uptake of antibody-conjugated Au nanocages by two-photon microscopy and inductively coupled plasma mass spectrometry.	Au L, Zhang Q, Cobley CM, Gidding M, Schwartz AG, Chen J, Xia Y	ACS nano	19954236	ACS Nano	2010 Jan 26	https://www.ncbi.nlm.nih.gov/pubmed/19954236
Probing the photothermal effect of gold-based nanocages with surface-enhanced Raman scattering (SERS).	Rycenga M, Wang Z, Gordon E, Cobley CM, Schwartz AG, Lo CS, Xia Y	Angewandte Chemie (International ed. in English)	20014343	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/20014343
The effects of size, shape, and surface functional group of gold nanostructures on their adsorption and internalization by cells.	Cho EC, Au L, Zhang Q, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	20029850	Small	2010 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/20029850
Engineering the Properties of Metal Nanostructures via Galvanic Replacement Reactions.	Cobley CM, Xia Y	Materials science & engineering. R, Reports : a review journal	21180400	Mater Sci Eng R Rep	2010 Nov 22	https://www.ncbi.nlm.nih.gov/pubmed/21180400
Controlling the synthesis and assembly of silver nanostructures for plasmonic applications.	Rycenga M, Cobley CM, Zeng J, Li W, Moran CH, Zhang Q, Qin D, Xia Y	Chemical reviews	21395318	Chem Rev	2011 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/21395318
A new theranostic system based on gold nanocages and phase-change materials with unique features for photoacoustic imaging and controlled release.	Moon GD, Choi SW, Cai X, Li W, Cho EC, Jeong U, Wang LV, Xia Y	Journal of the American Chemical Society	21401092	J Am Chem Soc	2011 Apr 6	https://www.ncbi.nlm.nih.gov/pubmed/21401092
Quantitative analysis of the role played by poly(vinylpyrrolidone) in seed-mediated growth of Ag nanocrystals.	Xia X, Zeng J, Oetjen LK, Li Q, Xia Y	Journal of the American Chemical Society	22206387	J Am Chem Soc	2012 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/22206387
Gold nanocages: from synthesis to theranostic applications.	Xia Y, Li W, Cobley CM, Chen J, Xia X, Zhang Q, Yang M, Cho EC, Brown PK	Accounts of chemical research	21528889	Acc Chem Res	2011 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/21528889
Surface-enhanced Raman scattering: comparison of three different molecules on single-crystal nanocubes and nanospheres of silver.	Rycenga M, Kim MH, Camargo PH, Cobley C, Li ZY, Xia Y	The journal of physical chemistry. A	19175302	J Phys Chem A	2009 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/19175302
Near-infrared gold nanocages as a new class of tracers for photoacoustic sentinel lymph node mapping on a rat model.	Song KH, Kim C, Cobley CM, Xia Y, Wang LV	Nano letters	19072058	Nano Lett	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19072058
A facile synthesis of asymmetric hybrid colloidal particles.	Ohnuma A, Cho EC, Camargo PH, Au L, Ohtani B, Xia Y	Journal of the American Chemical Society	19140763	J Am Chem Soc	2009 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/19140763
Understanding the SERS Effects of Single Silver Nanoparticles and Their Dimers, One at a Time.	Rycenga M, Camargo PH, Li W, Moran CH, Xia Y	The journal of physical chemistry letters	20368749	J Phys Chem Lett	2010 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/20368749
Measuring the SERS Enhancement Factors of Dimers with Different Structures Constructed from Silver Nanocubes.	Camargo PH, Au L, Rycenga M, Li W, Xia Y	Chemical physics letters	20209069	Chem Phys Lett	2010 Jan	https://www.ncbi.nlm.nih.gov/pubmed/20209069
Gold nanocages as photothermal transducers for cancer treatment.	Chen J, Glaus C, Laforest R, Zhang Q, Yang M, Gidding M, Welch MJ, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	20225187	Small	2010 Apr 9	https://www.ncbi.nlm.nih.gov/pubmed/20225187
Au@Ag core-shell nanocubes with finely tuned and well-controlled sizes, shell thicknesses, and optical properties.	Ma Y, Li W, Cho EC, Li Z, Yu T, Zeng J, Xie Z, Xia Y	ACS nano	20964400	ACS Nano	2010 Nov 23	https://www.ncbi.nlm.nih.gov/pubmed/20964400
Radially aligned, electrospun nanofibers as dural substitutes for wound closure and tissue regeneration applications.	Xie J, Macewan MR, Ray WZ, Liu W, Siewe DY, Xia Y	ACS nano	20695478	ACS Nano	2010 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/20695478
Conductive Core-Sheath Nanofibers and Their Potential Application in Neural Tissue Engineering.	Xie J, Macewan MR, Willerth SM, Li X, Moran DW, Sakiyama-Elbert SE, Xia Y	Advanced functional materials	19830261	Adv Funct Mater	2009 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/19830261
Facile synthesis of Ag nanocubes of 30 to 70 nm in edge length with CF(3)COOAg as a precursor.	Zhang Q, Li W, Wen LP, Chen J, Xia Y	Chemistry (Weinheim an der Bergstrasse, Germany)	20593441	Chemistry	2010 Sep 3	https://www.ncbi.nlm.nih.gov/pubmed/20593441
Measuring the Optical Absorption Cross-sections of Au-Ag Nanocages and Au Nanorods by Photoacoustic Imaging.	Cho EC, Kim C, Zhou F, Cobley CM, Song KH, Chen J, Li ZY, Wang LV, Xia Y	The journal of physical chemistry. C, Nanomaterials and interfaces	19680423	J Phys Chem C Nanomater Interfaces	2009 May 28	https://www.ncbi.nlm.nih.gov/pubmed/19680423
Probing the surface-enhanced Raman scattering properties of Au-Ag nanocages at two different excitation wavelengths.	Rycenga M, Hou KK, Cobley CM, Schwartz AG, Camargo PH, Xia Y	Physical chemistry chemical physics : PCCP	19588011	Phys Chem Chem Phys	2009 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/19588011
Facile synthesis of tadpole-like nanostructures consisting of Au heads and Pd tails.	Camargo PH, Xiong Y, Ji L, Zuo JM, Xia Y	Journal of the American Chemical Society	18027954	J Am Chem Soc	2007 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/18027954
Gold Nanocages for Biomedical Applications.	Skrabalak SE, Chen J, Au L, Lu X, Li X, Xia Y	Advanced materials (Deerfield Beach, Fla.)	18648528	Adv Mater	2007 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/18648528
Investigation of neovascularization in three-dimensional porous scaffolds in vivo by a combination of multiscale photoacoustic microscopy and optical coherence tomography.	Cai X, Zhang Y, Li L, Choi SW, MacEwan MR, Yao J, Kim C, Xia Y, Wang LV	Tissue engineering. Part C, Methods	22838500	Tissue Eng Part C Methods	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/22838500
Gold nanocages covered with thermally-responsive polymers for controlled release by high-intensity focused ultrasound.	Li W, Cai X, Kim C, Sun G, Zhang Y, Deng R, Yang M, Chen J, Achilefu S, Wang LV, Xia Y	Nanoscale	21321760	Nanoscale	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21321760
Seed-mediated synthesis of truncated gold decahedrons with a AuCl/oleylamine complex as precursor.	Ma Y, Zeng J, Li W, McKiernan M, Xie Z, Xia Y	Advanced materials (Deerfield Beach, Fla.)	20301132	Adv Mater	2010 May 4	https://www.ncbi.nlm.nih.gov/pubmed/20301132
Synthesis and Optical Properties of Cubic Gold Nanoframes.	Au L, Chen Y, Zhou F, Camargo PH, Lim B, Li ZY, Ginger DS, Xia Y	Nano research	20200595	Nano Res	2008 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/20200595
Fabrication of cubic nanocages and nanoframes by dealloying Au/Ag alloy nanoboxes with an aqueous etchant based on Fe(NO3)3 or NH4OH.	Lu X, Au L, McLellan J, Li ZY, Marquez M, Xia Y	Nano letters	17489641	Nano Lett	2007 Jun	https://www.ncbi.nlm.nih.gov/pubmed/17489641
Dissolving Ag from Au-Ag Alloy Nanoboxes with H(2)O(2): A Method for Both Tailoring the Optical Properties and Measuring the H(2)O(2) Concentration.	Zhang Q, Cobley CM, Zeng J, Wen LP, Chen J, Xia Y	The journal of physical chemistry. C, Nanomaterials and interfaces	20495675	J Phys Chem C Nanomater Interfaces	2010 Mar 5	https://www.ncbi.nlm.nih.gov/pubmed/20495675
Bright three-photon luminescence from gold/silver alloyed nanostructures for bioimaging with negligible photothermal toxicity.	Tong L, Cobley CM, Chen J, Xia Y, Cheng JX	Angewandte Chemie (International ed. in English)	20544899	Angew Chem Int Ed Engl	2010 May 3	https://www.ncbi.nlm.nih.gov/pubmed/20544899
The mechanics of PLGA nanofiber scaffolds with biomimetic gradients in mineral for tendon-to-bone repair.	Lipner J, Liu W, Liu Y, Boyle J, Genin GM, Xia Y, Thomopoulos S	Journal of the mechanical behavior of biomedical materials	25194525	J Mech Behav Biomed Mater	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25194525
Neovascularization in biodegradable inverse opal scaffolds with uniform and precisely controlled pore sizes.	Choi SW, Zhang Y, Macewan MR, Xia Y	Advanced healthcare materials	23184495	Adv Healthc Mater	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23184495
A plasmon-assisted optofluidic (PAOF) system for measuring the photothermal conversion efficiencies of gold nanostructures and controlling an electrical switch.	Zeng J, Goldfeld D, Xia Y	Angewandte Chemie (International ed. in English)	23494970	Angew Chem Int Ed Engl	2013 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/23494970
A bioreducible polymer for efficient delivery of Fas-silencing siRNA into stem cell spheroids and enhanced therapeutic angiogenesis.	Shim MS, Bhang SH, Yoon K, Choi K, Xia Y	Angewandte Chemie (International ed. in English)	23074025	Angew Chem Int Ed Engl	2012 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/23074025
In Vivo Evaluation of Adipose-Derived Stromal Cells Delivered with a Nanofiber Scaffold for Tendon-to-Bone Repair.	Lipner J, Shen H, Cavinatto L, Liu W, Havlioglu N, Xia Y, Galatz LM, Thomopoulos S	Tissue engineering. Part A	26414599	Tissue Eng Part A	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26414599
Using well-defined Ag nanocubes as substrates to quantify the spatial resolution and penetration depth of surface-enhanced Raman scattering imaging.	Moran CH, Rycenga M, Xia X, Cobley CM, Xia Y	Nanotechnology	24334508	Nanotechnology	2014 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/24334508
Silica-coated dimers of silver nanospheres as surface-enhanced Raman scattering tags for imaging cancer cells.	Xia X, Li W, Zhang Y, Xia Y	Interface focus	24427538	Interface Focus	2013 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/24427538
A Facile and General Method for the Encapsulation of Different Types of Imaging Contrast Agents Within Micrometer-Sized Polymer Beads.	Bai MY, Moran CH, Zhang L, Liu C, Zhang Y, Wang LV, Xia Y	Advanced functional materials	31866803	Adv Funct Mater	2012 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/31866803
Nanobottles for Controlled Release and Drug Delivery.	Qiu J, Xu J, Xia Y	Advanced healthcare materials	32543127	Adv Healthc Mater	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/32543127
Quantifying the coverage density of poly(ethylene glycol) chains on the surface of gold nanostructures.	Xia X, Yang M, Wang Y, Zheng Y, Li Q, Chen J, Xia Y	ACS nano	22148912	ACS Nano	2012 Jan 24	https://www.ncbi.nlm.nih.gov/pubmed/22148912
Electrospun nanofibers for neural tissue engineering.	Xie J, MacEwan MR, Schwartz AG, Xia Y	Nanoscale	20648362	Nanoscale	2010 Jan	https://www.ncbi.nlm.nih.gov/pubmed/20648362
Production of Ag nanocubes on a scale of 0.1 g per batch by protecting the NaHS-mediated polyol synthesis with argon.	Zhang Q, Cobley C, Au L, McKiernan M, Schwartz A, Wen LP, Chen J, Xia Y	ACS applied materials & interfaces	20305725	ACS Appl Mater Interfaces	2009 Sep	https://www.ncbi.nlm.nih.gov/pubmed/20305725
Facile synthesis of gold nanoparticles with narrow size distribution by using AuCl or AuBr as the precursor.	Lu X, Tuan HY, Korgel BA, Xia Y	Chemistry (Weinheim an der Bergstrasse, Germany)	18058964	Chemistry	2008	https://www.ncbi.nlm.nih.gov/pubmed/18058964
Targeting gold nanocages to cancer cells for photothermal destruction and drug delivery.	Cobley CM, Au L, Chen J, Xia Y	Expert opinion on drug delivery	20345327	Expert Opin Drug Deliv	2010 May	https://www.ncbi.nlm.nih.gov/pubmed/20345327
Non-invasive and in situ characterization of the degradation of biomaterial scaffolds by volumetric photoacoustic microscopy.	Zhang YS, Cai X, Yao J, Xing W, Wang LV, Xia Y	Angewandte Chemie (International ed. in English)	24130155	Angew Chem Int Ed Engl	2014 Jan 3	https://www.ncbi.nlm.nih.gov/pubmed/24130155
Microscale polymer bottles corked with a phase-change material for temperature-controlled release.	Hyun DC, Lu P, Choi SI, Jeong U, Xia Y	Angewandte Chemie (International ed. in English)	23959631	Angew Chem Int Ed Engl	2013 Sep 27	https://www.ncbi.nlm.nih.gov/pubmed/23959631
Fabrication of Cell Patches Using Biodegradable Scaffolds with a Hexagonal Array of Interconnected Pores (SHAIPs).	Zhang YS, Yao J, Wang LV, Xia Y	Polymer	24443593	Polymer (Guildf)	2014 Jan 14	https://www.ncbi.nlm.nih.gov/pubmed/24443593
Nanofiber scaffolds with gradations in mineral content for mimicking the tendon-to-bone insertion site.	Li X, Xie J, Lipner J, Yuan X, Thomopoulos S, Xia Y	Nano letters	19537737	Nano Lett	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19537737
Neurite outgrowth on nanofiber scaffolds with different orders, structures, and surface properties.	Xie J, MacEwan MR, Li X, Sakiyama-Elbert SE, Xia Y	ACS nano	19397333	ACS Nano	2009 May 26	https://www.ncbi.nlm.nih.gov/pubmed/19397333
Shape-controlled synthesis of metal nanocrystals: simple chemistry meets complex physics?	Xia Y, Xiong Y, Lim B, Skrabalak SE	Angewandte Chemie (International ed. in English)	19053095	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19053095
Etching and dimerization: a simple and versatile route to dimers of silver nanospheres with a range of sizes.	Li W, Camargo PH, Au L, Zhang Q, Rycenga M, Xia Y	Angewandte Chemie (International ed. in English)	19943304	Angew Chem Int Ed Engl	2010	https://www.ncbi.nlm.nih.gov/pubmed/19943304
Facile synthesis of gold icosahedra in an aqueous solution by reacting HAuCl(4) with N-vinyl pyrrolidone.	Yavuz MS, Li W, Xia Y	Chemistry (Weinheim an der Bergstrasse, Germany)	19876970	Chemistry	2009 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/19876970
Dark-field microscopy studies of single metal nanoparticles: understanding the factors that influence the linewidth of the localized surface plasmon resonance.	Hu M, Novo C, Funston A, Wang H, Staleva H, Zou S, Mulvaney P, Xia Y, Hartland GV	Journal of materials chemistry	18846243	J Mater Chem	2008	https://www.ncbi.nlm.nih.gov/pubmed/18846243
Gold nanocages: synthesis, properties, and applications.	Skrabalak SE, Chen J, Sun Y, Lu X, Au L, Cobley CM, Xia Y	Accounts of chemical research	18570442	Acc Chem Res	2008 Dec	https://www.ncbi.nlm.nih.gov/pubmed/18570442
An enzyme-sensitive probe for photoacoustic imaging and fluorescence detection of protease activity.	Xia X, Yang M, Oetjen LK, Zhang Y, Li Q, Chen J, Xia Y	Nanoscale	21225037	Nanoscale	2011 Mar	https://www.ncbi.nlm.nih.gov/pubmed/21225037
Isolating and probing the hot spot formed between two silver nanocubes.	Camargo PH, Rycenga M, Au L, Xia Y	Angewandte Chemie (International ed. in English)	19199309	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19199309
Correlated Rayleigh Scattering Spectroscopy and Scanning Electron Microscopy Studies of Au-Ag Bimetallic Nanoboxes and Nanocages.	Hu M, Chen J, Marquez M, Xia Y, Hartland GV	The journal of physical chemistry. C, Nanomaterials and interfaces	18629346	J Phys Chem C Nanomater Interfaces	2007	https://www.ncbi.nlm.nih.gov/pubmed/18629346
Radiolabeling of Gold Nanocages for Potential Applications in Tracking, Diagnosis, and Image-Guided Therapy.	Qiu J, Liu Y, Xia Y	Advanced healthcare materials	33470560	Adv Healthc Mater	2021 Aug	https://www.ncbi.nlm.nih.gov/pubmed/33470560
Protein capsules with cross-linked, semipermeable, and enzyme-degradable surface barriers for controlled release.	Zhou J, Hyun DC, Liu H, Wu H, Xia Y	Macromolecular rapid communications	24957975	Macromol Rapid Commun	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/24957975
Optical-resolution photoacoustic microscopy for volumetric and spectral analysis of histological and immunochemical samples.	Zhang YS, Yao J, Zhang C, Li L, Wang LV, Xia Y	Angewandte Chemie (International ed. in English)	24961608	Angew Chem Int Ed Engl	2014 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/24961608
Multiple facets for extracellular matrix mimicking in regenerative medicine.	Zhang YS, Xia Y	Nanomedicine (London, England)	25816873	Nanomedicine (Lond)	2015	https://www.ncbi.nlm.nih.gov/pubmed/25816873
Nanomaterial-Enabled Photothermal Heating and Its Use for Cancer Therapy via Localized Hyperthermia.	Shen S, Qiu J, Huo D, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	37803412	Small	2024 Feb	https://www.ncbi.nlm.nih.gov/pubmed/37803412
Fabrication of Microbeads with a Controllable Hollow Interior and Porous Wall Using a Capillary Fluidic Device.	Choi SW, Zhang Y, Xia Y	Advanced functional materials	20191106	Adv Funct Mater	2009 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/20191106
Three-dimensional scaffolds for tissue engineering: the importance of uniformity in pore size and structure.	Choi SW, Zhang Y, Xia Y	Langmuir : the ACS journal of surfaces and colloids	21090781	Langmuir	2010 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/21090781
Noninvasive photoacoustic microscopy of living cells in two and three dimensions through enhancement by a metabolite dye.	Zhang Y, Cai X, Wang Y, Zhang C, Li L, Choi SW, Wang LV, Xia Y	Angewandte Chemie (International ed. in English)	21681876	Angew Chem Int Ed Engl	2011 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/21681876
A temperature-sensitive drug release system based on phase-change materials.	Choi SW, Zhang Y, Xia Y	Angewandte Chemie (International ed. in English)	20839209	Angew Chem Int Ed Engl	2010 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/20839209
Radioluminescent gold nanocages with controlled radioactivity for real-time in vivo imaging.	Wang Y, Liu Y, Luehmann H, Xia X, Wan D, Cutler C, Xia Y	Nano letters	23360442	Nano Lett	2013 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/23360442
Synthesis of Ag nanocubes 18-32 nm in edge length: the effects of polyol on reduction kinetics, size control, and reproducibility.	Wang Y, Zheng Y, Huang CZ, Xia Y	Journal of the American Chemical Society	23317148	J Am Chem Soc	2013 Feb 6	https://www.ncbi.nlm.nih.gov/pubmed/23317148
SV119-gold nanocage conjugates: a new platform for targeting cancer cells via sigma-2 receptors.	Wang Y, Xu J, Xia X, Yang M, Vangveravong S, Chen J, Mach RH, Xia Y	Nanoscale	22113350	Nanoscale	2012 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/22113350
Silver nanocube on gold microplate as a well-defined and highly active substrate for SERS detection.	Xia X, Rycenga M, Qin D, Xia Y	Journal of materials chemistry. C	24187611	J Mater Chem C Mater	2013 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/24187611
Electrospun nanofibers for regenerative medicine.	Liu W, Thomopoulos S, Xia Y	Advanced healthcare materials	23184683	Adv Healthc Mater	2012 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/23184683
Photoacoustic Microscopy in Tissue Engineering.	Cai X, Zhang YS, Xia Y, Wang LV	Materials today (Kidlington, England)	23766667	Mater Today (Kidlington)	2013 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/23766667
Vibrational response of Au-Ag nanoboxes and nanocages to ultrafast laser-induced heating.	Petrova H, Lin CH, Hu M, Chen J, Siekkinen AR, Xia Y, Sader JE, Hartland GV	Nano letters	17358093	Nano Lett	2007 Apr	https://www.ncbi.nlm.nih.gov/pubmed/17358093
Facile synthesis of branched au nanostructures by templating against a self-destructive lattice of magnetic fe nanoparticles.	Li Z, Li W, Camargo PH, Xia Y	Angewandte Chemie (International ed. in English)	18988222	Angew Chem Int Ed Engl	2008	https://www.ncbi.nlm.nih.gov/pubmed/18988222
A Comparative Study of Galvanic Replacement Reactions Involving Ag Nanocubes and AuCl(2) or AuCl(4).	Au L, Lu X, Xia Y	Advanced materials (Deerfield Beach, Fla.)	18725963	Adv Mater	2008	https://www.ncbi.nlm.nih.gov/pubmed/18725963
Tailoring the Optical and Catalytic Properties of Gold-Silver Nanoboxes and Nanocages by Introducing Palladium.	Cobley CM, Campbell DJ, Xia Y	Advanced materials (Deerfield Beach, Fla.)	18568091	Adv Mater	2008 Feb	https://www.ncbi.nlm.nih.gov/pubmed/18568091
Morphological Evolution of Single-Crystal Ag Nanospheres during the Galvanic Replacement Reaction with HAuCl(4).	Kim MH, Lu X, Wiley B, Lee EP, Xia Y	The journal of physical chemistry. C, Nanomaterials and interfaces	18787649	J Phys Chem C Nanomater Interfaces	2008	https://www.ncbi.nlm.nih.gov/pubmed/18787649
Gold nanocages for cancer detection and treatment.	Skrabalak SE, Au L, Lu X, Li X, Xia Y	Nanomedicine (London, England)	17976028	Nanomedicine (Lond)	2007 Oct	https://www.ncbi.nlm.nih.gov/pubmed/17976028
Photoacoustic tomography of a rat cerebral cortex in vivo with au nanocages as an optical contrast agent.	Yang X, Skrabalak SE, Li ZY, Xia Y, Wang LV	Nano letters	18020475	Nano Lett	2007 Dec	https://www.ncbi.nlm.nih.gov/pubmed/18020475
A SERS study of the molecular structure of alkanethiol monolayers on Ag nanocubes in the presence of aqueous glucose.	Rycenga M, McLellan JM, Xia Y	Chemical physics letters	20160847	Chem Phys Lett	2009 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/20160847
In vitro mineralization by preosteoblasts in poly(DL-lactide-co-glycolide) inverse opal scaffolds reinforced with hydroxyapatite nanoparticles.	Choi SW, Zhang Y, Thomopoulos S, Xia Y	Langmuir : the ACS journal of surfaces and colloids	20450216	Langmuir	2010 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/20450216
In vivo molecular photoacoustic tomography of melanomas targeted by bioconjugated gold nanocages.	Kim C, Cho EC, Chen J, Song KH, Au L, Favazza C, Zhang Q, Cobley CM, Gao F, Xia Y, Wang LV	ACS nano	20731439	ACS Nano	2010 Aug 24	https://www.ncbi.nlm.nih.gov/pubmed/20731439
Emerging applications of phase-change materials (PCMs): teaching an old dog new tricks.	Hyun DC, Levinson NS, Jeong U, Xia Y	Angewandte Chemie (International ed. in English)	24470287	Angew Chem Int Ed Engl	2014 Apr 7	https://www.ncbi.nlm.nih.gov/pubmed/24470287
A reactive oxygen species (ROS)-responsive polymer for safe, efficient, and targeted gene delivery in cancer cells.	Shim MS, Xia Y	Angewandte Chemie (International ed. in English)	23716349	Angew Chem Int Ed Engl	2013 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/23716349
Using SV119-gold nanocage conjugates to eradicate cancer stem cells through a combination of photothermal and chemo therapies.	Sun T, Wang Y, Wang Y, Xu J, Zhao X, Vangveravong S, Mach RH, Xia Y	Advanced healthcare materials	24677807	Adv Healthc Mater	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/24677807
Nerve guidance conduits based on double-layered scaffolds of electrospun nanofibers for repairing the peripheral nervous system.	Xie J, MacEwan MR, Liu W, Jesuraj N, Li X, Hunter D, Xia Y	ACS applied materials & interfaces	24806389	ACS Appl Mater Interfaces	2014 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/24806389
Etching and growth: an intertwined pathway to silver nanocrystals with exotic shapes.	Cobley CM, Rycenga M, Zhou F, Li ZY, Xia Y	Angewandte Chemie (International ed. in English)	19479923	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19479923
Preparation of uniform microspheres using a simple fluidic device and their crystallization into close-packed lattices.	Choi SW, Cheong IW, Kim JH, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	19189332	Small	2009 Apr	https://www.ncbi.nlm.nih.gov/pubmed/19189332
Synthesis of gold microplates using bovine serum albumin as a reductant and a stabilizer.	Au L, Lim B, Colletti P, Jun YS, Xia Y	Chemistry, an Asian journal	19967737	Chem Asian J	2010 Jan 4	https://www.ncbi.nlm.nih.gov/pubmed/19967737
Putting Electrospun Nanofibers to Work for Biomedical Research.	Xie J, Li X, Xia Y	Macromolecular rapid communications	20011452	Macromol Rapid Commun	2008 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/20011452
Measuring the surface-enhanced Raman scattering enhancement factors of hot spots formed between an individual Ag nanowire and a single Ag nanocube.	Camargo PH, Cobley CM, Rycenga M, Xia Y	Nanotechnology	19801754	Nanotechnology	2009 Oct 28	https://www.ncbi.nlm.nih.gov/pubmed/19801754
Metal-polymer hybrid colloidal particles with an eccentric structure.	Ohnuma A, Cho EC, Jiang M, Ohtani B, Xia Y	Langmuir : the ACS journal of surfaces and colloids	19621917	Langmuir	2009 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/19621917
Improving biomedical imaging with gold nanocages.	Xia Y, Skrabalak SE	SPIE newsroom	19704778	SPIE Newsroom	2008 May 12	https://www.ncbi.nlm.nih.gov/pubmed/19704778
Fine tuning the optical properties of Au-Ag nanocages by selectively etching Ag with oxygen and a water-soluble thiol.	Cho EC, Cobley CM, Rycenga M, Xia Y	Journal of materials chemistry	19829745	J Mater Chem	2009 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/19829745
Gold Nanocages: A Novel Class of Multifunctional Nanomaterials for Theranostic Applications.	Chen J, Yang M, Zhang Q, Cho EC, Cobley CM, Kim C, Glaus C, Wang LV, Welch MJ, Xia Y	Advanced functional materials	33907543	Adv Funct Mater	2010 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/33907543
Enhancing the Tactile and Near-Infrared Sensing Capabilities of Electrospun PVDF Nanofibers with the Use of Gold Nanocages.	Li H, Wu T, Xie M, Shi Y, Shen S, Zhao M, Yang X, Figueroa-Cosme LM, Ke Q, Xia Y	Journal of materials chemistry. C	30911394	J Mater Chem C Mater	2018 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/30911394
Electrospun Nanofibers: New Concepts, Materials, and Applications.	Xue J, Xie J, Liu W, Xia Y	Accounts of chemical research	28777535	Acc Chem Res	2017 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/28777535
Seeing Through the Surface: Non-invasive Characterization of Biomaterial-Tissue Interactions Using Photoacoustic Microscopy.	Zhang YS, Wang LV, Xia Y	Annals of biomedical engineering	26471785	Ann Biomed Eng	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26471785
Quantitative analysis of the fate of gold nanocages in vitro and in vivo after uptake by U87-MG tumor cells.	Cho EC, Zhang Y, Cai X, Moran CM, Wang LV, Xia Y	Angewandte Chemie (International ed. in English)	23225223	Angew Chem Int Ed Engl	2013 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/23225223
In vivo quantitative evaluation of the transport kinetics of gold nanocages in a lymphatic system by noninvasive photoacoustic tomography.	Cai X, Li W, Kim CH, Yuan Y, Wang LV, Xia Y	ACS nano	22054348	ACS Nano	2011 Dec 27	https://www.ncbi.nlm.nih.gov/pubmed/22054348
Gold nanocages as contrast agents for photoacoustic imaging.	Li W, Brown PK, Wang LV, Xia Y	Contrast media & molecular imaging	22025337	Contrast Media Mol Imaging	2011 Sep-Oct	https://www.ncbi.nlm.nih.gov/pubmed/22025337
Comparison study of gold nanohexapods, nanorods, and nanocages for photothermal cancer treatment.	Wang Y, Black KC, Luehmann H, Li W, Zhang Y, Cai X, Wan D, Liu SY, Li M, Kim P, Li ZY, Wang LV, Liu Y, Xia Y	ACS nano	23383982	ACS Nano	2013 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/23383982
Colloidal hollow spheres of conducting polymers with smooth surface and uniform, controllable sizes.	Bai MY, Cheng YJ, Wickline SA, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	19384880	Small	2009 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/19384880
Chronic label-free volumetric photoacoustic microscopy of melanoma cells in three-dimensional porous scaffolds.	Zhang Y, Cai X, Choi SW, Kim C, Wang LV, Xia Y	Biomaterials	20727581	Biomaterials	2010 Nov	https://www.ncbi.nlm.nih.gov/pubmed/20727581
Uniform beads with controllable pore sizes for biomedical applications.	Choi SW, Yeh YC, Zhang Y, Sung HW, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	20578116	Small	2010 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/20578116
Nanofiber membranes with controllable microwells and structural cues and their use in forming cell microarrays and neuronal networks.	Xie J, Liu W, MacEwan MR, Yeh YC, Thomopoulos S, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	21294253	Small	2011 Feb 7	https://www.ncbi.nlm.nih.gov/pubmed/21294253
Inorganic nanoparticle-based contrast agents for molecular imaging.	Cho EC, Glaus C, Chen J, Welch MJ, Xia Y	Trends in molecular medicine	21074494	Trends Mol Med	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/21074494
Stimuli-Responsive Materials for Controlled Release of Theranostic Agents.	Wang Y, Shim MS, Levinson NS, Sung HW, Xia Y	Advanced functional materials	25477774	Adv Funct Mater	2014 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/25477774
Chitosan-Based Inverse Opals: Three-Dimensional Scaffolds with Uniform Pore Structures for Cell Culture.	Choi SW, Xie J, Xia Y	Advanced materials (Deerfield Beach, Fla.)	19710950	Adv Mater	2009 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/19710950
Total synthesis of the polycyclic fungal metabolite (+/-)-communesin F.	Liu P, Seo JH, Weinreb SM	Angewandte Chemie (International ed. in English)	20175174	Angew Chem Int Ed Engl	2010 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/20175174
Gold nanocages covered by smart polymers for controlled release with near-infrared light.	Yavuz MS, Cheng Y, Chen J, Cobley CM, Zhang Q, Rycenga M, Xie J, Kim C, Song KH, Schwartz AG, Wang LV, Xia Y	Nature materials	19881498	Nat Mater	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19881498
A simple spectroscopic method for differentiating cellular uptakes of gold nanospheres and nanorods from their mixtures.	Cho EC, Liu Y, Xia Y	Angewandte Chemie (International ed. in English)	20146292	Angew Chem Int Ed Engl	2010 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/20146292
The differentiation of embryonic stem cells seeded on electrospun nanofibers into neural lineages.	Xie J, Willerth SM, Li X, Macewan MR, Rader A, Sakiyama-Elbert SE, Xia Y	Biomaterials	18930315	Biomaterials	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/18930315
Dimers of silver nanospheres: facile synthesis and their use as hot spots for surface-enhanced Raman scattering.	Li W, Camargo PH, Lu X, Xia Y	Nano letters	19143509	Nano Lett	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19143509
Facile synthesis of Ag nanocubes and Au nanocages.	Skrabalak SE, Au L, Li X, Xia Y	Nature protocols	17853874	Nat Protoc	2007	https://www.ncbi.nlm.nih.gov/pubmed/17853874
Modifying the pores of an inverse opal scaffold with chitosan microstructures for truly three-dimensional cell culture.	Zhang Y, Choi SW, Xia Y	Macromolecular rapid communications	22231861	Macromol Rapid Commun	2012 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/22231861
The effect of sedimentation and diffusion on cellular uptake of gold nanoparticles.	Cho EC, Zhang Q, Xia Y	Nature nanotechnology	21516092	Nat Nanotechnol	2011 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/21516092
25th anniversary article: galvanic replacement: a simple and versatile route to hollow nanostructures with tunable and well-controlled properties.	Xia X, Wang Y, Ruditskiy A, Xia Y	Advanced materials (Deerfield Beach, Fla.)	24027074	Adv Mater	2013 Nov 26	https://www.ncbi.nlm.nih.gov/pubmed/24027074
Neurite outgrowth on electrospun nanofibers with uniaxial alignment: the effects of fiber density, surface coating, and supporting substrate.	Xie J, Liu W, MacEwan MR, Bridgman PC, Xia Y	ACS nano	24444076	ACS Nano	2014 Feb 25	https://www.ncbi.nlm.nih.gov/pubmed/24444076
Protein-protected Au clusters as a new class of nanoscale biosensor for label-free fluorescence detection of proteases.	Wang Y, Wang Y, Zhou F, Kim P, Xia Y	Small (Weinheim an der Bergstrasse, Germany)	22969016	Small	2012 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/22969016
Recent Developments in Shape-Controlled Synthesis of Silver Nanocrystals.	Xia X, Zeng J, Zhang Q, Moran CH, Xia Y	The journal of physical chemistry. C, Nanomaterials and interfaces	23105955	J Phys Chem C Nanomater Interfaces	2012	https://www.ncbi.nlm.nih.gov/pubmed/23105955
Putting gold nanocages to work for optical imaging, controlled release and cancer theranostics.	Pang B, Yang X, Xia Y	Nanomedicine (London, England)	27348546	Nanomedicine (Lond)	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/27348546
Phase-Change Materials for Controlled Release and Related Applications.	Qiu J, Huo D, Xia Y	Advanced materials (Deerfield Beach, Fla.)	32383215	Adv Mater	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/32383215
Inverse Opal Scaffolds and Their Biomedical Applications.	Zhang YS, Zhu C, Xia Y	Advanced materials (Deerfield Beach, Fla.)	28649794	Adv Mater	2017 Sep	https://www.ncbi.nlm.nih.gov/pubmed/28649794
Design and Fabrication of a Hierarchically Structured Scaffold for Tendon-to-Bone Repair.	Zhu C, Pongkitwitoon S, Qiu J, Thomopoulos S, Xia Y	Advanced materials (Deerfield Beach, Fla.)	29534316	Adv Mater	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29534316
Gold Nanomaterials at Work in Biomedicine.	Yang X, Yang M, Pang B, Vara M, Xia Y	Chemical reviews	26293344	Chem Rev	2015 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/26293344
Protein (19)F NMR in Escherichia coli.	Li C, Wang GF, Wang Y, Creager-Allen R, Lutz EA, Scronce H, Slade KM, Ruf RA, Mehl RA, Pielak GJ	Journal of the American Chemical Society	20050707	J Am Chem Soc	2010 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/20050707
19F NMR studies of alpha-synuclein conformation and fibrillation.	Li C, Lutz EA, Slade KM, Ruf RA, Wang GF, Pielak GJ	Biochemistry	19655784	Biochemistry	2009 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/19655784
Translational and rotational diffusion of a small globular protein under crowded conditions.	Li C, Wang Y, Pielak GJ	The journal of physical chemistry. B	19791823	J Phys Chem B	2009 Oct 8	https://www.ncbi.nlm.nih.gov/pubmed/19791823
Disordered Protein Diffusion under Crowded Conditions.	Wang Y, Benton LA, Singh V, Pielak GJ	The journal of physical chemistry letters	23185649	J Phys Chem Lett	2012 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/23185649
In-cell protein NMR and protein leakage.	Barnes CO, Pielak GJ	Proteins	21120863	Proteins	2011 Feb	https://www.ncbi.nlm.nih.gov/pubmed/21120863
A bioreactor for in-cell protein NMR.	Sharaf NG, Barnes CO, Charlton LM, Young GB, Pielak GJ	Journal of magnetic resonance (San Diego, Calif. : 1997)	19910228	J Magn Reson	2010 Feb	https://www.ncbi.nlm.nih.gov/pubmed/19910228
Alpha-Synuclein conformation affects its tyrosine-dependent oxidative aggregation.	Ruf RA, Lutz EA, Zigoneanu IG, Pielak GJ	Biochemistry	19049426	Biochemistry	2008 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/19049426
Effects of proteins on protein diffusion.	Wang Y, Li C, Pielak GJ	Journal of the American Chemical Society	20560582	J Am Chem Soc	2010 Jul 14	https://www.ncbi.nlm.nih.gov/pubmed/20560582
Volume exclusion and soft interaction effects on protein stability under crowded conditions.	Miklos AC, Li C, Sharaf NG, Pielak GJ	Biochemistry	20672856	Biochemistry	2010 Aug 24	https://www.ncbi.nlm.nih.gov/pubmed/20672856
Probing the micelle-bound aggregation-prone state of α-synuclein with (19)F NMR spectroscopy.	Wang GF, Li C, Pielak GJ	Chembiochem : a European journal of chemical biology	20730847	Chembiochem	2010 Sep 24	https://www.ncbi.nlm.nih.gov/pubmed/20730847
Interaction of α-synuclein and a cell penetrating fusion peptide with higher eukaryotic cell membranes assessed by ¹⁹F NMR.	Zigoneanu IG, Pielak GJ	Molecular pharmaceutics	22376087	Mol Pharm	2012 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/22376087
Effects of recombinant protein expression on green fluorescent protein diffusion in Escherichia coli.	Slade KM, Baker R, Chua M, Thompson NL, Pielak GJ	Biochemistry	19413350	Biochemistry	2009 Jun 16	https://www.ncbi.nlm.nih.gov/pubmed/19413350
Protein nuclear magnetic resonance under physiological conditions.	Pielak GJ, Li C, Miklos AC, Schlesinger AP, Slade KM, Wang GF, Zigoneanu IG	Biochemistry	19113834	Biochemistry	2009 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/19113834
Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy.	Li C, Charlton LM, Lakkavaram A, Seagle C, Wang G, Young GB, Macdonald JM, Pielak GJ	Journal of the American Chemical Society	18419123	J Am Chem Soc	2008 May 21	https://www.ncbi.nlm.nih.gov/pubmed/18419123
Quantifying green fluorescent protein diffusion in Escherichia coli by using continuous photobleaching with evanescent illumination.	Slade KM, Steele BL, Pielak GJ, Thompson NL	The journal of physical chemistry. B	19296673	J Phys Chem B	2009 Apr 9	https://www.ncbi.nlm.nih.gov/pubmed/19296673
Interaction of α-synuclein with vesicles that mimic mitochondrial membranes.	Zigoneanu IG, Yang YJ, Krois AS, Haque E, Pielak GJ	Biochimica et biophysica acta	22155643	Biochim Biophys Acta	2012 Mar	https://www.ncbi.nlm.nih.gov/pubmed/22155643
In situ structural characterization of a recombinant protein in native Escherichia coli membranes with solid-state magic-angle-spinning NMR.	Fu R, Wang X, Li C, Santiago-Miranda AN, Pielak GJ, Tian F	Journal of the American Chemical Society	21774553	J Am Chem Soc	2011 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/21774553
Using NMR to distinguish viscosity effects from nonspecific protein binding under crowded conditions.	Li C, Pielak GJ	Journal of the American Chemical Society	19140727	J Am Chem Soc	2009 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/19140727
Residue-level interrogation of macromolecular crowding effects on protein stability.	Charlton LM, Barnes CO, Li C, Orans J, Young GB, Pielak GJ	Journal of the American Chemical Society	18459780	J Am Chem Soc	2008 May 28	https://www.ncbi.nlm.nih.gov/pubmed/18459780
Macromolecular crowding fails to fold a globular protein in cells.	Schlesinger AP, Wang Y, Tadeo X, Millet O, Pielak GJ	Journal of the American Chemical Society	21534566	J Am Chem Soc	2011 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/21534566
Selective toxin sequestrants for the treatment of bacterial infections.	Simpson LS, Burdine L, Dutta AK, Feranchak AP, Kodadek T	Journal of the American Chemical Society	19351156	J Am Chem Soc	2009 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/19351156
Steroid receptor coactivator-3 expression in lung cancer and its role in the regulation of cancer cell survival and proliferation.	Cai D, Shames DS, Raso MG, Xie Y, Kim YH, Pollack JR, Girard L, Sullivan JP, Gao B, Peyton M, Nanjundan M, Byers L, Heymach J, Mills G, Gazdar AF, Wistuba I, Kodadek T, Minna JD	Cancer research	20663904	Cancer Res	2010 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/20663904
Development of antibody surrogates for the treatment of cancers and autoimmune disease.	Kodadek T	Current opinion in chemical biology	20674470	Curr Opin Chem Biol	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20674470
Potent and selective photo-inactivation of proteins with peptoid-ruthenium conjugates.	Lee J, Udugamasooriya DG, Lim HS, Kodadek T	Nature chemical biology	20228793	Nat Chem Biol	2010 Apr	https://www.ncbi.nlm.nih.gov/pubmed/20228793
Identification of a peptoid inhibitor of the proteasome 19S regulatory particle.	Lim HS, Archer CT, Kodadek T	Journal of the American Chemical Society	17536803	J Am Chem Soc	2007 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/17536803
Periodate-triggered cross-linking reveals Sug2/Rpt4 as the molecular target of a peptoid inhibitor of the 19S proteasome regulatory particle.	Lim HS, Cai D, Archer CT, Kodadek T	Journal of the American Chemical Society	17929816	J Am Chem Soc	2007 Oct 31	https://www.ncbi.nlm.nih.gov/pubmed/17929816
High-throughput evaluation of relative cell permeability between peptoids and peptides.	Tan NC, Yu P, Kwon YU, Kodadek T	Bioorganic & medicinal chemistry	18490170	Bioorg Med Chem	2008 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/18490170
Identification of candidate IgG biomarkers for Alzheimer's disease via combinatorial library screening.	Reddy MM, Wilson R, Wilson J, Connell S, Gocke A, Hynan L, German D, Kodadek T	Cell	21215375	Cell	2011 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/21215375
Synthetic receptors with antibody-like binding affinities.	Kodadek T	Current opinion in chemical biology	20674471	Curr Opin Chem Biol	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20674471
Seamless bead to microarray screening: rapid identification of the highest affinity protein ligands from large combinatorial libraries.	Astle JM, Simpson LS, Huang Y, Reddy MM, Wilson R, Connell S, Wilson J, Kodadek T	Chemistry & biology	20142039	Chem Biol	2010 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/20142039
Isolation of antagonists of antigen-specific autoimmune T cell proliferation.	Gocke AR, Udugamasooriya DG, Archer CT, Lee J, Kodadek T	Chemistry & biology	19942136	Chem Biol	2009 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/19942136
A peptoid antagonist of VEGF receptor 2 recognizes a 'hotspot' in the extracellular domain distinct from the hormone-binding site.	Udugamasooriya DG, Ritchie C, Brekken RA, Kodadek T	Bioorganic & medicinal chemistry	18501615	Bioorg Med Chem	2008 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/18501615
Upregulation of retinal dehydrogenase 2 in alternatively activated macrophages during retinoid-dependent type-2 immunity to helminth infection in mice.	Broadhurst MJ, Leung JM, Lim KC, Girgis NM, Gundra UM, Fallon PG, Premenko-Lanier M, McKerrow JH, McCune JM, Loke P	PLoS pathogens	22927819	PLoS Pathog	2012	https://www.ncbi.nlm.nih.gov/pubmed/22927819
Continuous Antigenic Stimulation of DO11.10 TCR Transgenic Mice in the Presence or Absence of IL-1β: Possible Implications for Mechanisms of T Cell Depletion in HIV Disease.	Ladell K, Hazenberg MD, Fitch M, Emson C, McEvoy-Hein Asgarian BK, Mold JE, Miller C, Busch R, Price DA, Hellerstein MK, McCune JM	Journal of immunology (Baltimore, Md. : 1950)	26416271	J Immunol	2015 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/26416271
Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells.	Bunis DG, Bronevetsky Y, Krow-Lucal E, Bhakta NR, Kim CC, Nerella S, Jones N, Mendoza VF, Bryson YJ, Gern JE, Rutishauser RL, Ye CJ, Sirota M, McCune JM, Burt TD	Cell reports	33406429	Cell Rep	2021 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/33406429
Composition and function of T cell subpopulations are slow to change despite effective antiretroviral treatment of HIV disease.	Emu B, Moretto WJ, Hoh R, Krone M, Martin JN, Nixon DF, Deeks SG, McCune JM	PloS one	24465619	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24465619
Expression of the autoimmune susceptibility gene FcRL3 on human regulatory T cells is associated with dysfunction and high levels of programmed cell death-1.	Swainson LA, Mold JE, Bajpai UD, McCune JM	Journal of immunology (Baltimore, Md. : 1950)	20190142	J Immunol	2010 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/20190142
Design, construction, and validation of a modular library of sequence diversity standards for polymerase chain reaction.	Baum PD, Young JJ, Zhang Q, Kasakow Z, McCune JM	Analytical biochemistry	21111699	Anal Biochem	2011 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/21111699
Correlating cellular and molecular signatures of mucosal immunity that distinguish HIV controllers from noncontrollers.	Loke P, Favre D, Hunt PW, Leung JM, Kanwar B, Martin JN, Deeks SG, McCune JM	Blood	20160163	Blood	2010 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/20160163
Central memory CD8+ T cells appear to have a shorter lifespan and reduced abundance as a function of HIV disease progression.	Ladell K, Hellerstein MK, Cesar D, Busch R, Boban D, McCune JM	Journal of immunology (Baltimore, Md. : 1950)	18523254	J Immunol	2008 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/18523254
Immune activation, CD4+ T cell counts, and viremia exhibit oscillatory patterns over time in patients with highly resistant HIV infection.	Kitchen CM, Yeghiazarian L, Hoh R, McCune JM, Sinclair E, Martin JN, Deeks SG	PloS one	21701594	PLoS One	2011	https://www.ncbi.nlm.nih.gov/pubmed/21701594
Hematopoietic-stem-cell-based gene therapy for HIV disease.	Kiem HP, Jerome KR, Deeks SG, McCune JM	Cell stem cell	22305563	Cell Stem Cell	2012 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/22305563
A role for cytomegalovirus-specific CD4+CX3CR1+ T cells and cytomegalovirus-induced T-cell immunopathology in HIV-associated atherosclerosis.	Sacre K, Hunt PW, Hsue PY, Maidji E, Martin JN, Deeks SG, Autran B, McCune JM	AIDS (London, England)	22313962	AIDS	2012 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/22313962
A functional variant in FCRL3 is associated with higher Fc receptor-like 3 expression on T cell subsets and rheumatoid arthritis disease activity.	Bajpai UD, Swainson LA, Mold JE, Graf JD, Imboden JB, McCune JM	Arthritis and rheumatism	22392608	Arthritis Rheum	2012 Aug	https://www.ncbi.nlm.nih.gov/pubmed/22392608
Evidence for persistent low-level viremia in individuals who control human immunodeficiency virus in the absence of antiretroviral therapy.	Hatano H, Delwart EL, Norris PJ, Lee TH, Dunn-Williams J, Hunt PW, Hoh R, Stramer SL, Linnen JM, McCune JM, Martin JN, Busch MP, Deeks SG	Journal of virology	18945778	J Virol	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/18945778
Maternal alloantigens promote the development of tolerogenic fetal regulatory T cells in utero.	Mold JE, Michaëlsson J, Burt TD, Muench MO, Beckerman KP, Busch MP, Lee TH, Nixon DF, McCune JM	Science (New York, N.Y.)	19056990	Science	2008 Dec 5	https://www.ncbi.nlm.nih.gov/pubmed/19056990
Persistent systemic inflammation and atypical enterocolitis in patients with NEMO syndrome.	Cheng LE, Kanwar B, Tcheurekdjian H, Grenert JP, Muskat M, Heyman MB, McCune JM, Wara DW	Clinical immunology (Orlando, Fla.)	19375390	Clin Immunol	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19375390
Levels of circulating myeloid subpopulations and of heme oxygenase-1 do not predict CD4(+) T cell recovery after the initiation of antiretroviral therapy for HIV disease.	Seu L, Ortiz GM, Burt TD, Deeks SG, Martin JN, McCune JM	AIDS research and therapy	25180041	AIDS Res Ther	2014	https://www.ncbi.nlm.nih.gov/pubmed/25180041
Higher CD27+CD8+ T cells percentages during suppressive antiretroviral therapy predict greater subsequent CD4+ T cell recovery in treated HIV infection.	Seu L, Ortiz GM, Epling L, Sinclair E, Swainson LA, Bajpai UD, Huang Y, Deeks SG, Hunt PW, Martin JN, McCune JM	PloS one	24391889	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24391889
Preclinical evaluation of HIV eradication strategies in the simian immunodeficiency virus-infected rhesus macaque: a pilot study testing inhibition of indoleamine 2,3-dioxygenase.	Dunham RM, Gordon SN, Vaccari M, Piatak M, Huang Y, Deeks SG, Lifson J, Franchini G, McCune JM	AIDS research and human retroviruses	22924680	AIDS Res Hum Retroviruses	2013 Feb	https://www.ncbi.nlm.nih.gov/pubmed/22924680
HIV-specific CD4+ T cells may contribute to viral persistence in HIV controllers.	Hunt PW, Hatano H, Sinclair E, Lee TH, Busch MP, Martin JN, McCune JM, Deeks SG	Clinical infectious diseases : an official publication of the Infectious Diseases Society of America	21245154	Clin Infect Dis	2011 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/21245154
Measurement of absolute T cell receptor rearrangement diversity.	Baum PD, Young JJ, McCune JM	Journal of immunological methods	21385585	J Immunol Methods	2011 May 31	https://www.ncbi.nlm.nih.gov/pubmed/21385585
A randomized, controlled trial of raltegravir intensification in antiretroviral-treated, HIV-infected patients with a suboptimal CD4+ T cell response.	Hatano H, Hayes TL, Dahl V, Sinclair E, Lee TH, Hoh R, Lampiris H, Hunt PW, Palmer S, McCune JM, Martin JN, Busch MP, Shacklett BL, Deeks SG	The Journal of infectious diseases	21402547	J Infect Dis	2011 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/21402547
SIV replication in the infected rhesus macaque is limited by the size of the preexisting TH17 cell compartment.	Hartigan-O'Connor DJ, Abel K, Van Rompay KK, Kanwar B, McCune JM	Science translational medicine	22649090	Sci Transl Med	2012 May 30	https://www.ncbi.nlm.nih.gov/pubmed/22649090
Direct measurement of T-cell receptor repertoire diversity with AmpliCot.	Baum PD, McCune JM	Nature methods	17060913	Nat Methods	2006 Nov	https://www.ncbi.nlm.nih.gov/pubmed/17060913
Increased circulating interleukin-7 levels in HIV-1-infected women.	Napolitano LA, Burt TD, Bacchetti P, Barrón Y, French AL, Kovacs A, Anastos K, Young M, McCune JM, Greenblatt RM	Journal of acquired immune deficiency syndromes (1999)	16284535	J Acquir Immune Defic Syndr	2005 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/16284535
IL-22+ CD4+ T cells are associated with therapeutic trichuris trichiura infection in an ulcerative colitis patient.	Broadhurst MJ, Leung JM, Kashyap V, McCune JM, Mahadevan U, McKerrow JH, Loke P	Science translational medicine	21123809	Sci Transl Med	2010 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/21123809
Naive human T cells are activated and proliferate in response to the heme oxygenase-1 inhibitor tin mesoporphyrin.	Burt TD, Seu L, Mold JE, Kappas A, McCune JM	Journal of immunology (Baltimore, Md. : 1950)	20921523	J Immunol	2010 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/20921523
Transcriptional profiling in pathogenic and non-pathogenic SIV infections reveals significant distinctions in kinetics and tissue compartmentalization.	Lederer S, Favre D, Walters KA, Proll S, Kanwar B, Kasakow Z, Baskin CR, Palermo R, McCune JM, Katze MG	PLoS pathogens	19214219	PLoS Pathog	2009 Feb	https://www.ncbi.nlm.nih.gov/pubmed/19214219
Suberoylanilide hydroxamic acid reactivates HIV from latently infected cells.	Contreras X, Schweneker M, Chen CS, McCune JM, Deeks SG, Martin J, Peterlin BM	The Journal of biological chemistry	19136668	J Biol Chem	2009 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/19136668
IFN-alpha-induced upregulation of CCR5 leads to expanded HIV tropism in vivo.	Stoddart CA, Keir ME, McCune JM	PLoS pathogens	20174557	PLoS Pathog	2010 Feb 19	https://www.ncbi.nlm.nih.gov/pubmed/20174557
Analysis of maternal microchimerism in rhesus monkeys (Macaca mulatta) using real-time quantitative PCR amplification of MHC polymorphisms.	Bakkour S, Baker CA, Tarantal AF, Wen L, Busch MP, Lee TH, McCune JM	Chimerism	24451553	Chimerism	2014 Jan-Mar	https://www.ncbi.nlm.nih.gov/pubmed/24451553
Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon.	Broadhurst MJ, Ardeshir A, Kanwar B, Mirpuri J, Gundra UM, Leung JM, Wiens KE, Vujkovic-Cvijin I, Kim CC, Yarovinsky F, Lerche NW, McCune JM, Loke P	PLoS pathogens	23166490	PLoS Pathog	2012	https://www.ncbi.nlm.nih.gov/pubmed/23166490
Cytotrophoblast induction of arterial apoptosis and lymphangiogenesis in an in vivo model of human placentation.	Red-Horse K, Rivera J, Schanz A, Zhou Y, Winn V, Kapidzic M, Maltepe E, Okazaki K, Kochman R, Vo KC, Giudice L, Erlebacher A, McCune JM, Stoddart CA, Fisher SJ	The Journal of clinical investigation	16998586	J Clin Invest	2006 Oct	https://www.ncbi.nlm.nih.gov/pubmed/16998586
Gag p27-specific B- and T-cell responses in Simian immunodeficiency virus SIVagm-infected African green monkeys.	Lozano Reina JM, Favre D, Kasakow Z, Mayau V, Nugeyre MT, Ka T, Faye A, Miller CJ, Scott-Algara D, McCune JM, Barré-Sinoussi F, Diop OM, Müller-Trutwin MC	Journal of virology	19109377	J Virol	2009 Mar	https://www.ncbi.nlm.nih.gov/pubmed/19109377
Human CD4+ regulatory T cells express lower levels of the IL-7 receptor alpha chain (CD127), allowing consistent identification and sorting of live cells.	Hartigan-O'Connor DJ, Poon C, Sinclair E, McCune JM	Journal of immunological methods	17173927	J Immunol Methods	2007 Jan 30	https://www.ncbi.nlm.nih.gov/pubmed/17173927
Loss of T cell responses following long-term cryopreservation.	Owen RE, Sinclair E, Emu B, Heitman JW, Hirschkorn DF, Epling CL, Tan QX, Custer B, Harris JM, Jacobson MA, McCune JM, Martin JN, Hecht FM, Deeks SG, Norris PJ	Journal of immunological methods	17707394	J Immunol Methods	2007 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/17707394
In vivo imaging of mucosal CD4+ T cells using single photon emission computed tomography in a murine model of colitis.	Kanwar B, Gao DW, Hwang AB, Grenert JP, Williams SP, Franc B, McCune JM	Journal of immunological methods	17964595	J Immunol Methods	2008 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/17964595
CD57(+) Memory T Cells Proliferate In Vivo.	Ahmed R, Miners KL, Lahoz-Beneytez J, Jones RE, Roger L, Baboonian C, Zhang Y, Wang ECY, Hellerstein MK, McCune JM, Baird DM, Price DA, Macallan DC, Asquith B, Ladell K	Cell reports	33326780	Cell Rep	2020 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/33326780
Rooted in risk: genetic predisposition for low-density lipoprotein cholesterol level associates with diminished low-density lipoprotein cholesterol response to statin treatment.	Smit RA, Postmus I, Trompet S, Barnes MR, Warren H, Arsenault BJ, Chasman DI, Cupples LA, Hitman GA, Krauss RM, Li X, Psaty BM, Stein CM, Rotter JI, Jukema JW	Pharmacogenomics	27648687	Pharmacogenomics	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27648687
Exposure to SIV in utero results in reduced viral loads and altered responsiveness to postnatal challenge.	Baker CA, Swainson L, Lin DL, Wong S, Hartigan-O'Connor DJ, Lifson JD, Tarantal AF, McCune JM	Science translational medicine	26268312	Sci Transl Med	2015 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/26268312
Abacavir increases platelet reactivity via competitive inhibition of soluble guanylyl cyclase.	Baum PD, Sullam PM, Stoddart CA, McCune JM	AIDS (London, England)	21941165	AIDS	2011 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/21941165
The role of transplacental microtransfusions of maternal lymphocytes in in utero HIV transmission.	Lee TH, Chafets DM, Biggar RJ, McCune JM, Busch MP	Journal of acquired immune deficiency syndromes (1999)	20683195	J Acquir Immune Defic Syndr	2010 Oct	https://www.ncbi.nlm.nih.gov/pubmed/20683195
Prevalence of CXCR4 tropism among antiretroviral-treated HIV-1-infected patients with detectable viremia.	Hunt PW, Harrigan PR, Huang W, Bates M, Williamson DW, McCune JM, Price RW, Spudich SS, Lampiris H, Hoh R, Leigler T, Martin JN, Deeks SG	The Journal of infectious diseases	16960780	J Infect Dis	2006 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/16960780
Increased carotid intima-media thickness in HIV patients is associated with increased cytomegalovirus-specific T-cell responses.	Hsue PY, Hunt PW, Sinclair E, Bredt B, Franklin A, Killian M, Hoh R, Martin JN, McCune JM, Waters DD, Deeks SG	AIDS (London, England)	17117013	AIDS	2006 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/17117013
Cytomegalovirus-specific T cells persist at very high levels during long-term antiretroviral treatment of HIV disease.	Naeger DM, Martin JN, Sinclair E, Hunt PW, Bangsberg DR, Hecht F, Hsue P, McCune JM, Deeks SG	PloS one	20126452	PLoS One	2010 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/20126452
Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism.	Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M, Deeks SG, Hunt PW, Lynch SV, McCune JM	Science translational medicine	23843452	Sci Transl Med	2013 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/23843452
IL-7 production in murine lymphatic endothelial cells and induction in the setting of peripheral lymphopenia.	Miller CN, Hartigan-O'Connor DJ, Lee MS, Laidlaw G, Cornelissen IP, Matloubian M, Coughlin SR, McDonald DM, McCune JM	International immunology	23657000	Int Immunol	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23657000
Hydroxychloroquine is associated with impaired interferon-alpha and tumor necrosis factor-alpha production by plasmacytoid dendritic cells in systemic lupus erythematosus.	Sacre K, Criswell LA, McCune JM	Arthritis research & therapy	22734582	Arthritis Res Ther	2012 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/22734582
Fetal and adult hematopoietic stem cells give rise to distinct T cell lineages in humans.	Mold JE, Venkatasubrahmanyam S, Burt TD, Michaëlsson J, Rivera JM, Galkina SA, Weinberg K, Stoddart CA, McCune JM	Science (New York, N.Y.)	21164017	Science	2010 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/21164017
Suppression of SIV-specific CD4+ T cells by infant but not adult macaque regulatory T cells: implications for SIV disease progression.	Hartigan-O'Connor DJ, Abel K, McCune JM	The Journal of experimental medicine	17954571	J Exp Med	2007 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/17954571
Growth hormone enhances thymic function in HIV-1-infected adults.	Napolitano LA, Schmidt D, Gotway MB, Ameli N, Filbert EL, Ng MM, Clor JL, Epling L, Sinclair E, Baum PD, Li K, Killian ML, Bacchetti P, McCune JM	The Journal of clinical investigation	18292808	J Clin Invest	2008 Mar	https://www.ncbi.nlm.nih.gov/pubmed/18292808
Relationship between T cell activation and CD4+ T cell count in HIV-seropositive individuals with undetectable plasma HIV RNA levels in the absence of therapy.	Hunt PW, Brenchley J, Sinclair E, McCune JM, Roland M, Page-Shafer K, Hsue P, Emu B, Krone M, Lampiris H, Douek D, Martin JN, Deeks SG	The Journal of infectious diseases	18171295	J Infect Dis	2008 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/18171295
HIV-induced changes in T cell signaling pathways.	Schweneker M, Favre D, Martin JN, Deeks SG, McCune JM	Journal of immunology (Baltimore, Md. : 1950)	18453567	J Immunol	2008 May 15	https://www.ncbi.nlm.nih.gov/pubmed/18453567
Identification of cinnabarinic acid as a novel endogenous aryl hydrocarbon receptor ligand that drives IL-22 production.	Lowe MM, Mold JE, Kanwar B, Huang Y, Louie A, Pollastri MP, Wang C, Patel G, Franks DG, Schlezinger J, Sherr DH, Silverstone AE, Hahn ME, McCune JM	PloS one	24498387	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24498387
IL-2 production correlates with effector cell differentiation in HIV-specific CD8+ T cells.	Nomura LE, Emu B, Hoh R, Haaland P, Deeks SG, Martin JN, McCune JM, Nixon DF, Maecker HT	AIDS research and therapy	16859558	AIDS Res Ther	2006 Jul 21	https://www.ncbi.nlm.nih.gov/pubmed/16859558
Antiviral antibodies are necessary for control of simian immunodeficiency virus replication.	Miller CJ, Genescà M, Abel K, Montefiori D, Forthal D, Bost K, Li J, Favre D, McCune JM	Journal of virology	17329327	J Virol	2007 May	https://www.ncbi.nlm.nih.gov/pubmed/17329327
Regulation of T cell responses in the developing human fetus.	Michaëlsson J, Mold JE, McCune JM, Nixon DF	Journal of immunology (Baltimore, Md. : 1950)	16670279	J Immunol	2006 May 15	https://www.ncbi.nlm.nih.gov/pubmed/16670279
Tim-3 expression defines a novel population of dysfunctional T cells with highly elevated frequencies in progressive HIV-1 infection.	Jones RB, Ndhlovu LC, Barbour JD, Sheth PM, Jha AR, Long BR, Wong JC, Satkunarajah M, Schweneker M, Chapman JM, Gyenes G, Vali B, Hyrcza MD, Yue FY, Kovacs C, Sassi A, Loutfy M, Halpenny R, Persad D, Spotts G, Hecht FM, Chun TW, McCune JM, Kaul R, Rini JM, Nixon DF, Ostrowski MA	The Journal of experimental medicine	19001139	J Exp Med	2008 Nov 24	https://www.ncbi.nlm.nih.gov/pubmed/19001139
Blood T-cell receptor diversity decreases during the course of HIV infection, but the potential for a diverse repertoire persists.	Baum PD, Young JJ, Schmidt D, Zhang Q, Hoh R, Busch M, Martin J, Deeks S, McCune JM	Blood	22371879	Blood	2012 Apr 12	https://www.ncbi.nlm.nih.gov/pubmed/22371879
Cell-based measures of viral persistence are associated with immune activation and programmed cell death protein 1 (PD-1)-expressing CD4+ T cells.	Hatano H, Jain V, Hunt PW, Lee TH, Sinclair E, Do TD, Hoh R, Martin JN, McCune JM, Hecht F, Busch MP, Deeks SG	The Journal of infectious diseases	23089590	J Infect Dis	2013 Jul	https://www.ncbi.nlm.nih.gov/pubmed/23089590
HIV disease progression correlates with the generation of dysfunctional naive CD8(low) T cells.	Favre D, Stoddart CA, Emu B, Hoh R, Martin JN, Hecht FM, Deeks SG, McCune JM	Blood	21200021	Blood	2011 Feb 17	https://www.ncbi.nlm.nih.gov/pubmed/21200021
A low T regulatory cell response may contribute to both viral control and generalized immune activation in HIV controllers.	Hunt PW, Landay AL, Sinclair E, Martinson JA, Hatano H, Emu B, Norris PJ, Busch MP, Martin JN, Brooks C, McCune JM, Deeks SG	PloS one	21305005	PLoS One	2011 Jan 31	https://www.ncbi.nlm.nih.gov/pubmed/21305005
Tryptophan catabolism by indoleamine 2,3-dioxygenase 1 alters the balance of TH17 to regulatory T cells in HIV disease.	Favre D, Mold J, Hunt PW, Kanwar B, Loke P, Seu L, Barbour JD, Lowe MM, Jayawardene A, Aweeka F, Huang Y, Douek DC, Brenchley JM, Martin JN, Hecht FM, Deeks SG, McCune JM	Science translational medicine	20484731	Sci Transl Med	2010 May 19	https://www.ncbi.nlm.nih.gov/pubmed/20484731
Critical loss of the balance between Th17 and T regulatory cell populations in pathogenic SIV infection.	Favre D, Lederer S, Kanwar B, Ma ZM, Proll S, Kasakow Z, Mold J, Swainson L, Barbour JD, Baskin CR, Palermo R, Pandrea I, Miller CJ, Katze MG, McCune JM	PLoS pathogens	19214220	PLoS Pathog	2009 Feb	https://www.ncbi.nlm.nih.gov/pubmed/19214220
Variations in the heme oxygenase-1 microsatellite polymorphism are associated with plasma CD14 and viral load in HIV-infected African-Americans.	Seu L, Burt TD, Witte JS, Martin JN, Deeks SG, McCune JM	Genes and immunity	22048453	Genes Immun	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22048453
Breaking free of sample size dogma to perform innovative translational research.	Bacchetti P, Deeks SG, McCune JM	Science translational medicine	21677197	Sci Transl Med	2011 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/21677197
On-wire lithography: synthesis, encoding and biological applications.	Banholzer MJ, Qin L, Millstone JE, Osberg KD, Mirkin CA	Nature protocols	19444241	Nat Protoc	2009	https://www.ncbi.nlm.nih.gov/pubmed/19444241
Multiplexed protein arrays enabled by polymer pen lithography: addressing the inking challenge.	Zheng Z, Daniel WL, Giam LR, Huo F, Senesi AJ, Zheng G, Mirkin CA	Angewandte Chemie (International ed. in English)	19731290	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19731290
Aptamer nano-flares for molecular detection in living cells.	Zheng D, Seferos DS, Giljohann DA, Patel PC, Mirkin CA	Nano letters	19645478	Nano Lett	2009 Sep	https://www.ncbi.nlm.nih.gov/pubmed/19645478
Establishing the design rules for DNA-mediated programmable colloidal crystallization.	Macfarlane RJ, Jones MR, Senesi AJ, Young KL, Lee B, Wu J, Mirkin CA	Angewandte Chemie (International ed. in English)	20486143	Angew Chem Int Ed Engl	2010 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/20486143
Fluorescence recovery assay for the detection of protein-DNA binding.	Xu X, Zhao Z, Qin L, Wei W, Levine JE, Mirkin CA	Analytical chemistry	18498181	Anal Chem	2008 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/18498181
Polyvalent DNA nanoparticle conjugates stabilize nucleic acids.	Seferos DS, Prigodich AE, Giljohann DA, Patel PC, Mirkin CA	Nano letters	19099465	Nano Lett	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19099465
The role radius of curvature plays in thiolated oligonucleotide loading on gold nanoparticles.	Hill HD, Millstone JE, Banholzer MJ, Mirkin CA	ACS nano	19236080	ACS Nano	2009 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/19236080
Templated spherical high density lipoprotein nanoparticles.	Thaxton CS, Daniel WL, Giljohann DA, Thomas AD, Mirkin CA	Journal of the American Chemical Society	19133723	J Am Chem Soc	2009 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/19133723
Polymer pen lithography.	Huo F, Zheng Z, Zheng G, Giam LR, Zhang H, Mirkin CA	Science (New York, N.Y.)	18703709	Science	2008 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/18703709
PCR-like cascade reactions in the context of an allosteric enzyme mimic.	Yoon HJ, Mirkin CA	Journal of the American Chemical Society	18681433	J Am Chem Soc	2008 Sep 3	https://www.ncbi.nlm.nih.gov/pubmed/18681433
Silver nanoparticle-oligonucleotide conjugates based on DNA with triple cyclic disulfide moieties.	Lee JS, Lytton-Jean AK, Hurst SJ, Mirkin CA	Nano letters	17571909	Nano Lett	2007 Jul	https://www.ncbi.nlm.nih.gov/pubmed/17571909
Nano-flares: probes for transfection and mRNA detection in living cells.	Seferos DS, Giljohann DA, Hill HD, Prigodich AE, Mirkin CA	Journal of the American Chemical Society	18034495	J Am Chem Soc	2007 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/18034495
Microarray detection of duplex and triplex DNA binders with DNA-modified gold nanoparticles.	Lytton-Jean AK, Han MS, Mirkin CA	Analytical chemistry	17614366	Anal Chem	2007 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/17614366
Topographically flat, chemically patterned PDMS stamps made by dip-pen nanolithography.	Zheng Z, Jang JW, Zheng G, Mirkin CA	Angewandte Chemie (International ed. in English)	19012308	Angew Chem Int Ed Engl	2008	https://www.ncbi.nlm.nih.gov/pubmed/19012308
Redox-activating dip-pen nanolithography (RA-DPN).	Braunschweig AB, Senesi AJ, Mirkin CA	Journal of the American Chemical Society	19128060	J Am Chem Soc	2009 Jan 28	https://www.ncbi.nlm.nih.gov/pubmed/19128060
Curvature-induced base pair "slipping" effects in DNA-nanoparticle hybridization.	Hill HD, Hurst SJ, Mirkin CA	Nano letters	19072317	Nano Lett	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19072317
Oligonucleotide loading determines cellular uptake of DNA-modified gold nanoparticles.	Giljohann DA, Seferos DS, Patel PC, Millstone JE, Rosi NL, Mirkin CA	Nano letters	17997588	Nano Lett	2007 Dec	https://www.ncbi.nlm.nih.gov/pubmed/17997588
Nano-flares for mRNA regulation and detection.	Prigodich AE, Seferos DS, Massich MD, Giljohann DA, Lane BC, Mirkin CA	ACS nano	19702321	ACS Nano	2009 Aug 25	https://www.ncbi.nlm.nih.gov/pubmed/19702321
Pyrene-Appended Fluorescent Tweezers Generated via the Weak-Link Approach and Their Halide Recognition Properties.	Jeon YM, Kim D, Mirkin CA, Golen JA, Rheingold AL	Tetrahedron	22180669	Tetrahedron	2008 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/22180669
Asymmetric functionalization of gold nanoparticles with oligonucleotides.	Xu X, Rosi NL, Wang Y, Huo F, Mirkin CA	Journal of the American Chemical Society	16848436	J Am Chem Soc	2006 Jul 26	https://www.ncbi.nlm.nih.gov/pubmed/16848436
Multipole plasmon resonances in gold nanorods.	Payne EK, Shuford KL, Park S, Schatz GC, Mirkin CA	The journal of physical chemistry. B	16471797	J Phys Chem B	2006 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/16471797
Thermodynamically controlled separation of polyvalent 2-nm gold nanoparticle-oligonucleotide conjugates.	Lee JS, Seferos DS, Giljohann DA, Mirkin CA	Journal of the American Chemical Society	18370386	J Am Chem Soc	2008 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/18370386
Polyethylene glycol as a novel resist and sacrificial material for generating positive and negative nanostructures.	Sanedrin RG, Huang L, Jang JW, Kakkassery J, Mirkin CA	Small (Weinheim an der Bergstrasse, Germany)	18563746	Small	2008 Jul	https://www.ncbi.nlm.nih.gov/pubmed/18563746
Iodide ions control seed-mediated growth of anisotropic gold nanoparticles.	Millstone JE, Wei W, Jones MR, Yoo H, Mirkin CA	Nano letters	18642955	Nano Lett	2008 Aug	https://www.ncbi.nlm.nih.gov/pubmed/18642955
Cellular response of polyvalent oligonucleotide-gold nanoparticle conjugates.	Massich MD, Giljohann DA, Schmucker AL, Patel PC, Mirkin CA	ACS nano	20860397	ACS Nano	2010 Oct 26	https://www.ncbi.nlm.nih.gov/pubmed/20860397
Colorimetric Cu(2+) detection using DNA-modified gold-nanoparticle aggregates as probes and click chemistry.	Xu X, Daniel WL, Wei W, Mirkin CA	Small (Weinheim an der Bergstrasse, Germany)	20108231	Small	2010 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/20108231
DNA-gold triangular nanoprism conjugates.	Millstone JE, Georganopoulou DG, Xu X, Wei W, Li S, Mirkin CA	Small (Weinheim an der Bergstrasse, Germany)	19016498	Small	2008 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19016498
"Three-dimensional hybridization" with polyvalent DNA-gold nanoparticle conjugates.	Hurst SJ, Hill HD, Mirkin CA	Journal of the American Chemical Society	18710229	J Am Chem Soc	2008 Sep 10	https://www.ncbi.nlm.nih.gov/pubmed/18710229
Surface plasmon-mediated energy transfer in heterogap Au-Ag nanowires.	Wei W, Li S, Qin L, Xue C, Millstone JE, Xu X, Schatz GC, Mirkin CA	Nano letters	18767888	Nano Lett	2008 Oct	https://www.ncbi.nlm.nih.gov/pubmed/18767888
In-wire conversion of a metal nanorod segment into an organic semiconductor.	Chen X, Zheng G, Cutler JI, Jang JW, Mirkin CA	Small (Weinheim an der Bergstrasse, Germany)	19387988	Small	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19387988
Regulating immune response using polyvalent nucleic acid-gold nanoparticle conjugates.	Massich MD, Giljohann DA, Seferos DS, Ludlow LE, Horvath CM, Mirkin CA	Molecular pharmaceutics	19810673	Mol Pharm	2009 Nov-Dec	https://www.ncbi.nlm.nih.gov/pubmed/19810673
On-wire lithography-generated molecule-based transport junctions: a new testbed for molecular electronics.	Chen X, Jeon YM, Jang JW, Qin L, Huo F, Wei W, Mirkin CA	Journal of the American Chemical Society	18528994	J Am Chem Soc	2008 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/18528994
Separation of tricomponent protein mixtures with triblock nanorods.	Oh BK, Park S, Millstone JE, Lee SW, Lee KB, Mirkin CA	Journal of the American Chemical Society	16953622	J Am Chem Soc	2006 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/16953622
Mechanistic study of photomediated triangular silver nanoprism growth.	Xue C, Métraux GS, Millstone JE, Mirkin CA	Journal of the American Chemical Society	18533653	J Am Chem Soc	2008 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/18533653
Triple-Decker Complexes Formed via the Weak Link Approach.	Jeon YM, Heo J, Brown AM, Mirkin CA	Organometallics	19060957	Organometallics	2006 May 22	https://www.ncbi.nlm.nih.gov/pubmed/19060957
Supramolecular allosteric cofacial porphyrin complexes.	Oliveri CG, Gianneschi NC, Nguyen ST, Mirkin CA, Stern CL, Wawrzak Z, Pink M	Journal of the American Chemical Society	17165783	J Am Chem Soc	2006 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/17165783
Maximizing DNA loading on a range of gold nanoparticle sizes.	Hurst SJ, Lytton-Jean AK, Mirkin CA	Analytical chemistry	17165821	Anal Chem	2006 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/17165821
A gold nanoparticle based approach for screening triplex DNA binders.	Han MS, Lytton-Jean AK, Mirkin CA	Journal of the American Chemical Society	16608320	J Am Chem Soc	2006 Apr 19	https://www.ncbi.nlm.nih.gov/pubmed/16608320
Inversion of product selectivity in an enzyme-inspired metallosupramolecular tweezer catalyzed epoxidation reaction.	Ulmann PA, Braunschweig AB, Lee OS, Wiester MJ, Schatz GC, Mirkin CA	Chemical communications (Cambridge, England)	20448966	Chem Commun (Camb)	2009 Sep 14	https://www.ncbi.nlm.nih.gov/pubmed/20448966
Plasmon-mediated synthesis of silver triangular bipyramids.	Zhang J, Li S, Wu J, Schatz GC, Mirkin CA	Angewandte Chemie (International ed. in English)	19760687	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19760687
Carborane-based pincers: synthesis and structure of SeBSe and SBS Pd(II) complexes.	Spokoyny AM, Reuter MG, Stern CL, Ratner MA, Seideman T, Mirkin CA	Journal of the American Chemical Society	19583431	J Am Chem Soc	2009 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/19583431
Gold nanoparticles for biology and medicine.	Giljohann DA, Seferos DS, Daniel WL, Massich MD, Patel PC, Mirkin CA	Angewandte Chemie (International ed. in English)	20401880	Angew Chem Int Ed Engl	2010 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/20401880
Dynamic interconversion of amorphous microparticles and crystalline rods in salen-based homochiral infinite coordination polymers.	Jeon YM, Heo J, Mirkin CA	Journal of the American Chemical Society	17523645	J Am Chem Soc	2007 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/17523645
Heteroligated supramolecular coordination complexes formed via the halide-induced ligand rearrangement reaction.	Oliveri CG, Ulmann PA, Wiester MJ, Mirkin CA	Accounts of chemical research	18642933	Acc Chem Res	2008 Dec	https://www.ncbi.nlm.nih.gov/pubmed/18642933
Complementary electrical and spectroscopic detection assays with on-wire-lithography-based nanostructures.	Zheng G, Chen X, Mirkin CA	Small (Weinheim an der Bergstrasse, Germany)	19697306	Small	2009 Nov	https://www.ncbi.nlm.nih.gov/pubmed/19697306
Surprisingly long-range surface-enhanced Raman scattering (SERS) on Au-Ni multisegmented nanowires.	Wei W, Li S, Millstone JE, Banholzer MJ, Chen X, Xu X, Schatz GC, Mirkin CA	Angewandte Chemie (International ed. in English)	19431164	Angew Chem Int Ed Engl	2009	https://www.ncbi.nlm.nih.gov/pubmed/19431164
A self-correcting inking strategy for cantilever arrays addressed by an inkjet printer and used for dip-pen nanolithography.	Wang Y, Giam LR, Park M, Lenhert S, Fuchs H, Mirkin CA	Small (Weinheim an der Bergstrasse, Germany)	18654990	Small	2008 Oct	https://www.ncbi.nlm.nih.gov/pubmed/18654990
Dip-pen nanolithography of high-melting-temperature molecules.	Huang L, Chang YH, Kakkassery JJ, Mirkin CA	The journal of physical chemistry. B	17048882	J Phys Chem B	2006 Oct 26	https://www.ncbi.nlm.nih.gov/pubmed/17048882
Nonenzymatic detection of bacterial genomic DNA using the bio bar code assay.	Hill HD, Vega RA, Mirkin CA	Analytical chemistry	17927207	Anal Chem	2007 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/17927207
Plasmonic focusing in rod-sheath heteronanostructures.	Chen X, Li S, Xue C, Banholzer MJ, Schatz GC, Mirkin CA	ACS nano	19206253	ACS Nano	2009 Jan 27	https://www.ncbi.nlm.nih.gov/pubmed/19206253
Controlling the lattice parameters of gold nanoparticle FCC crystals with duplex DNA linkers.	Hill HD, Macfarlane RJ, Senesi AJ, Lee B, Park SY, Mirkin CA	Nano letters	18572967	Nano Lett	2008 Aug	https://www.ncbi.nlm.nih.gov/pubmed/18572967
Gene regulation with polyvalent siRNA-nanoparticle conjugates.	Giljohann DA, Seferos DS, Prigodich AE, Patel PC, Mirkin CA	Journal of the American Chemical Society	19170493	J Am Chem Soc	2009 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/19170493
Tröger's-base-derived infinite co-ordination polymer microparticles.	Jeon YM, Armatas GS, Kim D, Kanatzidis MG, Mirkin CA	Small (Weinheim an der Bergstrasse, Germany)	19058289	Small	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19058289
Plasmonically controlled nucleic acid dehybridization with gold nanoprisms.	Jones MR, Millstone JE, Giljohann DA, Seferos DS, Young KL, Mirkin CA	Chemphyschem : a European journal of chemical physics and physical chemistry	19431161	Chemphyschem	2009 Jul 13	https://www.ncbi.nlm.nih.gov/pubmed/19431161
An Electrochemical Approach to and the Physical Consequences of Preparing Nanostructures from Gold Nanorods with Smooth Ends.	Banholzer MJ, Li S, Ketter JB, Rozkiewicz DI, Schatz GC, Mirkin CA	The journal of physical chemistry. C, Nanomaterials and interfaces	22180788	J Phys Chem C Nanomater Interfaces	2008 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/22180788
Nanodisk codes.	Qin L, Banholzer MJ, Millstone JE, Mirkin CA	Nano letters	18041858	Nano Lett	2007 Dec	https://www.ncbi.nlm.nih.gov/pubmed/18041858
A new approach to amplified telomerase detection with polyvalent oligonucleotide nanoparticle conjugates.	Zheng G, Daniel WL, Mirkin CA	Journal of the American Chemical Society	18597453	J Am Chem Soc	2008 Jul 30	https://www.ncbi.nlm.nih.gov/pubmed/18597453
Amorphous Infinite Coordination Polymer Microparticles: A New Class of Selective Hydrogen Storage Materials.	Jeon YM, Armatas GS, Heo J, Kanatzidis MG, Mirkin CA	Advanced materials (Deerfield Beach, Fla.)	34539086	Adv Mater	2008 Jun 4	https://www.ncbi.nlm.nih.gov/pubmed/34539086
Reversible Ligand Pairing and Sorting Processes Leading to Heteroligated Palladium(II) Complexes with Hemilabile Ligands.	Ulmann PA, Mirkin CA, DiPasquale AG, Liable-Sands LM, Rheingold AL	Organometallics	34446977	Organometallics	2009 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/34446977
Core-shell triangular bifrustums.	Yoo H, Millstone JE, Li S, Jang JW, Wei W, Wu J, Schatz GC, Mirkin CA	Nano letters	19603815	Nano Lett	2009 Aug	https://www.ncbi.nlm.nih.gov/pubmed/19603815
Water-soluble macrocycles synthesized via the weak-link approach.	Wiester MJ, Mirkin CA	Inorganic chemistry	19637852	Inorg Chem	2009 Sep 7	https://www.ncbi.nlm.nih.gov/pubmed/19637852
Stochastic protein expression in individual cells at the single molecule level.	Cai L, Friedman N, Xie XS	Nature	16541077	Nature	2006 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/16541077
Chemically specific imaging of cryptosporidium oocysts using coherent anti-Stokes Raman scattering (CARS) microscopy.	Murugkar S, Evans CL, Xie XS, Anis H	Journal of microscopy	19220690	J Microsc	2009 Feb	https://www.ncbi.nlm.nih.gov/pubmed/19220690
Mechanism of transcriptional bursting in bacteria.	Chong S, Chen C, Ge H, Xie XS	Cell	25036631	Cell	2014 Jul 17	https://www.ncbi.nlm.nih.gov/pubmed/25036631
Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: II. adenovirus proteinase is activated in an unusual one-dimensional biochemical reaction.	Graziano V, Luo G, Blainey PC, Pérez-Berná AJ, McGrath WJ, Flint SJ, San Martín C, Xie XS, Mangel WF	The Journal of biological chemistry	23043137	J Biol Chem	2013 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/23043137
A stochastic single-molecule event triggers phenotype switching of a bacterial cell.	Choi PJ, Cai L, Frieda K, Xie XS	Science (New York, N.Y.)	18927393	Science	2008 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/18927393
Probing transcription factor dynamics at the single-molecule level in a living cell.	Elf J, Li GW, Xie XS	Science (New York, N.Y.)	17525339	Science	2007 May 25	https://www.ncbi.nlm.nih.gov/pubmed/17525339
Probing dynein and kinesin stepping with mechanical manipulation in a living cell.	Sims PA, Xie XS	Chemphyschem : a European journal of chemical physics and physical chemistry	19504528	Chemphyschem	2009 Jul 13	https://www.ncbi.nlm.nih.gov/pubmed/19504528
Central dogma at the single-molecule level in living cells.	Li GW, Xie XS	Nature	21776076	Nature	2011 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/21776076
Modeling spatial correlation of DNA deformation: DNA allostery in protein binding.	Xu X, Ge H, Gu C, Gao YQ, Wang SS, Thio BJ, Hynes JT, Xie XS, Cao J	The journal of physical chemistry. B	23795567	J Phys Chem B	2013 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/23795567
Probing allostery through DNA.	Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su XD, Sun Y, Xie XS	Science (New York, N.Y.)	23413354	Science	2013 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/23413354
Label-free biomedical imaging with high sensitivity by stimulated Raman scattering microscopy.	Freudiger CW, Min W, Saar BG, Lu S, Holtom GR, He C, Tsai JC, Kang JX, Xie XS	Science (New York, N.Y.)	19095943	Science	2008 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/19095943
Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA templates.	Kim S, Schroeder CM, Xie XS	Journal of molecular biology	19968999	J Mol Biol	2010 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/19968999
Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state.	Ge H, Wu P, Qian H, Xie XS	PLoS computational biology	29529037	PLoS Comput Biol	2018 Mar	https://www.ncbi.nlm.nih.gov/pubmed/29529037
Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: I. binding to DNA AND to hexon of the precursor to protein VI, pVI, of human adenovirus.	Graziano V, McGrath WJ, Suomalainen M, Greber UF, Freimuth P, Blainey PC, Luo G, Xie XS, Mangel WF	The Journal of biological chemistry	23043136	J Biol Chem	2013 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/23043136
Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: IV. viral proteinase slides along DNA to locate and process its substrates.	Blainey PC, Graziano V, Pérez-Berná AJ, McGrath WJ, Flint SJ, San Martín C, Xie XS, Mangel WF	The Journal of biological chemistry	23043138	J Biol Chem	2013 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/23043138
Multicolored stain-free histopathology with coherent Raman imaging.	Freudiger CW, Pfannl R, Orringer DA, Saar BG, Ji M, Zeng Q, Ottoboni L, Wei Y, Waeber C, Sims JR, De Jager PL, Sagher O, Philbert MA, Xu X, Kesari S, Xie XS, Young GS	Laboratory investigation; a journal of technical methods and pathology	22906986	Lab Invest	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22906986
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.	Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS	Science (New York, N.Y.)	20671182	Science	2010 Jul 30	https://www.ncbi.nlm.nih.gov/pubmed/20671182
Development of proneurogenic, neuroprotective small molecules.	MacMillan KS, Naidoo J, Liang J, Melito L, Williams NS, Morlock L, Huntington PJ, Estill SJ, Longgood J, Becker GL, McKnight SL, Pieper AA, De Brabander JK, Ready JM	Journal of the American Chemical Society	21210688	J Am Chem Soc	2011 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/21210688
Discovery of a proneurogenic, neuroprotective chemical.	Pieper AA, Xie S, Capota E, Estill SJ, Zhong J, Long JM, Becker GL, Huntington P, Goldman SE, Shen CH, Capota M, Britt JK, Kotti T, Ure K, Brat DJ, Williams NS, MacMillan KS, Naidoo J, Melito L, Hsieh J, De Brabander J, Ready JM, McKnight SL	Cell	20603013	Cell	2010 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/20603013
Lin28 promotes transformation and is associated with advanced human malignancies.	Viswanathan SR, Powers JT, Einhorn W, Hoshida Y, Ng TL, Toffanin S, O'Sullivan M, Lu J, Phillips LA, Lockhart VL, Shah SP, Tanwar PS, Mermel CH, Beroukhim R, Azam M, Teixeira J, Meyerson M, Hughes TP, Llovet JM, Radich J, Mullighan CG, Golub TR, Sorensen PH, Daley GQ	Nature genetics	19483683	Nat Genet	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19483683
Bone-marrow adipocytes as negative regulators of the haematopoietic microenvironment.	Naveiras O, Nardi V, Wenzel PL, Hauschka PV, Fahey F, Daley GQ	Nature	19516257	Nature	2009 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/19516257
Telomere elongation in induced pluripotent stem cells from dyskeratosis congenita patients.	Agarwal S, Loh YH, McLoughlin EM, Huang J, Park IH, Miller JD, Huo H, Okuka M, Dos Reis RM, Loewer S, Ng HH, Keefe DL, Goldman FD, Klingelhutz AJ, Liu L, Daley GQ	Nature	20164838	Nature	2010 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/20164838
Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies.	Zhu H, Shah S, Shyh-Chang N, Shinoda G, Einhorn WS, Viswanathan SR, Takeuchi A, Grasemann C, Rinn JL, Lopez MF, Hirschhorn JN, Palmert MR, Daley GQ	Nature genetics	20512147	Nat Genet	2010 Jul	https://www.ncbi.nlm.nih.gov/pubmed/20512147
Selective blockade of microRNA processing by Lin28.	Viswanathan SR, Daley GQ, Gregory RI	Science (New York, N.Y.)	18292307	Science	2008 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/18292307
Interactions between Cdx genes and retinoic acid modulate early cardiogenesis.	Lengerke C, Wingert R, Beeretz M, Grauer M, Schmidt AG, Konantz M, Daley GQ, Davidson AJ	Developmental biology	21466798	Dev Biol	2011 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/21466798
Generation of functional human hepatic endoderm from human induced pluripotent stem cells.	Sullivan GJ, Hay DC, Park IH, Fletcher J, Hannoun Z, Payne CM, Dalgetty D, Black JR, Ross JA, Samuel K, Wang G, Daley GQ, Lee JH, Church GM, Forbes SJ, Iredale JP, Wilmut I	Hepatology (Baltimore, Md.)	19877180	Hepatology	2010 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19877180
Autologous blood cell therapies from pluripotent stem cells.	Lengerke C, Daley GQ	Blood reviews	19910091	Blood Rev	2010 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19910091
AP24163 inhibits the gatekeeper mutant of BCR-ABL and suppresses in vitro resistance.	Azam M, Powers JT, Einhorn W, Huang WS, Shakespeare WC, Zhu X, Dalgarno D, Clackson T, Sawyer TK, Daley GQ	Chemical biology & drug design	20028401	Chem Biol Drug Des	2010 Feb	https://www.ncbi.nlm.nih.gov/pubmed/20028401
Epigenetic memory in induced pluripotent stem cells.	Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ	Nature	20644535	Nature	2010 Sep 16	https://www.ncbi.nlm.nih.gov/pubmed/20644535
Knockdown of Fanconi anemia genes in human embryonic stem cells reveals early developmental defects in the hematopoietic lineage.	Tulpule A, Lensch MW, Miller JD, Austin K, D'Andrea A, Schlaeger TM, Shimamura A, Daley GQ	Blood	20089964	Blood	2010 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/20089964
Hematopoietic development from human induced pluripotent stem cells.	Lengerke C, Grauer M, Niebuhr NI, Riedt T, Kanz L, Park IH, Daley GQ	Annals of the New York Academy of Sciences	19796250	Ann N Y Acad Sci	2009 Sep	https://www.ncbi.nlm.nih.gov/pubmed/19796250
Ras-MAPK signaling promotes trophectoderm formation from embryonic stem cells and mouse embryos.	Lu CW, Yabuuchi A, Chen L, Viswanathan S, Kim K, Daley GQ	Nature genetics	18536715	Nat Genet	2008 Jul	https://www.ncbi.nlm.nih.gov/pubmed/18536715
Enhanced plating efficiency of trypsin-adapted human embryonic stem cells is reversible and independent of trisomy 12/17.	Chan EM, Yates F, Boyer LF, Schlaeger TM, Daley GQ	Cloning and stem cells	18241122	Cloning Stem Cells	2008 Mar	https://www.ncbi.nlm.nih.gov/pubmed/18241122
Disease-specific induced pluripotent stem cells.	Park IH, Arora N, Huo H, Maherali N, Ahfeldt T, Shimamura A, Lensch MW, Cowan C, Hochedlinger K, Daley GQ	Cell	18691744	Cell	2008 Sep 5	https://www.ncbi.nlm.nih.gov/pubmed/18691744
A role for Lin28 in primordial germ-cell development and germ-cell malignancy.	West JA, Viswanathan SR, Yabuuchi A, Cunniff K, Takeuchi A, Park IH, Sero JE, Zhu H, Perez-Atayde A, Frazier AL, Surani MA, Daley GQ	Nature	19578360	Nature	2009 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/19578360
Activation of tyrosine kinases by mutation of the gatekeeper threonine.	Azam M, Seeliger MA, Gray NS, Kuriyan J, Daley GQ	Nature structural & molecular biology	18794843	Nat Struct Mol Biol	2008 Oct	https://www.ncbi.nlm.nih.gov/pubmed/18794843
9-(Arenethenyl)purines as dual Src/Abl kinase inhibitors targeting the inactive conformation: design, synthesis, and biological evaluation.	Huang WS, Zhu X, Wang Y, Azam M, Wen D, Sundaramoorthi R, Thomas RM, Liu S, Banda G, Lentini SP, Das S, Xu Q, Keats J, Wang F, Wardwell S, Ning Y, Snodgrass JT, Broudy MI, Russian K, Daley GQ, Iuliucci J, Dalgarno DC, Clackson T, Sawyer TK, Shakespeare WC	Journal of medicinal chemistry	19572547	J Med Chem	2009 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/19572547
High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation.	Wu AR, Kawahara TL, Rapicavoli NA, van Riggelen J, Shroff EH, Xu L, Felsher DW, Chang HY, Quake SR	Lab on a chip	22566096	Lab Chip	2012 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/22566096
Single-molecule sequencing of an individual human genome.	Pushkarev D, Neff NF, Quake SR	Nature biotechnology	19668243	Nat Biotechnol	2009 Sep	https://www.ncbi.nlm.nih.gov/pubmed/19668243
Whole-genome molecular haplotyping of single cells.	Fan HC, Wang J, Potanina A, Quake SR	Nature biotechnology	21170043	Nat Biotechnol	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21170043
Non-invasive prenatal measurement of the fetal genome.	Fan HC, Gu W, Wang J, Blumenfeld YJ, El-Sayed YY, Quake SR	Nature	22763444	Nature	2012 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/22763444
Versatile, fully automated, microfluidic cell culture system.	Gómez-Sjöberg R, Leyrat AA, Pirone DM, Chen CS, Quake SR	Analytical chemistry	17953452	Anal Chem	2007 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/17953452
Biocompatibility and reduced drug absorption of sol-gel-treated poly(dimethyl siloxane) for microfluidic cell culture applications.	Gomez-Sjoberg R, Leyrat AA, Houseman BT, Shokat K, Quake SR	Analytical chemistry	20936785	Anal Chem	2010 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/20936785
A "window of opportunity:" the reduction of coronary heart disease and total mortality with menopausal therapies is age- and time-dependent.	Hodis HN, Mack WJ	Brain research	20977895	Brain Res	2011 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/20977895
Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis.	Einav S, Gerber D, Bryson PD, Sklan EH, Elazar M, Maerkl SJ, Glenn JS, Quake SR	Nature biotechnology	18758449	Nat Biotechnol	2008 Sep	https://www.ncbi.nlm.nih.gov/pubmed/18758449
High-throughput sequencing of the zebrafish antibody repertoire.	Weinstein JA, Jiang N, White RA 3rd, Fisher DS, Quake SR	Science (New York, N.Y.)	19423829	Science	2009 May 8	https://www.ncbi.nlm.nih.gov/pubmed/19423829
Enhanced signals and fast nucleic acid hybridization by microfluidic chaotic mixing.	Liu J, Williams BA, Gwirtz RM, Wold BJ, Quake S	Angewandte Chemie (International ed. in English)	16639763	Angew Chem Int Ed Engl	2006 May 26	https://www.ncbi.nlm.nih.gov/pubmed/16639763
Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines.	Powell AA, Talasaz AH, Zhang H, Coram MA, Reddy A, Deng G, Telli ML, Advani RH, Carlson RW, Mollick JA, Sheth S, Kurian AW, Ford JM, Stockdale FE, Quake SR, Pease RF, Mindrinos MN, Bhanot G, Dairkee SH, Davis RW, Jeffrey SS	PloS one	22586443	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22586443
High-throughput single-molecule optofluidic analysis.	Kim S, Streets AM, Lin RR, Quake SR, Weiss S, Majumdar DS	Nature methods	21297618	Nat Methods	2011 Mar	https://www.ncbi.nlm.nih.gov/pubmed/21297618
An in vitro microfluidic approach to generating protein-interaction networks.	Gerber D, Maerkl SJ, Quake SR	Nature methods	19098921	Nat Methods	2009 Jan	https://www.ncbi.nlm.nih.gov/pubmed/19098921
Dissecting genomic diversity, one cell at a time.	Blainey PC, Quake SR	Nature methods	24524132	Nat Methods	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24524132
Automated microfluidic chromatin immunoprecipitation from 2,000 cells.	Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR	Lab on a chip	19417902	Lab Chip	2009 May 21	https://www.ncbi.nlm.nih.gov/pubmed/19417902
High-performance binary protein interaction screening in a microfluidic format.	Meier M, Sit R, Pan W, Quake SR	Analytical chemistry	23051662	Anal Chem	2012 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/23051662
Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis.	Blainey PC, Milla CE, Cornfield DN, Quake SR	Science translational medicine	23019655	Sci Transl Med	2012 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/23019655
Ostwald ripening of clusters during protein crystallization.	Streets AM, Quake SR	Physical review letters	20482145	Phys Rev Lett	2010 Apr 30	https://www.ncbi.nlm.nih.gov/pubmed/20482145
Temporal response of the human virome to immunosuppression and antiviral therapy.	De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, Okamoto J, Snyder TM, Cornfield DN, Nicolls MR, Weill D, Bernstein D, Valantine HA, Quake SR	Cell	24267896	Cell	2013 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/24267896
Noninvasive prenatal diagnosis in a fetus at risk for methylmalonic acidemia.	Gu W, Koh W, Blumenfeld YJ, El-Sayed YY, Hudgins L, Hintz SR, Quake SR	Genetics in medicine : official journal of the American College of Medical Genetics	24406457	Genet Med	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24406457
Design Principles of Length Control of Cytoskeletal Structures.	Mohapatra L, Goode BL, Jelenkovic P, Phillips R, Kondev J	Annual review of biophysics	27145876	Annu Rev Biophys	2016 Jul 5	https://www.ncbi.nlm.nih.gov/pubmed/27145876
Connecting the Dots between Mechanosensitive Channel Abundance, Osmotic Shock, and Survival at Single-Cell Resolution.	Chure G, Lee HJ, Rasmussen A, Phillips R	Journal of bacteriology	30201782	J Bacteriol	2018 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/30201782
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.	Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R	Proceedings of the National Academy of Sciences of the United States of America	29728462	Proc Natl Acad Sci U S A	2018 May 22	https://www.ncbi.nlm.nih.gov/pubmed/29728462
Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.	Razo-Mejia M, Barnes SL, Belliveau NM, Chure G, Einav T, Lewis M, Phillips R	Cell systems	29574055	Cell Syst	2018 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/29574055
Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression.	Phillips R, Belliveau NM, Chure G, Garcia HG, Razo-Mejia M, Scholes C	Annual review of biophysics	31084583	Annu Rev Biophys	2019 May 6	https://www.ncbi.nlm.nih.gov/pubmed/31084583
Napoleon Is in Equilibrium.	Phillips R	Annual review of condensed matter physics	27429713	Annu Rev Condens Matter Phys	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/27429713
Morphology and interaction between lipid domains.	Ursell TS, Klug WS, Phillips R	Proceedings of the National Academy of Sciences of the United States of America	19620730	Proc Natl Acad Sci U S A	2009 Aug 11	https://www.ncbi.nlm.nih.gov/pubmed/19620730
Ion-dependent dynamics of DNA ejections for bacteriophage lambda.	Wu D, Van Valen D, Hu Q, Phillips R	Biophysical journal	20712993	Biophys J	2010 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/20712993
Biochemistry on a leash: the roles of tether length and geometry in signal integration proteins.	Van Valen D, Haataja M, Phillips R	Biophysical journal	19217847	Biophys J	2009 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/19217847
Entropic tension in crowded membranes.	Lindén M, Sens P, Phillips R	PLoS computational biology	22438801	PLoS Comput Biol	2012	https://www.ncbi.nlm.nih.gov/pubmed/22438801
Building enhancers from the ground up: a synthetic biology approach.	Amit R, Garcia HG, Phillips R, Fraser SE	Cell	21729783	Cell	2011 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/21729783
First-principles calculation of DNA looping in tethered particle experiments.	Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC	Physical biology	19571369	Phys Biol	2009 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/19571369
Membrane mechanics as a probe of ion-channel gating mechanisms.	Reeves D, Ursell T, Sens P, Kondev J, Phillips R	Physical review. E, Statistical, nonlinear, and soft matter physics	18999449	Phys Rev E Stat Nonlin Soft Matter Phys	2008 Oct	https://www.ncbi.nlm.nih.gov/pubmed/18999449
Tuning promoter strength through RNA polymerase binding site design in Escherichia coli.	Brewster RC, Jones DL, Phillips R	PLoS computational biology	23271961	PLoS Comput Biol	2012	https://www.ncbi.nlm.nih.gov/pubmed/23271961
Exact theory of kinkable elastic polymers.	Wiggins PA, Phillips R, Nelson PC	Physical review. E, Statistical, nonlinear, and soft matter physics	15783354	Phys Rev E Stat Nonlin Soft Matter Phys	2005 Feb	https://www.ncbi.nlm.nih.gov/pubmed/15783354
Transcriptional regulation by the numbers: applications.	Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R	Current opinion in genetics & development	15797195	Curr Opin Genet Dev	2005 Apr	https://www.ncbi.nlm.nih.gov/pubmed/15797195
Directional interactions and cooperativity between mechanosensitive membrane proteins.	Haselwandter CA, Phillips R	Europhysics letters	25309021	Europhys Lett	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25309021
Elastic energy of polyhedral bilayer vesicles.	Haselwandter CA, Phillips R	Physical review. E, Statistical, nonlinear, and soft matter physics	21797397	Phys Rev E Stat Nonlin Soft Matter Phys	2011 Jun	https://www.ncbi.nlm.nih.gov/pubmed/21797397
A single-molecule Hershey-Chase experiment.	Van Valen D, Wu D, Chen YJ, Tuson H, Wiggins P, Phillips R	Current biology : CB	22727695	Curr Biol	2012 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/22727695
Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.	Garcia HG, Sanchez A, Boedicker JQ, Osborne M, Gelles J, Kondev J, Phillips R	Cell reports	22840405	Cell Rep	2012 Jul 26	https://www.ncbi.nlm.nih.gov/pubmed/22840405
Theoretical and experimental dissection of DNA loop-mediated repression.	Boedicker JQ, Garcia HG, Phillips R	Physical review letters	23383841	Phys Rev Lett	2013 Jan 4	https://www.ncbi.nlm.nih.gov/pubmed/23383841
The transcription factor titration effect dictates level of gene expression.	Brewster RC, Weinert FM, Garcia HG, Song D, Rydenfelt M, Phillips R	Cell	24612990	Cell	2014 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/24612990
Volume-exclusion effects in tethered-particle experiments: bead size matters.	Segall DE, Nelson PC, Phillips R	Physical review letters	16606235	Phys Rev Lett	2006 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/16606235
Concentration and length dependence of DNA looping in transcriptional regulation.	Han L, Garcia HG, Blumberg S, Towles KB, Beausang JF, Nelson PC, Phillips R	PloS one	19479049	PLoS One	2009 May 25	https://www.ncbi.nlm.nih.gov/pubmed/19479049
Mapping DNA sequence to transcription factor binding energy in vivo.	Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R	PLoS computational biology	30716072	PLoS Comput Biol	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30716072
Predicting the impact of promoter variability on regulatory outputs.	Kreamer NN, Phillips R, Newman DK, Boedicker JQ	Scientific reports	26675057	Sci Rep	2015 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/26675057
Theory in Biology: Figure 1 or Figure 7?	Phillips R	Trends in cell biology	26584768	Trends Cell Biol	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26584768
Scaling of gene expression with transcription-factor fugacity.	Weinert FM, Brewster RC, Rydenfelt M, Phillips R, Kegel WK	Physical review letters	25554908	Phys Rev Lett	2014 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/25554908
Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD.	Travers T, López CA, Agamasu C, Hettige JJ, Messing S, García AE, Stephen AG, Gnanakaran S	Biophysical journal	32649863	Biophys J	2020 Aug 4	https://www.ncbi.nlm.nih.gov/pubmed/32649863
Statistical Mechanics of Allosteric Enzymes.	Einav T, Mazutis L, Phillips R	The journal of physical chemistry. B	27070509	J Phys Chem B	2016 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/27070509
Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants.	Einav T, Duque J, Phillips R	PloS one	30256816	PLoS One	2018	https://www.ncbi.nlm.nih.gov/pubmed/30256816
Predictive shifts in free energy couple mutations to their phenotypic consequences.	Chure G, Razo-Mejia M, Belliveau NM, Einav T, Kaczmarek ZA, Barnes SL, Lewis M, Phillips R	Proceedings of the National Academy of Sciences of the United States of America	31451655	Proc Natl Acad Sci U S A	2019 Sep 10	https://www.ncbi.nlm.nih.gov/pubmed/31451655
Combinatorial Control through Allostery.	Galstyan V, Funk L, Einav T, Phillips R	The journal of physical chemistry. B	30768906	J Phys Chem B	2019 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/30768906
Schrödinger's What Is Life? at 75.	Phillips R	Cell systems	34139159	Cell Syst	2021 Jun 16	https://www.ncbi.nlm.nih.gov/pubmed/34139159
The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli.	Rydenfelt M, Garcia HG, Cox RS 3rd, Phillips R	PloS one	25549361	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/25549361
Self-consistent theory of transcriptional control in complex regulatory architectures.	Landman J, Brewster RC, Weinert FM, Phillips R, Kegel WK	PloS one	28686609	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28686609
The effect of genome length on ejection forces in bacteriophage lambda.	Grayson P, Evilevitch A, Inamdar MM, Purohit PK, Gelbart WM, Knobler CM, Phillips R	Virology	16469346	Virology	2006 May 10	https://www.ncbi.nlm.nih.gov/pubmed/16469346
Transcription by the numbers redux: experiments and calculations that surprise.	Garcia HG, Sanchez A, Kuhlman T, Kondev J, Phillips R	Trends in cell biology	20801657	Trends Cell Biol	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/20801657
Single-cell census of mechanosensitive channels in living bacteria.	Bialecka-Fornal M, Lee HJ, DeBerg HA, Gandhi CS, Phillips R	PloS one	22427953	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/22427953
Connection between oligomeric state and gating characteristics of mechanosensitive ion channels.	Haselwandter CA, Phillips R	PLoS computational biology	23696720	PLoS Comput Biol	2013	https://www.ncbi.nlm.nih.gov/pubmed/23696720
Sequence dependence of transcription factor-mediated DNA looping.	Johnson S, Lindén M, Phillips R	Nucleic acids research	22718983	Nucleic Acids Res	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22718983
Effect of promoter architecture on the cell-to-cell variability in gene expression.	Sanchez A, Garcia HG, Jones D, Phillips R, Kondev J	PLoS computational biology	21390269	PLoS Comput Biol	2011 Mar	https://www.ncbi.nlm.nih.gov/pubmed/21390269
Thermodynamics of biological processes.	Garcia HG, Kondev J, Orme N, Theriot JA, Phillips R	Methods in enzymology	21333788	Methods Enzymol	2011	https://www.ncbi.nlm.nih.gov/pubmed/21333788
Cooperative gating and spatial organization of membrane proteins through elastic interactions.	Ursell T, Huang KC, Peterson E, Phillips R	PLoS computational biology	17480116	PLoS Comput Biol	2007 May	https://www.ncbi.nlm.nih.gov/pubmed/17480116
Measuring flux distributions for diffusion in the small-numbers limit.	Seitaridou E, Inamdar MM, Phillips R, Ghosh K, Dill K	The journal of physical chemistry. B	17295536	J Phys Chem B	2007 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/17295536
Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration.	Rydenfelt M, Cox RS 3rd, Garcia H, Phillips R	Physical review. E, Statistical, nonlinear, and soft matter physics	24580252	Phys Rev E Stat Nonlin Soft Matter Phys	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24580252
Comparison of the theoretical and real-world evolutionary potential of a genetic circuit.	Razo-Mejia M, Boedicker JQ, Jones D, DeLuna A, Kinney JB, Phillips R	Physical biology	24685590	Phys Biol	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24685590
Emerging roles for lipids in shaping membrane-protein function.	Phillips R, Ursell T, Wiggins P, Sens P	Nature	19458714	Nature	2009 May 21	https://www.ncbi.nlm.nih.gov/pubmed/19458714
Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation.	Ngo HB, Lovely GA, Phillips R, Chan DC	Nature communications	24435062	Nat Commun	2014	https://www.ncbi.nlm.nih.gov/pubmed/24435062
Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants.	Einav T, Phillips R	The journal of physical chemistry. B	28134524	J Phys Chem B	2017 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/28134524
Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity.	Garcia HG, Grayson P, Han L, Inamdar M, Kondev J, Nelson PC, Phillips R, Widom J, Wiggins PA	Biopolymers	17103419	Biopolymers	2007 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/17103419
Dynamics of DNA ejection from bacteriophage.	Inamdar MM, Gelbart WM, Phillips R	Biophysical journal	16679360	Biophys J	2006 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/16679360
Transcriptional regulation by the numbers: models.	Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R	Current opinion in genetics & development	15797194	Curr Opin Genet Dev	2005 Apr	https://www.ncbi.nlm.nih.gov/pubmed/15797194
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment.	Peterson EL, Kondev J, Theriot JA, Phillips R	Bioinformatics (Oxford, England)	19351620	Bioinformatics	2009 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/19351620
Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.	Wu D, Ghosh K, Inamdar M, Lee HJ, Fraser S, Dill K, Phillips R	Physical review letters	19792475	Phys Rev Lett	2009 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/19792475
Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.	Mulligan PJ, Chen YJ, Phillips R, Spakowitz AJ	Biophysical journal	26244743	Biophys J	2015 Aug 4	https://www.ncbi.nlm.nih.gov/pubmed/26244743
Promoter architecture dictates cell-to-cell variability in gene expression.	Jones DL, Brewster RC, Phillips R	Science (New York, N.Y.)	25525251	Science	2014 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/25525251
Statistical mechanics of Monod-Wyman-Changeux (MWC) models.	Marzen S, Garcia HG, Phillips R	Journal of molecular biology	23499654	J Mol Biol	2013 May 13	https://www.ncbi.nlm.nih.gov/pubmed/23499654
A feeling for the numbers in biology.	Phillips R, Milo R	Proceedings of the National Academy of Sciences of the United States of America	20018695	Proc Natl Acad Sci U S A	2009 Dec 22	https://www.ncbi.nlm.nih.gov/pubmed/20018695
Real-time observations of single bacteriophage lambda DNA ejections in vitro.	Grayson P, Han L, Winther T, Phillips R	Proceedings of the National Academy of Sciences of the United States of America	17804798	Proc Natl Acad Sci U S A	2007 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/17804798
The rate of osmotic downshock determines the survival probability of bacterial mechanosensitive channel mutants.	Bialecka-Fornal M, Lee HJ, Phillips R	Journal of bacteriology	25349158	J Bacteriol	2015 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/25349158
Using synthetic biology to make cells tomorrow's test tubes.	Garcia HG, Brewster RC, Phillips R	Integrative biology : quantitative biosciences from nano to macro	26952708	Integr Biol (Camb)	2016 Apr 18	https://www.ncbi.nlm.nih.gov/pubmed/26952708
Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time.	Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R	eLife	32955440	Elife	2020 Sep 21	https://www.ncbi.nlm.nih.gov/pubmed/32955440
Musings on mechanism: quest for a quark theory of proteins?	Phillips R	FASEB journal : official publication of the Federation of American Societies for Experimental Biology	28963318	FASEB J	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28963318
Comparison and calibration of different reporters for quantitative analysis of gene expression.	Garcia HG, Lee HJ, Boedicker JQ, Phillips R	Biophysical journal	21806921	Biophys J	2011 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/21806921
Minimal bending energies of bilayer polyhedra.	Haselwandter CA, Phillips R	Physical review letters	21231425	Phys Rev Lett	2010 Nov 26	https://www.ncbi.nlm.nih.gov/pubmed/21231425
Morphological phase diagram for lipid membrane domains with entropic tension.	Rim JE, Ursell TS, Phillips R, Klug WS	Physical review letters	21405437	Phys Rev Lett	2011 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/21405437
Probing individual environmental bacteria for viruses by using microfluidic digital PCR.	Tadmor AD, Ottesen EA, Leadbetter JR, Phillips R	Science (New York, N.Y.)	21719670	Science	2011 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/21719670
Quantitative dissection of the simple repression input-output function.	Garcia HG, Phillips R	Proceedings of the National Academy of Sciences of the United States of America	21730194	Proc Natl Acad Sci U S A	2011 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/21730194
Teaching the principles of statistical dynamics.	Ghosh K, Dill KA, Inamdar MM, Seitaridou E, Phillips R	American journal of physics	23585693	Am J Phys	2006 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/23585693
DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.	Boedicker JQ, Garcia HG, Johnson S, Phillips R	Physical biology	24231252	Phys Biol	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24231252
Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping.	Johnson S, Chen YJ, Phillips R	PloS one	24146776	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24146776
Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein-protein interactions directly from DNA.	Layton CJ, Hellinga HW	Protein science : a publication of the Protein Society	21674663	Protein Sci	2011 Aug	https://www.ncbi.nlm.nih.gov/pubmed/21674663
Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates.	Rizk SS, Cuneo MJ, Hellinga HW	Protein science : a publication of the Protein Society	16751609	Protein Sci	2006 Jul	https://www.ncbi.nlm.nih.gov/pubmed/16751609
A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.	Isom DG, Marguet PR, Oas TG, Hellinga HW	Proteins	21387407	Proteins	2011 Apr	https://www.ncbi.nlm.nih.gov/pubmed/21387407
Protein fabrication automation.	Cox JC, Lape J, Sayed MA, Hellinga HW	Protein science : a publication of the Protein Society	17242375	Protein Sci	2007 Mar	https://www.ncbi.nlm.nih.gov/pubmed/17242375
Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein.	Tian Y, Cuneo MJ, Changela A, Höcker B, Beese LS, Hellinga HW	Protein science : a publication of the Protein Society	17766373	Protein Sci	2007 Oct	https://www.ncbi.nlm.nih.gov/pubmed/17766373
Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes.	Layton CJ, Hellinga HW	Biochemistry	21050007	Biochemistry	2010 Dec 28	https://www.ncbi.nlm.nih.gov/pubmed/21050007
Wharton's Jelly Mesenchymal Stromal Cells and Derived Extracellular Vesicles as Post-Myocardial Infarction Therapeutic Toolkit: An Experienced View.	Muñoz-Domínguez N, Roura S, Prat-Vidal C, Vives J	Pharmaceutics	34575412	Pharmaceutics	2021 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/34575412
Multifactorial determinants of protein expression in prokaryotic open reading frames.	Allert M, Cox JC, Hellinga HW	Journal of molecular biology	20727358	J Mol Biol	2010 Oct 8	https://www.ncbi.nlm.nih.gov/pubmed/20727358
The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog.	Cuneo MJ, Tian Y, Allert M, Hellinga HW	BMC structural biology	18373848	BMC Struct Biol	2008 Mar 28	https://www.ncbi.nlm.nih.gov/pubmed/18373848
Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport.	Cuneo MJ, Changela A, Miklos AE, Beese LS, Krueger JK, Hellinga HW	The Journal of biological chemistry	18723845	J Biol Chem	2008 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/18723845
Ligand-induced conformational changes in a thermophilic ribose-binding protein.	Cuneo MJ, Beese LS, Hellinga HW	BMC structural biology	19019243	BMC Struct Biol	2008 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/19019243
Local encoding of computationally designed enzyme activity.	Allert M, Dwyer MA, Hellinga HW	Journal of molecular biology	17196220	J Mol Biol	2007 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/17196220
The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites.	Cuneo MJ, Changela A, Warren JJ, Beese LS, Hellinga HW	Journal of molecular biology	16904687	J Mol Biol	2006 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/16904687
Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins.	de Lorimier RM, Tian Y, Hellinga HW	Protein science : a publication of the Protein Society	16823040	Protein Sci	2006 Aug	https://www.ncbi.nlm.nih.gov/pubmed/16823040
Structural adaptations that modulate monosaccharide, disaccharide, and trisaccharide specificities in periplasmic maltose-binding proteins.	Cuneo MJ, Changela A, Beese LS, Hellinga HW	Journal of molecular biology	19361522	J Mol Biol	2009 May 29	https://www.ncbi.nlm.nih.gov/pubmed/19361522
Picomole-scale characterization of protein stability and function by quantitative cysteine reactivity.	Isom DG, Vardy E, Oas TG, Hellinga HW	Proceedings of the National Academy of Sciences of the United States of America	20194783	Proc Natl Acad Sci U S A	2010 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/20194783
Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold.	Cuneo MJ, Beese LS, Hellinga HW	The Journal of biological chemistry	19801540	J Biol Chem	2009 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/19801540
Visualization of synaptic inhibition with an optogenetic sensor developed by cell-free protein engineering automation.	Grimley JS, Li L, Wang W, Wen L, Beese LS, Hellinga HW, Augustine GJ	The Journal of neuroscience : the official journal of the Society for Neuroscience	24107961	J Neurosci	2013 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/24107961
Gating multiple signals through detailed balance of excitation and inhibition in spiking networks.	Vogels TP, Abbott LF	Nature neuroscience	19305402	Nat Neurosci	2009 Apr	https://www.ncbi.nlm.nih.gov/pubmed/19305402
HCN hyperpolarization-activated cation channels inhibit EPSPs by interactions with M-type K(+) channels.	George MS, Abbott LF, Siegelbaum SA	Nature neuroscience	19363490	Nat Neurosci	2009 May	https://www.ncbi.nlm.nih.gov/pubmed/19363490
Generating coherent patterns of activity from chaotic neural networks.	Sussillo D, Abbott LF	Neuron	19709635	Neuron	2009 Aug 27	https://www.ncbi.nlm.nih.gov/pubmed/19709635
Modular realignment of entorhinal grid cell activity as a basis for hippocampal remapping.	Monaco JD, Abbott LF	The Journal of neuroscience : the official journal of the Society for Neuroscience	21697391	J Neurosci	2011 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/21697391
Stimulus-dependent suppression of chaos in recurrent neural networks.	Rajan K, Abbott LF, Sompolinsky H	Physical review. E, Statistical, nonlinear, and soft matter physics	20866644	Phys Rev E Stat Nonlin Soft Matter Phys	2010 Jul	https://www.ncbi.nlm.nih.gov/pubmed/20866644
A brainstem map of orofacial rhythms.	Kaku H, Liu LD, Gao R, West S, Liao SM, Finkelstein A, Kleinfeld D, Thomas A, Tipparaju SL, Svoboda K, Li N	bioRxiv : the preprint server for biology	39975015	bioRxiv	2025 Jan 27	https://www.ncbi.nlm.nih.gov/pubmed/39975015
A frugal CRISPR kit for equitable and accessible education in gene editing and synthetic biology.	Collins M, Lau MB, Ma W, Shen A, Wang B, Cai S, La Russa M, Jewett MC, Qi LS	Nature communications	39095367	Nat Commun	2024 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/39095367
The realization of CRISPR gene therapy.	Ma Y, Qi LS	Nature chemical biology	38872012	Nat Chem Biol	2024 Jul	https://www.ncbi.nlm.nih.gov/pubmed/38872012
Programmable macromolecule delivery via engineered trogocytosis.	Chen X, Situ Y, Yang Y, Fu ML, Lyu L, Qi LS	bioRxiv : the preprint server for biology	40161588	bioRxiv	2025 Mar 14	https://www.ncbi.nlm.nih.gov/pubmed/40161588
Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications.	Roth GV, Gengaro IR, Qi LS	Cell chemical biology	39137782	Cell Chem Biol	2024 Aug 6	https://www.ncbi.nlm.nih.gov/pubmed/39137782
Cortical activity emerges in region-specific patterns during early brain development.	Suárez R, Bluett T, McCullough MH, Avitan L, Black DA, Paolino A, Fenlon LR, Goodhill GJ, Richards LJ	Proceedings of the National Academy of Sciences of the United States of America	37216522	Proc Natl Acad Sci U S A	2023 May 30	https://www.ncbi.nlm.nih.gov/pubmed/37216522
Cortical activity emerges in region-specific patterns during early brain development.	Suárez R, Bluett T, McCullough MH, Avitan L, Black DA, Paolino A, Fenlon LR, Goodhill GJ, Richards LJ	bioRxiv : the preprint server for biology	36824827	bioRxiv	2023 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/36824827
Diverse axonal morphologies of individual callosal projection neurons reveal new insights into brain connectivity.	Pal S, Lim JWC, Richards LJ	Current opinion in neurobiology	38271848	Curr Opin Neurobiol	2024 Feb	https://www.ncbi.nlm.nih.gov/pubmed/38271848
Seizure Detection in Continuous Inpatient EEG: A Comparison of Human vs Automated Review.	Ganguly TM, Ellis CA, Tu D, Shinohara RT, Davis KA, Litt B, Pathmanathan J	Neurology	35410905	Neurology	2022 May 31	https://www.ncbi.nlm.nih.gov/pubmed/35410905
Addressing spatial bias in intracranial EEG functional connectivity analyses for epilepsy surgical planning.	Conrad EC, Bernabei JM, Sinha N, Ghosn NJ, Stein JM, Shinohara RT, Litt B	Journal of neural engineering	36084621	J Neural Eng	2022 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/36084621
Fractional-order model predictive control as a framework for electrical neurostimulation in epilepsy.	Chatterjee S, Romero O, Ashourvan A, Pequito S	Journal of neural engineering	33142281	J Neural Eng	2020 Dec 16	https://www.ncbi.nlm.nih.gov/pubmed/33142281
Spike patterns surrounding sleep and seizures localize the seizure-onset zone in focal epilepsy.	Conrad EC, Revell AY, Greenblatt AS, Gallagher RS, Pattnaik AR, Hartmann N, Gugger JJ, Shinohara RT, Litt B, Marsh ED, Davis KA	Epilepsia	36484572	Epilepsia	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36484572
iEEG-recon: A Fast and Scalable Pipeline for Accurate Reconstruction of Intracranial Electrodes and Implantable Devices.	Lucas A, Scheid BH, Pattnaik AR, Gallagher R, Mojena M, Tranquille A, Prager B, Gleichgerrcht E, Gong R, Litt B, Davis KA, Das S, Stein JM, Sinha N	medRxiv : the preprint server for health sciences	37398160	medRxiv	2023 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/37398160
Generalization of finetuned transformer language models to new clinical contexts.	Xie K, Terman SW, Gallagher RS, Hill CE, Davis KA, Litt B, Roth D, Ellis CA	JAMIA open	37600072	JAMIA Open	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37600072
Disparities in seizure outcomes revealed by large language models.	Xie K, Ojemann WKS, Gallagher RS, Lucas A, Hill CE, Hamilton RH, Johnson KB, Roth D, Litt B, Ellis CA	medRxiv : the preprint server for health sciences	37790442	medRxiv	2023 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/37790442
Model-based design for seizure control by stimulation.	Ashourvan A, Pequito S, Khambhati AN, Mikhail F, Baldassano SN, Davis KA, Lucas TH, Vettel JM, Litt B, Pappas GJ, Bassett DS	Journal of neural engineering	32103826	J Neural Eng	2020 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/32103826
Low-field MRI: Clinical promise and challenges.	Arnold TC, Freeman CW, Litt B, Stein JM	Journal of magnetic resonance imaging : JMRI	36120962	J Magn Reson Imaging	2023 Jan	https://www.ncbi.nlm.nih.gov/pubmed/36120962
Electrocorticography and stereo EEG provide distinct measures of brain connectivity: implications for network models.	Bernabei JM, Arnold TC, Shah P, Revell A, Ong IZ, Kini LG, Stein JM, Shinohara RT, Lucas TH, Davis KA, Bassett DS, Litt B	Brain communications	34396112	Brain Commun	2021	https://www.ncbi.nlm.nih.gov/pubmed/34396112
Intracranial electroencephalographic biomarker predicts effective responsive neurostimulation for epilepsy prior to treatment.	Scheid BH, Bernabei JM, Khambhati AN, Mouchtaris S, Jeschke J, Bassett DS, Becker D, Davis KA, Lucas T, Doyle W, Chang EF, Friedman D, Rao VR, Litt B	Epilepsia	34997577	Epilepsia	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/34997577
A Full-Stack Application for Detecting Seizures and Reducing Data During Continuous Electroencephalogram Monitoring.	Bernabei JM, Owoputi O, Small SD, Nyema NT, Dumenyo E, Kim J, Baldassano SN, Painter C, Conrad EC, Ganguly TM, Balu R, Davis KA, Levine JM, Pathmanathan J, Litt B	Critical care explorations	34278312	Crit Care Explor	2021 Jul	https://www.ncbi.nlm.nih.gov/pubmed/34278312
Normative intracranial EEG maps epileptogenic tissues in focal epilepsy.	Bernabei JM, Sinha N, Arnold TC, Conrad E, Ong I, Pattnaik AR, Stein JM, Shinohara RT, Lucas TH, Bassett DS, Davis KA, Litt B	Brain : a journal of neurology	35640886	Brain	2022 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/35640886
Development of a natural language processing algorithm to extract seizure types and frequencies from the electronic health record.	Decker BM, Turco A, Xu J, Terman SW, Kosaraju N, Jamil A, Davis KA, Litt B, Ellis CA, Khankhanian P, Hill CE	Seizure	35882104	Seizure	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/35882104
Implanting intracranial electrodes does not affect spikes or network connectivity in nearby or connected brain regions.	Conrad EC, Shinohara RT, Gugger JJ, Revell AY, Das S, Stein JM, Marsh ED, Davis KA, Litt B	Network neuroscience (Cambridge, Mass.)	36607198	Netw Neurosci	2022 Jul	https://www.ncbi.nlm.nih.gov/pubmed/36607198
Quantitative approaches to guide epilepsy surgery from intracranial EEG.	Bernabei JM, Li A, Revell AY, Smith RJ, Gunnarsdottir KM, Ong IZ, Davis KA, Sinha N, Sarma S, Litt B	Brain : a journal of neurology	36623936	Brain	2023 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/36623936
Quantifying trial-by-trial variability during cortico-cortical evoked potential mapping of epileptogenic tissue.	Cornblath EJ, Lucas A, Armstrong C, Greenblatt AS, Stein JM, Hadar PN, Raghupathi R, Marsh E, Litt B, Davis KA, Conrad EC	Epilepsia	36728906	Epilepsia	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/36728906
Disparities in seizure outcomes revealed by large language models.	Xie K, Ojemann WKS, Gallagher RS, Shinohara RT, Lucas A, Hill CE, Hamilton RH, Johnson KB, Roth D, Litt B, Ellis CA	Journal of the American Medical Informatics Association : JAMIA	38481027	J Am Med Inform Assoc	2024 May 20	https://www.ncbi.nlm.nih.gov/pubmed/38481027
Quantitative EEG Spectral Features Differentiate Genetic Epilepsies and Predict Neurologic Outcomes.	Galer PD, McKee JL, Ruggiero SM, Kaufman MC, McSalley I, Ganesan S, Ojemann WKS, Gonzalez AK, Cao Q, Litt B, Helbig I, Conrad EC	medRxiv : the preprint server for health sciences	39417111	medRxiv	2024 Oct 10	https://www.ncbi.nlm.nih.gov/pubmed/39417111
Interictal intracranial EEG asymmetry lateralizes temporal lobe epilepsy.	Conrad EC, Lucas A, Ojemann WKS, Aguila CA, Mojena M, LaRocque JJ, Pattnaik AR, Gallagher R, Greenblatt A, Tranquille A, Parashos A, Gleichgerrcht E, Bonilha L, Litt B, Sinha S, Ungar L, Davis KA	medRxiv : the preprint server for health sciences	38168158	medRxiv	2023 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/38168158
Multi-contrast high-field quality image synthesis for portable low-field MRI using generative adversarial networks and paired data.	Lucas A, Campbell Arnold T, Okar SV, Vadali C, Kawatra KD, Ren Z, Cao Q, Shinohara RT, Schindler MK, Davis KA, Litt B, Reich DS, Stein JM	medRxiv : the preprint server for health sciences	38234785	medRxiv	2023 Dec 29	https://www.ncbi.nlm.nih.gov/pubmed/38234785
On-Demand Seizures Facilitate Rapid Screening of Therapeutics for Epilepsy.	Chen Y, Litt B, Vitale F, Takano H	bioRxiv : the preprint server for biology	39464023	bioRxiv	2025 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/39464023
Simulated diagnostic performance of low-field MRI: Harnessing open-access datasets to evaluate novel devices.	Arnold TC, Baldassano SN, Litt B, Stein JM	Magnetic resonance imaging	34968700	Magn Reson Imaging	2022 Apr	https://www.ncbi.nlm.nih.gov/pubmed/34968700
A framework For brain atlases: Lessons from seizure dynamics.	Revell AY, Silva AB, Arnold TC, Stein JM, Das SR, Shinohara RT, Bassett DS, Litt B, Davis KA	NeuroImage	35339683	Neuroimage	2022 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/35339683
Remote effects of temporal lobe epilepsy surgery: Long-term morphological changes after surgical resection.	Arnold TC, Kini LG, Bernabei JM, Revell AY, Das SR, Stein JM, Lucas TH, Englot DJ, Morgan VL, Litt B, Davis KA	Epilepsia open	36944585	Epilepsia Open	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/36944585
Long-term epilepsy outcome dynamics revealed by natural language processing of clinic notes.	Xie K, Gallagher RS, Shinohara RT, Xie SX, Hill CE, Conrad EC, Davis KA, Roth D, Litt B, Ellis CA	Epilepsia	37114472	Epilepsia	2023 Jul	https://www.ncbi.nlm.nih.gov/pubmed/37114472
Characterizing the treatment gap in the United States among adult patients with a new diagnosis of epilepsy.	Decker BM, Ellis CA, Schriver E, Fischbein K, Smith D, Moyer JT, Kulick-Soper CV, Mowery D, Litt B, Hill CE	Epilepsia	37150944	Epilepsia	2023 Jul	https://www.ncbi.nlm.nih.gov/pubmed/37150944
The seizure severity score: a quantitative tool for comparing seizures and their response to therapy.	Pattnaik AR, Ghosn NJ, Ong IZ, Revell AY, Ojemann WKS, Scheid BH, Georgostathi G, Bernabei JM, Conrad EC, Sinha SR, Davis KA, Sinha N, Litt B	Journal of neural engineering	37531949	J Neural Eng	2023 Aug 10	https://www.ncbi.nlm.nih.gov/pubmed/37531949
Sensitivity of portable low-field magnetic resonance imaging for multiple sclerosis lesions.	Arnold TC, Tu D, Okar SV, Nair G, By S, Kawatra KD, Robert-Fitzgerald TE, Desiderio LM, Schindler MK, Shinohara RT, Reich DS, Stein JM	NeuroImage. Clinical	35792417	Neuroimage Clin	2022	https://www.ncbi.nlm.nih.gov/pubmed/35792417
Utility of intracranial EEG networks depends on re-referencing and connectivity choice.	Shi H, Pattnaik AR, Aguila C, Lucas A, Sinha N, Prager B, Mojena M, Gallagher R, Parashos A, Bonilha L, Gleichgerrcht E, Davis KA, Litt B, Conrad EC	Brain communications	38799618	Brain Commun	2024	https://www.ncbi.nlm.nih.gov/pubmed/38799618
Clinical signatures of genetic epilepsies precede diagnosis in electronic medical records of 32,000 individuals.	Galer PD, Parthasarathy S, Xian J, McKee JL, Ruggiero SM, Ganesan S, Kaufman MC, Cohen SR, Haag S, Chen C, Ojemann WKS, Kim D, Wilmarth O, Vaidiswaran P, Sederman C, Ellis CA, Gonzalez AK, Boßelmann CM, Lal D, Sederman R, Lewis-Smith D, Litt B, Helbig I	Genetics in medicine : official journal of the American College of Medical Genetics	39011766	Genet Med	2024 Nov	https://www.ncbi.nlm.nih.gov/pubmed/39011766
MXene-infused bioelectronic interfaces for multiscale electrophysiology and stimulation.	Driscoll N, Erickson B, Murphy BB, Richardson AG, Robbins G, Apollo NV, Mentzelopoulos G, Mathis T, Hantanasirisakul K, Bagga P, Gullbrand SE, Sergison M, Reddy R, Wolf JA, Chen HI, Lucas TH, Dillingham TR, Davis KA, Gogotsi Y, Medaglia JD, Vitale F	Science translational medicine	34550728	Sci Transl Med	2021 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/34550728
Extracting seizure frequency from epilepsy clinic notes: a machine reading approach to natural language processing.	Xie K, Gallagher RS, Conrad EC, Garrick CO, Baldassano SN, Bernabei JM, Galer PD, Ghosn NJ, Greenblatt AS, Jennings T, Kornspun A, Kulick-Soper CV, Panchal JM, Pattnaik AR, Scheid BH, Wei D, Weitzman M, Muthukrishnan R, Kim J, Litt B, Ellis CA, Roth D	Journal of the American Medical Informatics Association : JAMIA	35190834	J Am Med Inform Assoc	2022 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/35190834
Thalamic stereo-EEG in epilepsy surgery: where do we stand?	Bernabei JM, Litt B, Cajigas I	Brain : a journal of neurology	37226526	Brain	2023 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/37226526
Resting-state background features demonstrate multidien cycles in long-term EEG device recordings.	Ojemann WKS, Scheid BH, Mouchtaris S, Lucas A, LaRocque JJ, Aguila C, Ashourvan A, Caciagli L, Davis KA, Conrad EC, Litt B	medRxiv : the preprint server for health sciences	37461688	medRxiv	2023 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/37461688
Quantifying interictal intracranial EEG to predict focal epilepsy.	Gallagher RS, Sinha N, Pattnaik AR, Ojemann WKS, Lucas A, LaRocque JJ, Bernabei JM, Greenblatt AS, Sweeney EM, Chen HI, Davis KA, Conrad EC, Litt B	ArXiv	37547655	ArXiv	2023 Jul 27	https://www.ncbi.nlm.nih.gov/pubmed/37547655
Time-evolving controllability of effective connectivity networks during seizure progression.	Scheid BH, Ashourvan A, Stiso J, Davis KA, Mikhail F, Pasqualetti F, Litt B, Bassett DS	Proceedings of the National Academy of Sciences of the United States of America	33495341	Proc Natl Acad Sci U S A	2021 Feb 2	https://www.ncbi.nlm.nih.gov/pubmed/33495341
A pharmacokinetic model of antiseizure medication load to guide care in the epilepsy monitoring unit.	Ghosn NJ, Xie K, Pattnaik AR, Gugger JJ, Ellis CA, Sweeney E, Fox E, Bernabei JM, Johnson J, Boccanfuso J, Litt B, Conrad EC	Epilepsia	36815252	Epilepsia	2023 May	https://www.ncbi.nlm.nih.gov/pubmed/36815252
Artificial intelligence in epilepsy phenotyping.	Knight A, Gschwind T, Galer P, Worrell GA, Litt B, Soltesz I, Beniczky S	Epilepsia	37983589	Epilepsia	2023 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/37983589
Alcohol for seizure induction in the epilepsy monitoring unit.	Emmert BE, Xie K, Conrad EC, Ghosn NJ, Bauman K, Korzun J, Kulick-Soper CV, Naveed O, Hartmann N, LaRocque JJ, Mindy Ganguly T, Gugger JJ, Raghupathi R, Gelfand MA, Davis KA, Sinha SR, Litt B, Shinohara RT, Ellis CA	Epilepsy & behavior : E&B	38070406	Epilepsy Behav	2024 Jan	https://www.ncbi.nlm.nih.gov/pubmed/38070406
iEEG-recon: A fast and scalable pipeline for accurate reconstruction of intracranial electrodes and implantable devices.	Lucas A, Scheid BH, Pattnaik AR, Gallagher R, Mojena M, Tranquille A, Prager B, Gleichgerrcht E, Gong R, Litt B, Davis KA, Das S, Stein JM, Sinha N	Epilepsia	38148517	Epilepsia	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38148517
Solving brain circuit function and dysfunction with computational modeling and optogenetic fMRI.	Lee JH, Liu Q, Dadgar-Kiani E	Science (New York, N.Y.)	36327349	Science	2022 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/36327349
Repeated hippocampal seizures lead to brain-wide reorganization of circuits and seizure propagation pathways.	Choy M, Dadgar-Kiani E, Cron GO, Duffy BA, Schmid F, Edelman BJ, Asaad M, Chan RW, Vahdat S, Lee JH	Neuron	34706219	Neuron	2022 Jan 19	https://www.ncbi.nlm.nih.gov/pubmed/34706219
Distinct local and brain-wide networks are activated by optogenetic stimulation of neurons specific to each layer of motor cortex.	Chan RW, Cron GO, Asaad M, Edelman BJ, Lee HJ, Adesnik H, Feinberg D, Lee JH	NeuroImage	36176220	Neuroimage	2022 Nov	https://www.ncbi.nlm.nih.gov/pubmed/36176220
Hemispherically lateralized rhythmic oscillations in the cingulate-amygdala circuit drive affective empathy in mice.	Kim SW, Kim M, Baek J, Latchoumane CF, Gangadharan G, Yoon Y, Kim DS, Lee JH, Shin HS	Neuron	36460007	Neuron	2023 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/36460007
Quantitative 3D histochemistry reveals region-specific amyloid-β reduction by the antidiabetic drug netoglitazone.	Catto F, Dadgar-Kiani E, Kirschenbaum D, Economides A, Reuss AM, Trevisan C, Caredio D, Mirzet D, Frick L, Weber-Stadlbauer U, Litvinov S, Koumoutsakos P, Hyung Lee J, Aguzzi A	bioRxiv : the preprint server for biology	39185170	bioRxiv	2024 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/39185170
In patients with late-life depression and cognitive decline, adding tDCS to cognitive training does not significantly affect depressive symptoms but shows potential benefits on cognition as measured by fMRI.	Ha J, Fang Y, Cron GO, Heo J, Jung E, Lee D, Kim H, Kim E, Park JY, Lee JH	Brain stimulation	38367933	Brain Stimul	2024 Mar-Apr	https://www.ncbi.nlm.nih.gov/pubmed/38367933
High-sensitivity detection of optogenetically-induced neural activity with functional ultrasound imaging.	Edelman BJ, Ielacqua GD, Chan RW, Asaad M, Choy M, Lee JH	NeuroImage	34333106	Neuroimage	2021 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/34333106
Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9.	Yang S, Park D, Manning L, Hill SE, Cao M, Xuan Z, Gonzalez I, Dong Y, Clark B, Shao L, Okeke I, Almoril-Porras A, Bai J, De Camilli P, Colón-Ramos DA	Neuron	35065714	Neuron	2022 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/35065714
A genetically encoded tool for reconstituting synthetic modulatory neurotransmission and reconnect neural circuits in vivo.	Hawk JD, Wisdom EM, Sengupta T, Kashlan ZD, Colón-Ramos DA	Nature communications	34373460	Nat Commun	2021 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/34373460
Structural and developmental principles of neuropil assembly in C. elegans.	Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, Bao Z, Shroff H, Mohler WA, Colón-Ramos DA	Nature	33627875	Nature	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33627875
Transmembrane protein ATG-9 links presynaptic autophagy with the synaptic vesicle cycle.	Yang S, Colón-Ramos DA	Autophagy	35349396	Autophagy	2022 Jul	https://www.ncbi.nlm.nih.gov/pubmed/35349396
Transforming the development and dissemination of cutting-edge microscopy and computation.	Colón-Ramos DA, La Riviere P, Shroff H, Oldenbourg R	Nature methods	31363203	Nat Methods	2019 Aug	https://www.ncbi.nlm.nih.gov/pubmed/31363203
The active zone protein Clarinet regulates synaptic sorting of ATG-9 and presynaptic autophagy.	Xuan Z, Yang S, Clark B, Hill SE, Manning L, Colón-Ramos DA	PLoS biology	37053235	PLoS Biol	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/37053235
Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy.	Guo M, Wu Y, Hobson CM, Su Y, Qian S, Krueger E, Christensen R, Kroeschell G, Bui J, Chaw M, Zhang L, Liu J, Hou X, Han X, Lu Z, Ma X, Zhovmer A, Combs C, Moyle M, Yemini E, Liu H, Liu Z, Benedetto A, La Riviere P, Colón-Ramos D, Shroff H	bioRxiv : the preprint server for biology	37986950	bioRxiv	2024 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/37986950
Antagonism between neuropeptides and monoamines in a distributed circuit for pathogen avoidance.	Marquina-Solis J, Feng L, Vandewyer E, Beets I, Hawk J, Colón-Ramos DA, Yu J, Fox BW, Schroeder FC, Bargmann CI	Cell reports	38573858	Cell Rep	2024 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/38573858
NeuroSCAN: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks.	Koonce NL, Emerson SE, Bhaskar D, Kuchroo M, Moyle MW, Arroyo-Morales P, Martínez NV, Krishnaswamy S, Mohler W, Colón-Ramos D	bioRxiv : the preprint server for biology	39484462	bioRxiv	2024 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/39484462
Configuration of electrical synapses filters sensory information to drive behavioral choices.	Almoril-Porras A, Calvo AC, Niu L, Beagan J, Díaz García M, Hawk JD, Aljobeh A, Wisdom EM, Ren I, Wang ZW, Colón-Ramos DA	Cell	39742807	Cell	2025 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/39742807
Phosphofructokinase relocalizes into subcellular compartments with liquid-like properties in vivo.	Jang S, Xuan Z, Lagoy RC, Jawerth LM, Gonzalez IJ, Singh M, Prashad S, Kim HS, Patel A, Albrecht DR, Hyman AA, Colón-Ramos DA	Biophysical journal	32853565	Biophys J	2021 Apr 6	https://www.ncbi.nlm.nih.gov/pubmed/32853565
Multiview confocal super-resolution microscopy.	Wu Y, Han X, Su Y, Glidewell M, Daniels JS, Liu J, Sengupta T, Rey-Suarez I, Fischer R, Patel A, Combs C, Sun J, Wu X, Christensen R, Smith C, Bao L, Sun Y, Duncan LH, Chen J, Pommier Y, Shi YB, Murphy E, Roy S, Upadhyaya A, Colón-Ramos D, La Riviere P, Shroff H	Nature	34837071	Nature	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34837071
Local and dynamic regulation of neuronal glycolysis in vivo.	Wolfe AD, Koberstein JN, Smith CB, Stewart ML, Gonzalez IJ, Hammarlund M, Hyman AA, Stork PJS, Goodman RH, Colón-Ramos DA	Proceedings of the National Academy of Sciences of the United States of America	38198527	Proc Natl Acad Sci U S A	2024 Jan 16	https://www.ncbi.nlm.nih.gov/pubmed/38198527
A muscle-epidermis-glia signaling axis sustains synaptic specificity during allometric growth in Caenorhabditis elegans.	Fan J, Ji T, Wang K, Huang J, Wang M, Manning L, Dong X, Shi Y, Zhang X, Shao Z, Colón-Ramos DA	eLife	32255430	Elife	2020 Apr 7	https://www.ncbi.nlm.nih.gov/pubmed/32255430
Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior.	Kochersberger A, Torkashvand MM, Lee D, Baskoylu S, Sengupta T, Koonce N, Emerson CE, Patel NV, Colón-Ramos D, Flavell S, Horvitz HR, Venkatachalam V, Hammarlund M	bioRxiv : the preprint server for biology	37745399	bioRxiv	2023 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/37745399
Differential adhesion regulates neurite placement via a retrograde zippering mechanism.	Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler WA, Shroff H, Colón-Ramos DA	eLife	34783657	Elife	2021 Nov 16	https://www.ncbi.nlm.nih.gov/pubmed/34783657
Local and dynamic regulation of neuronal glycolysis in vivo.	Wolfe AD, Koberstein JN, Smith CB, Stewart ML, Hammarlund M, Hyman A, Stork PJ, Goodman R, Colón-Ramos DA	bioRxiv : the preprint server for biology	37662365	bioRxiv	2023 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/37662365
The active zone protein CLA-1 (Clarinet) bridges two subsynaptic domains to regulate presynaptic sorting of ATG-9.	Xuan Z, Colón-Ramos DA	Autophagy	37389488	Autophagy	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37389488
Specific configurations of electrical synapses filter sensory information to drive choices in behavior.	Almoril-Porras A, Calvo AC, Niu L, Beagan J, Hawk JD, Aljobeh A, Wisdom EM, Ren I, Díaz-García M, Wang ZW, Colón-Ramos DA	bioRxiv : the preprint server for biology	37577611	bioRxiv	2023 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/37577611
Sleep Analysis in Adult C. elegans Reveals State-Dependent Alteration of Neural and Behavioral Responses.	Lawler DE, Chew YL, Hawk JD, Aljobeh A, Schafer WR, Albrecht DR	The Journal of neuroscience : the official journal of the Society for Neuroscience	33446520	J Neurosci	2021 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/33446520
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates.	Chen X, Wolfe DA, Bindu DS, Zhang M, Taskin N, Goertsen D, Shay TF, Sullivan EE, Huang SF, Ravindra Kumar S, Arokiaraj CM, Plattner VM, Campos LJ, Mich JK, Monet D, Ngo V, Ding X, Omstead V, Weed N, Bishaw Y, Gore BB, Lein ES, Akrami A, Miller C, Levi BP, Keller A, Ting JT, Fox AS, Eroglu C, Gradinaru V	Nature communications	37291094	Nat Commun	2023 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/37291094
Spatial transcriptomics for profiling the tropism of viral vectors in tissues.	Jang MJ, Coughlin GM, Jackson CR, Chen X, Chuapoco MR, Vendemiatti JL, Wang AZ, Gradinaru V	Nature biotechnology	36702899	Nat Biotechnol	2023 Sep	https://www.ncbi.nlm.nih.gov/pubmed/36702899
Primate-conserved carbonic anhydrase IV and murine-restricted LY6C1 enable blood-brain barrier crossing by engineered viral vectors.	Shay TF, Sullivan EE, Ding X, Chen X, Ravindra Kumar S, Goertsen D, Brown D, Crosby A, Vielmetter J, Borsos M, Wolfe DA, Lam AW, Gradinaru V	Science advances	37075114	Sci Adv	2023 Apr 21	https://www.ncbi.nlm.nih.gov/pubmed/37075114
Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types.	Ravindra Kumar S, Miles TF, Chen X, Brown D, Dobreva T, Huang Q, Ding X, Luo Y, Einarsson PH, Greenbaum A, Jang MJ, Deverman BE, Gradinaru V	Nature methods	32313222	Nat Methods	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/32313222
Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain.	Chuapoco MR, Flytzanis NC, Goeden N, Christopher Octeau J, Roxas KM, Chan KY, Scherrer J, Winchester J, Blackburn RJ, Campos LJ, Man KNM, Sun J, Chen X, Lefevre A, Singh VP, Arokiaraj CM, Shay TF, Vendemiatti J, Jang MJ, Mich JK, Bishaw Y, Gore BB, Omstead V, Taskin N, Weed N, Levi BP, Ting JT, Miller CT, Deverman BE, Pickel J, Tian L, Fox AS, Gradinaru V	Nature nanotechnology	37430038	Nat Nanotechnol	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37430038
Engineered AAVs for non-invasive gene delivery to rodent and non-human primate nervous systems.	Chen X, Ravindra Kumar S, Adams CD, Yang D, Wang T, Wolfe DA, Arokiaraj CM, Ngo V, Campos LJ, Griffiths JA, Ichiki T, Mazmanian SK, Osborne PB, Keast JR, Miller CT, Fox AS, Chiu IM, Gradinaru V	Neuron	35643078	Neuron	2022 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/35643078
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.	Bedbrook CN, Yang KK, Robinson JE, Mackey ED, Gradinaru V, Arnold FH	Nature methods	31611694	Nat Methods	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31611694
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates.	Chen X, Wolfe DA, Bindu DS, Zhang M, Taskin N, Goertsen D, Shay TF, Sullivan E, Huang SF, Kumar SR, Arokiaraj CM, Plattner V, Campos LJ, Mich J, Monet D, Ngo V, Ding X, Omstead V, Weed N, Bishaw Y, Gore B, Lein ES, Akrami A, Miller C, Levi BP, Keller A, Ting JT, Fox AS, Eroglu C, Gradinaru V	bioRxiv : the preprint server for biology	36711773	bioRxiv	2023 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/36711773
Human cell surface-AAV interactomes identify LRP6 as blood-brain barrier transcytosis receptor and immune cytokine IL3 as AAV9 binder.	Shay TF, Jang S, Brittain TJ, Chen X, Walker B, Tebbutt C, Fan Y, Wolfe DA, Arokiaraj CM, Sullivan EE, Ding X, Wang TY, Lei Y, Chuapoco MR, Chou TF, Gradinaru V	Nature communications	39245720	Nat Commun	2024 Sep 8	https://www.ncbi.nlm.nih.gov/pubmed/39245720
Electrical and synaptic integration of glioma into neural circuits.	Venkatesh HS, Morishita W, Geraghty AC, Silverbush D, Gillespie SM, Arzt M, Tam LT, Espenel C, Ponnuswami A, Ni L, Woo PJ, Taylor KR, Agarwal A, Regev A, Brang D, Vogel H, Hervey-Jumper S, Bergles DE, Suvà ML, Malenka RC, Monje M	Nature	31534222	Nature	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31534222
Roadmap for the Emerging Field of Cancer Neuroscience.	Monje M, Borniger JC, D'Silva NJ, Deneen B, Dirks PB, Fattahi F, Frenette PS, Garzia L, Gutmann DH, Hanahan D, Hervey-Jumper SL, Hondermarck H, Hurov JB, Kepecs A, Knox SM, Lloyd AC, Magnon C, Saloman JL, Segal RA, Sloan EK, Sun X, Taylor MD, Tracey KJ, Trotman LC, Tuveson DA, Wang TC, White RA, Winkler F	Cell	32302564	Cell	2020 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/32302564
Microenvironmental interactions of oligodendroglial cells.	Yalçın B, Monje M	Developmental cell	34192527	Dev Cell	2021 Jul 12	https://www.ncbi.nlm.nih.gov/pubmed/34192527
Transition to a mesenchymal state in neuroblastoma confers resistance to anti-GD2 antibody via reduced expression of ST8SIA1.	Mabe NW, Huang M, Dalton GN, Alexe G, Schaefer DA, Geraghty AC, Robichaud AL, Conway AS, Khalid D, Mader MM, Belk JA, Ross KN, Sheffer M, Linde MH, Ly N, Yao W, Rotiroti MC, Smith BAH, Wernig M, Bertozzi CR, Monje M, Mitsiades CS, Majeti R, Satpathy AT, Stegmaier K, Majzner RG	Nature cancer	35817829	Nat Cancer	2022 Aug	https://www.ncbi.nlm.nih.gov/pubmed/35817829
Neural Signaling in Cancer.	Keough MB, Monje M	Annual review of neuroscience	35259916	Annu Rev Neurosci	2022 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/35259916
Neuronal hyperexcitability drives central and peripheral nervous system tumor progression in models of neurofibromatosis-1.	Anastasaki C, Mo J, Chen JK, Chatterjee J, Pan Y, Scheaffer SM, Cobb O, Monje M, Le LQ, Gutmann DH	Nature communications	35589737	Nat Commun	2022 May 19	https://www.ncbi.nlm.nih.gov/pubmed/35589737
Diffuse Intrinsic Pontine Glioma: From Diagnosis to Next-Generation Clinical Trials.	Vitanza NA, Monje M	Current treatment options in neurology	31290035	Curr Treat Options Neurol	2019 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/31290035
NF1 mutation drives neuronal activity-dependent initiation of optic glioma.	Pan Y, Hysinger JD, Barron T, Schindler NF, Cobb O, Guo X, Yalçın B, Anastasaki C, Mulinyawe SB, Ponnuswami A, Scheaffer S, Ma Y, Chang KC, Xia X, Toonen JA, Lennon JJ, Gibson EM, Huguenard JR, Liau LM, Goldberg JL, Monje M, Gutmann DH	Nature	34040258	Nature	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/34040258
Neuron-Glial Interactions in Health and Brain Cancer.	Pan Y, Monje M	Advanced biology	35957525	Adv Biol (Weinh)	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35957525
Remote neuronal activity drives glioma infiltration via Sema4f.	Huang-Hobbs E, Cheng YT, Ko Y, Luna-Figueroa E, Lozzi B, Taylor KR, McDonald M, He P, Chen HC, Yang Y, Maleki E, Lee ZF, Murali S, Williamson M, Choi D, Curry R, Bayley J, Woo J, Jalali A, Monje M, Noebels JL, Harmanci AS, Rao G, Deneen B	bioRxiv : the preprint server for biology	36993539	bioRxiv	2023 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/36993539
Cholinergic Neuronal Activity Promotes Diffuse Midline Glioma Growth through Muscarinic Signaling.	Drexler R, Drinnenberg A, Gavish A, Yalcin B, Shamardani K, Rogers A, Mancusi R, Taylor KR, Kim YS, Woo PJ, Ravel A, Tatlock E, Ramakrishnan C, Ayala-Sarmiento AE, Pacheco DRF, Siverts L, Daigle TL, Tasic B, Zeng H, Breunig JJ, Deisseroth K, Monje M	bioRxiv : the preprint server for biology	39386427	bioRxiv	2024 Sep 24	https://www.ncbi.nlm.nih.gov/pubmed/39386427
Emerging mechanistic underpinnings and therapeutic targets for chemotherapy-related cognitive impairment.	Gibson EM, Monje M	Current opinion in oncology	31449084	Curr Opin Oncol	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31449084
GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas.	Majzner RG, Ramakrishna S, Yeom KW, Patel S, Chinnasamy H, Schultz LM, Richards RM, Jiang L, Barsan V, Mancusi R, Geraghty AC, Good Z, Mochizuki AY, Gillespie SM, Toland AMS, Mahdi J, Reschke A, Nie EH, Chau IJ, Rotiroti MC, Mount CW, Baggott C, Mavroukakis S, Egeler E, Moon J, Erickson C, Green S, Kunicki M, Fujimoto M, Ehlinger Z, Reynolds W, Kurra S, Warren KE, Prabhu S, Vogel H, Rasmussen L, Cornell TT, Partap S, Fisher PG, Campen CJ, Filbin MG, Grant G, Sahaf B, Davis KL, Feldman SA, Mackall CL, Monje M	Nature	35130560	Nature	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/35130560
A light-gated transcriptional recorder for detecting cell-cell contacts.	Cho KF, Gillespie SM, Kalogriopoulos NA, Quezada MA, Jacko M, Monje M, Ting AY	eLife	35311648	Elife	2022 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/35311648
Cancer hallmarks intersect with neuroscience in the tumor microenvironment.	Hanahan D, Monje M	Cancer cell	36917953	Cancer Cell	2023 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/36917953
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.	Liu I, Jiang L, Samuelsson ER, Marco Salas S, Beck A, Hack OA, Jeong D, Shaw ML, Englinger B, LaBelle J, Mire HM, Madlener S, Mayr L, Quezada MA, Trissal M, Panditharatna E, Ernst KJ, Vogelzang J, Gatesman TA, Halbert ME, Palova H, Pokorna P, Sterba J, Slaby O, Geyeregger R, Diaz A, Findlay IJ, Dun MD, Resnick A, Suvà ML, Jones DTW, Agnihotri S, Svedlund J, Koschmann C, Haberler C, Czech T, Slavc I, Cotter JA, Ligon KL, Alexandrescu S, Yung WKA, Arrillaga-Romany I, Gojo J, Monje M, Nilsson M, Filbin MG	Nature genetics	36471067	Nat Genet	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36471067
A prognostic neural epigenetic signature in high-grade glioma.	Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann JE, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Göller PC, Sahm F, Menstel JA, Zimmer DN, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL	Nature medicine	38760585	Nat Med	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/38760585
Neuron-oligodendroglial interactions in health and malignant disease.	Taylor KR, Monje M	Nature reviews. Neuroscience	37857838	Nat Rev Neurosci	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37857838
Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State.	Nagaraja S, Quezada MA, Gillespie SM, Arzt M, Lennon JJ, Woo PJ, Hovestadt V, Kambhampati M, Filbin MG, Suva ML, Nazarian J, Monje M	Molecular cell	31588023	Mol Cell	2019 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/31588023
Loss of Adaptive Myelination Contributes to Methotrexate Chemotherapy-Related Cognitive Impairment.	Geraghty AC, Gibson EM, Ghanem RA, Greene JJ, Ocampo A, Goldstein AK, Ni L, Yang T, Marton RM, Paşca SP, Greenberg ME, Longo FM, Monje M	Neuron	31122677	Neuron	2019 Jul 17	https://www.ncbi.nlm.nih.gov/pubmed/31122677
Developmental origins and emerging therapeutic opportunities for childhood cancer.	Filbin M, Monje M	Nature medicine	30842674	Nat Med	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30842674
Microglia in Cancer Therapy-Related Cognitive Impairment.	Gibson EM, Monje M	Trends in neurosciences	33674135	Trends Neurosci	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33674135
Therapeutic strategies for diffuse midline glioma from high-throughput combination drug screening.	Lin GL, Wilson KM, Ceribelli M, Stanton BZ, Woo PJ, Kreimer S, Qin EY, Zhang X, Lennon J, Nagaraja S, Morris PJ, Quezada M, Gillespie SM, Duveau DY, Michalowski AM, Shinn P, Guha R, Ferrer M, Klumpp-Thomas C, Michael S, McKnight C, Minhas P, Itkin Z, Raabe EH, Chen L, Ghanem R, Geraghty AC, Ni L, Andreasson KI, Vitanza NA, Warren KE, Thomas CJ, Monje M	Science translational medicine	31748226	Sci Transl Med	2019 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/31748226
Synaptic Communication in Brain Cancer.	Monje M	Cancer research	32381657	Cancer Res	2020 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/32381657
The bright and the dark side of myelin plasticity: Neuron-glial interactions in health and disease.	Monje M, Káradóttir RT	Seminars in cell & developmental biology	33293232	Semin Cell Dev Biol	2021 Aug	https://www.ncbi.nlm.nih.gov/pubmed/33293232
The neuroscience of cancer.	Mancusi R, Monje M	Nature	37316719	Nature	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/37316719
Glioma synapses recruit mechanisms of adaptive plasticity.	Taylor KR, Barron T, Hui A, Spitzer A, Yalçin B, Ivec AE, Geraghty AC, Hartmann GG, Arzt M, Gillespie SM, Kim YS, Maleki Jahan S, Zhang H, Shamardani K, Su M, Ni L, Du PP, Woo PJ, Silva-Torres A, Venkatesh HS, Mancusi R, Ponnuswami A, Mulinyawe S, Keough MB, Chau I, Aziz-Bose R, Tirosh I, Suvà ML, Monje M	Nature	37914930	Nature	2023 Nov	https://www.ncbi.nlm.nih.gov/pubmed/37914930
Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability.	Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann J, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL	bioRxiv : the preprint server for biology	37609137	bioRxiv	2023 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/37609137
Mild respiratory COVID can cause multi-lineage neural cell and myelin dysregulation.	Fernández-Castañeda A, Lu P, Geraghty AC, Song E, Lee MH, Wood J, O'Dea MR, Dutton S, Shamardani K, Nwangwu K, Mancusi R, Yalçın B, Taylor KR, Acosta-Alvarez L, Malacon K, Keough MB, Ni L, Woo PJ, Contreras-Esquivel D, Toland AMS, Gehlhausen JR, Klein J, Takahashi T, Silva J, Israelow B, Lucas C, Mao T, Peña-Hernández MA, Tabachnikova A, Homer RJ, Tabacof L, Tosto-Mancuso J, Breyman E, Kontorovich A, McCarthy D, Quezado M, Vogel H, Hefti MM, Perl DP, Liddelow S, Folkerth R, Putrino D, Nath A, Iwasaki A, Monje M	Cell	35768006	Cell	2022 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/35768006
Cancer neuroscience: State of the field, emerging directions.	Winkler F, Venkatesh HS, Amit M, Batchelor T, Demir IE, Deneen B, Gutmann DH, Hervey-Jumper S, Kuner T, Mabbott D, Platten M, Rolls A, Sloan EK, Wang TC, Wick W, Venkataramani V, Monje M	Cell	37059069	Cell	2023 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/37059069
Tumor inflammation-associated neurotoxicity.	Mahdi J, Dietrich J, Straathof K, Roddie C, Scott BJ, Davidson TB, Prolo LM, Batchelor TT, Campen CJ, Davis KL, Gust J, Lim M, Majzner RG, Park JR, Partap S, Ramakrishna S, Richards R, Schultz L, Vitanza NA, Wang LD, Mackall CL, Monje M	Nature medicine	37024595	Nat Med	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/37024595
Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas.	Bredel M, Espinosa L, Kim H, Scholtens DM, McElroy JP, Rajbhandari R, Meng W, Kollmeyer TM, Malta TM, Quezada MA, Harsh GR, Lobo-Jarne T, Solé L, Merati A, Nagaraja S, Nair S, White JJ, Thudi NK, Fleming JL, Webb A, Natsume A, Ogawa S, Weber RG, Bertran J, Haque SJ, Hentschel B, Miller CR, Furnari FB, Chan TA, Grosu AL, Weller M, Barnholtz-Sloan JS, Monje M, Noushmehr H, Jenkins RB, Rogers CL, MacDonald DR, Pugh SL, Chakravarti A	Cell reports. Medicine	37343523	Cell Rep Med	2023 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/37343523
The neurobiology of long COVID.	Monje M, Iwasaki A	Neuron	36288726	Neuron	2022 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/36288726
Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain.	Fernández-Castañeda A, Lu P, Geraghty AC, Song E, Lee MH, Wood J, Yalçın B, Taylor KR, Dutton S, Acosta-Alvarez L, Ni L, Contreras-Esquivel D, Gehlhausen JR, Klein J, Lucas C, Mao T, Silva J, Peña-Hernández MA, Tabachnikova A, Takahashi T, Tabacof L, Tosto-Mancuso J, Breyman E, Kontorovich A, McCarthy D, Quezado M, Hefti M, Perl D, Folkerth R, Putrino D, Nath A, Iwasaki A, Monje M	bioRxiv : the preprint server for biology	35043113	bioRxiv	2022 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/35043113
Diffuse intrinsic pontine glioma: molecular landscape and emerging therapeutic targets.	Aziz-Bose R, Monje M	Current opinion in oncology	31464759	Curr Opin Oncol	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31464759
Monosynaptic tracing maps brain-wide afferent oligodendrocyte precursor cell connectivity.	Mount CW, Yalçın B, Cunliffe-Koehler K, Sundaresh S, Monje M	eLife	31625910	Elife	2019 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/31625910
Remote neuronal activity drives glioma progression through SEMA4F.	Huang-Hobbs E, Cheng YT, Ko Y, Luna-Figueroa E, Lozzi B, Taylor KR, McDonald M, He P, Chen HC, Yang Y, Maleki E, Lee ZF, Murali S, Williamson MR, Choi D, Curry R, Bayley J, Woo J, Jalali A, Monje M, Noebels JL, Harmanci AS, Rao G, Deneen B	Nature	37380778	Nature	2023 Jul	https://www.ncbi.nlm.nih.gov/pubmed/37380778
Glioblastoma remodelling of human neural circuits decreases survival.	Krishna S, Choudhury A, Keough MB, Seo K, Ni L, Kakaizada S, Lee A, Aabedi A, Popova G, Lipkin B, Cao C, Nava Gonzales C, Sudharshan R, Egladyous A, Almeida N, Zhang Y, Molinaro AM, Venkatesh HS, Daniel AGS, Shamardani K, Hyer J, Chang EF, Findlay A, Phillips JJ, Nagarajan S, Raleigh DR, Brang D, Monje M, Hervey-Jumper SL	Nature	37138086	Nature	2023 May	https://www.ncbi.nlm.nih.gov/pubmed/37138086
Maladaptive myelination promotes generalized epilepsy progression.	Knowles JK, Xu H, Soane C, Batra A, Saucedo T, Frost E, Tam LT, Fraga D, Ni L, Villar K, Talmi S, Huguenard JR, Monje M	Nature neuroscience	35501379	Nat Neurosci	2022 May	https://www.ncbi.nlm.nih.gov/pubmed/35501379
Activity Shapes Neural Circuit Form and Function: A Historical Perspective.	Pan Y, Monje M	The Journal of neuroscience : the official journal of the Society for Neuroscience	31996470	J Neurosci	2020 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/31996470
Immunotherapy-related cognitive impairment after CAR T cell therapy in mice.	Geraghty AC, Acosta-Alvarez L, Rotiroti M, Dutton S, O'Dea MR, Woo PJ, Xu H, Shamardani K, Mancusi R, Ni L, Mulinyawe SB, Kim WJ, Liddelow SA, Majzner RG, Monje M	bioRxiv : the preprint server for biology	38798554	bioRxiv	2024 May 14	https://www.ncbi.nlm.nih.gov/pubmed/38798554
Nf1 mutation disrupts activity-dependent oligodendroglial plasticity and motor learning in mice.	Pan Y, Hysinger JD, Yalçın B, Lennon JJ, Byun YG, Raghavan P, Schindler NF, Anastasaki C, Chatterjee J, Ni L, Xu H, Malacon K, Jahan SM, Ivec AE, Aghoghovwia BE, Mount CW, Nagaraja S, Scheaffer S, Attardi LD, Gutmann DH, Monje M	Nature neuroscience	38816530	Nat Neurosci	2024 Aug	https://www.ncbi.nlm.nih.gov/pubmed/38816530
Myelin plasticity in the ventral tegmental area is required for opioid reward.	Yalçın B, Pomrenze MB, Malacon K, Drexler R, Rogers AE, Shamardani K, Chau IJ, Taylor KR, Ni L, Contreras-Esquivel D, Malenka RC, Monje M	Nature	38839962	Nature	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/38839962
GABAergic neuron-to-glioma synapses in diffuse midline gliomas.	Barron T, Yalçın B, Su M, Byun YG, Gavish A, Shamardani K, Xu H, Ni L, Soni N, Mehta V, Maleki Jahan S, Kim YS, Taylor KR, Keough MB, Quezada MA, Geraghty AC, Mancusi R, Vo LT, Castañeda EH, Woo PJ, Petritsch CK, Vogel H, Kaila K, Monje M	Nature	39972132	Nature	2025 Mar	https://www.ncbi.nlm.nih.gov/pubmed/39972132
Crim1 and Kelch-like 14 exert complementary dual-directional developmental control over segmentally specific corticospinal axon projection targeting.	Sahni V, Itoh Y, Shnider SJ, Macklis JD	Cell reports	34686337	Cell Rep	2021 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/34686337
Dynamic subtype- and context-specific subcellular RNA regulation in growth cones of developing neurons of the cerebral cortex.	Veeraraghavan P, Engmann AK, Hatch JJ, Itoh Y, Nguyen D, Addison T, Macklis JD	bioRxiv : the preprint server for biology	38328182	bioRxiv	2024 Jan 23	https://www.ncbi.nlm.nih.gov/pubmed/38328182
Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized human neural progenitor cells.	Peter M, Shipman S, Heo J, Macklis JD	iScience	38784012	iScience	2024 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/38784012
BEAM: A combinatorial recombinase toolbox for binary gene expression and mosaic genetic analysis.	Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD	Cell reports	39159043	Cell Rep	2024 Aug 27	https://www.ncbi.nlm.nih.gov/pubmed/39159043
An evolutionarily acquired microRNA shapes development of mammalian cortical projections.	Diaz JL, Siththanandan VB, Lu V, Gonzalez-Nava N, Pasquina L, MacDonald JL, Woodworth MB, Ozkan A, Nair R, He Z, Sahni V, Sarnow P, Palmer TD, Macklis JD, Tharin S	Proceedings of the National Academy of Sciences of the United States of America	33139574	Proc Natl Acad Sci U S A	2020 Nov 17	https://www.ncbi.nlm.nih.gov/pubmed/33139574
Subcellular transcriptomes and proteomes of developing axon projections in the cerebral cortex.	Poulopoulos A, Murphy AJ, Ozkan A, Davis P, Hatch J, Kirchner R, Macklis JD	Nature	30626971	Nature	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30626971
Neuronal subtype-specific growth cone and soma purification from mammalian CNS via fractionation and fluorescent sorting for subcellular analyses and spatial mapping of local transcriptomes and proteomes.	Engmann AK, Hatch JJ, Nanda P, Veeraraghavan P, Ozkan A, Poulopoulos A, Murphy AJ, Macklis JD	Nature protocols	35022617	Nat Protoc	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/35022617
Inter-axonal molecular crosstalk via Lumican proteoglycan sculpts murine cervical corticospinal innervation by distinct subpopulations.	Itoh Y, Sahni V, Shnider SJ, McKee H, Macklis JD	Cell reports	36934325	Cell Rep	2023 Mar 28	https://www.ncbi.nlm.nih.gov/pubmed/36934325
Symmetry in levels of axon-axon homophilic adhesion establishes topography in the corpus callosum and development of connectivity between brain hemispheres.	Poulopoulos A, Davis P, Brandenburg C, Itoh Y, Galazo MJ, Greig LC, Romanowski AJ, Budnik B, Macklis JD	bioRxiv : the preprint server for biology	38585721	bioRxiv	2024 Mar 31	https://www.ncbi.nlm.nih.gov/pubmed/38585721
Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized cortically differentiating human pluripotent stem cells.	Peter M, Shipman S, Macklis JD	bioRxiv : the preprint server for biology	37609140	bioRxiv	2023 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/37609140
Cortical projection neurons with distinct axonal connectivity employ ribosomal complexes with distinct protein compositions.	Tran TP, Budnik B, Froberg JE, Macklis JD	bioRxiv : the preprint server for biology	39763931	bioRxiv	2024 Dec 28	https://www.ncbi.nlm.nih.gov/pubmed/39763931
Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes.	Froberg JE, Durak O, Macklis JD	Cell reports	37624698	Cell Rep	2023 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/37624698
Corticospinal neuron subpopulation-specific developmental genes prospectively indicate mature segmentally specific axon projection targeting.	Sahni V, Shnider SJ, Jabaudon D, Song JHT, Itoh Y, Greig LC, Macklis JD	Cell reports	34686320	Cell Rep	2021 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/34686320
Tle4 controls both developmental acquisition and early post-natal maturation of corticothalamic projection neuron identity.	Galazo MJ, Sweetser DA, Macklis JD	Cell reports	37561632	Cell Rep	2023 Aug 29	https://www.ncbi.nlm.nih.gov/pubmed/37561632
Cbln1 Directs Axon Targeting by Corticospinal Neurons Specifically toward Thoraco-Lumbar Spinal Cord.	Song JHT, Ruven C, Patel P, Ding F, Macklis JD, Sahni V	The Journal of neuroscience : the official journal of the Society for Neuroscience	36823038	J Neurosci	2023 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/36823038
Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors.	Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh C, Basak AN, Macklis JD	bioRxiv : the preprint server for biology	38712174	bioRxiv	2024 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/38712174
Live imaging of follicle stimulating hormone receptors in gonads and bones using near infrared II fluorophore.	Feng Y, Zhu S, Antaris AL, Chen H, Xiao Y, Lu X, Jiang L, Diao S, Yu K, Wang Y, Herraiz S, Yue J, Hong X, Hong G, Cheng Z, Dai H, Hsueh AJ	Chemical science	28626555	Chem Sci	2017 May 1	https://www.ncbi.nlm.nih.gov/pubmed/28626555
Cross-Link-Functionalized Nanoparticles for Rapid Excretion in Nanotheranostic Applications.	Ma Z, Wang F, Zhong Y, Salazar F, Li J, Zhang M, Ren F, Wu AM, Dai H	Angewandte Chemie (Weinheim an der Bergstrasse, Germany)	34334834	Angew Chem Weinheim Bergstr Ger	2020 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/34334834
Rational Design of Molecular Fluorophores for Biological Imaging in the NIR-II Window.	Yang Q, Ma Z, Wang H, Zhou B, Zhu S, Zhong Y, Wang J, Wan H, Antaris A, Ma R, Zhang X, Yang J, Zhang X, Sun H, Liu W, Liang Y, Dai H	Advanced materials (Deerfield Beach, Fla.)	28117499	Adv Mater	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28117499
Boosting the down-shifting luminescence of rare-earth nanocrystals for biological imaging beyond 1500 nm.	Zhong Y, Ma Z, Zhu S, Yue J, Zhang M, Antaris AL, Yuan J, Cui R, Wan H, Zhou Y, Wang W, Huang NF, Luo J, Hu Z, Dai H	Nature communications	28963467	Nat Commun	2017 Sep 29	https://www.ncbi.nlm.nih.gov/pubmed/28963467
Molecular Cancer Imaging in the Second Near-Infrared Window Using a Renal-Excreted NIR-II Fluorophore-Peptide Probe.	Wang W, Ma Z, Zhu S, Wan H, Yue J, Ma H, Ma R, Yang Q, Wang Z, Li Q, Qian Y, Yue C, Wang Y, Fan L, Zhong Y, Zhou Y, Gao H, Ruan J, Hu Z, Liang Y, Dai H	Advanced materials (Deerfield Beach, Fla.)	29682821	Adv Mater	2018 May	https://www.ncbi.nlm.nih.gov/pubmed/29682821
Light-sheet microscopy in the near-infrared II window.	Wang F, Wan H, Ma Z, Zhong Y, Sun Q, Tian Y, Qu L, Du H, Zhang M, Li L, Ma H, Luo J, Liang Y, Li WJ, Hong G, Liu L, Dai H	Nature methods	31086342	Nat Methods	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31086342
In vivo NIR-II structured-illumination light-sheet microscopy.	Wang F, Ma Z, Zhong Y, Salazar F, Xu C, Ren F, Qu L, Wu AM, Dai H	Proceedings of the National Academy of Sciences of the United States of America	33526701	Proc Natl Acad Sci U S A	2021 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/33526701
3D NIR-II Molecular Imaging Distinguishes Targeted Organs with High-Performance NIR-II Bioconjugates.	Zhu S, Herraiz S, Yue J, Zhang M, Wan H, Yang Q, Ma Z, Wang Y, He J, Antaris AL, Zhong Y, Diao S, Feng Y, Zhou Y, Yu K, Hong G, Liang Y, Hsueh AJ, Dai H	Advanced materials (Deerfield Beach, Fla.)	29446156	Adv Mater	2018 Mar	https://www.ncbi.nlm.nih.gov/pubmed/29446156
A bright organic NIR-II nanofluorophore for three-dimensional imaging into biological tissues.	Wan H, Yue J, Zhu S, Uno T, Zhang X, Yang Q, Yu K, Hong G, Wang J, Li L, Ma Z, Gao H, Zhong Y, Su J, Antaris AL, Xia Y, Luo J, Liang Y, Dai H	Nature communications	29563581	Nat Commun	2018 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/29563581
Deep learning for in vivo near-infrared imaging.	Ma Z, Wang F, Wang W, Zhong Y, Dai H	Proceedings of the National Academy of Sciences of the United States of America	33372162	Proc Natl Acad Sci U S A	2021 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/33372162
Shortwave-infrared-light-emitting probes for the in vivo tracking of cancer vaccines and the elicited immune responses.	Ren F, Wang F, Baghdasaryan A, Li Y, Liu H, Hsu R, Wang C, Li J, Zhong Y, Salazar F, Xu C, Jiang Y, Ma Z, Zhu G, Zhao X, Wong KK, Willis R, Christopher Garcia K, Wu A, Mellins E, Dai H	Nature biomedical engineering	37620621	Nat Biomed Eng	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/37620621
Intratumor injected gold molecular clusters for NIR-II imaging and cancer therapy.	Baghdasaryan A, Liu H, Ren F, Hsu R, Jiang Y, Wang F, Zhang M, Grigoryan L, Dai H	Proceedings of the National Academy of Sciences of the United States of America	38261618	Proc Natl Acad Sci U S A	2024 Jan 30	https://www.ncbi.nlm.nih.gov/pubmed/38261618
A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging.	Antaris AL, Chen H, Diao S, Ma Z, Zhang Z, Zhu S, Wang J, Lozano AX, Fan Q, Chew L, Zhu M, Cheng K, Hong X, Dai H, Cheng Z	Nature communications	28524850	Nat Commun	2017 May 19	https://www.ncbi.nlm.nih.gov/pubmed/28524850
Near-Infrared-II Molecular Dyes for Cancer Imaging and Surgery.	Zhu S, Tian R, Antaris AL, Chen X, Dai H	Advanced materials (Deerfield Beach, Fla.)	31025403	Adv Mater	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31025403
Near-Infrared IIb Fluorescence Imaging of Vascular Regeneration with Dynamic Tissue Perfusion Measurement and High Spatial Resolution.	Ma Z, Zhang M, Yue J, Alcazar C, Zhong Y, Doyle TC, Dai H, Huang NF	Advanced functional materials	31327961	Adv Funct Mater	2018 Sep 5	https://www.ncbi.nlm.nih.gov/pubmed/31327961
Bright quantum dots emitting at ∼1,600 nm in the NIR-IIb window for deep tissue fluorescence imaging.	Zhang M, Yue J, Cui R, Ma Z, Wan H, Wang F, Zhu S, Zhou Y, Kuang Y, Zhong Y, Pang DW, Dai H	Proceedings of the National Academy of Sciences of the United States of America	29891702	Proc Natl Acad Sci U S A	2018 Jun 26	https://www.ncbi.nlm.nih.gov/pubmed/29891702
Developing a Bright NIR-II Fluorophore with Fast Renal Excretion and Its Application in Molecular Imaging of Immune Checkpoint PD-L1.	Wan H, Ma H, Zhu S, Wang F, Tian Y, Ma R, Yang Q, Hu Z, Zhu T, Wang W, Ma Z, Zhang M, Zhong Y, Sun H, Liang Y, Dai H	Advanced functional materials	31832053	Adv Funct Mater	2018 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/31832053
In vivo non-invasive confocal fluorescence imaging beyond 1,700 nm using superconducting nanowire single-photon detectors.	Wang F, Ren F, Ma Z, Qu L, Gourgues R, Xu C, Baghdasaryan A, Li J, Zadeh IE, Los JWN, Fognini A, Qin-Dregely J, Dai H	Nature nanotechnology	35606441	Nat Nanotechnol	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35606441
A theranostic agent for cancer therapy and imaging in the second near-infrared window.	Ma Z, Wan H, Wang W, Zhang X, Uno T, Yang Q, Yue J, Gao H, Zhong Y, Tian Y, Sun Q, Liang Y, Dai H	Nano research	31832124	Nano Res	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/31832124
A mini-review on rare-earth down-conversion nanoparticles for NIR-II imaging of biological systems.	Zhong Y, Dai H	Nano research	34336144	Nano Res	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/34336144
Molecular imaging in the second near-infrared window.	Wan H, Du H, Wang F, Dai H	Advanced functional materials	31885529	Adv Funct Mater	2019 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/31885529
In vivo molecular imaging for immunotherapy using ultra-bright near-infrared-IIb rare-earth nanoparticles.	Zhong Y, Ma Z, Wang F, Wang X, Yang Y, Liu Y, Zhao X, Li J, Du H, Zhang M, Cui Q, Zhu S, Sun Q, Wan H, Tian Y, Liu Q, Wang W, Garcia KC, Dai H	Nature biotechnology	31570897	Nat Biotechnol	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31570897
Phosphorylcholine-conjugated gold-molecular clusters improve signal for Lymph Node NIR-II fluorescence imaging in preclinical cancer models.	Baghdasaryan A, Wang F, Ren F, Ma Z, Li J, Zhou X, Grigoryan L, Xu C, Dai H	Nature communications	36153336	Nat Commun	2022 Sep 24	https://www.ncbi.nlm.nih.gov/pubmed/36153336
High-precision tumor resection down to few-cell level guided by NIR-IIb molecular fluorescence imaging.	Wang F, Qu L, Ren F, Baghdasaryan A, Jiang Y, Hsu R, Liang P, Li J, Zhu G, Ma Z, Dai H	Proceedings of the National Academy of Sciences of the United States of America	35380898	Proc Natl Acad Sci U S A	2022 Apr 12	https://www.ncbi.nlm.nih.gov/pubmed/35380898
A SARS-CoV-2 vaccine on an NIR-II/SWIR emitting nanoparticle platform.	Jiang Y, Sanyal M, Hussein NA, Baghdasaryan A, Zhang M, Wang F, Ren F, Li J, Zhu G, Meng Y, Adamska JZ, Mellins E, Dai H	Science advances	39919189	Sci Adv	2025 Feb 7	https://www.ncbi.nlm.nih.gov/pubmed/39919189
How We Think about Targeting RNA with Small Molecules.	Costales MG, Childs-Disney JL, Haniff HS, Disney MD	Journal of medicinal chemistry	32212706	J Med Chem	2020 Sep 10	https://www.ncbi.nlm.nih.gov/pubmed/32212706
Progress toward the development of the small molecule equivalent of small interfering RNA.	Disney MD, Suresh BM, Benhamou RI, Childs-Disney JL	Current opinion in chemical biology	32036231	Curr Opin Chem Biol	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/32036231
A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex.	Angelbello AJ, Benhamou RI, Rzuczek SG, Choudhary S, Tang Z, Chen JL, Roy M, Wang KW, Yildirim I, Jun AS, Thornton CA, Disney MD	Cell chemical biology	33157036	Cell Chem Biol	2021 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/33157036
Precise small-molecule recognition of a toxic CUG RNA repeat expansion.	Rzuczek SG, Colgan LA, Nakai Y, Cameron MD, Furling D, Yasuda R, Disney MD	Nature chemical biology	27941760	Nat Chem Biol	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/27941760
A blood-brain penetrant RNA-targeted small molecule triggers elimination of r(G(4)C(2))(exp) in c9ALS/FTD via the nuclear RNA exosome.	Bush JA, Meyer SM, Fuerst R, Tong Y, Li Y, Benhamou RI, Aikawa H, Zanon PRA, Gibaut QMR, Angelbello AJ, Gendron TF, Zhang YJ, Petrucelli L, Heick Jensen T, Childs-Disney JL, Disney MD	Proceedings of the National Academy of Sciences of the United States of America	36409902	Proc Natl Acad Sci U S A	2022 Nov 29	https://www.ncbi.nlm.nih.gov/pubmed/36409902
Using Genome Sequence to Enable the Design of Medicines and Chemical Probes.	Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD	Chemical reviews	29322778	Chem Rev	2018 Feb 28	https://www.ncbi.nlm.nih.gov/pubmed/29322778
Decreasing the intrinsically disordered protein α-synuclein levels by targeting its structured mRNA with a ribonuclease-targeting chimera.	Tong Y, Zhang P, Yang X, Liu X, Zhang J, Grudniewska M, Jung I, Abegg D, Liu J, Childs-Disney JL, Gibaut QMR, Haniff HS, Adibekian A, Mouradian MM, Disney MD	Proceedings of the National Academy of Sciences of the United States of America	38181056	Proc Natl Acad Sci U S A	2024 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/38181056
Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine.	Disney MD	Journal of the American Chemical Society	30896935	J Am Chem Soc	2019 May 1	https://www.ncbi.nlm.nih.gov/pubmed/30896935
Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence.	Disney MD, Angelbello AJ	Accounts of chemical research	27993012	Acc Chem Res	2016 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/27993012
Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer.	Costales MG, Aikawa H, Li Y, Childs-Disney JL, Abegg D, Hoch DG, Pradeep Velagapudi S, Nakai Y, Khan T, Wang KW, Yildirim I, Adibekian A, Wang ET, Disney MD	Proceedings of the National Academy of Sciences of the United States of America	31964809	Proc Natl Acad Sci U S A	2020 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/31964809
Small molecule alteration of RNA sequence in cells and animals.	Guan L, Luo Y, Ja WW, Disney MD	Bioorganic & medicinal chemistry letters	29079470	Bioorg Med Chem Lett	2018 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/29079470
Methods to identify and optimize small molecules interacting with RNA (SMIRNAs).	Ursu A, Vézina-Dawod S, Disney MD	Drug discovery today	31356880	Drug Discov Today	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31356880
Identifying and validating small molecules interacting with RNA (SMIRNAs).	Disney MD, Velagapudi SP, Li Y, Costales MG, Childs-Disney JL	Methods in enzymology	31239057	Methods Enzymol	2019	https://www.ncbi.nlm.nih.gov/pubmed/31239057
Targeted Degradation of a Hypoxia-Associated Non-coding RNA Enhances the Selectivity of a Small Molecule Interacting with RNA.	Costales MG, Suresh B, Vishnu K, Disney MD	Cell chemical biology	31130520	Cell Chem Biol	2019 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/31130520
Drugging the RNA World.	Disney MD, Dwyer BG, Childs-Disney JL	Cold Spring Harbor perspectives in biology	30385607	Cold Spring Harb Perspect Biol	2018 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/30385607
Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model.	Angelbello AJ, Rzuczek SG, Mckee KK, Chen JL, Olafson H, Cameron MD, Moss WN, Wang ET, Disney MD	Proceedings of the National Academy of Sciences of the United States of America	30926669	Proc Natl Acad Sci U S A	2019 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/30926669
The Hairpin Form of r(G(4)C(2))(exp) in c9ALS/FTD Is Repeat-Associated Non-ATG Translated and a Target for Bioactive Small Molecules.	Wang ZF, Ursu A, Childs-Disney JL, Guertler R, Yang WY, Bernat V, Rzuczek SG, Fuerst R, Zhang YJ, Gendron TF, Yildirim I, Dwyer BG, Rice JE, Petrucelli L, Disney MD	Cell chemical biology	30503283	Cell Chem Biol	2019 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/30503283
A Toxic RNA Catalyzes the Cellular Synthesis of Its Own Inhibitor, Shunting It to Endogenous Decay Pathways.	Benhamou RI, Angelbello AJ, Wang ET, Disney MD	Cell chemical biology	31981476	Cell Chem Biol	2020 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/31981476
Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.	Chen JL, VanEtten DM, Fountain MA, Yildirim I, Disney MD	Biochemistry	28617590	Biochemistry	2017 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/28617590
Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing.	Chen JL, Zhang P, Abe M, Aikawa H, Zhang L, Frank AJ, Zembryski T, Hubbs C, Park H, Withka J, Steppan C, Rogers L, Cabral S, Pettersson M, Wager TT, Fountain MA, Rumbaugh G, Childs-Disney JL, Disney MD	Journal of the American Chemical Society	32364710	J Am Chem Soc	2020 May 13	https://www.ncbi.nlm.nih.gov/pubmed/32364710
Gini Coefficients as a Single Value Metric to Define Chemical Probe Selectivity.	Ursu A, Childs-Disney JL, Angelbello AJ, Costales MG, Meyer SM, Disney MD	ACS chemical biology	32568503	ACS Chem Biol	2020 Aug 21	https://www.ncbi.nlm.nih.gov/pubmed/32568503
Poly(GP) proteins are a useful pharmacodynamic marker for C9ORF72-associated amyotrophic lateral sclerosis.	Gendron TF, Chew J, Stankowski JN, Hayes LR, Zhang YJ, Prudencio M, Carlomagno Y, Daughrity LM, Jansen-West K, Perkerson EA, O'Raw A, Cook C, Pregent L, Belzil V, van Blitterswijk M, Tabassian LJ, Lee CW, Yue M, Tong J, Song Y, Castanedes-Casey M, Rousseau L, Phillips V, Dickson DW, Rademakers R, Fryer JD, Rush BK, Pedraza O, Caputo AM, Desaro P, Palmucci C, Robertson A, Heckman MG, Diehl NN, Wiggs E, Tierney M, Braun L, Farren J, Lacomis D, Ladha S, Fournier CN, McCluskey LF, Elman LB, Toledo JB, McBride JD, Tiloca C, Morelli C, Poletti B, Solca F, Prelle A, Wuu J, Jockel-Balsarotti J, Rigo F, Ambrose C, Datta A, Yang W, Raitcheva D, Antognetti G, McCampbell A, Van Swieten JC, Miller BL, Boxer AL, Brown RH, Bowser R, Miller TM, Trojanowski JQ, Grossman M, Berry JD, Hu WT, Ratti A, Traynor BJ, Disney MD, Benatar M, Silani V, Glass JD, Floeter MK, Rothstein JD, Boylan KB, Petrucelli L	Science translational medicine	28356511	Sci Transl Med	2017 Mar 29	https://www.ncbi.nlm.nih.gov/pubmed/28356511
Studying a Drug-like, RNA-Focused Small Molecule Library Identifies Compounds That Inhibit RNA Toxicity in Myotonic Dystrophy.	Rzuczek SG, Southern MR, Disney MD	ACS chemical biology	26414664	ACS Chem Biol	2015 Dec 18	https://www.ncbi.nlm.nih.gov/pubmed/26414664
Design of a bioactive small molecule that targets r(AUUCU) repeats in spinocerebellar ataxia 10.	Yang WY, Gao R, Southern M, Sarkar PS, Disney MD	Nature communications	27248057	Nat Commun	2016 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/27248057
Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(G(4)C(2)) repeat expansion in vitro and in vivo ALS models.	Bush JA, Aikawa H, Fuerst R, Li Y, Ursu A, Meyer SM, Benhamou RI, Chen JL, Khan T, Wagner-Griffin S, Van Meter MJ, Tong Y, Olafson H, McKee KK, Childs-Disney JL, Gendron TF, Zhang Y, Coyne AN, Wang ET, Yildirim I, Wang KW, Petrucelli L, Rothstein JD, Disney MD	Science translational medicine	34705518	Sci Transl Med	2021 Oct 27	https://www.ncbi.nlm.nih.gov/pubmed/34705518
Small molecule recognition of disease-relevant RNA structures.	Meyer SM, Williams CC, Akahori Y, Tanaka T, Aikawa H, Tong Y, Childs-Disney JL, Disney MD	Chemical Society reviews	32975549	Chem Soc Rev	2020 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/32975549
Development of pharmacophore models for small molecules targeting RNA: Application to the RNA repeat expansion in myotonic dystrophy type 1.	Angelbello AJ, González ÀL, Rzuczek SG, Disney MD	Bioorganic & medicinal chemistry letters	27839685	Bioorg Med Chem Lett	2016 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/27839685
Small Molecule Recognition and Tools to Study Modulation of r(CGG)(exp) in Fragile X-Associated Tremor Ataxia Syndrome.	Yang WY, He F, Strack RL, Oh SY, Frazer M, Jaffrey SR, Todd PK, Disney MD	ACS chemical biology	27276216	ACS Chem Biol	2016 Sep 16	https://www.ncbi.nlm.nih.gov/pubmed/27276216
Small molecule targeting of RNA structures in neurological disorders.	Angelbello AJ, Chen JL, Disney MD	Annals of the New York Academy of Sciences	30964958	Ann N Y Acad Sci	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/30964958
Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA.	Zhang P, Park HJ, Zhang J, Junn E, Andrews RJ, Velagapudi SP, Abegg D, Vishnu K, Costales MG, Childs-Disney JL, Adibekian A, Moss WN, Mouradian MM, Disney MD	Proceedings of the National Academy of Sciences of the United States of America	31900363	Proc Natl Acad Sci U S A	2020 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/31900363
Structure-Specific Cleavage of an RNA Repeat Expansion with a Dimeric Small Molecule Is Advantageous over Sequence-Specific Recognition by an Oligonucleotide.	Benhamou RI, Angelbello AJ, Andrews RJ, Wang ET, Moss WN, Disney MD	ACS chemical biology	31927948	ACS Chem Biol	2020 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/31927948
Optimization of the Linker Domain in a Dimeric Compound that Degrades an r(CUG) Repeat Expansion in Cells.	Benhamou RI, Abe M, Choudhary S, Meyer SM, Angelbello AJ, Disney MD	Journal of medicinal chemistry	32657583	J Med Chem	2020 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/32657583
Macrocyclization of a Ligand Targeting a Toxic RNA Dramatically Improves Potency.	Benhamou RI, Vezina-Dawod S, Choudhary S, Won Wang K, Meyer SM, Yildirim I, Disney MD	Chembiochem : a European journal of chemical biology	32649032	Chembiochem	2020 Nov 16	https://www.ncbi.nlm.nih.gov/pubmed/32649032
Target-Directed Approaches for Screening Small Molecules against RNA Targets.	Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL	SLAS discovery : advancing life sciences R & D	32419578	SLAS Discov	2020 Sep	https://www.ncbi.nlm.nih.gov/pubmed/32419578
Fragment-Based Approaches to Identify RNA Binders.	Suresh BM, Taghavi A, Childs-Disney JL, Disney MD	Journal of medicinal chemistry	37186875	J Med Chem	2023 May 25	https://www.ncbi.nlm.nih.gov/pubmed/37186875
The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology.	Chen JL, Moss WN, Spencer A, Zhang P, Childs-Disney JL, Disney MD	PloS one	31291322	PLoS One	2019	https://www.ncbi.nlm.nih.gov/pubmed/31291322
Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD.	Ursu A, Wang KW, Bush JA, Choudhary S, Chen JL, Baisden JT, Zhang YJ, Gendron TF, Petrucelli L, Yildirim I, Disney MD	ACS chemical biology	33196168	ACS Chem Biol	2020 Dec 18	https://www.ncbi.nlm.nih.gov/pubmed/33196168
A Toxic RNA Templates the Synthesis of Its Own Fluorogenic Inhibitor by Using a Bio-orthogonal Tetrazine Ligation in Cells and Tissues.	Angelbello AJ, Disney MD	ACS chemical biology	32551539	ACS Chem Biol	2020 Jul 17	https://www.ncbi.nlm.nih.gov/pubmed/32551539
Kinetics of Endogenous CaMKII Required for Synaptic Plasticity Revealed by Optogenetic Kinase Inhibitor.	Murakoshi H, Shin ME, Parra-Bueno P, Szatmari EM, Shibata ACE, Yasuda R	Neuron	28318784	Neuron	2017 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/28318784
Rapid Ultrastructural Changes in the PSD and Surrounding Membrane after Induction of Structural LTP in Single Dendritic Spines.	Sun Y, Smirnov M, Kamasawa N, Yasuda R	The Journal of neuroscience : the official journal of the Society for Neuroscience	34266899	J Neurosci	2021 Aug 18	https://www.ncbi.nlm.nih.gov/pubmed/34266899
RGS14 Restricts Plasticity in Hippocampal CA2 by Limiting Postsynaptic Calcium Signaling.	Evans PR, Parra-Bueno P, Smirnov MS, Lustberg DJ, Dudek SM, Hepler JR, Yasuda R	eNeuro	29911178	eNeuro	2018 May-Jun	https://www.ncbi.nlm.nih.gov/pubmed/29911178
Mechanisms of Ca(2+)/calmodulin-dependent kinase II activation in single dendritic spines.	Chang JY, Nakahata Y, Hayano Y, Yasuda R	Nature communications	31239443	Nat Commun	2019 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/31239443
Longitudinal Two-Photon Imaging of Dorsal Hippocampal CA1 in Live Mice.	Ulivi AF, Castello-Waldow TP, Weston G, Yan L, Yasuda R, Chen A, Attardo A	Journal of visualized experiments : JoVE	31282875	J Vis Exp	2019 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/31282875
Rho GTPase complementation underlies BDNF-dependent homo- and heterosynaptic plasticity.	Hedrick NG, Harward SC, Hall CE, Murakoshi H, McNamara JO, Yasuda R	Nature	27680697	Nature	2016 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/27680697
Autocrine BDNF-TrkB signalling within a single dendritic spine.	Harward SC, Hedrick NG, Hall CE, Parra-Bueno P, Milner TA, Pan E, Laviv T, Hempstead BL, Yasuda R, McNamara JO	Nature	27680698	Nature	2016 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/27680698
An open-source tool for analysis and automatic identification of dendritic spines using machine learning.	Smirnov MS, Garrett TR, Yasuda R	PloS one	29975722	PLoS One	2018	https://www.ncbi.nlm.nih.gov/pubmed/29975722
Reciprocal Activation within a Kinase-Effector Complex Underlying Persistence of Structural LTP.	Saneyoshi T, Matsuno H, Suzuki A, Murakoshi H, Hedrick NG, Agnello E, O'Connell R, Stratton MM, Yasuda R, Hayashi Y	Neuron	31078368	Neuron	2019 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/31078368
Virus-Mediated Genome Editing via Homology-Directed Repair in Mitotic and Postmitotic Cells in Mammalian Brain.	Nishiyama J, Mikuni T, Yasuda R	Neuron	29056297	Neuron	2017 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/29056297
PKCα integrates spatiotemporally distinct Ca(2+) and autocrine BDNF signaling to facilitate synaptic plasticity.	Colgan LA, Hu M, Misler JA, Parra-Bueno P, Moran CM, Leitges M, Yasuda R	Nature neuroscience	30013171	Nat Neurosci	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/30013171
ADAP1/Centaurin-α1 Negatively Regulates Dendritic Spine Function and Memory Formation in the Hippocampus.	Szatmari EM, Moran C, Cohen S, Jacob A, Parra-Bueno P, Kamasawa N, Guerrero-Given D, Klein M, Stackman R Jr, Yasuda R	eNeuro	33139322	eNeuro	2021 Jan-Feb	https://www.ncbi.nlm.nih.gov/pubmed/33139322
The NMDA receptor subunit GluN3A regulates synaptic activity-induced and myocyte enhancer factor 2C (MEF2C)-dependent transcription.	Chen LF, Lyons MR, Liu F, Green MV, Hedrick NG, Williams AB, Narayanan A, Yasuda R, West AE	The Journal of biological chemistry	32393578	J Biol Chem	2020 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/32393578
Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins.	Laviv T, Kim BB, Chu J, Lam AJ, Lin MZ, Yasuda R	Nature methods	27798609	Nat Methods	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27798609
Imaging ERK and PKA Activation in Single Dendritic Spines during Structural Plasticity.	Tang S, Yasuda R	Neuron	28285819	Neuron	2017 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/28285819
High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing.	Mikuni T, Nishiyama J, Sun Y, Kamasawa N, Yasuda R	Cell	27180908	Cell	2016 Jun 16	https://www.ncbi.nlm.nih.gov/pubmed/27180908
Automated Remote Focusing, Drift Correction, and Photostimulation to Evaluate Structural Plasticity in Dendritic Spines.	Smirnov MS, Evans PR, Garrett TR, Yan L, Yasuda R	PloS one	28114380	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28114380
In Vivo Imaging of the Coupling between Neuronal and CREB Activity in the Mouse Brain.	Laviv T, Scholl B, Parra-Bueno P, Foote B, Zhang C, Yan L, Hayano Y, Chu J, Yasuda R	Neuron	31883788	Neuron	2020 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/31883788
FRET Imaging of Rho GTPase Activity with Red Fluorescent Protein-Based FRET Pairs.	Bajar BT, Guan X, Lam A, Lin MZ, Yasuda R, Laviv T, Chu J	Methods in molecular biology (Clifton, N.J.)	35147933	Methods Mol Biol	2022	https://www.ncbi.nlm.nih.gov/pubmed/35147933
CaMKII Autophosphorylation Is Necessary for Optimal Integration of Ca(2+) Signals during LTP Induction, but Not Maintenance.	Chang JY, Parra-Bueno P, Laviv T, Szatmari EM, Lee SR, Yasuda R	Neuron	28521133	Neuron	2017 May 17	https://www.ncbi.nlm.nih.gov/pubmed/28521133
Blood-Brain Barrier Permeability Is Regulated by Lipid Transport-Dependent Suppression of Caveolae-Mediated Transcytosis.	Andreone BJ, Chow BW, Tata A, Lacoste B, Ben-Zvi A, Bullock K, Deik AA, Ginty DD, Clish CB, Gu C	Neuron	28416077	Neuron	2017 May 3	https://www.ncbi.nlm.nih.gov/pubmed/28416077
Development and Cell Biology of the Blood-Brain Barrier.	Langen UH, Ayloo S, Gu C	Annual review of cell and developmental biology	31299172	Annu Rev Cell Dev Biol	2019 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/31299172
Control of cerebrovascular patterning by neural activity during postnatal development.	Lacoste B, Gu C	Mechanisms of development	26116138	Mech Dev	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26116138
Bridging barriers: a comparative look at the blood-brain barrier across organisms.	O'Brown NM, Pfau SJ, Gu C	Genes & development	29692355	Genes Dev	2018 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/29692355
Temporal modulation of collective cell behavior controls vascular network topology.	Kur E, Kim J, Tata A, Comin CH, Harrington KI, Costa Lda F, Bentley K, Gu C	eLife	26910011	Elife	2016 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/26910011
Caveolae in CNS arterioles mediate neurovascular coupling.	Chow BW, Nuñez V, Kaplan L, Granger AJ, Bistrong K, Zucker HL, Kumar P, Sabatini BL, Gu C	Nature	32076269	Nature	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/32076269
Neuronal and vascular interactions.	Andreone BJ, Lacoste B, Gu C	Annual review of neuroscience	25782970	Annu Rev Neurosci	2015 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/25782970
Pericyte-to-endothelial cell signaling via vitronectin-integrin regulates blood-CNS barrier.	Ayloo S, Lazo CG, Sun S, Zhang W, Cui B, Gu C	Neuron	35294899	Neuron	2022 May 18	https://www.ncbi.nlm.nih.gov/pubmed/35294899
Transcytosis at the blood-brain barrier.	Ayloo S, Gu C	Current opinion in neurobiology	30708291	Curr Opin Neurobiol	2019 Aug	https://www.ncbi.nlm.nih.gov/pubmed/30708291
Structure and mechanism of blood-brain-barrier lipid transporter MFSD2A.	Wood CAP, Zhang J, Aydin D, Xu Y, Andreone BJ, Langen UH, Dror RO, Gu C, Feng L	Nature	34349262	Nature	2021 Aug	https://www.ncbi.nlm.nih.gov/pubmed/34349262
Neuronal regulation of the blood-brain barrier and neurovascular coupling.	Kaplan L, Chow BW, Gu C	Nature reviews. Neuroscience	32636528	Nat Rev Neurosci	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32636528
Suppression of transcytosis regulates zebrafish blood-brain barrier function.	O'Brown NM, Megason SG, Gu C	eLife	31429822	Elife	2019 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/31429822
Gradual Suppression of Transcytosis Governs Functional Blood-Retinal Barrier Formation.	Chow BW, Gu C	Neuron	28334606	Neuron	2017 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/28334606
The molecular constituents of the blood-brain barrier.	Chow BW, Gu C	Trends in neurosciences	26442694	Trends Neurosci	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26442694
Spreading depolarizations trigger caveolin-1-dependent endothelial transcytosis.	Sadeghian H, Lacoste B, Qin T, Toussay X, Rosa R, Oka F, Chung DY, Takizawa T, Gu C, Ayata C	Annals of neurology	30014540	Ann Neurol	2018 Sep	https://www.ncbi.nlm.nih.gov/pubmed/30014540
Characteristics of blood-brain barrier heterogeneity between brain regions revealed by profiling vascular and perivascular cells.	Pfau SJ, Langen UH, Fisher TM, Prakash I, Nagpurwala F, Lozoya RA, Lee WA, Wu Z, Gu C	Nature neuroscience	39210068	Nat Neurosci	2024 Oct	https://www.ncbi.nlm.nih.gov/pubmed/39210068
Physical principles for scalable neural recording.	Marblestone AH, Zamft BM, Maguire YG, Shapiro MG, Cybulski TR, Glaser JI, Amodei D, Stranges PB, Kalhor R, Dalrymple DA, Seo D, Alon E, Maharbiz MM, Carmena JM, Rabaey JM, Boyden ES, Church GM, Kording KP	Frontiers in computational neuroscience	24187539	Front Comput Neurosci	2013	https://www.ncbi.nlm.nih.gov/pubmed/24187539
Population imaging of neural activity in awake behaving mice.	Piatkevich KD, Bensussen S, Tseng HA, Shroff SN, Lopez-Huerta VG, Park D, Jung EE, Shemesh OA, Straub C, Gritton HJ, Romano MF, Costa E, Sabatini BL, Fu Z, Boyden ES, Han X	Nature	31597963	Nature	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31597963
Cell diversity and network dynamics in photosensitive human brain organoids.	Quadrato G, Nguyen T, Macosko EZ, Sherwood JL, Min Yang S, Berger DR, Maria N, Scholvin J, Goldman M, Kinney JP, Boyden ES, Lichtman JW, Williams ZM, McCarroll SA, Arlotta P	Nature	28445462	Nature	2017 May 4	https://www.ncbi.nlm.nih.gov/pubmed/28445462
Sonofragmentation of Ultrathin 1D Nanomaterials.	Gao R, Gupta I, Boyden ES	Particle & particle systems characterization : measurement and description of particle properties and behavior in powders and other disperse systems	28804214	Part Part Syst Charact	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/28804214
Multiplexed neural recording along a single optical fiber via optical reflectometry.	Rodriques SG, Marblestone AH, Scholvin J, Dapello J, Sarkar D, Mankin M, Gao R, Wood L, Boyden ES	Journal of biomedical optics	27194640	J Biomed Opt	2016 May 1	https://www.ncbi.nlm.nih.gov/pubmed/27194640
Automated in vivo patch-clamp evaluation of extracellular multielectrode array spike recording capability.	Allen BD, Moore-Kochlacs C, Bernstein JG, Kinney JP, Scholvin J, Seoane LF, Chronopoulos C, Lamantia C, Kodandaramaiah SB, Tegmark M, Boyden ES	Journal of neurophysiology	29995597	J Neurophysiol	2018 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/29995597
Evidence for Long-Timescale Patterns of Synaptic Inputs in CA1 of Awake Behaving Mice.	Kolb I, Talei Franzesi G, Wang M, Kodandaramaiah SB, Forest CR, Boyden ES, Singer AC	The Journal of neuroscience : the official journal of the Society for Neuroscience	29279309	J Neurosci	2018 Feb 14	https://www.ncbi.nlm.nih.gov/pubmed/29279309
Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues.	Asano SM, Gao R, Wassie AT, Tillberg PW, Chen F, Boyden ES	Current protocols in cell biology	30070431	Curr Protoc Cell Biol	2018 Sep	https://www.ncbi.nlm.nih.gov/pubmed/30070431
Oxytocin-dependent reopening of a social reward learning critical period with MDMA.	Nardou R, Lewis EM, Rothhaas R, Xu R, Yang A, Boyden E, Dölen G	Nature	30944474	Nature	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/30944474
A theoretical analysis of single molecule protein sequencing via weak binding spectra.	Rodriques SG, Marblestone AH, Boyden ES	PloS one	30921350	PLoS One	2019	https://www.ncbi.nlm.nih.gov/pubmed/30921350
Scalable, Modular Three-Dimensional Silicon Microelectrode Assembly via Electroless Plating.	Scholvin J, Zorzos A, Kinney J, Bernstein J, Moore-Kochlacs C, Kopell N, Fonstad C, Boyden ES	Micromachines	30424369	Micromachines (Basel)	2018 Aug 30	https://www.ncbi.nlm.nih.gov/pubmed/30424369
Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies.	Tillberg PW, Chen F, Piatkevich KD, Zhao Y, Yu CC, English BP, Gao L, Martorell A, Suk HJ, Yoshida F, DeGennaro EM, Roossien DH, Gong G, Seneviratne U, Tannenbaum SR, Desimone R, Cai D, Boyden ES	Nature biotechnology	27376584	Nat Biotechnol	2016 Sep	https://www.ncbi.nlm.nih.gov/pubmed/27376584
Nanoscale imaging of RNA with expansion microscopy.	Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES	Nature methods	27376770	Nat Methods	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27376770
Principles of designing interpretable optogenetic behavior experiments.	Allen BD, Singer AC, Boyden ES	Learning & memory (Cold Spring Harbor, N.Y.)	25787711	Learn Mem	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25787711
Optical imaging. Expansion microscopy.	Chen F, Tillberg PW, Boyden ES	Science (New York, N.Y.)	25592419	Science	2015 Jan 30	https://www.ncbi.nlm.nih.gov/pubmed/25592419
Engineering genetic circuit interactions within and between synthetic minimal cells.	Adamala KP, Martin-Alarcon DA, Guthrie-Honea KR, Boyden ES	Nature chemistry	28430194	Nat Chem	2017 May	https://www.ncbi.nlm.nih.gov/pubmed/28430194
Designing tools for assumption-proof brain mapping.	Marblestone AH, Boyden ES	Neuron	25233303	Neuron	2014 Sep 17	https://www.ncbi.nlm.nih.gov/pubmed/25233303
Temporally precise single-cell-resolution optogenetics.	Shemesh OA, Tanese D, Zampini V, Linghu C, Piatkevich K, Ronzitti E, Papagiakoumou E, Boyden ES, Emiliani V	Nature neuroscience	29184208	Nat Neurosci	2017 Dec	https://www.ncbi.nlm.nih.gov/pubmed/29184208
Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain.	Singer AC, Talei Franzesi G, Kodandaramaiah SB, Flores FJ, Cohen JD, Lee AK, Borgers C, Forest CR, Kopell NJ, Boyden ES	Journal of neurophysiology	28566460	J Neurophysiol	2017 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/28566460
Noninvasive Deep Brain Stimulation via Temporally Interfering Electric Fields.	Grossman N, Bono D, Dedic N, Kodandaramaiah SB, Rudenko A, Suk HJ, Cassara AM, Neufeld E, Kuster N, Tsai LH, Pascual-Leone A, Boyden ES	Cell	28575667	Cell	2017 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/28575667
A novel flexible cuff-like microelectrode for dual purpose, acute and chronic electrical interfacing with the mouse cervical vagus nerve.	Caravaca AS, Tsaava T, Goldman L, Silverman H, Riggott G, Chavan SS, Bouton C, Tracey KJ, Desimone R, Boyden ES, Sohal HS, Olofsson PS	Journal of neural engineering	28628030	J Neural Eng	2017 Dec	https://www.ncbi.nlm.nih.gov/pubmed/28628030
Advances in the automation of whole-cell patch clamp technology.	Suk HJ, Boyden ES, van Welie I	Journal of neuroscience methods	31336060	J Neurosci Methods	2019 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/31336060
Expansion microscopy: principles and uses in biological research.	Wassie AT, Zhao Y, Boyden ES	Nature methods	30573813	Nat Methods	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30573813
Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications.	Zhang YS, Chang JB, Alvarez MM, Trujillo-de Santiago G, Aleman J, Batzaya B, Krishnadoss V, Ramanujam AA, Kazemzadeh-Narbat M, Chen F, Tillberg PW, Dokmeci MR, Boyden ES, Khademhosseini A	Scientific reports	26975883	Sci Rep	2016 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/26975883
In situ genome sequencing resolves DNA sequence and structure in intact biological samples.	Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F	Science (New York, N.Y.)	33384301	Science	2021 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/33384301
Closed-loop, ultraprecise, automated craniotomies.	Pak N, Siegle JH, Kinney JP, Denman DJ, Blanche TJ, Boyden ES	Journal of neurophysiology	25855700	J Neurophysiol	2015 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/25855700
A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters.	Piatkevich KD, Jung EE, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES	Nature chemical biology	29483642	Nat Chem Biol	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29483642
Programmable RNA-binding protein composed of repeats of a single modular unit.	Adamala KP, Martin-Alarcon DA, Boyden ES	Proceedings of the National Academy of Sciences of the United States of America	27118836	Proc Natl Acad Sci U S A	2016 May 10	https://www.ncbi.nlm.nih.gov/pubmed/27118836
Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.	Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, Rodriguez A, Mosaliganti KR, Sheu SH, Pasolli HA, Pang S, Xu CS, Megason SG, Hess H, Lippincott-Schwartz J, Hantman A, Rubin GM, Kirchhausen T, Saalfeld S, Aso Y, Boyden ES, Betzig E	Science (New York, N.Y.)	30655415	Science	2019 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/30655415
Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration.	Yoon YG, Dai P, Wohlwend J, Chang JB, Marblestone AH, Boyden ES	Frontiers in computational neuroscience	29114215	Front Comput Neurosci	2017	https://www.ncbi.nlm.nih.gov/pubmed/29114215
Expansion Mini-Microscopy: An Enabling Alternative in Point-of-Care Diagnostics.	Zhang YS, Santiago GT, Alvarez MM, Schiff SJ, Boyden ES, Khademhosseini A	Current opinion in biomedical engineering	29062977	Curr Opin Biomed Eng	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/29062977
A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy.	Gao R, Yu CJ, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES	Nature nanotechnology	33782587	Nat Nanotechnol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33782587
Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy.	Sarkar D, Kang J, Wassie AT, Schroeder ME, Peng Z, Tarr TB, Tang AH, Niederst ED, Young JZ, Su H, Park D, Yin P, Tsai LH, Blanpied TA, Boyden ES	Nature biomedical engineering	36038771	Nat Biomed Eng	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/36038771
Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues.	Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, IMAXT Grand Challenge Consortium, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES	Nature communications	39939319	Nat Commun	2025 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/39939319
Spatial information in large-scale neural recordings.	Cybulski TR, Glaser JI, Marblestone AH, Zamft BM, Boyden ES, Church GM, Kording KP	Frontiers in computational neuroscience	25653613	Front Comput Neurosci	2014	https://www.ncbi.nlm.nih.gov/pubmed/25653613
Green fluorescent genetically encoded calcium indicator based on calmodulin/M13-peptide from fungi.	Barykina NV, Subach OM, Piatkevich KD, Jung EE, Malyshev AY, Smirnov IV, Bogorodskiy AO, Borshchevskiy VI, Varizhuk AM, Pozmogova GE, Boyden ES, Anokhin KV, Enikolopov GN, Subach FV	PloS one	28837632	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28837632
Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics.	Linghu C, Johnson SL, Valdes PA, Shemesh OA, Park WM, Park D, Piatkevich KD, Wassie AT, Liu Y, An B, Barnes SA, Celiker OT, Yao CC, Yu CJ, Wang R, Adamala KP, Bear MF, Keating AE, Boyden ES	Cell	33232692	Cell	2020 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/33232692
A direct-to-drive neural data acquisition system.	Kinney JP, Bernstein JG, Meyer AJ, Barber JB, Bolivar M, Newbold B, Scholvin J, Moore-Kochlacs C, Wentz CT, Kopell NJ, Boyden ES	Frontiers in neural circuits	26388740	Front Neural Circuits	2015	https://www.ncbi.nlm.nih.gov/pubmed/26388740
Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy.	Prevedel R, Yoon YG, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrödel T, Raskar R, Zimmer M, Boyden ES, Vaziri A	Nature methods	24836920	Nat Methods	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24836920
Gamma frequency entrainment attenuates amyloid load and modifies microglia.	Iaccarino HF, Singer AC, Martorell AJ, Rudenko A, Gao F, Gillingham TZ, Mathys H, Seo J, Kritskiy O, Abdurrob F, Adaikkan C, Canter RG, Rueda R, Brown EN, Boyden ES, Tsai LH	Nature	27929004	Nature	2016 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/27929004
Nucleotide-time alignment for molecular recorders.	Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP	PLoS computational biology	28459860	PLoS Comput Biol	2017 May	https://www.ncbi.nlm.nih.gov/pubmed/28459860
Iterative expansion microscopy.	Chang JB, Chen F, Yoon YG, Jung EE, Babcock H, Kang JS, Asano S, Suk HJ, Pak N, Tillberg PW, Wassie AT, Cai D, Boyden ES	Nature methods	28417997	Nat Methods	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28417997
Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator.	Shemesh OA, Linghu C, Piatkevich KD, Goodwin D, Celiker OT, Gritton HJ, Romano MF, Gao R, Yu CJ, Tseng HA, Bensussen S, Narayan S, Yang CT, Freifeld L, Siciliano CA, Gupta I, Wang J, Pak N, Yoon YG, Ullmann JFP, Guner-Ataman B, Noamany H, Sheinkopf ZR, Park WM, Asano S, Keating AE, Trimmer JS, Reimer J, Tolias AS, Bear MF, Tye KM, Han X, Ahrens MB, Boyden ES	Neuron	32592656	Neuron	2020 Aug 5	https://www.ncbi.nlm.nih.gov/pubmed/32592656
Close-Packed Silicon Microelectrodes for Scalable Spatially Oversampled Neural Recording.	Scholvin J, Kinney JP, Bernstein JG, Moore-Kochlacs C, Kopell N, Fonstad CG, Boyden ES	IEEE transactions on bio-medical engineering	26699649	IEEE Trans Biomed Eng	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26699649
Assembly and operation of the autopatcher for automated intracellular neural recording in vivo.	Kodandaramaiah SB, Holst GL, Wickersham IR, Singer AC, Franzesi GT, McKinnon ML, Forest CR, Boyden ES	Nature protocols	26938115	Nat Protoc	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/26938115
RNA timestamps identify the age of single molecules in RNA sequencing.	Rodriques SG, Chen LM, Liu S, Zhong ED, Scherrer JR, Boyden ES, Chen F	Nature biotechnology	33077959	Nat Biotechnol	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33077959
Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo.	Suk HJ, van Welie I, Kodandaramaiah SB, Allen B, Forest CR, Boyden ES	Neuron	28957673	Neuron	2017 Sep 27	https://www.ncbi.nlm.nih.gov/pubmed/28957673
Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy.	Zhao Y, Bucur O, Irshad H, Chen F, Weins A, Stancu AL, Oh EY, DiStasio M, Torous V, Glass B, Stillman IE, Schnitt SJ, Beck AH, Boyden ES	Nature biotechnology	28714966	Nat Biotechnol	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28714966
Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo.	Suk HJ, van Welie I, Kodandaramaiah SB, Allen B, Forest CR, Boyden ES	Neuron	28858614	Neuron	2017 Aug 30	https://www.ncbi.nlm.nih.gov/pubmed/28858614
3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds.	Oran D, Rodriques SG, Gao R, Asano S, Skylar-Scott MA, Chen F, Tillberg PW, Marblestone AH, Boyden ES	Science (New York, N.Y.)	30545883	Science	2018 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/30545883
Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues.	Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, IMAXT Grand Challenge Consortium, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES	bioRxiv : the preprint server for biology	38496681	bioRxiv	2024 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/38496681
A map of object space in primate inferotemporal cortex.	Bao P, She L, McGill M, Tsao DY	Nature	32494012	Nature	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32494012
Mice and primates use distinct strategies for visual segmentation.	Luongo FJ, Liu L, Ho CLA, Hesse JK, Wekselblatt JB, Lanfranchi FF, Huber D, Tsao DY	eLife	36790170	Elife	2023 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/36790170
A network for scene processing in the macaque temporal lobe.	Kornblith S, Cheng X, Ohayon S, Tsao DY	Neuron	23891401	Neuron	2013 Aug 21	https://www.ncbi.nlm.nih.gov/pubmed/23891401
Temporal multiplexing of perception and memory codes in IT cortex.	She L, Benna MK, Shi Y, Fusi S, Tsao DY	Nature	38750353	Nature	2024 May	https://www.ncbi.nlm.nih.gov/pubmed/38750353
Unsupervised deep learning identifies semantic disentanglement in single inferotemporal face patch neurons.	Higgins I, Chang L, Langston V, Hassabis D, Summerfield C, Tsao D, Botvinick M	Nature communications	34753913	Nat Commun	2021 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/34753913
Identification of nonvisual photomotor response cells in the vertebrate hindbrain.	Kokel D, Dunn TW, Ahrens MB, Alshut R, Cheung CY, Saint-Amant L, Bruni G, Mateus R, van Ham TJ, Shiraki T, Fukada Y, Kojima D, Yeh JR, Mikut R, von Lintig J, Engert F, Peterson RT	The Journal of neuroscience : the official journal of the Society for Neuroscience	23447595	J Neurosci	2013 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/23447595
Whole-brain activity mapping onto a zebrafish brain atlas.	Randlett O, Wee CL, Naumann EA, Nnaemeka O, Schoppik D, Fitzgerald JE, Portugues R, Lacoste AM, Riegler C, Engert F, Schier AF	Nature methods	26778924	Nat Methods	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26778924
A novel mechanism for mechanosensory-based rheotaxis in larval zebrafish.	Oteiza P, Odstrcil I, Lauder G, Portugues R, Engert F	Nature	28700578	Nature	2017 Jul 27	https://www.ncbi.nlm.nih.gov/pubmed/28700578
Neural control and modulation of swimming speed in the larval zebrafish.	Severi KE, Portugues R, Marques JC, O'Malley DM, Orger MB, Engert F	Neuron	25066084	Neuron	2014 Aug 6	https://www.ncbi.nlm.nih.gov/pubmed/25066084
Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior.	Portugues R, Feierstein CE, Engert F, Orger MB	Neuron	24656252	Neuron	2014 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/24656252
Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure.	Swinburne IA, Mosaliganti KR, Upadhyayula S, Liu TL, Hildebrand DGC, Tsai TY, Chen A, Al-Obeidi E, Fass AK, Malhotra S, Engert F, Lichtman JW, Kirchhausen T, Betzig E, Megason SG	eLife	29916365	Elife	2018 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/29916365
Visuomotor transformations underlying hunting behavior in zebrafish.	Bianco IH, Engert F	Current biology : CB	25754638	Curr Biol	2015 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/25754638
The structure and timescales of heat perception in larval zebrafish.	Haesemeyer M, Robson DN, Li JM, Schier AF, Engert F	Cell systems	26640823	Cell Syst	2015 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/26640823
Properties of the Visible Light Phototaxis and UV Avoidance Behaviors in the Larval Zebrafish.	Guggiana-Nilo DA, Engert F	Frontiers in behavioral neuroscience	27594828	Front Behav Neurosci	2016	https://www.ncbi.nlm.nih.gov/pubmed/27594828
Whole-brain serial-section electron microscopy in larval zebrafish.	Hildebrand DGC, Cicconet M, Torres RM, Choi W, Quan TM, Moon J, Wetzel AW, Scott Champion A, Graham BJ, Randlett O, Plummer GS, Portugues R, Bianco IH, Saalfeld S, Baden AD, Lillaney K, Burns R, Vogelstein JT, Schier AF, Lee WA, Jeong WK, Lichtman JW, Engert F	Nature	28489821	Nature	2017 May 18	https://www.ncbi.nlm.nih.gov/pubmed/28489821
Zebrafish neurobiology: from development to circuit function and behaviour.	Engert F, Wilson SW	Developmental neurobiology	22058058	Dev Neurobiol	2012 Mar	https://www.ncbi.nlm.nih.gov/pubmed/22058058
A convergent and essential interneuron pathway for Mauthner-cell-mediated escapes.	Lacoste AM, Schoppik D, Robson DN, Haesemeyer M, Portugues R, Li JM, Randlett O, Wee CL, Engert F, Schier AF	Current biology : CB	25959971	Curr Biol	2015 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/25959971
Whole-field visual motion drives swimming in larval zebrafish via a stochastic process.	Portugues R, Haesemeyer M, Blum ML, Engert F	The Journal of experimental biology	25792753	J Exp Biol	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25792753
Brain-wide neuronal dynamics during motor adaptation in zebrafish.	Ahrens MB, Li JM, Orger MB, Robson DN, Schier AF, Engert F, Portugues R	Nature	22622571	Nature	2012 May 9	https://www.ncbi.nlm.nih.gov/pubmed/22622571
The neural basis of visual behaviors in the larval zebrafish.	Portugues R, Engert F	Current opinion in neurobiology	19896836	Curr Opin Neurobiol	2009 Dec	https://www.ncbi.nlm.nih.gov/pubmed/19896836
From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response.	Naumann EA, Fitzgerald JE, Dunn TW, Rihel J, Sompolinsky H, Engert F	Cell	27814522	Cell	2016 Nov 3	https://www.ncbi.nlm.nih.gov/pubmed/27814522
Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents.	Hou JH, Kralj JM, Douglass AD, Engert F, Cohen AE	Frontiers in physiology	25309445	Front Physiol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25309445
The big data problem: turning maps into knowledge.	Engert F	Neuron	25233305	Neuron	2014 Sep 17	https://www.ncbi.nlm.nih.gov/pubmed/25233305
A high-throughput assay for quantifying appetite and digestive dynamics.	Jordi J, Guggiana-Nilo D, Soucy E, Song EY, Lei Wee C, Engert F	American journal of physiology. Regulatory, integrative and comparative physiology	26108871	Am J Physiol Regul Integr Comp Physiol	2015 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/26108871
Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.	Dunn TW, Mu Y, Narayan S, Randlett O, Naumann EA, Yang CT, Schier AF, Freeman J, Engert F, Ahrens MB	eLife	27003593	Elife	2016 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/27003593
A Brain-wide Circuit Model of Heat-Evoked Swimming Behavior in Larval Zebrafish.	Haesemeyer M, Robson DN, Li JM, Schier AF, Engert F	Neuron	29731253	Neuron	2018 May 16	https://www.ncbi.nlm.nih.gov/pubmed/29731253
Two-photon calcium imaging during fictive navigation in virtual environments.	Ahrens MB, Huang KH, Narayan S, Mensh BD, Engert F	Frontiers in neural circuits	23761738	Front Neural Circuits	2013	https://www.ncbi.nlm.nih.gov/pubmed/23761738
Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery.	Chang TY, Shi P, Steinmeyer JD, Chatnuntawech I, Tillberg P, Love KT, Eimon PM, Anderson DG, Yanik MF	Integrative biology : quantitative biosciences from nano to macro	25184623	Integr Biol (Camb)	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25184623
Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects.	Eimon PM, Ghannad-Rezaie M, De Rienzo G, Allalou A, Wu Y, Gao M, Roy A, Skolnick J, Yanik MF	Nature communications	29335539	Nat Commun	2018 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/29335539
Automated deep-phenotyping of the vertebrate brain.	Allalou A, Wu Y, Ghannad-Rezaie M, Eimon PM, Yanik MF	eLife	28406399	Elife	2017 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/28406399
Basal Forebrain Cholinergic Circuits and Signaling in Cognition and Cognitive Decline.	Ballinger EC, Ananth M, Talmage DA, Role LW	Neuron	27657448	Neuron	2016 Sep 21	https://www.ncbi.nlm.nih.gov/pubmed/27657448
hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function.	Ye J, Beetz N, O'Keeffe S, Tapia JC, Macpherson L, Chen WV, Bassel-Duby R, Olson EN, Maniatis T	Proceedings of the National Academy of Sciences of the United States of America	26039991	Proc Natl Acad Sci U S A	2015 Jun 9	https://www.ncbi.nlm.nih.gov/pubmed/26039991
Pcdhαc2 is required for axonal tiling and assembly of serotonergic circuitries in mice.	Chen WV, Nwakeze CL, Denny CA, O'Keeffe S, Rieger MA, Mountoufaris G, Kirner A, Dougherty JD, Hen R, Wu Q, Maniatis T	Science (New York, N.Y.)	28450636	Science	2017 Apr 28	https://www.ncbi.nlm.nih.gov/pubmed/28450636
Intricate interplay between astrocytes and motor neurons in ALS.	Phatnani HP, Guarnieri P, Friedman BA, Carrasco MA, Muratet M, O'Keeffe S, Nwakeze C, Pauli-Behn F, Newberry KM, Meadows SK, Tapia JC, Myers RM, Maniatis T	Proceedings of the National Academy of Sciences of the United States of America	23388633	Proc Natl Acad Sci U S A	2013 Feb 19	https://www.ncbi.nlm.nih.gov/pubmed/23388633
Astrocyte pathology and the absence of non-cell autonomy in an induced pluripotent stem cell model of TDP-43 proteinopathy.	Serio A, Bilican B, Barmada SJ, Ando DM, Zhao C, Siller R, Burr K, Haghi G, Story D, Nishimura AL, Carrasco MA, Phatnani HP, Shum C, Wilmut I, Maniatis T, Shaw CE, Finkbeiner S, Chandran S	Proceedings of the National Academy of Sciences of the United States of America	23401527	Proc Natl Acad Sci U S A	2013 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/23401527
Axonal transport of TDP-43 mRNA granules is impaired by ALS-causing mutations.	Alami NH, Smith RB, Carrasco MA, Williams LA, Winborn CS, Han SSW, Kiskinis E, Winborn B, Freibaum BD, Kanagaraj A, Clare AJ, Badders NM, Bilican B, Chaum E, Chandran S, Shaw CE, Eggan KC, Maniatis T, Taylor JP	Neuron	24507191	Neuron	2014 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/24507191
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.	Rizvi AH, Camara PG, Kandror EK, Roberts TJ, Schieren I, Maniatis T, Rabadan R	Nature biotechnology	28459448	Nat Biotechnol	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28459448
Key Features of Structural and Functional Organization of Zebrafish Facial Motor Neurons Are Resilient to Disruption of Neuronal Migration.	McArthur KL, Fetcho JR	Current biology : CB	28602649	Curr Biol	2017 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/28602649
Cell type specificity of neurovascular coupling in cerebral cortex.	Uhlirova H, Kılıç K, Tian P, Thunemann M, Desjardins M, Saisan PA, Sakadžić S, Ness TV, Mateo C, Cheng Q, Weldy KL, Razoux F, Vandenberghe M, Cremonesi JA, Ferri CG, Nizar K, Sridhar VB, Steed TC, Abashin M, Fainman Y, Masliah E, Djurovic S, Andreassen OA, Silva GA, Boas DA, Kleinfeld D, Buxton RB, Einevoll GT, Dale AM, Devor A	eLife	27244241	Elife	2016 May 31	https://www.ncbi.nlm.nih.gov/pubmed/27244241
Activation and measurement of free whisking in the lightly anesthetized rodent.	Moore JD, Deschênes M, Kurnikova A, Kleinfeld D	Nature protocols	24992095	Nat Protoc	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/24992095
Entrainment of Arteriole Vasomotor Fluctuations by Neural Activity Is a Basis of Blood-Oxygenation-Level-Dependent "Resting-State" Connectivity.	Mateo C, Knutsen PM, Tsai PS, Shih AY, Kleinfeld D	Neuron	29107517	Neuron	2017 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/29107517
Neurovascular and Immuno-Imaging: From Mechanisms to Therapies. Proceedings of the Inaugural Symposium.	Akassoglou K, Agalliu D, Chang CJ, Davalos D, Grutzendler J, Hillman EM, Khakh BS, Kleinfeld D, McGavern DB, Nelson SJ, Zlokovic BV	Frontiers in neuroscience	26941593	Front Neurosci	2016	https://www.ncbi.nlm.nih.gov/pubmed/26941593
Heightened lateral habenula activity during stress produces brainwide and behavioral substrates of susceptibility.	Zhukovskaya A, Zimmerman CA, Willmore L, Pan-Vazquez A, Janarthanan SR, Lynch LA, Falkner AL, Witten IB	Neuron	39393349	Neuron	2024 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/39393349
Pre-existing visual responses in a projection-defined dopamine population explain individual learning trajectories.	Pan-Vazquez A, Sanchez Araujo Y, McMannon B, Louka M, Bandi A, Haetzel L, Faulkner M, International Brain Laboratory, Pillow JW, Daw ND, Witten IB	Current biology : CB	39413788	Curr Biol	2024 Nov 18	https://www.ncbi.nlm.nih.gov/pubmed/39413788
A neural mechanism for learning from delayed postingestive feedback.	Zimmerman CA, Bolkan SS, Pan-Vazquez A, Wu B, Keppler EF, Meares-Garcia JB, Guthman EM, Fetcho RN, McMannon B, Lee J, Hoag AT, Lynch LA, Janarthanan SR, López Luna JF, Bondy AG, Falkner AL, Wang SS, Witten IB	bioRxiv : the preprint server for biology	37873112	bioRxiv	2024 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/37873112
Cohesin-dependence of neuronal gene expression relates to chromatin loop length.	Calderon L, Weiss FD, Beagan JA, Oliveira MS, Georgieva R, Wang YF, Carroll TS, Dharmalingam G, Gong W, Tossell K, de Paola V, Whilding C, Ungless MA, Fisher AG, Phillips-Cremins JE, Merkenschlager M	eLife	35471149	Elife	2022 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/35471149
Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains.	Girdhar K, Hoffman GE, Bendl J, Rahman S, Dong P, Liao W, Hauberg ME, Sloofman L, Brown L, Devillers O, Kassim BS, Wiseman JR, Park R, Zharovsky E, Jacobov R, Flatow E, Kozlenkov A, Gilgenast T, Johnson JS, Couto L, Peters MA, Phillips-Cremins JE, Hahn CG, Gur RE, Tamminga CA, Lewis DA, Haroutunian V, PsychENCODE Consortium, Dracheva S, Lipska BK, Marenco S, Kundakovic M, Fullard JF, Jiang Y, Roussos P, Akbarian S	Nature neuroscience	35332326	Nat Neurosci	2022 Apr	https://www.ncbi.nlm.nih.gov/pubmed/35332326
Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions.	Maury EA, Sherman MA, Genovese G, Gilgenast TG, Kamath T, Burris SJ, Rajarajan P, Flaherty E, Akbarian S, Chess A, McCarroll SA, Loh PR, Phillips-Cremins JE, Brennand KJ, Macosko EZ, Walters JTR, O'Donovan M, Sullivan P, Psychiatric Genomic Consortium Schizophrenia and CNV workgroup, Brain Somatic Mosaicism Network, Sebat J, Lee EA, Walsh CA	Cell genomics	37601975	Cell Genom	2023 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/37601975
G-quadruplexes associated with R-loops promote CTCF binding.	Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K	Molecular cell	37552993	Mol Cell	2023 Sep 7	https://www.ncbi.nlm.nih.gov/pubmed/37552993
FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data.	Patel R, Pham K, Chandrashekar H, Phillips-Cremins JE	bioRxiv : the preprint server for biology	38948824	bioRxiv	2024 Jun 18	https://www.ncbi.nlm.nih.gov/pubmed/38948824
Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation.	Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE	bioRxiv : the preprint server for biology	38106199	bioRxiv	2023 Dec 5	https://www.ncbi.nlm.nih.gov/pubmed/38106199
Cohesin-mediated loop anchors confine the locations of human replication origins.	Emerson DJ, Zhao PA, Cook AL, Barnett RJ, Klein KN, Saulebekova D, Ge C, Zhou L, Simandi Z, Minsk MK, Titus KR, Wang W, Gong W, Zhang D, Yang L, Venev SV, Gibcus JH, Yang H, Sasaki T, Kanemaki MT, Yue F, Dekker J, Chen CL, Gilbert DM, Phillips-Cremins JE	Nature	35676475	Nature	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35676475
Polygenic burden of short tandem repeat expansions promote risk for Alzheimer's disease.	Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins J	medRxiv : the preprint server for health sciences	38014121	medRxiv	2023 Nov 16	https://www.ncbi.nlm.nih.gov/pubmed/38014121
Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.	Malachowski T, Chandradoss KR, Boya R, Zhou L, Cook AL, Su C, Pham K, Haws SA, Kim JH, Ryu HS, Ge C, Luppino JM, Nguyen SC, Titus KR, Gong W, Wallace O, Joyce EF, Wu H, Rojas LA, Phillips-Cremins JE	Cell	38134876	Cell	2023 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/38134876
3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome.	Haws SA, Simandi Z, Barnett RJ, Phillips-Cremins JE	Cell	35868274	Cell	2022 Jul 21	https://www.ncbi.nlm.nih.gov/pubmed/35868274
A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations.	Chandrashekar H, Simandi Z, Choi H, Ryu HS, Waldman AJ, Nikish A, Muppidi SS, Gong W, Paquet D, Phillips-Cremins JE	bioRxiv : the preprint server for biology	38463966	bioRxiv	2024 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/38463966
MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing.	Su C, Chandradoss KR, Malachowski T, Boya R, Ryu HS, Brennand KJ, Phillips-Cremins JE	bioRxiv : the preprint server for biology	38746155	bioRxiv	2024 May 2	https://www.ncbi.nlm.nih.gov/pubmed/38746155
Programmable RNA sensing for cell monitoring and manipulation.	Qian Y, Li J, Zhao S, Matthews EA, Adoff M, Zhong W, An X, Yeo M, Park C, Yang X, Wang BS, Southwell DG, Huang ZJ	Nature	36198803	Nature	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36198803
The progenitor basis of cortical projection neuron diversity.	Huilgol D, Russ JB, Srivas S, Huang ZJ	Current opinion in neurobiology	37148649	Curr Opin Neurobiol	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37148649
Specific and comprehensive genetic targeting reveals brain-wide distribution and synaptic input patterns of GABAergic axo-axonic interneurons.	Raudales R, Kim G, Kelly SM, Hatfield J, Guan W, Zhao S, Paul A, Qian Y, Li B, Huang ZJ	eLife	39012795	Elife	2024 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/39012795
Direct and indirect neurogenesis generate a mosaic of distinct glutamatergic projection neuron types in cerebral cortex.	Huilgol D, Levine JM, Galbavy W, Wang BS, He M, Suryanarayana SM, Huang ZJ	Neuron	37348506	Neuron	2023 Aug 16	https://www.ncbi.nlm.nih.gov/pubmed/37348506
Cortical glutamatergic projection neuron types contribute to distinct functional subnetworks.	Mohan H, An X, Xu XH, Kondo H, Zhao S, Matho KS, Wang BS, Musall S, Mitra P, Huang ZJ	Nature neuroscience	36690901	Nat Neurosci	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36690901
Specific and comprehensive genetic targeting reveals brain-wide distribution and synaptic input patterns of GABAergic axo-axonic interneurons.	Raudales R, Kim G, Kelly SM, Hatfield J, Guan W, Zhao S, Paul A, Qian Y, Li B, Huang ZJ	bioRxiv : the preprint server for biology	37986757	bioRxiv	2024 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/37986757
RNA-programmable cell type monitoring and manipulation in the human cortex with CellREADR.	Matthews EA, Russ JB, Qian Y, Zhao S, Thompson P, Methani M, Vestal ML, Josh Huang Z, Southwell DG	bioRxiv : the preprint server for biology	39677799	bioRxiv	2024 Dec 6	https://www.ncbi.nlm.nih.gov/pubmed/39677799
Cognitive experience alters cortical involvement in goal-directed navigation.	Arlt C, Barroso-Luque R, Kira S, Bruno CA, Xia N, Chettih SN, Soares S, Pettit NL, Harvey CD	eLife	35735909	Elife	2022 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/35735909
Shared and specialized coding across posterior cortical areas for dynamic navigation decisions.	Tseng SY, Chettih SN, Arlt C, Barroso-Luque R, Harvey CD	Neuron	35679861	Neuron	2022 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/35679861
Representational drift: Emerging theories for continual learning and experimental future directions.	Driscoll LN, Duncker L, Harvey CD	Current opinion in neurobiology	35939861	Curr Opin Neurobiol	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/35939861
ArMo: An Articulated Mesh Approach for Mouse 3D Reconstruction.	Bohnslav JP, Osman MAM, Jaggi A, Soares S, Weinreb C, Datta SR, Harvey CD	bioRxiv : the preprint server for biology	36824774	bioRxiv	2023 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/36824774
A distributed and efficient population code of mixed selectivity neurons for flexible navigation decisions.	Kira S, Safaai H, Morcos AS, Panzeri S, Harvey CD	Nature communications	37055431	Nat Commun	2023 Apr 14	https://www.ncbi.nlm.nih.gov/pubmed/37055431
Cortical responses to touch reflect subcortical integration of LTMR signals.	Emanuel AJ, Lehnert BP, Panzeri S, Harvey CD, Ginty DD	Nature	34789880	Nature	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34789880
DeepEthogram, a machine learning pipeline for supervised behavior classification from raw pixels.	Bohnslav JP, Wimalasena NK, Clausing KJ, Dai YY, Yarmolinsky DA, Cruz T, Kashlan AD, Chiappe ME, Orefice LL, Woolf CJ, Harvey CD	eLife	34473051	Elife	2021 Sep 2	https://www.ncbi.nlm.nih.gov/pubmed/34473051
Mechanoreceptor synapses in the brainstem shape the central representation of touch.	Lehnert BP, Santiago C, Huey EL, Emanuel AJ, Renauld S, Africawala N, Alkislar I, Zheng Y, Bai L, Koutsioumpa C, Hong JT, Magee AR, Harvey CD, Ginty DD	Cell	34637701	Cell	2021 Oct 28	https://www.ncbi.nlm.nih.gov/pubmed/34637701
The structures and functions of correlations in neural population codes.	Panzeri S, Moroni M, Safaai H, Harvey CD	Nature reviews. Neuroscience	35732917	Nat Rev Neurosci	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35732917
Fos ensembles encode and shape stable spatial maps in the hippocampus.	Pettit NL, Yap EL, Greenberg ME, Harvey CD	Nature	36002569	Nature	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/36002569
A cell-type-specific error-correction signal in the posterior parietal cortex.	Green J, Bruno CA, Traunmüller L, Ding J, Hrvatin S, Wilson DE, Khodadad T, Samuels J, Greenberg ME, Harvey CD	Nature	37468637	Nature	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37468637
Specialized structure of neural population codes in parietal cortex outputs.	Safaai H, Wang AY, Kira S, Malerba SB, Panzeri S, Harvey CD	bioRxiv : the preprint server for biology	37662297	bioRxiv	2023 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/37662297
Synaptic wiring motifs in posterior parietal cortex support decision-making.	Kuan AT, Bondanelli G, Driscoll LN, Han J, Kim M, Hildebrand DGC, Graham BJ, Wilson DE, Thomas LA, Panzeri S, Harvey CD, Lee WA	Nature	38383788	Nature	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38383788
Mechanoreceptor signal convergence and transformation in the dorsal horn flexibly shape a diversity of outputs to the brain.	Chirila AM, Rankin G, Tseng SY, Emanuel AJ, Chavez-Martinez CL, Zhang D, Harvey CD, Ginty DD	Cell	36334588	Cell	2022 Nov 23	https://www.ncbi.nlm.nih.gov/pubmed/36334588
Hippocampal place codes are gated by behavioral engagement.	Pettit NL, Yuan XC, Harvey CD	Nature neuroscience	35449355	Nat Neurosci	2022 May	https://www.ncbi.nlm.nih.gov/pubmed/35449355
Intensiometric biosensors visualize the activity of multiple small GTPases in vivo.	Kim J, Lee S, Jung K, Oh WC, Kim N, Son S, Jo Y, Kwon HB, Heo WD	Nature communications	30643148	Nat Commun	2019 Jan 14	https://www.ncbi.nlm.nih.gov/pubmed/30643148
Neural circuitry for maternal oxytocin release induced by infant cries.	Valtcheva S, Issa HA, Bair-Marshall CJ, Martin KA, Jung K, Zhang Y, Kwon HB, Froemke RC	Nature	37730989	Nature	2023 Sep	https://www.ncbi.nlm.nih.gov/pubmed/37730989
Exuberant de novo dendritic spine growth in mature neurons.	Krüssel S, Deb I, Son S, Ewall G, Chang M, Lee HK, do Heo W, Kwon HB	bioRxiv : the preprint server for biology	37546796	bioRxiv	2023 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/37546796
Sleep and circadian rhythm disruption by NPTX2 loss of function.	Roh SE, Xiao M, Delgado A, Kwak C, Savonenko A, Bakker A, Kwon HB, Worley P	bioRxiv : the preprint server for biology	37808783	bioRxiv	2023 Sep 27	https://www.ncbi.nlm.nih.gov/pubmed/37808783
Dopamine-mediated formation of a memory module in the nucleus accumbens for goal-directed navigation.	Jung K, Krüssel S, Yoo S, An M, Burke B, Schappaugh N, Choi Y, Gu Z, Blackshaw S, Costa RM, Kwon HB	Nature neuroscience	39333785	Nat Neurosci	2024 Nov	https://www.ncbi.nlm.nih.gov/pubmed/39333785
Formation of cellular close-ended tunneling nanotubes through mechanical deformation.	Chang M, Lee OC, Bu G, Oh J, Yunn NO, Ryu SH, Kwon HB, Kolomeisky AB, Shim SH, Doh J, Jeon JH, Lee JB	Science advances	35353579	Sci Adv	2022 Apr	https://www.ncbi.nlm.nih.gov/pubmed/35353579
Dysregulation of the mesoprefrontal dopamine circuit mediates an early-life stress-induced synaptic imbalance in the prefrontal cortex.	Oh WC, Rodríguez G, Asede D, Jung K, Hwang IW, Ogelman R, Bolton MM, Kwon HB	Cell reports	33951422	Cell Rep	2021 May 4	https://www.ncbi.nlm.nih.gov/pubmed/33951422
Tagging active neurons by soma-targeted Cal-Light.	Hyun JH, Nagahama K, Namkung H, Mignocchi N, Roh SE, Hannan P, Krüssel S, Kwak C, McElroy A, Liu B, Cui M, Lee S, Lee D, Huganir RL, Worley PF, Sawa A, Kwon HB	Nature communications	36509775	Nat Commun	2022 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/36509775
Intersectional monosynaptic tracing for dissecting subtype-specific organization of GABAergic interneuron inputs.	Yetman MJ, Washburn E, Hyun JH, Osakada F, Hayano Y, Zeng H, Callaway EM, Kwon HB, Taniguchi H	Nature neuroscience	30692688	Nat Neurosci	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30692688
IgSF11 homophilic adhesion proteins promote layer-specific synaptic assembly of the cortical interneuron subtype.	Hayano Y, Ishino Y, Hyun JH, Orozco CG, Steinecke A, Potts E, Oisi Y, Thomas CI, Guerrero-Given D, Kim E, Kwon HB, Kamasawa N, Taniguchi H	Science advances	34261648	Sci Adv	2021 Jul	https://www.ncbi.nlm.nih.gov/pubmed/34261648
An adaptive behavioral control motif mediated by cortical axo-axonic inhibition.	Jung K, Chang M, Steinecke A, Berke B, Choi Y, Oisi Y, Fitzpatrick D, Taniguchi H, Kwon HB	bioRxiv : the preprint server for biology	36945592	bioRxiv	2023 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/36945592
Current and future techniques for detecting oxytocin: Focusing on genetically-encoded GPCR sensors.	Lee D, Kwon HB	Journal of neuroscience methods	34763021	J Neurosci Methods	2022 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/34763021
Environmental Enrichment Sharpens Sensory Acuity by Enhancing Information Coding in Barrel Cortex and Premotor Cortex.	Zheng HJV, Meagher JP, Xu D, Patel YA, O'Connor DH, Kwon HB	eNeuro	33893166	eNeuro	2021 May-Jun	https://www.ncbi.nlm.nih.gov/pubmed/33893166
An adaptive behavioral control motif mediated by cortical axo-axonic inhibition.	Jung K, Chang M, Steinecke A, Burke B, Choi Y, Oisi Y, Fitzpatrick D, Taniguchi H, Kwon HB	Nature neuroscience	37474640	Nat Neurosci	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37474640
H-Ras induces exuberant de novo dendritic protrusion growth in mature neurons regardless of cell type.	Krüssel S, Deb I, Son S, Ewall G, Chang M, Lee HK, Heo WD, Kwon HB	iScience	39220408	iScience	2024 Aug 16	https://www.ncbi.nlm.nih.gov/pubmed/39220408
Global connectivity and local excitability changes underlie antidepressant effects of repetitive transcranial magnetic stimulation.	Eshel N, Keller CJ, Wu W, Jiang J, Mills-Finnerty C, Huemer J, Wright R, Fonzo GA, Ichikawa N, Carreon D, Wong M, Yee A, Shpigel E, Guo Y, McTeague L, Maron-Katz A, Etkin A	Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology	32053828	Neuropsychopharmacology	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/32053828
Cortical Connectivity Moderators of Antidepressant vs Placebo Treatment Response in Major Depressive Disorder: Secondary Analysis of a Randomized Clinical Trial.	Rolle CE, Fonzo GA, Wu W, Toll R, Jha MK, Cooper C, Chin-Fatt C, Pizzagalli DA, Trombello JM, Deckersbach T, Fava M, Weissman MM, Trivedi MH, Etkin A	JAMA psychiatry	31895437	JAMA Psychiatry	2020 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/31895437
The Role of the Dorsal-Lateral Prefrontal Cortex in Reward Sensitivity During Approach-Avoidance Conflict.	Rolle CE, Pedersen ML, Johnson N, Amemori KI, Ironside M, Graybiel AM, Pizzagalli DA, Etkin A	Cerebral cortex (New York, N.Y. : 1991)	34464445	Cereb Cortex	2022 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/34464445
Individualized fMRI connectivity defines signatures of antidepressant and placebo responses in major depression.	Zhao K, Xie H, Fonzo GA, Tong X, Carlisle N, Chidharom M, Etkin A, Zhang Y	Molecular psychiatry	36732585	Mol Psychiatry	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/36732585
Discriminative functional connectivity signature of cocaine use disorder links to rTMS treatment response.	Zhao K, Fonzo GA, Xie H, Oathes DJ, Keller CJ, Carlisle NB, Etkin A, Garza-Villarreal EA, Zhang Y	Nature. Mental health	39279909	Nat Ment Health	2024 Apr	https://www.ncbi.nlm.nih.gov/pubmed/39279909
Identification of psychiatric disorder subtypes from functional connectivity patterns in resting-state electroencephalography.	Zhang Y, Wu W, Toll RT, Naparstek S, Maron-Katz A, Watts M, Gordon J, Jeong J, Astolfi L, Shpigel E, Longwell P, Sarhadi K, El-Said D, Li Y, Cooper C, Chin-Fatt C, Arns M, Goodkind MS, Trivedi MH, Marmar CR, Etkin A	Nature biomedical engineering	33077939	Nat Biomed Eng	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/33077939
Densely sampled stimulus-response map of human cortex with single pulse TMS-EEG and its relation to whole brain neuroimaging measures.	Sun Y, Lucas MV, Cline CC, Menezes MC, Kim S, Badami FS, Narayan M, Wu W, Daskalakis ZJ, Etkin A, Saggar M	bioRxiv : the preprint server for biology	38948696	bioRxiv	2024 Jun 17	https://www.ncbi.nlm.nih.gov/pubmed/38948696
Towards objective definition of psychopathology in post-traumatic stress disorder.	Etkin A	Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology	31488889	Neuropsychopharmacology	2020 Jan	https://www.ncbi.nlm.nih.gov/pubmed/31488889
Identification of Common Neural Circuit Disruptions in Emotional Processing Across Psychiatric Disorders.	McTeague LM, Rosenberg BM, Lopez JW, Carreon DM, Huemer J, Jiang Y, Chick CF, Eickhoff SB, Etkin A	The American journal of psychiatry	31964160	Am J Psychiatry	2020 May 1	https://www.ncbi.nlm.nih.gov/pubmed/31964160
An electroencephalographic signature predicts antidepressant response in major depression.	Wu W, Zhang Y, Jiang J, Lucas MV, Fonzo GA, Rolle CE, Cooper C, Chin-Fatt C, Krepel N, Cornelssen CA, Wright R, Toll RT, Trivedi HM, Monuszko K, Caudle TL, Sarhadi K, Jha MK, Trombello JM, Deckersbach T, Adams P, McGrath PJ, Weissman MM, Fava M, Pizzagalli DA, Arns M, Trivedi MH, Etkin A	Nature biotechnology	32042166	Nat Biotechnol	2020 Apr	https://www.ncbi.nlm.nih.gov/pubmed/32042166
A data-driven framework for mapping domains of human neurobiology.	Beam E, Potts C, Poldrack RA, Etkin A	Nature neuroscience	34764476	Nat Neurosci	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34764476
A generalizable functional connectivity signature characterizes brain dysfunction and links to rTMS treatment response in cocaine use disorder.	Zhao K, Fonzo GA, Xie H, Oathes DJ, Keller CJ, Carlisle N, Etkin A, Garza-Villarreal EA, Zhang Y	medRxiv : the preprint server for health sciences	37162878	medRxiv	2023 May 4	https://www.ncbi.nlm.nih.gov/pubmed/37162878
Individual Deviations from Normative Electroencephalographic Connectivity Predict Antidepressant Response.	Tong X, Xie H, Wu W, Keller C, Fonzo G, Chidharom M, Carlisle N, Etkin A, Zhang Y	medRxiv : the preprint server for health sciences	37292874	medRxiv	2023 May 28	https://www.ncbi.nlm.nih.gov/pubmed/37292874
Opportunities for use of neuroimaging in de-risking drug development and improving clinical outcomes in psychiatry: an industry perspective.	Etkin A, Powell J, Savitz AJ	Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology	39169213	Neuropsychopharmacology	2024 Nov	https://www.ncbi.nlm.nih.gov/pubmed/39169213
Individual deviations from normative electroencephalographic connectivity predict antidepressant response.	Tong X, Xie H, Wu W, Keller CJ, Fonzo GA, Chidharom M, Carlisle NB, Etkin A, Zhang Y	Journal of affective disorders	38281595	J Affect Disord	2024 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/38281595
Maternal Priming of Offspring Immune System in Drosophila.	Bozler J, Kacsoh BZ, Bosco G	G3 (Bethesda, Md.)	31685524	G3 (Bethesda)	2020 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/31685524
Nematocytes: Discovery and characterization of a novel anculeate hemocyte in Drosophila falleni and Drosophila phalerata.	Bozler J, Kacsoh BZ, Bosco G	PloS one	29141015	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/29141015
A novel paradigm for nonassociative long-term memory in Drosophila: predator-induced changes in oviposition behavior.	Kacsoh BZ, Bozler J, Hodge S, Ramaswami M, Bosco G	Genetics	25633088	Genetics	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25633088
Olfactory inputs regulate Drosophila melanogaster oogenesis.	Sadanandappa MK, Bosco G	The Journal of experimental biology	39660407	J Exp Biol	2024 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/39660407
Condensins exert force on chromatin-nuclear envelope tethers to mediate nucleoplasmic reticulum formation in Drosophila melanogaster.	Bozler J, Nguyen HQ, Rogers GC, Bosco G	G3 (Bethesda, Md.)	25552604	G3 (Bethesda)	2014 Dec 30	https://www.ncbi.nlm.nih.gov/pubmed/25552604
Machine Learning Analysis Identifies Drosophila Grunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning.	Kacsoh BZ, Greene CS, Bosco G	G3 (Bethesda, Md.)	28889104	G3 (Bethesda)	2017 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/28889104
A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes.	Bozler J, Kacsoh BZ, Chen H, Theurkauf WE, Weng Z, Bosco G	PLoS genetics	29084214	PLoS Genet	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/29084214
Neuropeptide F signaling regulates parasitoid-specific germline development and egg-laying in Drosophila.	Sadanandappa MK, Sathyanarayana SH, Kondo S, Bosco G	PLoS genetics	33770070	PLoS Genet	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33770070
Social communication of predator-induced changes in Drosophila behavior and germ line physiology.	Kacsoh BZ, Bozler J, Ramaswami M, Bosco G	eLife	25970035	Elife	2015 May 13	https://www.ncbi.nlm.nih.gov/pubmed/25970035
Neural circuitry of social learning in Drosophila requires multiple inputs to facilitate inter-species communication.	Kacsoh BZ, Bozler J, Hodge S, Bosco G	Communications biology	31428697	Commun Biol	2019	https://www.ncbi.nlm.nih.gov/pubmed/31428697
New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.	Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G	G3 (Bethesda, Md.)	30463884	G3 (Bethesda)	2019 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/30463884
The Photoconvertible Fluorescent Probe, CaMPARI, Labels Active Neurons in Freely-Moving Intact Adult Fruit Flies.	Edwards KA, Hoppa MB, Bosco G	Frontiers in neural circuits	32457580	Front Neural Circuits	2020	https://www.ncbi.nlm.nih.gov/pubmed/32457580
Drosophila species learn dialects through communal living.	Kacsoh BZ, Bozler J, Bosco G	PLoS genetics	30024883	PLoS Genet	2018 Jul	https://www.ncbi.nlm.nih.gov/pubmed/30024883
Transgeneratonal inheritance of ethanol preference is caused by maternal NPF repression.	Bozler J, Kacsoh BZ, Bosco G	eLife	31287057	Elife	2019 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/31287057
Correction: Drosophila species learn dialects through communal living.	Kacsoh BZ, Bozler J, Bosco G	PLoS genetics	30481167	PLoS Genet	2018 Nov	https://www.ncbi.nlm.nih.gov/pubmed/30481167
Parasitoid cues modulate Drosophila germline development and stem cell proliferation.	Sadanandappa MK, Bosco G	Cell reports	38175752	Cell Rep	2024 Jan 23	https://www.ncbi.nlm.nih.gov/pubmed/38175752
Physical bioenergetics: Energy fluxes, budgets, and constraints in cells.	Yang X, Heinemann M, Howard J, Huber G, Iyer-Biswas S, Le Treut G, Lynch M, Montooth KL, Needleman DJ, Pigolotti S, Rodenfels J, Ronceray P, Shankar S, Tavassoly I, Thutupalli S, Titov DV, Wang J, Foster PJ	Proceedings of the National Academy of Sciences of the United States of America	34140336	Proc Natl Acad Sci U S A	2021 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/34140336
Focal laser stimulation of fly nociceptors activates distinct axonal and dendritic Ca(2+) signals.	Basak R, Sutradhar S, Howard J	Biophysical journal	34175294	Biophys J	2021 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/34175294
The narrowing of dendrite branches across nodes follows a well-defined scaling law.	Liao M, Liang X, Howard J	Proceedings of the National Academy of Sciences of the United States of America	34215693	Proc Natl Acad Sci U S A	2021 Jul 6	https://www.ncbi.nlm.nih.gov/pubmed/34215693
Nicotinamide adenine dinucleotides and their precursor NMN have no direct effect on microtubule dynamics in purified brain tubulin.	Luchniak A, Mahamdeh M, Howard J	PloS one	31393939	PLoS One	2019	https://www.ncbi.nlm.nih.gov/pubmed/31393939
Predicted Effects of Severing Enzymes on the Length Distribution and Total Mass of Microtubules.	Kuo YW, Trottier O, Howard J	Biophysical journal	31708162	Biophys J	2019 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/31708162
Cutting, Amplifying, and Aligning Microtubules with Severing Enzymes.	Kuo YW, Howard J	Trends in cell biology	33183955	Trends Cell Biol	2021 Jan	https://www.ncbi.nlm.nih.gov/pubmed/33183955
Dynamic instability of dendrite tips generates the highly branched morphologies of sensory neurons.	Shree S, Sutradhar S, Trottier O, Tu Y, Liang X, Howard J	Science advances	35767611	Sci Adv	2022 Jul	https://www.ncbi.nlm.nih.gov/pubmed/35767611
Protocol for Imaging the Same Class IV Neurons at Different Stages of Development.	Shree S, Howard J	Bio-protocol	39210953	Bio Protoc	2024 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/39210953
In Vitro Reconstitution of Microtubule Dynamics and Severing Imaged by Label-Free Interference-Reflection Microscopy.	Kuo YW, Howard J	Methods in molecular biology (Clifton, N.J.)	35476326	Methods Mol Biol	2022	https://www.ncbi.nlm.nih.gov/pubmed/35476326
Spastin is a dual-function enzyme that severs microtubules and promotes their regrowth to increase the number and mass of microtubules.	Kuo YW, Trottier O, Mahamdeh M, Howard J	Proceedings of the National Academy of Sciences of the United States of America	30837315	Proc Natl Acad Sci U S A	2019 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/30837315
Structural Biology: Piezo Senses Tension through Curvature.	Liang X, Howard J	Current biology : CB	29689211	Curr Biol	2018 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/29689211
Enhancing GAT-3 in thalamic astrocytes promotes resilience to brain injury in rodents.	Cho FS, Vainchtein ID, Voskobiynyk Y, Morningstar AR, Aparicio F, Higashikubo B, Ciesielska A, Broekaart DWM, Anink JJ, van Vliet EA, Yu X, Khakh BS, Aronica E, Molofsky AV, Paz JT	Science translational medicine	35857628	Sci Transl Med	2022 Jul 6	https://www.ncbi.nlm.nih.gov/pubmed/35857628
Astrocyte-Neuron Interactions in the Striatum: Insights on Identity, Form, and Function.	Khakh BS	Trends in neurosciences	31351745	Trends Neurosci	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31351745
Diversity of astrocyte functions and phenotypes in neural circuits.	Khakh BS, Sofroniew MV	Nature neuroscience	26108722	Nat Neurosci	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26108722
Astrocyte calcium signaling: from observations to functions and the challenges therein.	Khakh BS, McCarthy KD	Cold Spring Harbor perspectives in biology	25605709	Cold Spring Harb Perspect Biol	2015 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/25605709
Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence.	Chai H, Diaz-Castro B, Shigetomi E, Monte E, Octeau JC, Yu X, Cohn W, Rajendran PS, Vondriska TM, Whitelegge JP, Coppola G, Khakh BS	Neuron	28712653	Neuron	2017 Aug 2	https://www.ncbi.nlm.nih.gov/pubmed/28712653
Imaging intracellular Ca²⁺ signals in striatal astrocytes from adult mice using genetically-encoded calcium indicators.	Jiang R, Haustein MD, Sofroniew MV, Khakh BS	Journal of visualized experiments : JoVE	25490346	J Vis Exp	2014 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/25490346
Conditions and constraints for astrocyte calcium signaling in the hippocampal mossy fiber pathway.	Haustein MD, Kracun S, Lu XH, Shih T, Jackson-Weaver O, Tong X, Xu J, Yang XW, O'Dell TJ, Marvin JS, Ellisman MH, Bushong EA, Looger LL, Khakh BS	Neuron	24742463	Neuron	2014 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/24742463
Astrocyte Kir4.1 ion channel deficits contribute to neuronal dysfunction in Huntington's disease model mice.	Tong X, Ao Y, Faas GC, Nwaobi SE, Xu J, Haustein MD, Anderson MA, Mody I, Olsen ML, Sofroniew MV, Khakh BS	Nature neuroscience	24686787	Nat Neurosci	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24686787
Astrocytes and Huntington's disease.	Khakh BS, Sofroniew MV	ACS chemical neuroscience	24842291	ACS Chem Neurosci	2014 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/24842291
Astrocyte scar formation aids central nervous system axon regeneration.	Anderson MA, Burda JE, Ren Y, Ao Y, O'Shea TM, Kawaguchi R, Coppola G, Khakh BS, Deming TJ, Sofroniew MV	Nature	27027288	Nature	2016 Apr 14	https://www.ncbi.nlm.nih.gov/pubmed/27027288
Unravelling and Exploiting Astrocyte Dysfunction in Huntington's Disease.	Khakh BS, Beaumont V, Cachope R, Munoz-Sanjuan I, Goldman SA, Grantyn R	Trends in neurosciences	28578789	Trends Neurosci	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28578789
Breakdown of spatial coding and interneuron synchronization in epileptic mice.	Shuman T, Aharoni D, Cai DJ, Lee CR, Chavlis S, Page-Harley L, Vetere LM, Feng Y, Yang CY, Mollinedo-Gajate I, Chen L, Pennington ZT, Taxidis J, Flores SE, Cheng K, Javaherian M, Kaba CC, Rao N, La-Vu M, Pandi I, Shtrahman M, Bakhurin KI, Masmanidis SC, Khakh BS, Poirazi P, Silva AJ, Golshani P	Nature neuroscience	31907437	Nat Neurosci	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/31907437
Context-Specific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable.	Yu X, Nagai J, Marti-Solano M, Soto JS, Coppola G, Babu MM, Khakh BS	Neuron	33086039	Neuron	2020 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/33086039
Making, Testing, and Using Potassium Ion Selective Microelectrodes in Tissue Slices of Adult Brain.	Octeau JC, Faas G, Mody I, Khakh BS	Journal of visualized experiments : JoVE	29781998	J Vis Exp	2018 May 7	https://www.ncbi.nlm.nih.gov/pubmed/29781998
An Optical Neuron-Astrocyte Proximity Assay at Synaptic Distance Scales.	Octeau JC, Chai H, Jiang R, Bonanno SL, Martin KC, Khakh BS	Neuron	29621490	Neuron	2018 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/29621490
Local and CNS-Wide Astrocyte Intracellular Calcium Signaling Attenuation In Vivo with CalEx(flox) Mice.	Yu X, Moye SL, Khakh BS	The Journal of neuroscience : the official journal of the Society for Neuroscience	33903221	J Neurosci	2021 May 26	https://www.ncbi.nlm.nih.gov/pubmed/33903221
Hyperactivity with Disrupted Attention by Activation of an Astrocyte Synaptogenic Cue.	Nagai J, Rajbhandari AK, Gangwani MR, Hachisuka A, Coppola G, Masmanidis SC, Fanselow MS, Khakh BS	Cell	31031006	Cell	2019 May 16	https://www.ncbi.nlm.nih.gov/pubmed/31031006
Transient, Consequential Increases in Extracellular Potassium Ions Accompany Channelrhodopsin2 Excitation.	Octeau JC, Gangwani MR, Allam SL, Tran D, Huang S, Hoang-Trong TM, Golshani P, Rumbell TH, Kozloski JR, Khakh BS	Cell reports	31116972	Cell Rep	2019 May 21	https://www.ncbi.nlm.nih.gov/pubmed/31116972
A genetically encoded single-wavelength sensor for imaging cytosolic and cell surface ATP.	Lobas MA, Tao R, Nagai J, Kronschläger MT, Borden PM, Marvin JS, Looger LL, Khakh BS	Nature communications	30755613	Nat Commun	2019 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/30755613
Probing the Complexities of Astrocyte Calcium Signaling.	Shigetomi E, Patel S, Khakh BS	Trends in cell biology	26896246	Trends Cell Biol	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/26896246
New Transgenic Mouse Lines for Selectively Targeting Astrocytes and Studying Calcium Signals in Astrocyte Processes In Situ and In Vivo.	Srinivasan R, Lu TY, Chai H, Xu J, Huang BS, Golshani P, Coppola G, Khakh BS	Neuron	27939582	Neuron	2016 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/27939582
New Insights on Astrocyte Ion Channels: Critical for Homeostasis and Neuron-Glia Signaling.	Olsen ML, Khakh BS, Skatchkov SN, Zhou M, Lee CJ, Rouach N	The Journal of neuroscience : the official journal of the Society for Neuroscience	26468182	J Neurosci	2015 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/26468182
Ca(2+) signaling in astrocytes from Ip3r2(-/-) mice in brain slices and during startle responses in vivo.	Srinivasan R, Huang BS, Venugopal S, Johnston AD, Chai H, Zeng H, Golshani P, Khakh BS	Nature neuroscience	25894291	Nat Neurosci	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25894291
Dysfunctional Calcium and Glutamate Signaling in Striatal Astrocytes from Huntington's Disease Model Mice.	Jiang R, Diaz-Castro B, Looger LL, Khakh BS	The Journal of neuroscience : the official journal of the Society for Neuroscience	27013675	J Neurosci	2016 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/27013675
Reducing Astrocyte Calcium Signaling In Vivo Alters Striatal Microcircuits and Causes Repetitive Behavior.	Yu X, Taylor AMW, Nagai J, Golshani P, Evans CJ, Coppola G, Khakh BS	Neuron	30174118	Neuron	2018 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/30174118
General anesthetics activate a potent central pain-suppression circuit in the amygdala.	Hua T, Chen B, Lu D, Sakurai K, Zhao S, Han BX, Kim J, Yin L, Chen Y, Lu J, Wang F	Nature neuroscience	32424286	Nat Neurosci	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32424286
Presynaptic Inputs to Any CNS Projection Neuron Identified by Dual Recombinant Virus Infection.	Bráz JM, Wang F, Basbaum AI	PloS one	26470056	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26470056
State-dependent architecture of thalamic reticular subnetworks.	Halassa MM, Chen Z, Wimmer RD, Brunetti PM, Zhao S, Zikopoulos B, Wang F, Brown EN, Wilson MA	Cell	25126786	Cell	2014 Aug 14	https://www.ncbi.nlm.nih.gov/pubmed/25126786
A craniofacial-specific monosynaptic circuit enables heightened affective pain.	Rodriguez E, Sakurai K, Xu J, Chen Y, Toda K, Zhao S, Han BX, Ryu D, Yin H, Liedtke W, Wang F	Nature neuroscience	29184209	Nat Neurosci	2017 Dec	https://www.ncbi.nlm.nih.gov/pubmed/29184209
MIN1PIPE: A Miniscope 1-Photon-Based Calcium Imaging Signal Extraction Pipeline.	Lu J, Li C, Singh-Alvarado J, Zhou ZC, Fröhlich F, Mooney R, Wang F	Cell reports	29925007	Cell Rep	2018 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/29925007
Capturing and Manipulating Activated Neuronal Ensembles with CANE Delineates a Hypothalamic Social-Fear Circuit.	Sakurai K, Zhao S, Takatoh J, Rodriguez E, Lu J, Leavitt AD, Fu M, Han BX, Wang F	Neuron	27974160	Neuron	2016 Nov 23	https://www.ncbi.nlm.nih.gov/pubmed/27974160
A Specialized Neural Circuit Gates Social Vocalizations in the Mouse.	Tschida K, Michael V, Takatoh J, Han BX, Zhao S, Sakurai K, Mooney R, Wang F	Neuron	31204083	Neuron	2019 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/31204083
A mast cell-thermoregulatory neuron circuit axis regulates hypothermia in anaphylaxis.	Bao C, Chen O, Sheng H, Zhang J, Luo Y, Hayes BW, Liang H, Liedtke W, Ji RR, Abraham SN	Science immunology	36930731	Sci Immunol	2023 Mar 17	https://www.ncbi.nlm.nih.gov/pubmed/36930731
A Common Neuroendocrine Substrate for Diverse General Anesthetics and Sleep.	Jiang-Xie LF, Yin L, Zhao S, Prevosto V, Han BX, Dzirasa K, Wang F	Neuron	31006556	Neuron	2019 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/31006556
Genome engineering using the CRISPR-Cas9 system.	Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F	Nature protocols	24157548	Nat Protoc	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24157548
Nucleic acid detection with CRISPR-Cas13a/C2c2.	Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F	Science (New York, N.Y.)	28408723	Science	2017 Apr 28	https://www.ncbi.nlm.nih.gov/pubmed/28408723
Rationally engineered Cas9 nucleases with improved specificity.	Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F	Science (New York, N.Y.)	26628643	Science	2016 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/26628643
Applications of CRISPR-Cas systems in neuroscience.	Heidenreich M, Zhang F	Nature reviews. Neuroscience	26656253	Nat Rev Neurosci	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26656253
Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.	Habib N, Li Y, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A	Science (New York, N.Y.)	27471252	Science	2016 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/27471252
GUIDES: sgRNA design for loss-of-function screens.	Meier JA, Zhang F, Sanjana NE	Nature methods	28858339	Nat Methods	2017 Aug 31	https://www.ncbi.nlm.nih.gov/pubmed/28858339
A cytosine deaminase for programmable single-base RNA editing.	Abudayyeh OO, Gootenberg JS, Franklin B, Koob J, Kellner MJ, Ladha A, Joung J, Kirchgatterer P, Cox DBT, Zhang F	Science (New York, N.Y.)	31296651	Science	2019 Jul 26	https://www.ncbi.nlm.nih.gov/pubmed/31296651
Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9.	Hirano S, Abudayyeh OO, Gootenberg JS, Horii T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O	Nature communications	31036811	Nat Commun	2019 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/31036811
CRISPR-Cas9: Prospects and Challenges.	Zhang F	Human gene therapy	26176430	Hum Gene Ther	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26176430
Mice with Shank3 Mutations Associated with ASD and Schizophrenia Display Both Shared and Distinct Defects.	Zhou Y, Kaiser T, Monteiro P, Zhang X, Van der Goes MS, Wang D, Barak B, Zeng M, Li C, Lu C, Wells M, Amaya A, Nguyen S, Lewis M, Sanjana N, Zhou Y, Zhang M, Zhang F, Fu Z, Feng G	Neuron	26687841	Neuron	2016 Jan 6	https://www.ncbi.nlm.nih.gov/pubmed/26687841
Crystal Structure of Staphylococcus aureus Cas9.	Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O	Cell	26317473	Cell	2015 Aug 27	https://www.ncbi.nlm.nih.gov/pubmed/26317473
AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma.	Chow RD, Guzman CD, Wang G, Schmidt F, Youngblood MW, Ye L, Errami Y, Dong MB, Martinez MA, Zhang S, Renauer P, Bilguvar K, Gunel M, Sharp PA, Zhang F, Platt RJ, Chen S	Nature neuroscience	28805815	Nat Neurosci	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28805815
Engineering and optimising deaminase fusions for genome editing.	Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G	Nature communications	27804970	Nat Commun	2016 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/27804970
Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array.	Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F	Nature biotechnology	27918548	Nat Biotechnol	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27918548
Improved vectors and genome-wide libraries for CRISPR screening.	Sanjana NE, Shalem O, Zhang F	Nature methods	25075903	Nat Methods	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/25075903
CRISPR-Cas9 knockin mice for genome editing and cancer modeling.	Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F	Cell	25263330	Cell	2014 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/25263330
Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains.	Cong L, Zhou R, Kuo YC, Cunniff M, Zhang F	Nature communications	22828628	Nat Commun	2012 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/22828628
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.	Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA	Nature biotechnology	24752079	Nat Biotechnol	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24752079
Global microRNA depletion suppresses tumor angiogenesis.	Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA	Genes & development	24788094	Genes Dev	2014 May 15	https://www.ncbi.nlm.nih.gov/pubmed/24788094
CRISPR-mediated direct mutation of cancer genes in the mouse liver.	Xue W, Chen S, Yin H, Tammela T, Papagiannakopoulos T, Joshi NS, Cai W, Yang G, Bronson R, Crowley DG, Zhang F, Anderson DG, Sharp PA, Jacks T	Nature	25119044	Nature	2014 Oct 16	https://www.ncbi.nlm.nih.gov/pubmed/25119044
Genome-scale CRISPR-Cas9 knockout screening in human cells.	Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F	Science (New York, N.Y.)	24336571	Science	2014 Jan 3	https://www.ncbi.nlm.nih.gov/pubmed/24336571
Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.	Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A	Cell reports	24981863	Cell Rep	2014 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/24981863
RNA-guided editing of bacterial genomes using CRISPR-Cas systems.	Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA	Nature biotechnology	23360965	Nat Biotechnol	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23360965
Multiplex genome engineering using CRISPR/Cas systems.	Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F	Science (New York, N.Y.)	23287718	Science	2013 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/23287718
Common genetic variants modulate pathogen-sensing responses in human dendritic cells.	Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N	Science (New York, N.Y.)	24604203	Science	2014 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/24604203
In vivo gene editing in dystrophic mouse muscle and muscle stem cells.	Tabebordbar M, Zhu K, Cheng JKW, Chew WL, Widrick JJ, Yan WX, Maesner C, Wu EY, Xiao R, Ran FA, Cong L, Zhang F, Vandenberghe LH, Church GM, Wagers AJ	Science (New York, N.Y.)	26721686	Science	2016 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/26721686
Engineered Cpf1 variants with altered PAM specificities.	Gao L, Cox DBT, Yan WX, Manteiga JC, Schneider MW, Yamano T, Nishimasu H, Nureki O, Crosetto N, Zhang F	Nature biotechnology	28581492	Nat Biotechnol	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28581492
RNA targeting with CRISPR-Cas13.	Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A, Lander ES, Voytas DF, Ting AY, Zhang F	Nature	28976959	Nature	2017 Oct 12	https://www.ncbi.nlm.nih.gov/pubmed/28976959
A Survey of Genome Editing Activity for 16 Cas12a Orthologs.	Zetsche B, Abudayyeh OO, Gootenberg JS, Scott DA, Zhang F	The Keio journal of medicine	31723075	Keio J Med	2020 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/31723075
In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy.	Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA, Castellanos Rivera RM, Madhavan S, Pan X, Ran FA, Yan WX, Asokan A, Zhang F, Duan D, Gersbach CA	Science (New York, N.Y.)	26721684	Science	2016 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/26721684
Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease.	Dahlman JE, Abudayyeh OO, Joung J, Gootenberg JS, Zhang F, Konermann S	Nature biotechnology	26436575	Nat Biotechnol	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26436575
In vivo genome editing using Staphylococcus aureus Cas9.	Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F	Nature	25830891	Nature	2015 Apr 9	https://www.ncbi.nlm.nih.gov/pubmed/25830891
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex.	Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F	Nature	25494202	Nature	2015 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/25494202
Brains, genes, and primates.	Izpisua Belmonte JC, Callaway EM, Caddick SJ, Churchland P, Feng G, Homanics GE, Lee KF, Leopold DA, Miller CT, Mitchell JF, Mitalipov S, Moutri AR, Movshon JA, Okano H, Reynolds JH, Ringach D, Sejnowski TJ, Silva AC, Strick PL, Wu J, Zhang F	Neuron	25950631	Neuron	2015 May 6	https://www.ncbi.nlm.nih.gov/pubmed/25950631
Structure and Engineering of Francisella novicida Cas9.	Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O	Cell	26875867	Cell	2016 Feb 25	https://www.ncbi.nlm.nih.gov/pubmed/26875867
A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.	Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A	Cell	26189680	Cell	2015 Jul 30	https://www.ncbi.nlm.nih.gov/pubmed/26189680
High-resolution interrogation of functional elements in the noncoding genome.	Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F	Science (New York, N.Y.)	27708104	Science	2016 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/27708104
SHERLOCK: nucleic acid detection with CRISPR nucleases.	Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F	Nature protocols	31548639	Nat Protoc	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31548639
Massively parallel single-nucleus RNA-seq with DroNc-seq.	Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A	Nature methods	28846088	Nat Methods	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28846088
CRISPR Tools for Systematic Studies of RNA Regulation.	Engreitz J, Abudayyeh O, Gootenberg J, Zhang F	Cold Spring Harbor perspectives in biology	31371352	Cold Spring Harb Perspect Biol	2019 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/31371352
Engineered CRISPR-Cas9 nuclease with expanded targeting space.	Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H, Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O	Science (New York, N.Y.)	30166441	Science	2018 Sep 21	https://www.ncbi.nlm.nih.gov/pubmed/30166441
A split-Cas9 architecture for inducible genome editing and transcription modulation.	Zetsche B, Volz SE, Zhang F	Nature biotechnology	25643054	Nat Biotechnol	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25643054
Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA.	Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O	Cell	27114038	Cell	2016 May 5	https://www.ncbi.nlm.nih.gov/pubmed/27114038
Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.	Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F	Cell	26422227	Cell	2015 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/26422227
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.	Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV	Molecular cell	26593719	Mol Cell	2015 Nov 5	https://www.ncbi.nlm.nih.gov/pubmed/26593719
Chd8 Mutation Leads to Autistic-like Behaviors and Impaired Striatal Circuits.	Platt RJ, Zhou Y, Slaymaker IM, Shetty AS, Weisbach NR, Kim JA, Sharma J, Desai M, Sood S, Kempton HR, Crabtree GR, Feng G, Zhang F	Cell reports	28402856	Cell Rep	2017 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/28402856
BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.	Yan WX, Mirzazadeh R, Garnerone S, Scott D, Schneider MW, Kallas T, Custodio J, Wernersson E, Li Y, Gao L, Federova Y, Zetsche B, Zhang F, Bienko M, Crosetto N	Nature communications	28497783	Nat Commun	2017 May 12	https://www.ncbi.nlm.nih.gov/pubmed/28497783
Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1.	Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R, Nureki O	Molecular cell	28595896	Mol Cell	2017 Jul 6	https://www.ncbi.nlm.nih.gov/pubmed/28595896
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.	Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE	Nature	26375006	Nature	2015 Nov 12	https://www.ncbi.nlm.nih.gov/pubmed/26375006
The effects of aging on diurnal water intake and melatonin binding in the suprachiasmatic nucleus.	Whealin JM, Burwell RD, Gallagher M	Neuroscience letters	8361631	Neurosci Lett	1993 May 14	https://www.ncbi.nlm.nih.gov/pubmed/8361631
Optical control of mammalian endogenous transcription and epigenetic states.	Konermann S, Brigham MD, Trevino A, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F	Nature	23877069	Nature	2013 Aug 22	https://www.ncbi.nlm.nih.gov/pubmed/23877069
DNA targeting specificity of RNA-guided Cas9 nucleases.	Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F	Nature biotechnology	23873081	Nat Biotechnol	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23873081
One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering.	Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R	Cell	23643243	Cell	2013 May 9	https://www.ncbi.nlm.nih.gov/pubmed/23643243
Crystal structure of Cas9 in complex with guide RNA and target DNA.	Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O	Cell	24529477	Cell	2014 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/24529477
In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9.	Swiech L, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, Sur M, Zhang F	Nature biotechnology	25326897	Nat Biotechnol	2015 Jan	https://www.ncbi.nlm.nih.gov/pubmed/25326897
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity.	Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F	Cell	23992846	Cell	2013 Sep 12	https://www.ncbi.nlm.nih.gov/pubmed/23992846
Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening.	Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F	Nature protocols	28333914	Nat Protoc	2017 Apr	https://www.ncbi.nlm.nih.gov/pubmed/28333914
Hypoxia as a therapy for mitochondrial disease.	Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman-Bone S, Dhillon H, Goldberger O, Peng J, Shalem O, Sanjana NE, Zhang F, Goessling W, Zapol WM, Mootha VK	Science (New York, N.Y.)	26917594	Science	2016 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/26917594
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.	Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F	Science (New York, N.Y.)	27256883	Science	2016 Aug 5	https://www.ncbi.nlm.nih.gov/pubmed/27256883
An RNA-aptamer-based two-color CRISPR labeling system.	Wang S, Su JH, Zhang F, Zhuang X	Scientific reports	27229896	Sci Rep	2016 May 27	https://www.ncbi.nlm.nih.gov/pubmed/27229896
Therapeutic genome editing: prospects and challenges.	Cox DB, Platt RJ, Zhang F	Nature medicine	25654603	Nat Med	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25654603
Development and applications of CRISPR-Cas9 for genome engineering.	Hsu PD, Lander ES, Zhang F	Cell	24906146	Cell	2014 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/24906146
Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum.	Wagner JC, Platt RJ, Goldfless SJ, Zhang F, Niles JC	Nature methods	25108687	Nat Methods	2014 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25108687
CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus.	Ramanan V, Shlomai A, Cox DB, Schwartz RE, Michailidis E, Bhatta A, Scott DA, Zhang F, Rice CM, Bhatia SN	Scientific reports	26035283	Sci Rep	2015 Jun 2	https://www.ncbi.nlm.nih.gov/pubmed/26035283
Sequence determinants of improved CRISPR sgRNA design.	Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS	Genome research	26063738	Genome Res	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26063738
Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis.	Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA	Cell	25748654	Cell	2015 Mar 12	https://www.ncbi.nlm.nih.gov/pubmed/25748654
High-throughput functional genomics using CRISPR-Cas9.	Shalem O, Sanjana NE, Zhang F	Nature reviews. Genetics	25854182	Nat Rev Genet	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25854182
Diversity and evolution of class 2 CRISPR-Cas systems.	Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV	Nature reviews. Microbiology	28111461	Nat Rev Microbiol	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28111461
Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28.	Smargon AA, Cox DBT, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, Koonin EV, Zhang F	Molecular cell	28065598	Mol Cell	2017 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/28065598
Multidimensional chemical control of CRISPR-Cas9.	Maji B, Moore CL, Zetsche B, Volz SE, Zhang F, Shoulders MD, Choudhary A	Nature chemical biology	27820801	Nat Chem Biol	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27820801
The Clustered, Regularly Interspaced, Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9)-created MDM2 T309G Mutation Enhances Vitreous-induced Expression of MDM2 and Proliferation and Survival of Cells.	Duan Y, Ma G, Huang X, D'Amore PA, Zhang F, Lei H	The Journal of biological chemistry	27246850	J Biol Chem	2016 Jul 29	https://www.ncbi.nlm.nih.gov/pubmed/27246850
Implications of human genetic variation in CRISPR-based therapeutic genome editing.	Scott DA, Zhang F	Nature medicine	28759051	Nat Med	2017 Sep	https://www.ncbi.nlm.nih.gov/pubmed/28759051
Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.	Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O	Molecular cell	28781234	Mol Cell	2017 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/28781234
Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood.	Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F	Nature	28792927	Nature	2017 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/28792927
Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states.	Jang S, Choubey S, Furchtgott L, Zou LN, Doyle A, Menon V, Loew EB, Krostag AR, Martinez RA, Madisen L, Levi BP, Ramanathan S	eLife	28296635	Elife	2017 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/28296635
Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.	Close JL, Yao Z, Levi BP, Miller JA, Bakken TE, Menon V, Ting JT, Wall A, Krostag AR, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass IA, Bort S, Shapovalova NV, Ngo NK, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E	Neuron	29144976	Neuron	2017 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/29144976
A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development.	Yao Z, Mich JK, Ku S, Menon V, Krostag AR, Martinez RA, Furchtgott L, Mulholland H, Bort S, Fuqua MA, Gregor BW, Hodge RD, Jayabalu A, May RC, Melton S, Nelson AM, Ngo NK, Shapovalova NV, Shehata SI, Smith MW, Tait LJ, Thompson CL, Thomsen ER, Ye C, Glass IA, Kaykas A, Yao S, Phillips JW, Grimley JS, Levi BP, Wang Y, Ramanathan S	Cell stem cell	28094016	Cell Stem Cell	2017 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/28094016
Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.	Close JL, Yao Z, Levi BP, Miller JA, Bakken TE, Menon V, Ting JT, Wall A, Krostag AR, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass IA, Bort S, Shapovalova NV, Ngo NK, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E	Neuron	28279351	Neuron	2017 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/28279351
Fixed single-cell transcriptomic characterization of human radial glial diversity.	Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, Shehata SI, Nelson AM, Shapovalova NV, Levi BP, Ramanathan S	Nature methods	26524239	Nat Methods	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26524239
Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behaviour.	Kocabas A, Shen CH, Guo ZV, Ramanathan S	Nature	23000898	Nature	2012 Oct 11	https://www.ncbi.nlm.nih.gov/pubmed/23000898
Discovering sparse transcription factor codes for cell states and state transitions during development.	Furchtgott LA, Melton S, Menon V, Ramanathan S	eLife	28296636	Elife	2017 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/28296636
A wireless transmission neural interface system for unconstrained non-human primates.	Fernandez-Leon JA, Parajuli A, Franklin R, Sorenson M, Felleman DJ, Hansen BJ, Hu M, Dragoi V	Journal of neural engineering	26269496	J Neural Eng	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26269496
The human brain in a dish: the promise of iPSC-derived neurons.	Dolmetsch R, Geschwind DH	Cell	21663789	Cell	2011 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/21663789
Interbrain cortical synchronization encodes multiple aspects of social interactions in monkey pairs.	Tseng PH, Rajangam S, Lehew G, Lebedev MA, Nicolelis MAL	Scientific reports	29599529	Sci Rep	2018 Mar 29	https://www.ncbi.nlm.nih.gov/pubmed/29599529
An automatic experimental apparatus to study arm reaching in New World monkeys.	Yin A, An J, Lehew G, Lebedev MA, Nicolelis MAL	Journal of neuroscience methods	26928257	J Neurosci Methods	2016 May 1	https://www.ncbi.nlm.nih.gov/pubmed/26928257
Wireless Cortical Brain-Machine Interface for Whole-Body Navigation in Primates.	Rajangam S, Tseng PH, Yin A, Lehew G, Schwarz D, Lebedev MA, Nicolelis MA	Scientific reports	26938468	Sci Rep	2016 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/26938468
Generating artificial sensations with spinal cord stimulation in primates and rodents.	Yadav AP, Li S, Krucoff MO, Lebedev MA, Abd-El-Barr MM, Nicolelis MAL	Brain stimulation	34015518	Brain Stimul	2021 Jul-Aug	https://www.ncbi.nlm.nih.gov/pubmed/34015518
Toward a whole-body neuroprosthetic.	Lebedev MA, Nicolelis MA	Progress in brain research	21867793	Prog Brain Res	2011	https://www.ncbi.nlm.nih.gov/pubmed/21867793
Expanding the primate body schema in sensorimotor cortex by virtual touches of an avatar.	Shokur S, O'Doherty JE, Winans JA, Bleuler H, Lebedev MA, Nicolelis MA	Proceedings of the National Academy of Sciences of the United States of America	23980141	Proc Natl Acad Sci U S A	2013 Sep 10	https://www.ncbi.nlm.nih.gov/pubmed/23980141
Joint cross-correlation analysis reveals complex, time-dependent functional relationship between cortical neurons and arm electromyograms.	Zhuang KZ, Lebedev MA, Nicolelis MA	Journal of neurophysiology	25210153	J Neurophysiol	2014 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/25210153
Simultaneous top-down modulation of the primary somatosensory cortex and thalamic nuclei during active tactile discrimination.	Pais-Vieira M, Lebedev MA, Wiest MC, Nicolelis MA	The Journal of neuroscience : the official journal of the Society for Neuroscience	23447616	J Neurosci	2013 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/23447616
Computing Arm Movements with a Monkey Brainet.	Ramakrishnan A, Ifft PJ, Pais-Vieira M, Byun YW, Zhuang KZ, Lebedev MA, Nicolelis MAL	Scientific reports	26158523	Sci Rep	2015 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/26158523
Building an organic computing device with multiple interconnected brains.	Pais-Vieira M, Chiuffa G, Lebedev M, Yadav A, Nicolelis MA	Scientific reports	26158615	Sci Rep	2015 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/26158615
Cortical and thalamic contributions to response dynamics across layers of the primary somatosensory cortex during tactile discrimination.	Pais-Vieira M, Kunicki C, Tseng PH, Martin J, Lebedev M, Nicolelis MA	Journal of neurophysiology	26180115	J Neurophysiol	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/26180115
Embedding a Panoramic Representation of Infrared Light in the Adult Rat Somatosensory Cortex through a Sensory Neuroprosthesis.	Hartmann K, Thomson EE, Zea I, Yun R, Mullen P, Canarick J, Huh A, Nicolelis MA	The Journal of neuroscience : the official journal of the Society for Neuroscience	26911689	J Neurosci	2016 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/26911689
Future developments in brain-machine interface research.	Lebedev MA, Tate AJ, Hanson TL, Li Z, O'Doherty JE, Winans JA, Ifft PJ, Zhuang KZ, Fitzsimmons NA, Schwarz DA, Fuller AM, An JH, Nicolelis MA	Clinics (Sao Paulo, Brazil)	21779720	Clinics (Sao Paulo)	2011	https://www.ncbi.nlm.nih.gov/pubmed/21779720
Perceiving invisible light through a somatosensory cortical prosthesis.	Thomson EE, Carra R, Nicolelis MA	Nature communications	23403583	Nat Commun	2013	https://www.ncbi.nlm.nih.gov/pubmed/23403583
A brain-to-brain interface for real-time sharing of sensorimotor information.	Pais-Vieira M, Lebedev M, Kunicki C, Wang J, Nicolelis MA	Scientific reports	23448946	Sci Rep	2013	https://www.ncbi.nlm.nih.gov/pubmed/23448946
A novel paraplegia model in awake behaving macaques.	Krucoff MO, Zhuang K, MacLeod D, Yin A, Byun YW, Manson RJ, Turner DA, Oliveira L, Lebedev MA	Journal of neurophysiology	28701540	J Neurophysiol	2017 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/28701540
A brain-machine interface enables bimanual arm movements in monkeys.	Ifft PJ, Shokur S, Li Z, Lebedev MA, Nicolelis MA	Science translational medicine	24197735	Sci Transl Med	2013 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/24197735
Elk-1 phosphorylated at threonine-417 is present in diverse cancers and correlates with differentiation grade of colonic adenocarcinoma.	Morris JF, Sul JY, Kim MS, Klein-Szanto AJ, Schochet T, Rustgi A, Eberwine JH	Human pathology	23114923	Hum Pathol	2013 May	https://www.ncbi.nlm.nih.gov/pubmed/23114923
Dendritic glutamate receptor mRNAs show contingent local hotspot-dependent translational dynamics.	Kim TK, Sul JY, Helmfors H, Langel U, Kim J, Eberwine J	Cell reports	24075992	Cell Rep	2013 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/24075992
Revisiting the role of the granuloma in tuberculosis.	Ramakrishnan L	Nature reviews. Immunology	22517424	Nat Rev Immunol	2012 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/22517424
mTOR-regulated mitochondrial metabolism limits mycobacterium-induced cytotoxicity.	Pagán AJ, Lee LJ, Edwards-Hicks J, Moens CB, Tobin DM, Busch-Nentwich EM, Pearce EL, Ramakrishnan L	Cell	36103894	Cell	2022 Sep 29	https://www.ncbi.nlm.nih.gov/pubmed/36103894
Drug tolerance in replicating mycobacteria mediated by a macrophage-induced efflux mechanism.	Adams KN, Takaki K, Connolly LE, Wiedenhoft H, Winglee K, Humbert O, Edelstein PH, Cosma CL, Ramakrishnan L	Cell	21376383	Cell	2011 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/21376383
An in vivo platform for rapid high-throughput antitubercular drug discovery.	Takaki K, Cosma CL, Troll MA, Ramakrishnan L	Cell reports	22840407	Cell Rep	2012 Jul 26	https://www.ncbi.nlm.nih.gov/pubmed/22840407
Neutrophils exert protection in the early tuberculous granuloma by oxidative killing of mycobacteria phagocytosed from infected macrophages.	Yang CT, Cambier CJ, Davis JM, Hall CJ, Crosier PS, Ramakrishnan L	Cell host & microbe	22980327	Cell Host Microbe	2012 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/22980327
TB: the Yin and Yang of lipid mediators.	Tobin DM, Ramakrishnan L	Current opinion in pharmacology	23849093	Curr Opin Pharmacol	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23849093
Insights into tuberculosis from the zebrafish model.	Berg RD, Ramakrishnan L	Trends in molecular medicine	23084762	Trends Mol Med	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23084762
An enzyme that inactivates the inflammatory mediator leukotriene b4 restricts mycobacterial infection.	Tobin DM, Roca FJ, Ray JP, Ko DC, Ramakrishnan L	PloS one	23874453	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23874453
Looking within the zebrafish to understand the tuberculous granuloma.	Ramakrishnan L	Advances in experimental medicine and biology	23468113	Adv Exp Med Biol	2013	https://www.ncbi.nlm.nih.gov/pubmed/23468113
Antimicrobial efflux pumps and Mycobacterium tuberculosis drug tolerance: evolutionary considerations.	Szumowski JD, Adams KN, Edelstein PH, Ramakrishnan L	Current topics in microbiology and immunology	23242857	Curr Top Microbiol Immunol	2013	https://www.ncbi.nlm.nih.gov/pubmed/23242857
Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections.	Tobin DM, Roca FJ, Oh SF, McFarland R, Vickery TW, Ray JP, Ko DC, Zou Y, Bang ND, Chau TT, Vary JC, Hawn TR, Dunstan SJ, Farrar JJ, Thwaites GE, King MC, Serhan CN, Ramakrishnan L	Cell	22304914	Cell	2012 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/22304914
Sexually dimorphic neurons in the ventromedial hypothalamus govern mating in both sexes and aggression in males.	Yang CF, Chiang MC, Gray DC, Prabhakaran M, Alvarado M, Juntti SA, Unger EK, Wells JA, Shah NM	Cell	23663785	Cell	2013 May 9	https://www.ncbi.nlm.nih.gov/pubmed/23663785
Spontaneous emergence of overgrown molar teeth in a colony of Prairie voles (Microtus ochrogaster).	Jheon AH, Prochazkova M, Sherman M, Manoli DS, Shah NM, Carbone L, Klein O	International journal of oral science	25634121	Int J Oral Sci	2015 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/25634121
Neural control of sexually dimorphic behaviors.	Manoli DS, Fan P, Fraser EJ, Shah NM	Current opinion in neurobiology	23680385	Curr Opin Neurobiol	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23680385
Representing sex in the brain, one module at a time.	Yang CF, Shah NM	Neuron	24742456	Neuron	2014 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/24742456
Turning on caspases with genetics and small molecules.	Morgan CW, Julien O, Unger EK, Shah NM, Wells JA	Methods in enzymology	24974291	Methods Enzymol	2014	https://www.ncbi.nlm.nih.gov/pubmed/24974291
Oxytocin receptor is not required for social attachment in prairie voles.	Berendzen KM, Sharma R, Mandujano MA, Wei Y, Rogers FD, Simmons TC, Seelke AMH, Bond JM, Larios R, Goodwin NL, Sherman M, Parthasarthy S, Espineda I, Knoedler JR, Beery A, Bales KL, Shah NM, Manoli DS	Neuron	36708707	Neuron	2023 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/36708707
Ensuring Equitable Access to Patient Portals-Closing the "Techquity" Gap.	Johnson KB, Ibrahim SA, Rosenbloom ST	JAMA health forum	37948065	JAMA Health Forum	2023 Nov 3	https://www.ncbi.nlm.nih.gov/pubmed/37948065
Denial-Artificial Intelligence Tools and Health Insurance Coverage Decisions.	Mello MM, Rose S	JAMA health forum	38451493	JAMA Health Forum	2024 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/38451493
A call for better validation of opioid overdose risk algorithms.	McElfresh DC, Chen L, Oliva E, Joyce V, Rose S, Tamang S	Journal of the American Medical Informatics Association : JAMIA	37428897	J Am Med Inform Assoc	2023 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/37428897
A novel decision modeling framework for health policy analyses when outcomes are influenced by social and disease processes.	Cusick MM, Alarid-Escudero F, Goldhaber-Fiebert JD, Rose S	medRxiv : the preprint server for health sciences	40061345	medRxiv	2025 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/40061345
Recommendations for the use of pediatric data in artificial intelligence and machine learning ACCEPT-AI.	Muralidharan V, Burgart A, Daneshjou R, Rose S	NPJ digital medicine	37673925	NPJ Digit Med	2023 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/37673925
Clinical Research Reporting Paradigms May Incompletely Describe Participant Identities.	Enache Oana M, Lisa GR, Sherri R	American journal of epidemiology	39191644	Am J Epidemiol	2024 Aug 27	https://www.ncbi.nlm.nih.gov/pubmed/39191644
Contractile force generation by 3D hiPSC-derived cardiac tissues is enhanced by rapid establishment of cellular interconnection in matrix with muscle-mimicking stiffness.	Lee S, Serpooshan V, Tong X, Venkatraman S, Lee M, Lee J, Chirikian O, Wu JC, Wu SM, Yang F	Biomaterials	28384492	Biomaterials	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28384492
Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response.	Zhu H, Rhee JW, Cheng P, Waliany S, Chang A, Witteles RM, Maecker H, Davis MM, Nguyen PK, Wu SM	Current cardiology reports	32318865	Curr Cardiol Rep	2020 Apr 21	https://www.ncbi.nlm.nih.gov/pubmed/32318865
Mammalian Heart Regeneration: The Race to the Finish Line.	Doppler SA, Deutsch MA, Serpooshan V, Li G, Dzilic E, Lange R, Krane M, Wu SM	Circulation research	28209796	Circ Res	2017 Feb 17	https://www.ncbi.nlm.nih.gov/pubmed/28209796
Lift NIH restrictions on chimera research.	Sharma A, Sebastiano V, Scott CT, Magnus D, Koyano-Nakagawa N, Garry DJ, Witte ON, Nakauchi H, Wu JC, Weissman IL, Wu SM	Science (New York, N.Y.)	26542560	Science	2015 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/26542560
devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data.	Galdos FX, Xu S, Goodyer WR, Duan L, Huang YV, Lee S, Zhu H, Lee C, Wei N, Lee D, Wu SM	Nature communications	36071107	Nat Commun	2022 Sep 7	https://www.ncbi.nlm.nih.gov/pubmed/36071107
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris.	Tabula Muris Consortium, Overall coordination, Logistical coordination, Organ collection and processing, Library preparation and sequencing, Computational data analysis, Cell type annotation, Writing group, Supplemental text writing group, Principal investigators	Nature	30283141	Nature	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30283141
Genome Editing Redefines Precision Medicine in the Cardiovascular Field.	Dzilic E, Lahm H, Dreßen M, Deutsch MA, Lange R, Wu SM, Krane M, Doppler SA	Stem cells international	29731778	Stem Cells Int	2018	https://www.ncbi.nlm.nih.gov/pubmed/29731778
Reactivation of the Nkx2.5 cardiac enhancer after myocardial infarction does not presage myogenesis.	Deutsch MA, Doppler SA, Li X, Lahm H, Santamaria G, Cuda G, Eichhorn S, Ratschiller T, Dzilic E, Dreßen M, Eckart A, Stark K, Massberg S, Bartels A, Rischpler C, Gilsbach R, Hein L, Fleischmann BK, Wu SM, Lange R, Krane M	Cardiovascular research	29579159	Cardiovasc Res	2018 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/29579159
Prometheus Unbound in Ya(p) Heart.	Buikema JW, Wu SM	Developmental cell	30913402	Dev Cell	2019 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/30913402
Big bottlenecks in cardiovascular tissue engineering.	Huang NF, Serpooshan V, Morris VB, Sayed N, Pardon G, Abilez OJ, Nakayama KH, Pruitt BL, Wu SM, Yoon YS, Zhang J, Wu JC	Communications biology	30480100	Commun Biol	2018	https://www.ncbi.nlm.nih.gov/pubmed/30480100
Harnessing the Induction of Cardiomyocyte Proliferation for Cardiac Regenerative Medicine.	Sharma A, Zhang Y, Wu SM	Current treatment options in cardiovascular medicine	26324824	Curr Treat Options Cardiovasc Med	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26324824
Members Only: Hypoxia-Induced Cell-Cycle Activation in Cardiomyocytes.	Sharma A, Wu SM	Cell metabolism	26331604	Cell Metab	2015 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/26331604
Patient-Specific Induced Pluripotent Stem Cells Implicate Intrinsic Impaired Contractility in Hypoplastic Left Heart Syndrome.	Paige SL, Galdos FX, Lee S, Chin ET, Ranjbarvaziri S, Feyen DAM, Darsha AK, Xu S, Ryan JA, Beck AL, Qureshi MY, Miao Y, Gu M, Bernstein D, Nelson TJ, Mercola M, Rabinovitch M, Ashley EA, Parikh VN, Wu SM	Circulation	33074758	Circulation	2020 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/33074758
In vivo visualization and molecular targeting of the cardiac conduction system.	Goodyer WR, Beyersdorf BM, Duan L, van den Berg NS, Mantri S, Galdos FX, Puluca N, Buikema JW, Lee S, Salmi D, Robinson ER, Rogalla S, Cogan DP, Khosla C, Rosenthal EL, Wu SM	The Journal of clinical investigation	35951416	J Clin Invest	2022 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/35951416
Strategies for the acquisition of transcriptional and epigenetic information in single cells.	Li G, Dzilic E, Flores N, Shieh A, Wu SM	Journal of thoracic disease	28446964	J Thorac Dis	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28446964
Partial Reprogramming of Pluripotent Stem Cell-Derived Cardiomyocytes into Neurons.	Chuang W, Sharma A, Shukla P, Li G, Mall M, Rajarajan K, Abilez OJ, Hamaguchi R, Wu JC, Wernig M, Wu SM	Scientific reports	28327614	Sci Rep	2017 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/28327614
Identification of cardiovascular lineage descendants at single-cell resolution.	Li G, Plonowska K, Kuppusamy R, Sturzu A, Wu SM	Development (Cambridge, England)	25633351	Development	2015 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/25633351
Ageing hallmarks exhibit organ-specific temporal signatures.	Schaum N, Lehallier B, Hahn O, Pálovics R, Hosseinzadeh S, Lee SE, Sit R, Lee DP, Losada PM, Zardeneta ME, Fehlmann T, Webber JT, McGeever A, Calcuttawala K, Zhang H, Berdnik D, Mathur V, Tan W, Zee A, Tan M, Tabula Muris Consortium, Pisco AO, Karkanias J, Neff NF, Keller A, Darmanis S, Quake SR, Wyss-Coray T	Nature	32669715	Nature	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32669715
4HNE Impairs Myocardial Bioenergetics in Congenital Heart Disease-Induced Right Ventricular Failure.	Hwang HV, Sandeep N, Paige SL, Ranjbarvaziri S, Hu DQ, Zhao M, Lan IS, Coronado M, Kooiker KB, Wu SM, Fajardo G, Bernstein D, Reddy S	Circulation	32806952	Circulation	2020 Oct 27	https://www.ncbi.nlm.nih.gov/pubmed/32806952
Intrinsic Endocardial Defects Contribute to Hypoplastic Left Heart Syndrome.	Miao Y, Tian L, Martin M, Paige SL, Galdos FX, Li J, Klein A, Zhang H, Ma N, Wei Y, Stewart M, Lee S, Moonen JR, Zhang B, Grossfeld P, Mital S, Chitayat D, Wu JC, Rabinovitch M, Nelson TJ, Nie S, Wu SM, Gu M	Cell stem cell	32810435	Cell Stem Cell	2020 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/32810435
Regenerative Medicine: Potential Mechanisms of Cardiac Recovery in Takotsubo Cardiomyopathy.	Chang AY, Kittle JT, Wu SM	Current treatment options in cardiovascular medicine	26874708	Curr Treat Options Cardiovasc Med	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26874708
iPSC-derived cardiomyocytes reveal abnormal TGF-β signalling in left ventricular non-compaction cardiomyopathy.	Kodo K, Ong SG, Jahanbani F, Termglinchan V, Hirono K, InanlooRahatloo K, Ebert AD, Shukla P, Abilez OJ, Churko JM, Karakikes I, Jung G, Ichida F, Wu SM, Snyder MP, Bernstein D, Wu JC	Nature cell biology	27642787	Nat Cell Biol	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27642787
Integrative Analysis of PRKAG2 Cardiomyopathy iPS and Microtissue Models Identifies AMPK as a Regulator of Metabolism, Survival, and Fibrosis.	Hinson JT, Chopra A, Lowe A, Sheng CC, Gupta RM, Kuppusamy R, O'Sullivan J, Rowe G, Wakimoto H, Gorham J, Burke MA, Zhang K, Musunuru K, Gerszten RE, Wu SM, Chen CS, Seidman JG, Seidman CE	Cell reports	28009297	Cell Rep	2016 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/28009297
Integrin Based Isolation Enables Purification of Murine Lineage Committed Cardiomyocytes.	Tarnawski L, Xian X, Monnerat G, Macaulay IC, Malan D, Borgman A, Wu SM, Fleischmann BK, Jovinge S	PloS one	26323090	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26323090
Fates Aligned: Origins and Mechanisms of Ventricular Conduction System and Ventricular Wall Development.	Goodyer WR, Wu SM	Pediatric cardiology	29594502	Pediatr Cardiol	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29594502
Levitating Cells to Sort the Fit and the Fat.	Puluca N, Durmus NG, Lee S, Belbachir N, Galdos FX, Ogut MG, Gupta R, Hirano KI, Krane M, Lange R, Wu JC, Wu SM, Demirci U	Advanced biosystems	32352239	Adv Biosyst	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/32352239
Cardiovascular tissue bioprinting: Physical and chemical processes.	Hu JB, Tomov ML, Buikema JW, Chen C, Mahmoudi M, Wu SM, Serpooshan V	Applied physics reviews	32550960	Appl Phys Rev	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/32550960
Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development.	Li G, Tian L, Goodyer W, Kort EJ, Buikema JW, Xu A, Wu JC, Jovinge S, Wu SM	Development (Cambridge, England)	31142541	Development	2019 Jun 14	https://www.ncbi.nlm.nih.gov/pubmed/31142541
In Vivo Rescue of the Hematopoietic Niche By Pluripotent Stem Cell Complementation of Defective Osteoblast Compartments.	Chubb R, Oh J, Riley AK, Kimura T, Wu SM, Wu JY	Stem cells (Dayton, Ohio)	28741855	Stem Cells	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28741855
Tissue Engineering of 3D Organotypic Microtissues by Acoustic Assembly.	Zhu Y, Serpooshan V, Wu S, Demirci U, Chen P, Güven S	Methods in molecular biology (Clifton, N.J.)	28921421	Methods Mol Biol	2019	https://www.ncbi.nlm.nih.gov/pubmed/28921421
Massive expansion and cryopreservation of functional human induced pluripotent stem cell-derived cardiomyocytes.	Maas RGC, Lee S, Harakalova M, Snijders Blok CJB, Goodyer WR, Hjortnaes J, Doevendans PAFM, Van Laake LW, van der Velden J, Asselbergs FW, Wu JC, Sluijter JPG, Wu SM, Buikema JW	STAR protocols	33615277	STAR Protoc	2021 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/33615277
Identification of Pathogenic Immune Cell Subsets Associated With Checkpoint Inhibitor-Induced Myocarditis.	Zhu H, Galdos FX, Lee D, Waliany S, Huang YV, Ryan J, Dang K, Neal JW, Wakelee HA, Reddy SA, Srinivas S, Lin LL, Witteles RM, Maecker HT, Davis MM, Nguyen PK, Wu SM	Circulation	35762356	Circulation	2022 Jul 26	https://www.ncbi.nlm.nih.gov/pubmed/35762356
Bioprinting Approaches to Engineering Vascularized 3D Cardiac Tissues.	Puluca N, Lee S, Doppler S, Münsterer A, Dreßen M, Krane M, Wu SM	Current cardiology reports	31352612	Curr Cardiol Rep	2019 Jul 27	https://www.ncbi.nlm.nih.gov/pubmed/31352612
Reassessment of c-Kit in Cardiac Cells: A Complex Interplay Between Expression, Fate, and Function.	Zhou B, Wu SM	Circulation research	29929968	Circ Res	2018 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/29929968
CRISPR/Cas9-based targeting of fluorescent reporters to human iPSCs to isolate atrial and ventricular-specific cardiomyocytes.	Chirikian O, Goodyer WR, Dzilic E, Serpooshan V, Buikema JW, McKeithan W, Wu H, Li G, Lee S, Merk M, Galdos F, Beck A, Ribeiro AJS, Paige S, Mercola M, Wu JC, Pruitt BL, Wu SM	Scientific reports	33542270	Sci Rep	2021 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/33542270
Fetal Mammalian Heart Generates a Robust Compensatory Response to Cell Loss.	Sturzu AC, Rajarajan K, Passer D, Plonowska K, Riley A, Tan TC, Sharma A, Xu AF, Engels MC, Feistritzer R, Li G, Selig MK, Geissler R, Robertson KD, Scherrer-Crosbie M, Domian IJ, Wu SM	Circulation	25995316	Circulation	2015 Jul 14	https://www.ncbi.nlm.nih.gov/pubmed/25995316
Effects of Spaceflight on Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Structure and Function.	Wnorowski A, Sharma A, Chen H, Wu H, Shao NY, Sayed N, Liu C, Countryman S, Stodieck LS, Rubins KH, Wu SM, Lee PHU, Wu JC	Stem cell reports	31708475	Stem Cell Reports	2019 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/31708475
The relationship between cardiac endothelium and fibroblasts: it's complicated.	Karra R, Walter AO, Wu SM	The Journal of clinical investigation	28650344	J Clin Invest	2017 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/28650344
Identification of a hybrid myocardial zone in the mammalian heart after birth.	Tian X, Li Y, He L, Zhang H, Huang X, Liu Q, Pu W, Zhang L, Li Y, Zhao H, Wang Z, Zhu J, Nie Y, Hu S, Sedmera D, Zhong TP, Yu Y, Zhang L, Yan Y, Qiao Z, Wang QD, Wu SM, Pu WT, Anderson RH, Zhou B	Nature communications	28729659	Nat Commun	2017 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/28729659
YY1 Expression Is Sufficient for the Maintenance of Cardiac Progenitor Cell State.	Gregoire S, Li G, Sturzu AC, Schwartz RJ, Wu SM	Stem cells (Dayton, Ohio)	28580685	Stem Cells	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28580685
Derivation of highly purified cardiomyocytes from human induced pluripotent stem cells using small molecule-modulated differentiation and subsequent glucose starvation.	Sharma A, Li G, Rajarajan K, Hamaguchi R, Burridge PW, Wu SM	Journal of visualized experiments : JoVE	25867738	J Vis Exp	2015 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/25867738
Bioacoustic-enabled patterning of human iPSC-derived cardiomyocytes into 3D cardiac tissue.	Serpooshan V, Chen P, Wu H, Lee S, Sharma A, Hu DA, Venkatraman S, Ganesan AV, Usta OB, Yarmush M, Yang F, Wu JC, Demirci U, Wu SM	Biomaterials	28376365	Biomaterials	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28376365
High-throughput screening of tyrosine kinase inhibitor cardiotoxicity with human induced pluripotent stem cells.	Sharma A, Burridge PW, McKeithan WL, Serrano R, Shukla P, Sayed N, Churko JM, Kitani T, Wu H, Holmström A, Matsa E, Zhang Y, Kumar A, Fan AC, Del Álamo JC, Wu SM, Moslehi JJ, Mercola M, Wu JC	Science translational medicine	28202772	Sci Transl Med	2017 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/28202772
Small RNAs make big impact in cardiac repair.	Krane M, Deutsch MA, Doppler S, Lange R, Wu SM	Circulation research	25634967	Circ Res	2015 Jan 30	https://www.ncbi.nlm.nih.gov/pubmed/25634967
Patching up broken hearts: cardiac cell therapy gets a bioengineered boost.	Serpooshan V, Wu SM	Cell stem cell	25479741	Cell Stem Cell	2014 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/25479741
Molecular regulation of cardiomyocyte differentiation.	Paige SL, Plonowska K, Xu A, Wu SM	Circulation research	25593278	Circ Res	2015 Jan 16	https://www.ncbi.nlm.nih.gov/pubmed/25593278
Cardiac Regeneration: Lessons From Development.	Galdos FX, Guo Y, Paige SL, VanDusen NJ, Wu SM, Pu WT	Circulation research	28302741	Circ Res	2017 Mar 17	https://www.ncbi.nlm.nih.gov/pubmed/28302741
Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells.	Li G, Xu A, Sim S, Priest JR, Tian X, Khan T, Quertermous T, Zhou B, Tsao PS, Quake SR, Wu SM	Developmental cell	27840109	Dev Cell	2016 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/27840109
Untangling the Biology of Genetic Cardiomyopathies with Pluripotent Stem Cell Disease Models.	Buikema JW, Wu SM	Current cardiology reports	28315121	Curr Cardiol Rep	2017 Apr	https://www.ncbi.nlm.nih.gov/pubmed/28315121
Nkx2.5+ Cardiomyoblasts Contribute to Cardiomyogenesis in the Neonatal Heart.	Serpooshan V, Liu YH, Buikema JW, Galdos FX, Chirikian O, Paige S, Venkatraman S, Kumar A, Rawnsley DR, Huang X, Pijnappels DA, Wu SM	Scientific reports	28974782	Sci Rep	2017 Oct 3	https://www.ncbi.nlm.nih.gov/pubmed/28974782
Distilling complexity to advance cardiac tissue engineering.	Ogle BM, Bursac N, Domian I, Huang NF, Menasché P, Murry CE, Pruitt B, Radisic M, Wu JC, Wu SM, Zhang J, Zimmermann WH, Vunjak-Novakovic G	Science translational medicine	27280684	Sci Transl Med	2016 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/27280684
Single-Cell Delineation of Who's on First and Second Heart Fields During Development.	Galdos FX, Wu SM	Circulation research	31518166	Circ Res	2019 Aug 2	https://www.ncbi.nlm.nih.gov/pubmed/31518166
Simple Lithography-Free Single Cell Micropatterning using Laser-Cut Stencils.	Lee S, Yang H, Chen C, Venkatraman S, Darsha A, Wu SM, Wu JC, Seeger T	Journal of visualized experiments : JoVE	32310234	J Vis Exp	2020 Apr 3	https://www.ncbi.nlm.nih.gov/pubmed/32310234
Cardiovascular Risks in Patients with COVID-19: Potential Mechanisms and Areas of Uncertainty.	Cheng P, Zhu H, Witteles RM, Wu JC, Quertermous T, Wu SM, Rhee JW	Current cardiology reports	32350632	Curr Cardiol Rep	2020 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/32350632
Wnt Activation and Reduced Cell-Cell Contact Synergistically Induce Massive Expansion of Functional Human iPSC-Derived Cardiomyocytes.	Buikema JW, Lee S, Goodyer WR, Maas RG, Chirikian O, Li G, Miao Y, Paige SL, Lee D, Wu H, Paik DT, Rhee S, Tian L, Galdos FX, Puluca N, Beyersdorf B, Hu J, Beck A, Venkamatran S, Swami S, Wijnker P, Schuldt M, Dorsch LM, van Mil A, Red-Horse K, Wu JY, Geisen C, Hesse M, Serpooshan V, Jovinge S, Fleischmann BK, Doevendans PA, van der Velden J, Garcia KC, Wu JC, Sluijter JPG, Wu SM	Cell stem cell	32619518	Cell Stem Cell	2020 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/32619518
Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution.	Goodyer WR, Beyersdorf BM, Paik DT, Tian L, Li G, Buikema JW, Chirikian O, Choi S, Venkatraman S, Adams EL, Tessier-Lavigne M, Wu JC, Wu SM	Circulation research	31284824	Circ Res	2019 Aug 2	https://www.ncbi.nlm.nih.gov/pubmed/31284824
Stage-specific Effects of Bioactive Lipids on Human iPSC Cardiac Differentiation and Cardiomyocyte Proliferation.	Sharma A, Zhang Y, Buikema JW, Serpooshan V, Chirikian O, Kosaric N, Churko JM, Dzilic E, Shieh A, Burridge PW, Wu JC, Wu SM	Scientific reports	29700394	Sci Rep	2018 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/29700394
Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.	Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW	Cell systems	28396000	Cell Syst	2017 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/28396000
Incorporation of flexible objectives and time-linked simulation with flux balance analysis.	Birch EW, Udell M, Covert MW	Journal of theoretical biology	24361328	J Theor Biol	2014 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/24361328
Determining host metabolic limitations on viral replication via integrated modeling and experimental perturbation.	Birch EW, Ruggero NA, Covert MW	PLoS computational biology	23093930	PLoS Comput Biol	2012	https://www.ncbi.nlm.nih.gov/pubmed/23093930
Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target.	Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK, Subramanian S, Samudrala R, Van Voorhis WC	Journal of biomolecular screening	27146385	J Biomol Screen	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27146385
An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load.	Herbeck JT, Mittler JE, Gottlieb GS, Mullins JI	PLoS computational biology	24945322	PLoS Comput Biol	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24945322
Structural optimization and de novo design of dengue virus entry inhibitory peptides.	Costin JM, Jenwitheesuk E, Lok SM, Hunsperger E, Conrads KA, Fontaine KA, Rees CR, Rossmann MG, Isern S, Samudrala R, Michael SF	PLoS neglected tropical diseases	20582308	PLoS Negl Trop Dis	2010 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/20582308
Probing the molecular mechanisms of quartz-binding peptides.	Oren EE, Notman R, Kim IW, Evans JS, Walsh TR, Samudrala R, Tamerler C, Sarikaya M	Langmuir : the ACS journal of surfaces and colloids	20499870	Langmuir	2010 Jul 6	https://www.ncbi.nlm.nih.gov/pubmed/20499870
Caries induced cytokine network in the odontoblast layer of human teeth.	Horst OV, Horst JA, Samudrala R, Dale BA	BMC immunology	21261944	BMC Immunol	2011 Jan 24	https://www.ncbi.nlm.nih.gov/pubmed/21261944
Cementomimetics-constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides.	Gungormus M, Oren EE, Horst JA, Fong H, Hnilova M, Somerman MJ, Snead ML, Samudrala R, Tamerler C, Sarikaya M	International journal of oral science	22743342	Int J Oral Sci	2012 Jun	https://www.ncbi.nlm.nih.gov/pubmed/22743342
Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin.	Lertkiatmongkol P, Assawamakin A, White G, Chopra G, Rongnoparut P, Samudrala R, Tongsima S	PloS one	24023924	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24023924
Computational prediction of type III and IV secreted effectors in gram-negative bacteria.	McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F	Infection and immunity	20974833	Infect Immun	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/20974833
A generalized knowledge-based discriminatory function for biomolecular interactions.	Bernard B, Samudrala R	Proteins	19127590	Proteins	2009 Jul	https://www.ncbi.nlm.nih.gov/pubmed/19127590
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.	Hung LH, Samudrala R	Bioinformatics (Oxford, England)	24532722	Bioinformatics	2014 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/24532722
Data access for the 1,000 Plants (1KP) project.	Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK	GigaScience	25625010	Gigascience	2014	https://www.ncbi.nlm.nih.gov/pubmed/25625010
The evolution and functional repertoire of translation proteins following the origin of life.	Goldman AD, Samudrala R, Baross JA	Biology direct	20377891	Biol Direct	2010 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/20377891
Disease risk of missense mutations using structural inference from predicted function.	Horst JA, Wang K, Horst OV, Cunningham ML, Samudrala R	Current protein & peptide science	20887259	Curr Protein Pept Sci	2010 Nov	https://www.ncbi.nlm.nih.gov/pubmed/20887259
GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition.	Hung LH, Guerquin M, Samudrala R	BMC research notes	21453553	BMC Res Notes	2011 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/21453553
Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial.	Campbell MS, Mullins JI, Hughes JP, Celum C, Wong KG, Raugi DN, Sorensen S, Stoddard JN, Zhao H, Deng W, Kahle E, Panteleeff D, Baeten JM, McCutchan FE, Albert J, Leitner T, Wald A, Corey L, Lingappa JR, Partners in Prevention HSV/HIV Transmission Study Team	PloS one	21399681	PLoS One	2011 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/21399681
Viral entry inhibitors block dengue antibody-dependent enhancement in vitro.	Nicholson CO, Costin JM, Rowe DK, Lin L, Jenwitheesuk E, Samudrala R, Isern S, Michael SF	Antiviral research	21093488	Antiviral Res	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21093488
Evolutionary transients in the rice transcriptome.	Wang J, Zhang J, Li R, Zheng H, Li J, Zhang Y, Li H, Ni P, Li S, Li S, Wang J, Liu D, McDermott J, Samudrala R, Liu S, Wang J, Yang H, Yu J, Wong GK	Genomics, proteomics & bioinformatics	21382590	Genomics Proteomics Bioinformatics	2010 Dec	https://www.ncbi.nlm.nih.gov/pubmed/21382590
IGF1R variants associated with isolated single suture craniosynostosis.	Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML	American journal of medical genetics. Part A	21204214	Am J Med Genet A	2011 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21204214
Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix.	Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak DJ, Parsek MR	Molecular microbiology	20088866	Mol Microbiol	2010 Feb	https://www.ncbi.nlm.nih.gov/pubmed/20088866
A protein sequence meta-functional signature for calcium binding residue prediction.	Horst JA, Samudrala R	Pattern recognition letters	20824111	Pattern Recognit Lett	2010 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/20824111
Solution study of engineered quartz binding peptides using replica exchange molecular dynamics.	Notman R, Oren EE, Tamerler C, Sarikaya M, Samudrala R, Walsh TR	Biomacromolecules	20964422	Biomacromolecules	2010 Dec 13	https://www.ncbi.nlm.nih.gov/pubmed/20964422
Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.	Manocheewa S, Mittler JE, Samudrala R, Mullins JI	Viruses	26556362	Viruses	2015 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/26556362
Adhesion and fusion efficiencies of human immunodeficiency virus type 1 (HIV-1) surface proteins.	Dobrowsky TM, Rabi SA, Nedellec R, Daniels BR, Mullins JI, Mosier DE, Siliciano RF, Wirtz D	Scientific reports	24145278	Sci Rep	2013 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/24145278
Nanopore molecular trajectories of a eukaryotic reverse transcriptase reveal a long-range RNA structure sensing mechanism.	Shaw A, Craig JM, Amiri H, Kim J, Upton HE, Pimentel SC, Huang JR, Marqusee S, Collins K, Gundlach JH, Bustamante CJ	bioRxiv : the preprint server for biology	37066208	bioRxiv	2023 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/37066208
eIF3 engages with 3'-UTR termini of highly translated mRNAs.	Mestre-Fos S, Ferguson L, Trinidad MI, Ingolia NT, Cate JHD	eLife	39879133	Elife	2025 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/39879133
Separable structural requirements for cDNA synthesis, nontemplated extension, and template jumping by a non-LTR retroelement reverse transcriptase.	Pimentel SC, Upton HE, Collins K	The Journal of biological chemistry	35065960	J Biol Chem	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/35065960
Structure of human telomerase holoenzyme with bound telomeric DNA.	Ghanim GE, Fountain AJ, van Roon AM, Rangan R, Das R, Collins K, Nguyen THD	Nature	33883742	Nature	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/33883742
Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein.	Rodríguez-Vargas A, Collins K	Nucleic acids research	38499488	Nucleic Acids Res	2024 Jun 24	https://www.ncbi.nlm.nih.gov/pubmed/38499488
Structure and sequence at an RNA template 5' end influence insertion of transgenes by an R2 retrotransposon protein.	Palm SM, Horton CA, Zhang X, Collins K	RNA (New York, N.Y.)	38960642	RNA	2024 Aug 16	https://www.ncbi.nlm.nih.gov/pubmed/38960642
Improved precision, sensitivity, and adaptability of ordered two-template relay cDNA library preparation for RNA sequencing.	Ferguson L, Upton HE, Pimentel SC, Jeans C, Ingolia NT, Collins K	RNA (New York, N.Y.)	39626888	RNA	2025 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/39626888
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells.	Ferguson L, Upton HE, Pimentel SC, Mok A, Lareau LF, Collins K, Ingolia NT	Nature methods	37783882	Nat Methods	2023 Nov	https://www.ncbi.nlm.nih.gov/pubmed/37783882
Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second strand nicking.	Thawani A, Rodríguez-Vargas A, Van Treeck B, Hassan NT, Adelson DL, Nogales E, Collins K	bioRxiv : the preprint server for biology	39605677	bioRxiv	2024 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/39605677
Low-bias ncRNA libraries using ordered two-template relay: Serial template jumping by a modified retroelement reverse transcriptase.	Upton HE, Ferguson L, Temoche-Diaz MM, Liu XM, Pimentel SC, Ingolia NT, Schekman R, Collins K	Proceedings of the National Academy of Sciences of the United States of America	34649994	Proc Natl Acad Sci U S A	2021 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/34649994
Template and target-site recognition by human LINE-1 in retrotransposition.	Thawani A, Ariza AJF, Nogales E, Collins K	Nature	38096901	Nature	2024 Feb	https://www.ncbi.nlm.nih.gov/pubmed/38096901
eIF3 engages with 3'-UTR termini of highly translated mRNAs.	Mestre-Fos S, Ferguson L, Trinidad M, Ingolia NT, Cate JHD	bioRxiv : the preprint server for biology	37986910	bioRxiv	2024 Nov 24	https://www.ncbi.nlm.nih.gov/pubmed/37986910
Conserved and divergent DNA recognition specificities and functions of R2 retrotransposon N-terminal domains.	Lee RJ, Horton CA, Van Treeck B, McIntyre JJR, Collins K	Cell reports	38753487	Cell Rep	2024 May 28	https://www.ncbi.nlm.nih.gov/pubmed/38753487
Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci.	Zhang X, Van Treeck B, Horton CA, McIntyre JJR, Palm SM, Shumate JL, Collins K	Nature biotechnology	38379101	Nat Biotechnol	2025 Jan	https://www.ncbi.nlm.nih.gov/pubmed/38379101
Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing.	Ferguson L, Upton HE, Pimentel SC, Jeans C, Ingolia NT, Collins K	bioRxiv : the preprint server for biology	39574714	bioRxiv	2024 Nov 10	https://www.ncbi.nlm.nih.gov/pubmed/39574714
Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening.	Wang G, Chow RD, Ye L, Guzman CD, Dai X, Dong MB, Zhang F, Sharp PA, Platt RJ, Chen S	Science advances	29503867	Sci Adv	2018 Feb	https://www.ncbi.nlm.nih.gov/pubmed/29503867
CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors.	Wang D, Zhang F, Gao G	Cell	32243786	Cell	2020 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/32243786
Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery.	Segel M, Lash B, Song J, Ladha A, Liu CC, Jin X, Mekhedov SL, Macrae RK, Koonin EV, Zhang F	Science (New York, N.Y.)	34413232	Science	2021 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/34413232
In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes.	Jin X, Simmons SK, Guo A, Shetty AS, Ko M, Nguyen L, Jokhi V, Robinson E, Oyler P, Curry N, Deangeli G, Lodato S, Levin JZ, Regev A, Zhang F, Arlotta P	Science (New York, N.Y.)	33243861	Science	2020 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/33243861
LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding.	Ludwig KU, Schmithausen RM, Li D, Jacobs ML, Hollstein R, Blumenstock K, Liebing J, Słabicki M, Ben-Shmuel A, Israeli O, Weiss S, Ebert TS, Paran N, Rüdiger W, Wilbring G, Feldman D, Lippke B, Ishorst N, Hochfeld LM, Beins EC, Kaltheuner IH, Schmitz M, Wöhler A, Döhla M, Sib E, Jentzsch M, Moench EC, Borrajo JD, Strecker J, Reinhardt J, Cleary B, Geyer M, Hölzel M, Macrae R, Nöthen MM, Hoffmann P, Exner M, Regev A, Zhang F, Schmid-Burgk JL	Nature biotechnology	34188222	Nat Biotechnol	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34188222
Microfluidic Enrichment and Computational Analysis of Rare Sequences from Mixed Genomic Samples for Metagenomic Mining.	Cui N, Faure G, Singh A, Macrae R, Zhang F	The CRISPR journal	36206017	CRISPR J	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36206017
Compact RNA editors with small Cas13 proteins.	Kannan S, Altae-Tran H, Jin X, Madigan VJ, Oshiro R, Makarova KS, Koonin EV, Zhang F	Nature biotechnology	34462587	Nat Biotechnol	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/34462587
RNA editing with CRISPR-Cas13.	Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F	Science (New York, N.Y.)	29070703	Science	2017 Nov 24	https://www.ncbi.nlm.nih.gov/pubmed/29070703
Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13.	Abudayyeh OO, Gootenberg JS, Kellner MJ, Zhang F	The CRISPR journal	31225754	CRISPR J	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31225754
DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction.	Weinstein JA, Regev A, Zhang F	Cell	31230717	Cell	2019 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/31230717
Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6.	Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F	Science (New York, N.Y.)	29449508	Science	2018 Apr 27	https://www.ncbi.nlm.nih.gov/pubmed/29449508
UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions.	Mestre MR, Gao LA, Shah SA, López-Beltrán A, González-Delgado A, Martínez-Abarca F, Iranzo J, Redrejo-Rodríguez M, Zhang F, Toro N	Nucleic acids research	35648479	Nucleic Acids Res	2022 Jun 24	https://www.ncbi.nlm.nih.gov/pubmed/35648479
RNA-activated protein cleavage with a CRISPR-associated endopeptidase.	Strecker J, Demircioglu FE, Li D, Faure G, Wilkinson ME, Gootenberg JS, Abudayyeh OO, Nishimasu H, Macrae RK, Zhang F	Science (New York, N.Y.)	36423276	Science	2022 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/36423276
Field-deployable viral diagnostics using CRISPR-Cas13.	Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, Kellner MJ, Tan AL, Paul LM, Parham LA, Garcia KF, Barnes KG, Chak B, Mondini A, Nogueira ML, Isern S, Michael SF, Lorenzana I, Yozwiak NL, MacInnis BL, Bosch I, Gehrke L, Zhang F, Sabeti PC	Science (New York, N.Y.)	29700266	Science	2018 Apr 27	https://www.ncbi.nlm.nih.gov/pubmed/29700266
Engineering of CRISPR-Cas12b for human genome editing.	Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F	Nature communications	30670702	Nat Commun	2019 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/30670702
Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing.	Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, Barretto RPJ, Ranu A, Macrae RK, Faure G, Ioannidi EI, Krajeski RN, Bruneau R, Huang MW, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F	The New England journal of medicine	32937062	N Engl J Med	2020 Oct 8	https://www.ncbi.nlm.nih.gov/pubmed/32937062
Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity.	Sorek M, Oweis W, Nissim-Rafinia M, Maman M, Simon S, Hession CC, Adiconis X, Simmons SK, Sanjana NE, Shi X, Lu C, Pan JQ, Xu X, Pouladi MA, Ellerby LM, Zhang F, Levin JZ, Meshorer E	Genome biology	33663567	Genome Biol	2021 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/33663567
High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage.	Slaymaker IM, Mesa P, Kellner MJ, Kannan S, Brignole E, Koob J, Feliciano PR, Stella S, Abudayyeh OO, Gootenberg JS, Strecker J, Montoya G, Zhang F	Cell reports	30917325	Cell Rep	2019 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/30917325
Unexpected connections between type VI-B CRISPR-Cas systems, bacterial natural competence, ubiquitin signaling network and DNA modification through a distinct family of membrane proteins.	Makarova KS, Gao L, Zhang F, Koonin EV	FEMS microbiology letters	31089700	FEMS Microbiol Lett	2019 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/31089700
Dual modes of CRISPR-associated transposon homing.	Saito M, Ladha A, Strecker J, Faure G, Neumann E, Altae-Tran H, Macrae RK, Zhang F	Cell	33770501	Cell	2021 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/33770501
Structure and engineering of the minimal type VI CRISPR-Cas13bt3.	Nakagawa R, Kannan S, Altae-Tran H, Takeda SN, Tomita A, Hirano H, Kusakizako T, Nishizawa T, Yamashita K, Zhang F, Nishimasu H, Nureki O	Molecular cell	36027912	Mol Cell	2022 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/36027912
A transcription factor atlas of directed differentiation.	Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F	Cell	36608654	Cell	2023 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/36608654
Programmable Inhibition and Detection of RNA Viruses Using Cas13.	Freije CA, Myhrvold C, Boehm CK, Lin AE, Welch NL, Carter A, Metsky HC, Luo CY, Abudayyeh OO, Gootenberg JS, Yozwiak NL, Zhang F, Sabeti PC	Molecular cell	31607545	Mol Cell	2019 Dec 5	https://www.ncbi.nlm.nih.gov/pubmed/31607545
Optical Pooled Screens in Human Cells.	Feldman D, Singh A, Schmid-Burgk JL, Carlson RJ, Mezger A, Garrity AJ, Zhang F, Blainey PC	Cell	31626775	Cell	2019 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/31626775
RNA-guided DNA insertion with CRISPR-associated transposases.	Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F	Science (New York, N.Y.)	31171706	Science	2019 Jul 5	https://www.ncbi.nlm.nih.gov/pubmed/31171706
Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons.	Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich M, Pan JQ, Levin JZ, Zhang F	Nature biomedical engineering	30271673	Nat Biomed Eng	2018 Jul	https://www.ncbi.nlm.nih.gov/pubmed/30271673
The evolution of red color vision is linked to coordinated rhodopsin tuning in lycaenid butterflies.	Liénard MA, Bernard GD, Allen A, Lassance JM, Song S, Childers RR, Yu N, Ye D, Stephenson A, Valencia-Montoya WA, Salzman S, Whitaker MRL, Calonje M, Zhang F, Pierce NE	Proceedings of the National Academy of Sciences of the United States of America	33547236	Proc Natl Acad Sci U S A	2021 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/33547236
Highly Parallel Profiling of Cas9 Variant Specificity.	Schmid-Burgk JL, Gao L, Li D, Gardner Z, Strecker J, Lash B, Zhang F	Molecular cell	32187529	Mol Cell	2020 May 21	https://www.ncbi.nlm.nih.gov/pubmed/32187529
Ongoing global and regional adaptive evolution of SARS-CoV-2.	Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV	Proceedings of the National Academy of Sciences of the United States of America	34292871	Proc Natl Acad Sci U S A	2021 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/34292871
Prokaryotic innate immunity through pattern recognition of conserved viral proteins.	Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F	Science (New York, N.Y.)	35951700	Science	2022 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/35951700
The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases.	Altae-Tran H, Kannan S, Demircioglu FE, Oshiro R, Nety SP, McKay LJ, Dlakić M, Inskeep WP, Makarova KS, Macrae RK, Koonin EV, Zhang F	Science (New York, N.Y.)	34591643	Science	2021 Oct	https://www.ncbi.nlm.nih.gov/pubmed/34591643
Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA.	Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F	Nature	36224386	Nature	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36224386
CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity.	Joung J, Kirchgatterer PC, Singh A, Cho JH, Nety SP, Larson RC, Macrae RK, Deasy R, Tseng YY, Maus MV, Zhang F	Nature communications	35338135	Nat Commun	2022 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/35338135
Diverse enzymatic activities mediate antiviral immunity in prokaryotes.	Gao L, Altae-Tran H, Böhning F, Makarova KS, Segel M, Schmid-Burgk JL, Koob J, Wolf YI, Koonin EV, Zhang F	Science (New York, N.Y.)	32855333	Science	2020 Aug 28	https://www.ncbi.nlm.nih.gov/pubmed/32855333
Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses.	Gussow AB, Auslander N, Faure G, Wolf YI, Zhang F, Koonin EV	Proceedings of the National Academy of Sciences of the United States of America	32522874	Proc Natl Acad Sci U S A	2020 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/32522874
Spatially Adaptive Multi-Scale Optimization for Local Parameter Estimation in Cardiac Electrophysiology.	Dhamala J, Arevalo HJ, Sapp J, Horacek M, Wu KC, Trayanova NA, Wang L	IEEE transactions on medical imaging	28459685	IEEE Trans Med Imaging	2017 Sep	https://www.ncbi.nlm.nih.gov/pubmed/28459685
Submillimeter diffusion tensor imaging and late gadolinium enhancement cardiovascular magnetic resonance of chronic myocardial infarction.	Pashakhanloo F, Herzka DA, Mori S, Zviman M, Halperin H, Gai N, Bluemke DA, Trayanova NA, McVeigh ER	Journal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance	28122618	J Cardiovasc Magn Reson	2017 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/28122618
Effect of KCNQ1 G229D mutation on cardiac pumping efficacy and reentrant dynamics in ventricles: Computational study.	Yuniarti AR, Setianto F, Marcellinus A, Hwang HJ, Choi SW, Trayanova N, Lim KM	International journal for numerical methods in biomedical engineering	29488358	Int J Numer Method Biomed Eng	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29488358
Virtual electrophysiological study as a tool for evaluating efficacy of MRI techniques in predicting adverse arrhythmic events in ischemic patients.	Ukwatta E, Nikolov P, Zabihollahy F, Trayanova NA, Wright GA	Physics in medicine and biology	30412472	Phys Med Biol	2018 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/30412472
New insights on the cardiac safety factor: Unraveling the relationship between conduction velocity and robustness of propagation.	Boyle PM, Franceschi WH, Constantin M, Hawks C, Desplantez T, Trayanova NA, Vigmond EJ	Journal of molecular and cellular cardiology	30677394	J Mol Cell Cardiol	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30677394
Computational Identification of Ventricular Arrhythmia Risk in Pediatric Myocarditis.	Cartoski MJ, Nikolov PP, Prakosa A, Boyle PM, Spevak PJ, Trayanova NA	Pediatric cardiology	30840104	Pediatr Cardiol	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30840104
The role of personalized atrial modeling in understanding atrial fibrillation mechanisms and improving treatment.	Aronis KN, Ali R, Trayanova NA	International journal of cardiology	30755334	Int J Cardiol	2019 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/30755334
Myofilament protein dynamics modulate EAD formation in human hypertrophic cardiomyopathy.	Zile MA, Trayanova NA	Progress in biophysics and molecular biology	28648627	Prog Biophys Mol Biol	2017 Nov	https://www.ncbi.nlm.nih.gov/pubmed/28648627
A feasibility study of arrhythmia risk prediction in patients with myocardial infarction and preserved ejection fraction.	Deng D, Arevalo HJ, Prakosa A, Callans DJ, Trayanova NA	Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology	28011832	Europace	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/28011832
Modeling the aging heart: from local respiratory defects to global rhythm disturbances.	Khrapko K, Trayanova N, Nattel S	Cell metabolism	25955202	Cell Metab	2015 May 5	https://www.ncbi.nlm.nih.gov/pubmed/25955202
Computational analysis of the effect of valvular regurgitation on ventricular mechanics using a 3D electromechanics model.	Lim KM, Hong SB, Lee BK, Shim EB, Trayanova N	The journal of physiological sciences : JPS	25644379	J Physiol Sci	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25644379
"Beauty is a light in the heart": the transformative potential of optogenetics for clinical applications in cardiovascular medicine.	Boyle PM, Karathanos TV, Trayanova NA	Trends in cardiovascular medicine	25453984	Trends Cardiovasc Med	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25453984
Corrigendum to "effects of fibrosis morphology on reentrant ventricular tachycardia inducibility and simulation fidelity in patient-derived models".	Ringenberg J, Deo M, Filgueiras-Rama D, Pizarro G, Ibañez B, Peinado R, Trayanova N, Miller M, Merino JL, Berenfeld O, Devabhaktuni V	Clinical Medicine Insights. Cardiology	25698881	Clin Med Insights Cardiol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25698881
Exploring susceptibility to atrial and ventricular arrhythmias resulting from remodeling of the passive electrical properties in the heart: a simulation approach.	Trayanova NA, Boyle PM, Arevalo HJ, Zahid S	Frontiers in physiology	25429272	Front Physiol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25429272
Virtual 3D heart models to aid pacemaker implantation in children.	Trayanova NA	Future cardiology	24344653	Future Cardiol	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24344653
Sodium current reduction unmasks a structure-dependent substrate for arrhythmogenesis in the normal ventricles.	Boyle PM, Park CJ, Arevalo HJ, Vigmond EJ, Trayanova NA	PloS one	24489810	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24489810
Optogenetics-enabled dynamic modulation of action potential duration in atrial tissue: feasibility of a novel therapeutic approach.	Karathanos TV, Boyle PM, Trayanova NA	Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology	25362173	Europace	2014 Nov	https://www.ncbi.nlm.nih.gov/pubmed/25362173
Mathematical approaches to understanding and imaging atrial fibrillation: significance for mechanisms and management.	Trayanova NA	Circulation research	24763468	Circ Res	2014 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/24763468
Degradation of T-Tubular Microdomains and Altered cAMP Compartmentation Lead to Emergence of Arrhythmogenic Triggers in Heart Failure Myocytes: An in silico Study.	Loucks AD, O'Hara T, Trayanova NA	Frontiers in physiology	30564142	Front Physiol	2018	https://www.ncbi.nlm.nih.gov/pubmed/30564142
Initiation of a High-Frequency Jet Ventilation Strategy for Catheter Ablation for Atrial Fibrillation: Safety and Outcomes Data.	Sivasambu B, Hakim JB, Barodka V, Chrispin J, Berger RD, Ashikaga H, Ciuffo L, Tao S, Calkins H, Marine JE, Trayanova N, Spragg DD	JACC. Clinical electrophysiology	30573114	JACC Clin Electrophysiol	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30573114
Image-based Reconstruction of 3D Myocardial Infarct Geometry for Patient Specific Applications.	Ukwatta E, Rajchl M, White J, Pashakhanloo F, Herzka DA, McVeigh E, Lardo AC, Trayanova N, Vadakkumpadan F	Proceedings of SPIE--the International Society for Optical Engineering	26633913	Proc SPIE Int Soc Opt Eng	2015 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/26633913
Opsin spectral sensitivity determines the effectiveness of optogenetic termination of ventricular fibrillation in the human heart: a simulation study.	Karathanos TV, Bayer JD, Wang D, Boyle PM, Trayanova NA	The Journal of physiology	26941055	J Physiol	2016 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/26941055
Computational rabbit models to investigate the initiation, perpetuation, and termination of ventricular arrhythmia.	Arevalo HJ, Boyle PM, Trayanova NA	Progress in biophysics and molecular biology	27334789	Prog Biophys Mol Biol	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/27334789
Computational modeling of cardiac optogenetics: Methodology overview & review of findings from simulations.	Boyle PM, Karathanos TV, Entcheva E, Trayanova NA	Computers in biology and medicine	26002074	Comput Biol Med	2015 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/26002074
Virtual electrophysiological study of atrial fibrillation in fibrotic remodeling.	McDowell KS, Zahid S, Vadakkumpadan F, Blauer J, MacLeod RS, Trayanova NA	PloS one	25692857	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/25692857
Myocardial infarct segmentation and reconstruction from 2D late-gadolinium enhanced magnetic resonance images.	Ukwatta E, Yuan J, Qiu W, Wu KC, Trayanova N, Vadakkumpadan F	Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention	25485423	Med Image Comput Comput Assist Interv	2014	https://www.ncbi.nlm.nih.gov/pubmed/25485423
Precisely parameterized experimental and computational models of tissue organization.	Molitoris JM, Paliwal S, Sekar RB, Blake R, Park J, Trayanova NA, Tung L, Levchenko A	Integrative biology : quantitative biosciences from nano to macro	26822672	Integr Biol (Camb)	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/26822672
Myocardial Infarct Segmentation From Magnetic Resonance Images for Personalized Modeling of Cardiac Electrophysiology.	Ukwatta E, Arevalo H, Li K, Yuan J, Qiu W, Malamas P, Wu KC, Trayanova NA, Vadakkumpadan F	IEEE transactions on medical imaging	26731693	IEEE Trans Med Imaging	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/26731693
Light-based Approaches to Cardiac Arrhythmia Research: From Basic Science to Translational Applications.	Karathanos TV, Boyle PM, Trayanova NA	Clinical Medicine Insights. Cardiology	27840581	Clin Med Insights Cardiol	2016	https://www.ncbi.nlm.nih.gov/pubmed/27840581
A New MRI-Based Model of Heart Function with Coupled Hemodynamics and Application to Normal and Diseased Canine Left Ventricles.	Choi YJ, Constantino J, Vedula V, Trayanova N, Mittal R	Frontiers in bioengineering and biotechnology	26442254	Front Bioeng Biotechnol	2015	https://www.ncbi.nlm.nih.gov/pubmed/26442254
Mechanisms of arrhythmogenesis related to calcium-driven alternans in a model of human atrial fibrillation.	Chang KC, Trayanova NA	Scientific reports	27812021	Sci Rep	2016 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/27812021
Feasibility of using patient-specific models and the "minimum cut" algorithm to predict optimal ablation targets for left atrial flutter.	Zahid S, Whyte KN, Schwarz EL, Blake RC 3rd, Boyle PM, Chrispin J, Prakosa A, Ipek EG, Pashakhanloo F, Halperin HR, Calkins H, Berger RD, Nazarian S, Trayanova NA	Heart rhythm	27108938	Heart Rhythm	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27108938
A comprehensive, multiscale framework for evaluation of arrhythmias arising from cell therapy in the whole post-myocardial infarcted heart.	Yu JK, Franceschi W, Huang Q, Pashakhanloo F, Boyle PM, Trayanova NA	Scientific reports	31239508	Sci Rep	2019 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/31239508
Ventricular arrhythmia risk prediction in repaired Tetralogy of Fallot using personalized computational cardiac models.	Shade JK, Cartoski MJ, Nikolov P, Prakosa A, Doshi A, Binka E, Olivieri L, Boyle PM, Spevak PJ, Trayanova NA	Heart rhythm	31589989	Heart Rhythm	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/31589989
Cardiac Optogenetics: 2018.	Boyle PM, Karathanos TV, Trayanova NA	JACC. Clinical electrophysiology	29749932	JACC Clin Electrophysiol	2018 Feb	https://www.ncbi.nlm.nih.gov/pubmed/29749932
Quantifying the uncertainty in model parameters using Gaussian process-based Markov chain Monte Carlo in cardiac electrophysiology.	Dhamala J, Arevalo HJ, Sapp J, Horácek BM, Wu KC, Trayanova NA, Wang L	Medical image analysis	29843078	Med Image Anal	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29843078
Plakophilin-2 is required for transcription of genes that control calcium cycling and cardiac rhythm.	Cerrone M, Montnach J, Lin X, Zhao YT, Zhang M, Agullo-Pascual E, Leo-Macias A, Alvarado FJ, Dolgalev I, Karathanos TV, Malkani K, Van Opbergen CJM, van Bavel JJA, Yang HQ, Vasquez C, Tester D, Fowler S, Liang F, Rothenberg E, Heguy A, Morley GE, Coetzee WA, Trayanova NA, Ackerman MJ, van Veen TAB, Valdivia HH, Delmar M	Nature communications	28740174	Nat Commun	2017 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/28740174
Personalized Imaging and Modeling Strategies for Arrhythmia Prevention and Therapy.	Trayanova NA, Boyle PM, Nikolov PP	Current opinion in biomedical engineering	29546250	Curr Opin Biomed Eng	2018 Mar	https://www.ncbi.nlm.nih.gov/pubmed/29546250
Sensitivity of reentrant driver localization to electrophysiological parameter variability in image-based computational models of persistent atrial fibrillation sustained by a fibrotic substrate.	Deng D, Murphy MJ, Hakim JB, Franceschi WH, Zahid S, Pashakhanloo F, Trayanova NA, Boyle PM	Chaos (Woodbury, N.Y.)	28964164	Chaos	2017 Sep	https://www.ncbi.nlm.nih.gov/pubmed/28964164
Biological substrate modification suppresses ventricular arrhythmias in a porcine model of chronic ischaemic cardiomyopathy.	Dawkins JF, Ehdaie A, Rogers R, Soetkamp D, Valle J, Holm K, Sanchez L, Tremmel I, Nawaz A, Shehata M, Wang X, Prakosa A, Yu J, Van Eyk JE, Trayanova N, Marbán E, Cingolani E	European heart journal	35262692	Eur Heart J	2022 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/35262692
Sensitivity of Ablation Targets Prediction to Electrophysiological Parameter Variability in Image-Based Computational Models of Ventricular Tachycardia in Post-infarction Patients.	Deng D, Prakosa A, Shade J, Nikolov P, Trayanova NA	Frontiers in physiology	31178758	Front Physiol	2019	https://www.ncbi.nlm.nih.gov/pubmed/31178758
4D cardiac electromechanical activation imaging.	Grondin J, Wang D, Grubb CS, Trayanova N, Konofagou EE	Computers in biology and medicine	31476587	Comput Biol Med	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31476587
Increased thin filament activation enhances alternans in human chronic atrial fibrillation.	Zile MA, Trayanova NA	American journal of physiology. Heart and circulatory physiology	30141984	Am J Physiol Heart Circ Physiol	2018 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/30141984
β-adrenergic stimulation augments transmural dispersion of repolarization via modulation of delayed rectifier currents I(Ks) and I(Kr) in the human ventricle.	Kang C, Badiceanu A, Brennan JA, Gloschat C, Qiao Y, Trayanova NA, Efimov IR	Scientific reports	29162896	Sci Rep	2017 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/29162896
Personalized virtual-heart technology for guiding the ablation of infarct-related ventricular tachycardia.	Prakosa A, Arevalo HJ, Deng D, Boyle PM, Nikolov PP, Ashikaga H, Blauer JJE, Ghafoori E, Park CJ, Blake RC 3rd, Han FT, MacLeod RS, Halperin HR, Callans DJ, Ranjan R, Chrispin J, Nazarian S, Trayanova NA	Nature biomedical engineering	30847259	Nat Biomed Eng	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30847259
Computational models in cardiology.	Niederer SA, Lumens J, Trayanova NA	Nature reviews. Cardiology	30361497	Nat Rev Cardiol	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30361497
From genetics to smart watches: developments in precision cardiology.	Trayanova N	Nature reviews. Cardiology	30568275	Nat Rev Cardiol	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30568275
Association of regional myocardial conduction velocity with the distribution of hypoattenuation on contrast-enhanced perfusion computed tomography in patients with postinfarct ventricular tachycardia.	Ustunkaya T, Desjardins B, Liu B, Zahid S, Park J, Saju N, Trayanova N, Zimmerman SL, Marchlinski FE, Nazarian S	Heart rhythm	30935494	Heart Rhythm	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30935494
Rate-dependent force, intracellular calcium, and action potential voltage alternans are modulated by sarcomere length and heart failure induced-remodeling of thin filament regulation in human heart failure: A myocyte modeling study.	Zile MA, Trayanova NA	Progress in biophysics and molecular biology	26724571	Prog Biophys Mol Biol	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26724571
Arrhythmia risk stratification of patients after myocardial infarction using personalized heart models.	Arevalo HJ, Vadakkumpadan F, Guallar E, Jebb A, Malamas P, Wu KC, Trayanova NA	Nature communications	27164184	Nat Commun	2016 May 10	https://www.ncbi.nlm.nih.gov/pubmed/27164184
Accurate Conduction Velocity Maps and Their Association With Scar Distribution on Magnetic Resonance Imaging in Patients With Postinfarction Ventricular Tachycardias.	Aronis KN, Ali RL, Prakosa A, Ashikaga H, Berger RD, Hakim JB, Liang J, Tandri H, Teng F, Chrispin J, Trayanova NA	Circulation. Arrhythmia and electrophysiology	32191131	Circ Arrhythm Electrophysiol	2020 Apr	https://www.ncbi.nlm.nih.gov/pubmed/32191131
Arrhythmogenic propensity of the fibrotic substrate after atrial fibrillation ablation: a longitudinal study using magnetic resonance imaging-based atrial models.	Ali RL, Hakim JB, Boyle PM, Zahid S, Sivasambu B, Marine JE, Calkins H, Trayanova NA, Spragg DD	Cardiovascular research	30977811	Cardiovasc Res	2019 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/30977811
Using personalized computer models to custom-tailor ablation procedures for atrial fibrillation patients: are we there yet?	Boyle PM, Zahid S, Trayanova NA	Expert review of cardiovascular therapy	28395557	Expert Rev Cardiovasc Ther	2017 May	https://www.ncbi.nlm.nih.gov/pubmed/28395557
Disrupted calcium release as a mechanism for atrial alternans associated with human atrial fibrillation.	Chang KC, Bayer JD, Trayanova NA	PLoS computational biology	25501557	PLoS Comput Biol	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25501557
Efficient preloading of the ventricles by a properly timed atrial contraction underlies stroke work improvement in the acute response to cardiac resynchronization therapy.	Hu Y, Gurev V, Constantino J, Trayanova N	Heart rhythm	23928177	Heart Rhythm	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23928177
Advances in modeling ventricular arrhythmias: from mechanisms to the clinic.	Trayanova NA, Boyle PM	Wiley interdisciplinary reviews. Systems biology and medicine	24375958	Wiley Interdiscip Rev Syst Biol Med	2014 Mar-Apr	https://www.ncbi.nlm.nih.gov/pubmed/24375958
Image-based left ventricular shape analysis for sudden cardiac death risk stratification.	Vadakkumpadan F, Trayanova N, Wu KC	Heart rhythm	24854217	Heart Rhythm	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24854217
Towards personalized computational modelling of the fibrotic substrate for atrial arrhythmia.	Boyle PM, Zahid S, Trayanova NA	Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology	28011841	Europace	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/28011841
Epicardial Conduction Speed, Electrogram Abnormality, and Computed Tomography Attenuation Associations in Arrhythmogenic Right Ventricular Cardiomyopathy.	Ustunkaya T, Desjardins B, Wedan R, Chahal CAA, Zimmerman SL, Saju N, Zahid S, Sharma A, Han Y, Trayanova N, Marchlinski FE, Calkins H, Tandri H, Nazarian S	JACC. Clinical electrophysiology	31648740	JACC Clin Electrophysiol	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31648740
Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology.	Ukwatta E, Arevalo H, Rajchl M, White J, Pashakhanloo F, Prakosa A, Herzka DA, McVeigh E, Lardo AC, Trayanova NA, Vadakkumpadan F	Medical physics	26233186	Med Phys	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26233186
Optogenetics-enabled assessment of viral gene and cell therapy for restoration of cardiac excitability.	Ambrosi CM, Boyle PM, Chen K, Trayanova NA, Entcheva E	Scientific reports	26621212	Sci Rep	2015 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/26621212
How computer simulations of the human heart can improve anti-arrhythmia therapy.	Trayanova NA, Chang KC	The Journal of physiology	26621489	J Physiol	2016 May 1	https://www.ncbi.nlm.nih.gov/pubmed/26621489
Association of left atrial epicardial adipose tissue with electrogram bipolar voltage and fractionation: Electrophysiologic substrates for atrial fibrillation.	Zghaib T, Ipek EG, Zahid S, Balouch MA, Misra S, Ashikaga H, Berger RD, Marine JE, Spragg DD, Zimmerman SL, Zipunnikov V, Trayanova N, Calkins H, Nazarian S	Heart rhythm	27546816	Heart Rhythm	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27546816
Early somatic mosaicism is a rare cause of long-QT syndrome.	Priest JR, Gawad C, Kahlig KM, Yu JK, O'Hara T, Boyle PM, Rajamani S, Clark MJ, Garcia ST, Ceresnak S, Harris J, Boyle S, Dewey FE, Malloy-Walton L, Dunn K, Grove M, Perez MV, Neff NF, Chen R, Maeda K, Dubin A, Belardinelli L, West J, Antolik C, Macaya D, Quertermous T, Trayanova NA, Quake SR, Ashley EA	Proceedings of the National Academy of Sciences of the United States of America	27681629	Proc Natl Acad Sci U S A	2016 Oct 11	https://www.ncbi.nlm.nih.gov/pubmed/27681629
Caveolin-3 regulates compartmentation of cardiomyocyte beta2-adrenergic receptor-mediated cAMP signaling.	Wright PT, Nikolaev VO, O'Hara T, Diakonov I, Bhargava A, Tokar S, Schobesberger S, Shevchuk AI, Sikkel MB, Wilkinson R, Trayanova NA, Lyon AR, Harding SE, Gorelik J	Journal of molecular and cellular cardiology	24345421	J Mol Cell Cardiol	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24345421
Methodology for image-based reconstruction of ventricular geometry for patient-specific modeling of cardiac electrophysiology.	Prakosa A, Malamas P, Zhang S, Pashakhanloo F, Arevalo H, Herzka DA, Lardo A, Halperin H, McVeigh E, Trayanova N, Vadakkumpadan F	Progress in biophysics and molecular biology	25148771	Prog Biophys Mol Biol	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/25148771
Association of Left Atrial Local Conduction Velocity With Late Gadolinium Enhancement on Cardiac Magnetic Resonance in Patients With Atrial Fibrillation.	Fukumoto K, Habibi M, Ipek EG, Zahid S, Khurram IM, Zimmerman SL, Zipunnikov V, Spragg D, Ashikaga H, Trayanova N, Tomaselli GF, Rickard J, Marine JE, Berger RD, Calkins H, Nazarian S	Circulation. Arrhythmia and electrophysiology	26917814	Circ Arrhythm Electrophysiol	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26917814
Mechanisms linking electrical alternans and clinical ventricular arrhythmia in human heart failure.	Bayer JD, Lalani GG, Vigmond EJ, Narayan SM, Trayanova NA	Heart rhythm	27215536	Heart Rhythm	2016 Sep	https://www.ncbi.nlm.nih.gov/pubmed/27215536
Computational models of heart disease.	Smith N, Trayanova N	Drug discovery today. Disease models	26843884	Drug Discov Today Dis Models	2014 Winter	https://www.ncbi.nlm.nih.gov/pubmed/26843884
Myofiber Architecture of the Human Atria as Revealed by Submillimeter Diffusion Tensor Imaging.	Pashakhanloo F, Herzka DA, Ashikaga H, Mori S, Gai N, Bluemke DA, Trayanova NA, McVeigh ER	Circulation. Arrhythmia and electrophysiology	27071829	Circ Arrhythm Electrophysiol	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/27071829
Intermittent drivers anchoring to structural heterogeneities as a major pathophysiological mechanism of human persistent atrial fibrillation.	Haissaguerre M, Shah AJ, Cochet H, Hocini M, Dubois R, Efimov I, Vigmond E, Bernus O, Trayanova N	The Journal of physiology	26890861	J Physiol	2016 May 1	https://www.ncbi.nlm.nih.gov/pubmed/26890861
Spatial dispersion analysis of LGE-CMR for prediction of ventricular arrhythmias in patients with cardiac sarcoidosis.	Aronis KN, Okada DR, Xie E, Daimee UA, Prakosa A, Gilotra NA, Wu KC, Trayanova N, Chrispin J	Pacing and clinical electrophysiology : PACE	34766627	Pacing Clin Electrophysiol	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34766627
Characterization of the Electrophysiologic Remodeling of Patients With Ischemic Cardiomyopathy by Clinical Measurements and Computer Simulations Coupled With Machine Learning.	Aronis KN, Prakosa A, Bergamaschi T, Berger RD, Boyle PM, Chrispin J, Ju S, Marine JE, Sinha S, Tandri H, Ashikaga H, Trayanova NA	Frontiers in physiology	34335294	Front Physiol	2021	https://www.ncbi.nlm.nih.gov/pubmed/34335294
Computational modeling of aberrant electrical activity following remuscularization with intramyocardially injected pluripotent stem cell-derived cardiomyocytes.	Yu JK, Liang JA, Weinberg SH, Trayanova NA	Journal of molecular and cellular cardiology	34487753	J Mol Cell Cardiol	2022 Jan	https://www.ncbi.nlm.nih.gov/pubmed/34487753
Modelling methodology of atrial fibrosis affects rotor dynamics and electrograms.	Roney CH, Bayer JD, Zahid S, Meo M, Boyle PM, Trayanova NA, Haïssaguerre M, Dubois R, Cochet H, Vigmond EJ	Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology	28011842	Europace	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/28011842
Imaging-Based Simulations for Predicting Sudden Death and Guiding Ventricular Tachycardia Ablation.	Trayanova NA, Pashakhanloo F, Wu KC, Halperin HR	Circulation. Arrhythmia and electrophysiology	28696219	Circ Arrhythm Electrophysiol	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28696219
Tropomyosin dynamics during cardiac muscle contraction as governed by a multi-well energy landscape.	Aboelkassem Y, Trayanova N	Progress in biophysics and molecular biology	30145015	Prog Biophys Mol Biol	2019 Jul	https://www.ncbi.nlm.nih.gov/pubmed/30145015
Optimal contrast-enhanced MRI image thresholding for accurate prediction of ventricular tachycardia using ex-vivo high resolution models.	Deng D, Nikolov P, Arevalo HJ, Trayanova NA	Computers in biology and medicine	30301573	Comput Biol Med	2018 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/30301573
Optogenetic defibrillation terminates ventricular arrhythmia in mouse hearts and human simulations.	Bruegmann T, Boyle PM, Vogt CC, Karathanos TV, Arevalo HJ, Fleischmann BK, Trayanova NA, Sasse P	The Journal of clinical investigation	27617859	J Clin Invest	2016 Oct 3	https://www.ncbi.nlm.nih.gov/pubmed/27617859
Role of 3-Dimensional Architecture of Scar and Surviving Tissue in Ventricular Tachycardia: Insights From High-Resolution Ex Vivo Porcine Models.	Pashakhanloo F, Herzka DA, Halperin H, McVeigh ER, Trayanova NA	Circulation. Arrhythmia and electrophysiology	29880529	Circ Arrhythm Electrophysiol	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29880529
Characterizing Conduction Channels in Postinfarction Patients Using a Personalized Virtual Heart.	Deng D, Prakosa A, Shade J, Nikolov P, Trayanova NA	Biophysical journal	31447108	Biophys J	2019 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/31447108
Computationally guided personalized targeted ablation of persistent atrial fibrillation.	Boyle PM, Zghaib T, Zahid S, Ali RL, Deng D, Franceschi WH, Hakim JB, Murphy MJ, Prakosa A, Zimmerman SL, Ashikaga H, Marine JE, Kolandaivelu A, Nazarian S, Spragg DD, Calkins H, Trayanova NA	Nature biomedical engineering	31427780	Nat Biomed Eng	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31427780
New insights into defibrillation of the heart from realistic simulation studies.	Trayanova NA, Rantner LJ	Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology	24798960	Europace	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24798960
Optimizing cardiac resynchronization therapy to minimize ATP consumption heterogeneity throughout the left ventricle: a simulation analysis using a canine heart failure model.	Hu Y, Gurev V, Constantino J, Trayanova N	Heart rhythm	24657430	Heart Rhythm	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24657430
Relationship Between Fibrosis Detected on Late Gadolinium-Enhanced Cardiac Magnetic Resonance and Re-Entrant Activity Assessed With Electrocardiographic Imaging in Human Persistent Atrial Fibrillation.	Cochet H, Dubois R, Yamashita S, Al Jefairi N, Berte B, Sellal JM, Hooks D, Frontera A, Amraoui S, Zemoura A, Denis A, Derval N, Sacher F, Corneloup O, Latrabe V, Clément-Guinaudeau S, Relan J, Zahid S, Boyle PM, Trayanova NA, Bernus O, Montaudon M, Laurent F, Hocini M, Haïssaguerre M, Jaïs P	JACC. Clinical electrophysiology	29479568	JACC Clin Electrophysiol	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29479568
Substrate Spatial Complexity Analysis for the Prediction of Ventricular Arrhythmias in Patients With Ischemic Cardiomyopathy.	Okada DR, Miller J, Chrispin J, Prakosa A, Trayanova N, Jones S, Maggioni M, Wu KC	Circulation. Arrhythmia and electrophysiology	32188287	Circ Arrhythm Electrophysiol	2020 Apr	https://www.ncbi.nlm.nih.gov/pubmed/32188287
Chronic centrosome amplification without tumorigenesis.	Vitre B, Holland AJ, Kulukian A, Shoshani O, Hirai M, Wang Y, Maldonado M, Cho T, Boubaker J, Swing DA, Tessarollo L, Evans SM, Fuchs E, Cleveland DW	Proceedings of the National Academy of Sciences of the United States of America	26578792	Proc Natl Acad Sci U S A	2015 Nov 17	https://www.ncbi.nlm.nih.gov/pubmed/26578792
Resident fibroblast lineages mediate pressure overload-induced cardiac fibrosis.	Moore-Morris T, Guimarães-Camboa N, Banerjee I, Zambon AC, Kisseleva T, Velayoudon A, Stallcup WB, Gu Y, Dalton ND, Cedenilla M, Gomez-Amaro R, Zhou B, Brenner DA, Peterson KL, Chen J, Evans SM	The Journal of clinical investigation	24937432	J Clin Invest	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24937432
Sorting out where fibroblasts come from.	Moore-Morris T, Tallquist MD, Evans SM	Circulation research	25214570	Circ Res	2014 Sep 12	https://www.ncbi.nlm.nih.gov/pubmed/25214570
Coordination of heart and lung co-development by a multipotent cardiopulmonary progenitor.	Peng T, Tian Y, Boogerd CJ, Lu MM, Kadzik RS, Stewart KM, Evans SM, Morrisey EE	Nature	23873040	Nature	2013 Aug 29	https://www.ncbi.nlm.nih.gov/pubmed/23873040
Mapping the dynamic expression of Wnt11 and the lineage contribution of Wnt11-expressing cells during early mouse development.	Sinha T, Lin L, Li D, Davis J, Evans S, Wynshaw-Boris A, Wang J	Developmental biology	25448697	Dev Biol	2015 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/25448697
Early postmyocardial infarction survival in Murphy Roths Large mice is mediated by attenuated apoptosis and inflammation but depends on genetic background.	Hunt DL, Campbell PH, Zambon AC, Vranizan K, Evans SM, Kuo HC, Yamaguchi KD, Omens JH, McCulloch AD	Experimental physiology	21967898	Exp Physiol	2012 Jan	https://www.ncbi.nlm.nih.gov/pubmed/21967898
Avian intervertebral disc arises from rostral sclerotome and lacks a nucleus pulposus: implications for evolution of the vertebrate disc.	Bruggeman BJ, Maier JA, Mohiuddin YS, Powers R, Lo Y, Guimarães-Camboa N, Evans SM, Harfe BD	Developmental dynamics : an official publication of the American Association of Anatomists	22354863	Dev Dyn	2012 Apr	https://www.ncbi.nlm.nih.gov/pubmed/22354863
Thymosin beta 4 is dispensable for murine cardiac development and function.	Banerjee I, Zhang J, Moore-Morris T, Lange S, Shen T, Dalton ND, Gu Y, Peterson KL, Evans SM, Chen J	Circulation research	22158707	Circ Res	2012 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/22158707
Origins of cardiac fibroblasts.	Moore-Morris T, Cattaneo P, Puceat M, Evans SM	Journal of molecular and cellular cardiology	26748307	J Mol Cell Cardiol	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/26748307
Tbx18 Regulates the Differentiation of Periductal Smooth Muscle Stroma and the Maintenance of Epithelial Integrity in the Prostate.	Bolt CC, Negi S, Guimarães-Camboa N, Zhang H, Troy JM, Lu X, Kispert A, Evans SM, Stubbs L	PloS one	27120339	PLoS One	2016	https://www.ncbi.nlm.nih.gov/pubmed/27120339
Transcription factor ISL1 is essential for pacemaker development and function.	Liang X, Zhang Q, Cattaneo P, Zhuang S, Gong X, Spann NJ, Jiang C, Cao X, Zhao X, Zhang X, Bu L, Wang G, Chen HS, Zhuang T, Yan J, Geng P, Luo L, Banerjee I, Chen Y, Glass CK, Zambon AC, Chen J, Sun Y, Evans SM	The Journal of clinical investigation	26193633	J Clin Invest	2015 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/26193633
Probing chromatin landscape reveals roles of endocardial TBX20 in septation.	Boogerd CJ, Aneas I, Sakabe N, Dirschinger RJ, Cheng QJ, Zhou B, Chen J, Nobrega MA, Evans SM	The Journal of clinical investigation	27348591	J Clin Invest	2016 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/27348591
Human pre-valvular endocardial cells derived from pluripotent stem cells recapitulate cardiac pathophysiological valvulogenesis.	Neri T, Hiriart E, van Vliet PP, Faure E, Norris RA, Farhat B, Jagla B, Lefrancois J, Sugi Y, Moore-Morris T, Zaffran S, Faustino RS, Zambon AC, Desvignes JP, Salgado D, Levine RA, de la Pompa JL, Terzic A, Evans SM, Markwald R, Pucéat M	Nature communications	31028265	Nat Commun	2019 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/31028265
Single-molecule states link transcription factor binding to gene expression.	Doughty BR, Hinks MM, Schaepe JM, Marinov GK, Thurm AR, Rios-Martinez C, Parks BE, Tan Y, Marklund E, Dubocanin D, Bintu L, Greenleaf WJ	Nature	39567683	Nature	2024 Dec	https://www.ncbi.nlm.nih.gov/pubmed/39567683
Concurrent genome and epigenome editing by CRISPR-mediated sequence replacement.	Alexander J, Findlay GM, Kircher M, Shendure J	BMC biology	31739790	BMC Biol	2019 Nov 18	https://www.ncbi.nlm.nih.gov/pubmed/31739790
Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks.	Agarwal V, Shendure J	Cell reports	32433972	Cell Rep	2020 May 19	https://www.ncbi.nlm.nih.gov/pubmed/32433972
The landscape of alternative polyadenylation in single cells of the developing mouse embryo.	Agarwal V, Lopez-Darwin S, Kelley DR, Shendure J	Nature communications	34429411	Nat Commun	2021 Aug 24	https://www.ncbi.nlm.nih.gov/pubmed/34429411
Comprehensive single-cell transcriptional profiling of a multicellular organism.	Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J	Science (New York, N.Y.)	28818938	Science	2017 Aug 18	https://www.ncbi.nlm.nih.gov/pubmed/28818938
Accurate classification of BRCA1 variants with saturation genome editing.	Findlay GM, Daza RM, Martin B, Zhang MD, Leith AP, Gasperini M, Janizek JD, Huang X, Starita LM, Shendure J	Nature	30209399	Nature	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30209399
Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data.	Gray VE, Hause RJ, Luebeck J, Shendure J, Fowler DM	Cell systems	29226803	Cell Syst	2018 Jan 24	https://www.ncbi.nlm.nih.gov/pubmed/29226803
FlashFry: a fast and flexible tool for large-scale CRISPR target design.	McKenna A, Shendure J	BMC biology	29976198	BMC Biol	2018 Jul 5	https://www.ncbi.nlm.nih.gov/pubmed/29976198
Genomic Medicine-Progress, Pitfalls, and Promise.	Shendure J, Findlay GM, Snyder MW	Cell	30901547	Cell	2019 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/30901547
The power of multiplexed functional analysis of genetic variants.	Gasperini M, Starita L, Shendure J	Nature protocols	27583640	Nat Protoc	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27583640
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.	Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J	Science (New York, N.Y.)	25953818	Science	2015 May 22	https://www.ncbi.nlm.nih.gov/pubmed/25953818
A general framework for estimating the relative pathogenicity of human genetic variants.	Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J	Nature genetics	24487276	Nat Genet	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24487276
High Sensitivity Profiling of Chromatin Structure by MNase-SSP.	Ramani V, Qiu R, Shendure J	Cell reports	30811994	Cell Rep	2019 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/30811994
Massively Parallel Functional Analysis of BRCA1 RING Domain Variants.	Starita LM, Young DL, Islam M, Kitzman JO, Gullingsrud J, Hause RJ, Fowler DM, Parvin JD, Shendure J, Fields S	Genetics	25823446	Genetics	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25823446
Massively parallel single-amino-acid mutagenesis.	Kitzman JO, Starita LM, Lo RS, Fields S, Shendure J	Nature methods	25559584	Nat Methods	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25559584
Massively multiplex single-cell Hi-C.	Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J	Nature methods	28135255	Nat Methods	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28135255
Multiplex assessment of protein variant abundance by massively parallel sequencing.	Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ, Bhatia S, Evans WE, Relling MV, Yang W, Shendure J, Fowler DM	Nature genetics	29785012	Nat Genet	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29785012
Variant Interpretation: Functional Assays to the Rescue.	Starita LM, Ahituv N, Dunham MJ, Kitzman JO, Roth FP, Seelig G, Shendure J, Fowler DM	American journal of human genetics	28886340	Am J Hum Genet	2017 Sep 7	https://www.ncbi.nlm.nih.gov/pubmed/28886340
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy.	McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ Jr, Shendure J, Trapnell C	bioRxiv : the preprint server for biology	37398090	bioRxiv	2023 Jun 14	https://www.ncbi.nlm.nih.gov/pubmed/37398090
Joint profiling of chromatin accessibility and gene expression in thousands of single cells.	Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J	Science (New York, N.Y.)	30166440	Science	2018 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/30166440
High-Throughput Single-Cell Sequencing with Linear Amplification.	Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J	Molecular cell	31495564	Mol Cell	2019 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/31495564
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.	Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J	Cell	30849375	Cell	2019 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/30849375
A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function.	Starita LM, Islam MM, Banerjee T, Adamovich AI, Gullingsrud J, Fields S, Shendure J, Parvin JD	American journal of human genetics	30219179	Am J Hum Genet	2018 Oct 4	https://www.ncbi.nlm.nih.gov/pubmed/30219179
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.	Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J	Cell	30078704	Cell	2018 Aug 23	https://www.ncbi.nlm.nih.gov/pubmed/30078704
High-throughput determination of RNA structure by proximity ligation.	Ramani V, Qiu R, Shendure J	Nature biotechnology	26237516	Nat Biotechnol	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/26237516
Copy-number variation and false positive prenatal aneuploidy screening results.	Snyder MW, Simmons LE, Kitzman JO, Coe BP, Henson JM, Daza RM, Eichler EE, Shendure J, Gammill HS	The New England journal of medicine	25830323	N Engl J Med	2015 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/25830323
Mapping 3D genome architecture through in situ DNase Hi-C.	Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z	Nature protocols	27685100	Nat Protoc	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/27685100
Whole-organism lineage tracing by combinatorial and cumulative genome editing.	McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J	Science (New York, N.Y.)	27229144	Science	2016 Jul 29	https://www.ncbi.nlm.nih.gov/pubmed/27229144
Saturation editing of genomic regions by multiplex homology-directed repair.	Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J	Nature	25141179	Nature	2014 Sep 4	https://www.ncbi.nlm.nih.gov/pubmed/25141179
The cis-regulatory dynamics of embryonic development at single-cell resolution.	Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM	Nature	29539636	Nature	2018 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/29539636
Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.	Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J	Cell	26771485	Cell	2016 Jan 14	https://www.ncbi.nlm.nih.gov/pubmed/26771485
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy.	McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ Jr, Shendure J, Trapnell C	Cell genomics	38278156	Cell Genom	2024 Feb 14	https://www.ncbi.nlm.nih.gov/pubmed/38278156
CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions.	Gasperini M, Findlay GM, McKenna A, Milbank JH, Lee C, Zhang MD, Cusanovich DA, Shendure J	American journal of human genetics	28712454	Am J Hum Genet	2017 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/28712454
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.	Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C	Molecular cell	30078726	Mol Cell	2018 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/30078726
Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.	Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF	Nature biotechnology	29608178	Nat Biotechnol	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29608178
Supervised classification enables rapid annotation of cell atlases.	Pliner HA, Shendure J, Trapnell C	Nature methods	31501545	Nat Methods	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31501545
Massively multiplex chemical transcriptomics at single-cell resolution.	Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C	Science (New York, N.Y.)	31806696	Science	2020 Jan 3	https://www.ncbi.nlm.nih.gov/pubmed/31806696
Sci-fate characterizes the dynamics of gene expression in single cells.	Cao J, Zhou W, Steemers F, Trapnell C, Shendure J	Nature biotechnology	32284584	Nat Biotechnol	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32284584
Multimodal single-cell analysis reveals distinct radioresistant stem-like and progenitor cell populations in murine glioma.	Alexander J, LaPlant QC, Pattwell SS, Szulzewsky F, Cimino PJ, Caruso FP, Pugliese P, Chen Z, Chardon F, Hill AJ, Spurrell C, Ahrendsen D, Pietras A, Starita LM, Hambardzumyan D, Iavarone A, Shendure J, Holland EC	Glia	32621641	Glia	2020 Dec	https://www.ncbi.nlm.nih.gov/pubmed/32621641
The single-cell transcriptional landscape of mammalian organogenesis.	Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J	Nature	30787437	Nature	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30787437
Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.	Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z	Methods (San Diego, Calif.)	31536770	Methods	2020 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/31536770
On the design of CRISPR-based single-cell molecular screens.	Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C	Nature methods	29457792	Nat Methods	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29457792
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.	Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J	Cell	30612741	Cell	2019 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/30612741
Analysis of Cre lines for targeting embryonic airway smooth muscle.	Goodwin K, Nelson CM	Developmental biology	36706974	Dev Biol	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/36706974
pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells.	Farahani PE, Yang X, Mesev EV, Fomby KA, Brumbaugh-Reed EH, Bashor CJ, Nelson CM, Toettcher JE	eLife	37212240	Elife	2023 May 22	https://www.ncbi.nlm.nih.gov/pubmed/37212240
Plasticity in airway smooth muscle differentiation during mouse lung development.	Goodwin K, Lemma B, Zhang P, Boukind A, Nelson CM	Developmental cell	36868232	Dev Cell	2023 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/36868232
Biophysics of morphogenesis in the vertebrate lung.	Banavar SP, Fowler EW, Nelson CM	Current topics in developmental biology	38937031	Curr Top Dev Biol	2024	https://www.ncbi.nlm.nih.gov/pubmed/38937031
Mesenchymal Vangl1 and Vangl2 facilitate airway elongation and widening independently of the planar cell polarity complex.	Paramore SV, Goodwin K, Fowler EW, Devenport D, Nelson CM	Development (Cambridge, England)	39225402	Development	2024 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/39225402
Mesenchymal Vangl facilitates airway elongation and widening independently of the planar cell polarity complex.	Paramore SV, Goodwin K, Devenport D, Nelson CM	bioRxiv : the preprint server for biology	37461477	bioRxiv	2023 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/37461477
Spatial patterning of energy metabolism during tissue morphogenesis.	Lemma B, Nelson CM	Current opinion in cell biology	37696131	Curr Opin Cell Biol	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37696131
Vangl-dependent mesenchymal thinning shapes the distal lung during murine sacculation.	Paramore SV, Trenado-Yuste C, Sharan R, Nelson CM, Devenport D	Developmental cell	38569553	Dev Cell	2024 May 20	https://www.ncbi.nlm.nih.gov/pubmed/38569553
Basement membrane remodelling regulates mouse embryogenesis.	Kyprianou C, Christodoulou N, Hamilton RS, Nahaboo W, Boomgaard DS, Amadei G, Migeotte I, Zernicka-Goetz M	Nature	32523119	Nature	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/32523119
Mouse embryo model derived exclusively from embryonic stem cells undergoes neurulation and heart development.	Lau KYC, Rubinstein H, Gantner CW, Hadas R, Amadei G, Stelzer Y, Zernicka-Goetz M	Cell stem cell	36084657	Cell Stem Cell	2022 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/36084657
Embryo size regulates the timing and mechanism of pluripotent tissue morphogenesis.	Orietti LC, Rosa VS, Antonica F, Kyprianou C, Mansfield W, Marques-Souza H, Shahbazi MN, Zernicka-Goetz M	Stem cell reports	33035465	Stem Cell Reports	2021 May 11	https://www.ncbi.nlm.nih.gov/pubmed/33035465
Modeling human embryo development with embryonic and extra-embryonic stem cells.	Weatherbee BAT, Cui T, Zernicka-Goetz M	Developmental biology	33333069	Dev Biol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33333069
Progress and challenges in stem cell biology.	Apostolou E, Blau H, Chien K, Lancaster MA, Tata PR, Trompouki E, Watt FM, Zeng YA, Zernicka-Goetz M	Nature cell biology	36788378	Nat Cell Biol	2023 Feb	https://www.ncbi.nlm.nih.gov/pubmed/36788378
Temporal BMP4 effects on mouse embryonic and extraembryonic development.	Hadas R, Rubinstein H, Mittnenzweig M, Mayshar Y, Ben-Yair R, Cheng S, Aguilera-Castrejon A, Reines N, Orenbuch AH, Lifshitz A, Chen DY, Elowitz MB, Zernicka-Goetz M, Hanna JH, Tanay A, Stelzer Y	Nature	39294373	Nature	2024 Oct	https://www.ncbi.nlm.nih.gov/pubmed/39294373
AI-based approach to dissect the variability of mouse stem cell-derived embryo models.	Caldarelli P, Deininger L, Zhao S, Panda P, Yang C, Mikut R, Zernicka-Goetz M	Nature communications	39971935	Nat Commun	2025 Feb 19	https://www.ncbi.nlm.nih.gov/pubmed/39971935
The dynamics of morphogenesis in stem cell-based embryology: Novel insights for symmetry breaking.	Sozen B, Cornwall-Scoones J, Zernicka-Goetz M	Developmental biology	33333067	Dev Biol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33333067
An in vitro stem cell model of human epiblast and yolk sac interaction.	Mackinlay KM, Weatherbee BA, Souza Rosa V, Handford CE, Hudson G, Coorens T, Pereira LV, Behjati S, Vallier L, Shahbazi MN, Zernicka-Goetz M	eLife	34403333	Elife	2021 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/34403333
Assembly of complete mouse embryo models from embryonic and induced stem cell types in vitro.	Lau KYC, Amadei G, Zernicka-Goetz M	Nature protocols	37821625	Nat Protoc	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37821625
Self-organization of stem cells into embryos: A window on early mammalian development.	Shahbazi MN, Siggia ED, Zernicka-Goetz M	Science (New York, N.Y.)	31171690	Science	2019 Jun 7	https://www.ncbi.nlm.nih.gov/pubmed/31171690
Integrin β1 coordinates survival and morphogenesis of the embryonic lineage upon implantation and pluripotency transition.	Molè MA, Weberling A, Fässler R, Campbell A, Fishel S, Zernicka-Goetz M	Cell reports	33691117	Cell Rep	2021 Mar 9	https://www.ncbi.nlm.nih.gov/pubmed/33691117
Trophectoderm mechanics direct epiblast shape upon embryo implantation.	Weberling A, Zernicka-Goetz M	Cell reports	33472064	Cell Rep	2021 Jan 19	https://www.ncbi.nlm.nih.gov/pubmed/33472064
Principles of Self-Organization of the Mammalian Embryo.	Zhu M, Zernicka-Goetz M	Cell	33306953	Cell	2020 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/33306953
Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension.	Bao M, Cornwall-Scoones J, Sanchez-Vasquez E, Cox AL, Chen DY, De Jonghe J, Shadkhoo S, Hollfelder F, Thomson M, Glover DM, Zernicka-Goetz M	Nature cell biology	36100738	Nat Cell Biol	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/36100738
spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content.	De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, Kohler TN, Amadei G, Handford CE, Findlay GM, Zernicka-Goetz M, Teichmann SA, Hollfelder F	Nature communications	37553326	Nat Commun	2023 Aug 8	https://www.ncbi.nlm.nih.gov/pubmed/37553326
Topical section: embryonic models (2023) for Current Opinion in Genetics & Development.	Handford CE, Junyent S, Jorgensen V, Zernicka-Goetz M	Current opinion in genetics & development	38052116	Curr Opin Genet Dev	2024 Feb	https://www.ncbi.nlm.nih.gov/pubmed/38052116
Stem-cell-based human and mouse embryo models.	Bao M, Cornwall-Scoones J, Zernicka-Goetz M	Current opinion in genetics & development	35988317	Curr Opin Genet Dev	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/35988317
Embryo model completes gastrulation to neurulation and organogenesis.	Amadei G, Handford CE, Qiu C, De Jonghe J, Greenfeld H, Tran M, Martin BK, Chen DY, Aguilera-Castrejon A, Hanna JH, Elowitz MB, Hollfelder F, Shendure J, Glover DM, Zernicka-Goetz M	Nature	36007540	Nature	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36007540
Inducible Stem-Cell-Derived Embryos Capture Mouse Morphogenetic Events In Vitro.	Amadei G, Lau KYC, De Jonghe J, Gantner CW, Sozen B, Chan C, Zhu M, Kyprianou C, Hollfelder F, Zernicka-Goetz M	Developmental cell	33378662	Dev Cell	2021 Feb 8	https://www.ncbi.nlm.nih.gov/pubmed/33378662
Unifying synthetic embryology.	Cornwall-Scoones J, Zernicka-Goetz M	Developmental biology	33753081	Dev Biol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33753081
Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid.	Sozen B, Cox AL, De Jonghe J, Bao M, Hollfelder F, Glover DM, Zernicka-Goetz M	Developmental cell	31846649	Dev Cell	2019 Dec 16	https://www.ncbi.nlm.nih.gov/pubmed/31846649
BMP signalling is required for extra-embryonic ectoderm development during pre-to-post-implantation transition of the mouse embryo.	Sozen B, Demir N, Zernicka-Goetz M	Developmental biology	33217407	Dev Biol	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33217407
Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts.	Shafer MER, Sawh AN, Schier AF	Nature ecology & evolution	34824389	Nat Ecol Evol	2022 Jan	https://www.ncbi.nlm.nih.gov/pubmed/34824389
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.	Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF	Science (New York, N.Y.)	29700225	Science	2018 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/29700225
Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT.	Raj B, Gagnon JA, Schier AF	Nature protocols	30353175	Nat Protoc	2018 Nov	https://www.ncbi.nlm.nih.gov/pubmed/30353175
Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions.	Thyme SB, Pieper LM, Li EH, Pandey S, Wang Y, Morris NS, Sha C, Choi JW, Herrera KJ, Soucy ER, Zimmerman S, Randlett O, Greenwood J, McCarroll SA, Schier AF	Cell	30929901	Cell	2019 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/30929901
Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level.	Lin Q, Manley J, Helmreich M, Schlumm F, Li JM, Robson DN, Engert F, Schier A, Nöbauer T, Vaziri A	Cell	31955849	Cell	2020 Feb 6	https://www.ncbi.nlm.nih.gov/pubmed/31955849
A single-cell transcriptome atlas of the maturing zebrafish telencephalon.	Pandey S, Moyer AJ, Thyme SB	Genome research	37072188	Genome Res	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/37072188
Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development.	Sur A, Wang Y, Capar P, Margolin G, Prochaska MK, Farrell JA	Developmental cell	37995681	Dev Cell	2023 Dec 18	https://www.ncbi.nlm.nih.gov/pubmed/37995681
Convergent Temperature Representations in Artificial and Biological Neural Networks.	Haesemeyer M, Schier AF, Engert F	Neuron	31376984	Neuron	2019 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/31376984
Emergence of Neuronal Diversity during Vertebrate Brain Development.	Raj B, Farrell JA, Liu J, El Kholtei J, Carte AN, Navajas Acedo J, Du LY, McKenna A, Relić Đ, Leslie JM, Schier AF	Neuron	33068532	Neuron	2020 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/33068532
Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq.	Pandey S, Shekhar K, Regev A, Schier AF	Current biology : CB	29576475	Curr Biol	2018 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/29576475
Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development.	Sur A, Wang Y, Capar P, Margolin G, Farrell JA	bioRxiv : the preprint server for biology	36993555	bioRxiv	2023 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/36993555
Zebrafish oxytocin neurons drive nocifensive behavior via brainstem premotor targets.	Wee CL, Nikitchenko M, Wang WC, Luks-Morgan SJ, Song E, Gagnon JA, Randlett O, Bianco IH, Lacoste AMB, Glushenkova E, Barrios JP, Schier AF, Kunes S, Engert F, Douglass AD	Nature neuroscience	31358991	Nat Neurosci	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31358991
Molecular mechanisms controlling the biogenesis of the TGF-β signal Vg1.	Dingal PCDP, Carte AN, Montague TG, Lim Suan MB Jr, Schier AF	Proceedings of the National Academy of Sciences of the United States of America	37844219	Proc Natl Acad Sci U S A	2023 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/37844219
Neural synchrony predicts children's learning of novel words.	Piazza EA, Cohen A, Trach J, Lew-Williams C	Cognition	33965782	Cognition	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/33965782
Measuring shared responses across subjects using intersubject correlation.	Nastase SA, Gazzola V, Hasson U, Keysers C	Social cognitive and affective neuroscience	31099394	Soc Cogn Affect Neurosci	2019 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/31099394
The default mode network: where the idiosyncratic self meets the shared social world.	Yeshurun Y, Nguyen M, Hasson U	Nature reviews. Neuroscience	33483717	Nat Rev Neurosci	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33483717
Information flow across the cortical timescale hierarchy during narrative construction.	Chang CHC, Nastase SA, Hasson U	Proceedings of the National Academy of Sciences of the United States of America	36508677	Proc Natl Acad Sci U S A	2022 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/36508677
A shared model-based linguistic space for transmitting our thoughts from brain to brain in natural conversations.	Zada Z, Goldstein A, Michelmann S, Simony E, Price A, Hasenfratz L, Barham E, Zadbood A, Doyle W, Friedman D, Dugan P, Melloni L, Devore S, Flinker A, Devinsky O, Nastase SA, Hasson U	Neuron	39096896	Neuron	2024 Sep 25	https://www.ncbi.nlm.nih.gov/pubmed/39096896
Linguistic coupling between neural systems for speech production and comprehension during real-time dyadic conversations.	Zada Z, Nastase SA, Speer S, Mwilambwe-Tshilobo L, Tsoi L, Burns S, Falk E, Hasson U, Tamir D	bioRxiv : the preprint server for biology	39990465	bioRxiv	2025 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/39990465
Propagation of Information Along the Cortical Hierarchy as a Function of Attention While Reading and Listening to Stories.	Regev M, Simony E, Lee K, Tan KM, Chen J, Hasson U	Cerebral cortex (New York, N.Y. : 1991)	30395174	Cereb Cortex	2019 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/30395174
Elucidating relations between fMRI, ECoG, and EEG through a common natural stimulus.	Haufe S, DeGuzman P, Henin S, Arcaro M, Honey CJ, Hasson U, Parra LC	NeuroImage	29902585	Neuroimage	2018 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/29902585
Shared understanding of narratives is correlated with shared neural responses.	Nguyen M, Vanderwal T, Hasson U	NeuroImage	30217543	Neuroimage	2019 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/30217543
Shared computational principles for language processing in humans and deep language models.	Goldstein A, Zada Z, Buchnik E, Schain M, Price A, Aubrey B, Nastase SA, Feder A, Emanuel D, Cohen A, Jansen A, Gazula H, Choe G, Rao A, Kim C, Casto C, Fanda L, Doyle W, Friedman D, Dugan P, Melloni L, Reichart R, Devore S, Flinker A, Hasenfratz L, Levy O, Hassidim A, Brenner M, Matias Y, Norman KA, Devinsky O, Hasson U	Nature neuroscience	35260860	Nat Neurosci	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/35260860
Alignment of brain embeddings and artificial contextual embeddings in natural language points to common geometric patterns.	Goldstein A, Grinstein-Dabush A, Schain M, Wang H, Hong Z, Aubrey B, Nastase SA, Zada Z, Ham E, Feder A, Gazula H, Buchnik E, Doyle W, Devore S, Dugan P, Reichart R, Friedman D, Brenner M, Hassidim A, Devinsky O, Flinker A, Hasson U	Nature communications	38553456	Nat Commun	2024 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/38553456
How a speaker herds the audience: multibrain neural convergence over time during naturalistic storytelling.	Chang CHC, Nastase SA, Zadbood A, Hasson U	Social cognitive and affective neuroscience	39223692	Soc Cogn Affect Neurosci	2024 Sep 24	https://www.ncbi.nlm.nih.gov/pubmed/39223692
A functional neuroimaging dataset acquired during naturalistic movie watching and narrated recall of a series of short cinematic films.	Lee H, Chen J, Hasson U	Data in brief	36506797	Data Brief	2023 Feb	https://www.ncbi.nlm.nih.gov/pubmed/36506797
Neural alignment predicts learning outcomes in students taking an introduction to computer science course.	Meshulam M, Hasenfratz L, Hillman H, Liu YF, Nguyen M, Norman KA, Hasson U	Nature communications	33771999	Nat Commun	2021 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/33771999
Direct Fit to Nature: An Evolutionary Perspective on Biological and Artificial Neural Networks.	Hasson U, Nastase SA, Goldstein A	Neuron	32027833	Neuron	2020 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/32027833
Keep it real: rethinking the primacy of experimental control in cognitive neuroscience.	Nastase SA, Goldstein A, Hasson U	NeuroImage	32800992	Neuroimage	2020 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/32800992
Measuring speaker-listener neural coupling with functional near infrared spectroscopy.	Liu Y, Piazza EA, Simony E, Shewokis PA, Onaral B, Hasson U, Ayaz H	Scientific reports	28240295	Sci Rep	2017 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/28240295
How a speaker herds the audience: Multi-brain neural convergence over time during naturalistic storytelling.	Chang CHC, Nastase SA, Hasson U	bioRxiv : the preprint server for biology	37873125	bioRxiv	2024 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/37873125
A shared linguistic space for transmitting our thoughts from brain to brain in natural conversations.	Zada Z, Goldstein A, Michelmann S, Simony E, Price A, Hasenfratz L, Barham E, Zadbood A, Doyle W, Friedman D, Dugan P, Melloni L, Devore S, Flinker A, Devinsky O, Nastase SA, Hasson U	bioRxiv : the preprint server for biology	37425747	bioRxiv	2023 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/37425747
Neural representations of naturalistic events are updated as our understanding of the past changes.	Zadbood A, Nastase S, Chen J, Norman KA, Hasson U	eLife	36519530	Elife	2022 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/36519530
The "Narratives" fMRI dataset for evaluating models of naturalistic language comprehension.	Nastase SA, Liu YF, Hillman H, Zadbood A, Hasenfratz L, Keshavarzian N, Chen J, Honey CJ, Yeshurun Y, Regev M, Nguyen M, Chang CHC, Baldassano C, Lositsky O, Simony E, Chow MA, Leong YC, Brooks PP, Micciche E, Choe G, Goldstein A, Vanderwal T, Halchenko YO, Norman KA, Hasson U	Scientific data	34584100	Sci Data	2021 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/34584100
In Search of a Neural Mechanism for Domain-General Value Comparison in Decision Making.	Samara A, Zada Z	The Journal of neuroscience : the official journal of the Society for Neuroscience	39939165	J Neurosci	2025 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/39939165
Teacher-student neural coupling during teaching and learning.	Nguyen M, Chang A, Micciche E, Meshulam M, Nastase SA, Hasson U	Social cognitive and affective neuroscience	34450637	Soc Cogn Affect Neurosci	2022 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/34450637
Infant and Adult Brains Are Coupled to the Dynamics of Natural Communication.	Piazza EA, Hasenfratz L, Hasson U, Lew-Williams C	Psychological science	31845827	Psychol Sci	2020 Jan	https://www.ncbi.nlm.nih.gov/pubmed/31845827
Bayesian Surprise Predicts Human Event Segmentation in Story Listening.	Kumar M, Goldstein A, Michelmann S, Zacks JM, Hasson U, Norman KA	Cognitive science	37867379	Cogn Sci	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37867379
Scale matters: Large language models with billions (rather than millions) of parameters better match neural representations of natural language.	Hong Z, Wang H, Zada Z, Gazula H, Turner D, Aubrey B, Niekerken L, Doyle W, Devore S, Dugan P, Friedman D, Devinsky O, Flinker A, Hasson U, Nastase SA, Goldstein A	bioRxiv : the preprint server for biology	39005394	bioRxiv	2024 Oct 16	https://www.ncbi.nlm.nih.gov/pubmed/39005394
The "Podcast" ECoG dataset for modeling neural activity during natural language comprehension.	Zada Z, Nastase SA, Aubrey B, Jalon I, Michelmann S, Wang H, Hasenfratz L, Doyle W, Friedman D, Dugan P, Melloni L, Devore S, Flinker A, Devinsky O, Goldstein A, Hasson U	bioRxiv : the preprint server for biology	39990398	bioRxiv	2025 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/39990398
The neural architecture of language: Integrative modeling converges on predictive processing.	Schrimpf M, Blank IA, Tuckute G, Kauf C, Hosseini EA, Kanwisher N, Tenenbaum JB, Fedorenko E	Proceedings of the National Academy of Sciences of the United States of America	34737231	Proc Natl Acad Sci U S A	2021 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/34737231
The Quest for the FFA and Where It Led.	Kanwisher N	The Journal of neuroscience : the official journal of the Society for Neuroscience	28148806	J Neurosci	2017 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/28148806
What is changing when: Decoding visual information in movies from human intracranial recordings.	Isik L, Singer J, Madsen JR, Kanwisher N, Kreiman G	NeuroImage	28823828	Neuroimage	2018 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/28823828
Invariant representation of physical stability in the human brain.	Pramod RT, Cohen MA, Tenenbaum JB, Kanwisher N	eLife	35635277	Elife	2022 May 30	https://www.ncbi.nlm.nih.gov/pubmed/35635277
Using child-friendly movie stimuli to study the development of face, place, and object regions from age 3 to 12 years.	Kamps FS, Richardson H, Murty NAR, Kanwisher N, Saxe R	Human brain mapping	35274789	Hum Brain Mapp	2022 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/35274789
Brain-like functional specialization emerges spontaneously in deep neural networks.	Dobs K, Martinez J, Kell AJE, Kanwisher N	Science advances	35294241	Sci Adv	2022 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/35294241
Toward a universal decoder of linguistic meaning from brain activation.	Pereira F, Lou B, Pritchett B, Ritter S, Gershman SJ, Kanwisher N, Botvinick M, Fedorenko E	Nature communications	29511192	Nat Commun	2018 Mar 6	https://www.ncbi.nlm.nih.gov/pubmed/29511192
Approximating Human-Level 3D Visual Inferences With Deep Neural Networks.	O'Connell TP, Bonnen T, Friedman Y, Tewari A, Sitzmann V, Tenenbaum JB, Kanwisher N	Open mind : discoveries in cognitive science	40013087	Open Mind (Camb)	2025	https://www.ncbi.nlm.nih.gov/pubmed/40013087
Divergence in the functional organization of human and macaque auditory cortex revealed by fMRI responses to harmonic tones.	Norman-Haignere SV, Kanwisher N, McDermott JH, Conway BR	Nature neuroscience	31182868	Nat Neurosci	2019 Jul	https://www.ncbi.nlm.nih.gov/pubmed/31182868
Facephenes and rainbows: Causal evidence for functional and anatomical specificity of face and color processing in the human brain.	Schalk G, Kapeller C, Guger C, Ogawa H, Hiroshima S, Lafer-Sousa R, Saygin ZM, Kamada K, Kanwisher N	Proceedings of the National Academy of Sciences of the United States of America	29087337	Proc Natl Acad Sci U S A	2017 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/29087337
A neural population selective for song in human auditory cortex.	Norman-Haignere SV, Feather J, Boebinger D, Brunner P, Ritaccio A, McDermott JH, Schalk G, Kanwisher N	Current biology : CB	35196507	Curr Biol	2022 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/35196507
Selective responses to faces, scenes, and bodies in the ventral visual pathway of infants.	Kosakowski HL, Cohen MA, Takahashi A, Keil B, Kanwisher N, Saxe R	Current biology : CB	34784506	Curr Biol	2022 Jan 24	https://www.ncbi.nlm.nih.gov/pubmed/34784506
A neural population selective for song in human auditory cortex.	Norman-Haignere SV, Feather J, Boebinger D, Brunner P, Ritaccio A, McDermott JH, Schalk G, Kanwisher N	Current biology : CB	35349804	Curr Biol	2022 Mar 28	https://www.ncbi.nlm.nih.gov/pubmed/35349804
Behavioral signatures of face perception emerge in deep neural networks optimized for face recognition.	Dobs K, Yuan J, Martinez J, Kanwisher N	Proceedings of the National Academy of Sciences of the United States of America	37523537	Proc Natl Acad Sci U S A	2023 Aug 8	https://www.ncbi.nlm.nih.gov/pubmed/37523537
Using artificial neural networks to ask 'why' questions of minds and brains.	Kanwisher N, Khosla M, Dobs K	Trends in neurosciences	36658072	Trends Neurosci	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36658072
Exploring early human brain development with structural and physiological neuroimaging.	Vasung L, Abaci Turk E, Ferradal SL, Sutin J, Stout JN, Ahtam B, Lin PY, Grant PE	NeuroImage	30041061	Neuroimage	2019 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/30041061
An integrative computational architecture for object-driven cortex.	Yildirim I, Wu J, Kanwisher N, Tenenbaum J	Current opinion in neurobiology	30825704	Curr Opin Neurobiol	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30825704
Music-selective neural populations arise without musical training.	Boebinger D, Norman-Haignere SV, McDermott JH, Kanwisher N	Journal of neurophysiology	33596723	J Neurophysiol	2021 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/33596723
Organization of high-level visual cortex in human infants.	Deen B, Richardson H, Dilks DD, Takahashi A, Keil B, Wald LL, Kanwisher N, Saxe R	Nature communications	28072399	Nat Commun	2017 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/28072399
How face perception unfolds over time.	Dobs K, Isik L, Pantazis D, Kanwisher N	Nature communications	30890707	Nat Commun	2019 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/30890707
Visual experience is not necessary for the development of face-selectivity in the lateral fusiform gyrus.	Ratan Murty NA, Teng S, Beeler D, Mynick A, Oliva A, Kanwisher N	Proceedings of the National Academy of Sciences of the United States of America	32839334	Proc Natl Acad Sci U S A	2020 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/32839334
Perceiving social interactions in the posterior superior temporal sulcus.	Isik L, Koldewyn K, Beeler D, Kanwisher N	Proceedings of the National Academy of Sciences of the United States of America	29073111	Proc Natl Acad Sci U S A	2017 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/29073111
A highly selective response to food in human visual cortex revealed by hypothesis-free voxel decomposition.	Khosla M, Ratan Murty NA, Kanwisher N	Current biology : CB	36027910	Curr Biol	2022 Oct 10	https://www.ncbi.nlm.nih.gov/pubmed/36027910
Representational similarity precedes category selectivity in the developing ventral visual pathway.	Cohen MA, Dilks DD, Koldewyn K, Weigelt S, Feather J, Kell AJ, Keil B, Fischl B, Zöllei L, Wald L, Saxe R, Kanwisher N	NeuroImage	31077844	Neuroimage	2019 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/31077844
Computational models of category-selective brain regions enable high-throughput tests of selectivity.	Ratan Murty NA, Bashivan P, Abate A, DiCarlo JJ, Kanwisher N	Nature communications	34545079	Nat Commun	2021 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/34545079
Stress-induced RNA-chromatin interactions promote endothelial dysfunction.	Calandrelli R, Xu L, Luo Y, Wu W, Fan X, Nguyen T, Chen CJ, Sriram K, Tang X, Burns AB, Natarajan R, Chen ZB, Zhong S	Nature communications	33060583	Nat Commun	2020 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/33060583
Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos.	Biase FH, Wu Q, Calandrelli R, Rivas-Astroza M, Zhou S, Chen Z, Zhong S	iScience	30267678	iScience	2018 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/30267678
RNA, Action through Interactions.	Nguyen TC, Zaleta-Rivera K, Huang X, Dai X, Zhong S	Trends in genetics : TIG	30177410	Trends Genet	2018 Nov	https://www.ncbi.nlm.nih.gov/pubmed/30177410
Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs.	Yan Z, Huang N, Wu W, Chen W, Jiang Y, Chen J, Huang X, Wen X, Xu J, Jin Q, Zhang K, Chen Z, Chien S, Zhong S	Proceedings of the National Academy of Sciences of the United States of America	30718424	Proc Natl Acad Sci U S A	2019 Feb 19	https://www.ncbi.nlm.nih.gov/pubmed/30718424
SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination.	Xiao S, Lu J, Sridhar B, Cao X, Yu P, Zhao T, Chen CC, McDee D, Sloofman L, Wang Y, Rivas-Astroza M, Telugu BPVL, Levasseur D, Zhang K, Liang H, Zhao JC, Tanaka TS, Stormo G, Zhong S	Cell reports	28355564	Cell Rep	2017 Mar 28	https://www.ncbi.nlm.nih.gov/pubmed/28355564
Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.	Tang X, Miao Y, Luo Y, Sriram K, Qi Z, Lin FM, Gu Y, Lai CH, Hsu CY, Peterson KL, Van Keuren-Jensen K, Fueger PT, Yeo GW, Natarajan R, Zhong S, Chen ZB	Circulation	32393053	Circulation	2020 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/32393053
Mapping RNA-chromatin interactions by sequencing with iMARGI.	Wu W, Yan Z, Nguyen TC, Bouman Chen Z, Chien S, Zhong S	Nature protocols	31619811	Nat Protoc	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31619811
GIVE: portable genome browsers for personal websites.	Cao X, Yan Z, Wu Q, Zheng A, Zhong S	Genome biology	30016975	Genome Biol	2018 Jul 18	https://www.ncbi.nlm.nih.gov/pubmed/30016975
From structure to function, how bioinformatics help to reveal functions of our genomes.	Zheng X, Zhong S	Genome biology	28950915	Genome Biol	2017 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/28950915
Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level.	Malhi NK, Luo Y, Tang X, Sriram K, Calandrelli R, Zhong S, Chen ZB	Journal of visualized experiments : JoVE	35343966	J Vis Exp	2022 Mar 14	https://www.ncbi.nlm.nih.gov/pubmed/35343966
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.	Lu J, Cao X, Zhong S	PLoS computational biology	30586383	PLoS Comput Biol	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30586383
Systematic Mapping of RNA-Chromatin Interactions In Vivo.	Sridhar B, Rivas-Astroza M, Nguyen TC, Chen W, Yan Z, Cao X, Hebert L, Zhong S	Current biology : CB	28132817	Curr Biol	2017 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/28132817
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.	Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, Zhong S	Nature communications	37845234	Nat Commun	2023 Oct 16	https://www.ncbi.nlm.nih.gov/pubmed/37845234
GeNemo: a search engine for web-based functional genomic data.	Zhang Y, Cao X, Zhong S	Nucleic acids research	27098038	Nucleic Acids Res	2016 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/27098038
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction.	Huang N, Fan X, Zaleta-Rivera K, Nguyen TC, Zhou J, Luo Y, Gao J, Fang RH, Yan Z, Chen ZB, Zhang L, Zhong S	Genome biology	32907628	Genome Biol	2020 Sep 10	https://www.ncbi.nlm.nih.gov/pubmed/32907628
Pattern-based Search of Epigenomic Data Using GeNemo.	Zheng A, Cao X, Zhong S	Journal of visualized experiments : JoVE	29053670	J Vis Exp	2017 Oct 8	https://www.ncbi.nlm.nih.gov/pubmed/29053670
Mapping RNA-RNA interactome and RNA structure in vivo by MARIO.	Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S	Nature communications	27338251	Nat Commun	2016 Jun 24	https://www.ncbi.nlm.nih.gov/pubmed/27338251
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome.	Chen W, Yan Z, Li S, Huang N, Huang X, Zhang J, Zhong S	iScience	30240742	iScience	2018 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/30240742
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data.	Calandrelli R, Wu Q, Guan J, Zhong S	Genomics, proteomics & bioinformatics	30553884	Genomics Proteomics Bioinformatics	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30553884
Heat-inducible CAR-T overcomes adverse mechanical tumor microenvironment in a 3D bioprinted glioblastoma model.	Tang M, Qu Y, He P, Yao E, Guo T, Yu D, Zhang N, Kiratitanaporn W, Sun Y, Liu L, Wang Y, Chen S	Materials today. Bio	38765247	Mater Today Bio	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/38765247
Gasdermin D activity in inflammation and host defense.	Lieberman J, Wu H, Kagan JC	Science immunology	31492708	Sci Immunol	2019 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/31492708
FDA-approved disulfiram inhibits pyroptosis by blocking gasdermin D pore formation.	Hu JJ, Liu X, Xia S, Zhang Z, Zhang Y, Zhao J, Ruan J, Luo X, Lou X, Bai Y, Wang J, Hollingsworth LR, Magupalli VG, Zhao L, Luo HR, Kim J, Lieberman J, Wu H	Nature immunology	32367036	Nat Immunol	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32367036
Structures and functions of the inflammasome engine.	Wang L, Sharif H, Vora SM, Zheng Y, Wu H	The Journal of allergy and clinical immunology	34092352	J Allergy Clin Immunol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/34092352
Conformational flexibility and inhibitor binding to unphosphorylated interleukin-1 receptor-associated kinase 4 (IRAK4).	Wang L, Ferrao R, Li Q, Hatcher JM, Choi HG, Buhrlage SJ, Gray NS, Wu H	The Journal of biological chemistry	30679311	J Biol Chem	2019 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/30679311
SERPINB1-mediated checkpoint of inflammatory caspase activation.	Choi YJ, Kim S, Choi Y, Nielsen TB, Yan J, Lu A, Ruan J, Lee HR, Wu H, Spellberg B, Jung JU	Nature immunology	30692621	Nat Immunol	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30692621
Inflammation NODs to Antagonists of RIP2-XIAP Interaction.	Xia S, Fu TM, Wu H	Molecular cell	29452633	Mol Cell	2018 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/29452633
DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation.	Hollingsworth LR, Sharif H, Griswold AR, Fontana P, Mintseris J, Dagbay KB, Paulo JA, Gygi SP, Bachovchin DA, Wu H	Nature	33731932	Nature	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/33731932
Mechanism of filament formation in UPA-promoted CARD8 and NLRP1 inflammasomes.	Robert Hollingsworth L, David L, Li Y, Griswold AR, Ruan J, Sharif H, Fontana P, Orth-He EL, Fu TM, Bachovchin DA, Wu H	Nature communications	33420033	Nat Commun	2021 Jan 8	https://www.ncbi.nlm.nih.gov/pubmed/33420033
Phase separation drives RNA virus-induced activation of the NLRP6 inflammasome.	Shen C, Li R, Negro R, Cheng J, Vora SM, Fu TM, Wang A, He K, Andreeva L, Gao P, Tian Z, Flavell RA, Zhu S, Wu H	Cell	34678144	Cell	2021 Nov 11	https://www.ncbi.nlm.nih.gov/pubmed/34678144
Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold.	Fontana P, Dong Y, Pi X, Tong AB, Hecksel CW, Wang L, Fu TM, Bustamante C, Wu H	Science (New York, N.Y.)	35679401	Science	2022 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/35679401
Chopped! Newfound GSDMD cleavage facilitates tolerance to food allergens.	Healy LB, Du G, Wu H	Trends in immunology	37414717	Trends Immunol	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37414717
ROS-dependent S-palmitoylation activates cleaved and intact gasdermin D.	Du G, Healy LB, David L, Walker C, El-Baba TJ, Lutomski CA, Goh B, Gu B, Pi X, Devant P, Fontana P, Dong Y, Ma X, Miao R, Balasubramanian A, Puthenveetil R, Banerjee A, Luo HR, Kagan JC, Oh SF, Robinson CV, Lieberman J, Wu H	Nature	38599239	Nature	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/38599239
Higher-order assemblies in innate immune and inflammatory signaling: A general principle in cell biology.	Shi M, Zhang P, Vora SM, Wu H	Current opinion in cell biology	32272435	Curr Opin Cell Biol	2020 Apr	https://www.ncbi.nlm.nih.gov/pubmed/32272435
Mimicry by a viral RHIM.	Mompeán M, Bozkurt G, Wu H	EMBO reports	30665943	EMBO Rep	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30665943
Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling.	Pan L, Fu TM, Zhao W, Zhao L, Chen W, Qiu C, Liu W, Liu Z, Piai A, Fu Q, Chen S, Wu H, Chou JJ	Cell	30827683	Cell	2019 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/30827683
Structural mechanisms of inflammasome assembly.	Lu A, Wu H	The FEBS journal	25354325	FEBS J	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25354325
AID Recognizes Structured DNA for Class Switch Recombination.	Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H	Molecular cell	28757211	Mol Cell	2017 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/28757211
Cryo-EM structure of the gasdermin A3 membrane pore.	Ruan J, Xia S, Liu X, Lieberman J, Wu H	Nature	29695864	Nature	2018 May	https://www.ncbi.nlm.nih.gov/pubmed/29695864
Molecular basis of caspase-1 polymerization and its inhibition by a new capping mechanism.	Lu A, Li Y, Schmidt FI, Yin Q, Chen S, Fu TM, Tong AB, Ploegh HL, Mao Y, Wu H	Nature structural & molecular biology	27043298	Nat Struct Mol Biol	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/27043298
Dipeptidyl peptidase 9 sets a threshold for CARD8 inflammasome formation by sequestering its active C-terminal fragment.	Sharif H, Hollingsworth LR, Griswold AR, Hsiao JC, Wang Q, Bachovchin DA, Wu H	Immunity	34019797	Immunity	2021 Jul 13	https://www.ncbi.nlm.nih.gov/pubmed/34019797
Pathogen blockade of TAK1 triggers caspase-8-dependent cleavage of gasdermin D and cell death.	Orning P, Weng D, Starheim K, Ratner D, Best Z, Lee B, Brooks A, Xia S, Wu H, Kelliher MA, Berger SB, Gough PJ, Bertin J, Proulx MM, Goguen JD, Kayagaki N, Fitzgerald KA, Lien E	Science (New York, N.Y.)	30361383	Science	2018 Nov 30	https://www.ncbi.nlm.nih.gov/pubmed/30361383
STING condensates on ER limit IFN response.	Andreeva L, Wu H	Nature cell biology	33833430	Nat Cell Biol	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/33833430
Disulfiram use is associated with lower risk of COVID-19: A retrospective cohort study.	Fillmore N, Bell S, Shen C, Nguyen V, La J, Dubreuil M, Strymish J, Brophy M, Mehta G, Wu H, Lieberman J, Do N, Sander C	PloS one	34710137	PLoS One	2021	https://www.ncbi.nlm.nih.gov/pubmed/34710137
Structural transitions enable interleukin-18 maturation and signaling.	Dong Y, Bonin JP, Devant P, Liang Z, Sever AIM, Mintseris J, Aramini JM, Du G, Gygi SP, Kagan JC, Kay LE, Wu H	Immunity	38733997	Immunity	2024 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/38733997
NINJ1 mediates plasma membrane rupture by cutting and releasing membrane disks.	David L, Borges JP, Hollingsworth LR, Volchuk A, Jansen I, Garlick E, Steinberg BE, Wu H	Cell	38614101	Cell	2024 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/38614101
Understanding CARD Tricks in Apoptosomes.	Wang L, Qiao Q, Wu H	Structure (London, England : 1993)	28380338	Structure	2017 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/28380338
Mechanism and Regulation of Gasdermin-Mediated Cell Death.	Xia S, Hollingsworth LR 4th, Wu H	Cold Spring Harbor perspectives in biology	31451512	Cold Spring Harb Perspect Biol	2020 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/31451512
Mechanism of TRPM2 channel gating revealed by cryo-EM.	Xia S, Wang L, Fu TM, Wu H	The FEBS journal	31144442	FEBS J	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31144442
Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome.	Sharif H, Wang L, Wang WL, Magupalli VG, Andreeva L, Qiao Q, Hauenstein AV, Wu Z, Núñez G, Mao Y, Wu H	Nature	31189953	Nature	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31189953
Cryo-EM structures of ASC and NLRC4 CARD filaments reveal a unified mechanism of nucleation and activation of caspase-1.	Li Y, Fu TM, Lu A, Witt K, Ruan J, Shen C, Wu H	Proceedings of the National Academy of Sciences of the United States of America	30279182	Proc Natl Acad Sci U S A	2018 Oct 23	https://www.ncbi.nlm.nih.gov/pubmed/30279182
The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules.	Wu H, Fuxreiter M	Cell	27203110	Cell	2016 May 19	https://www.ncbi.nlm.nih.gov/pubmed/27203110
Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex.	Fu TM, Li Y, Lu A, Li Z, Vajjhala PR, Cruz AC, Srivastava DB, DiMaio F, Penczek PA, Siegel RM, Stacey KJ, Egelman EH, Wu H	Molecular cell	27746017	Mol Cell	2016 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/27746017
The palmitoylation of gasdermin D directs its membrane translocation and pore formation during pyroptosis.	Balasubramanian A, Hsu AY, Ghimire L, Tahir M, Devant P, Fontana P, Du G, Liu X, Fabin D, Kambara H, Xie X, Liu F, Hasegawa T, Xu R, Yu H, Chen M, Kolakowski S, Trauger S, Larsen MR, Wei W, Wu H, Kagan JC, Lieberman J, Luo HR	Science immunology	38530158	Sci Immunol	2024 Apr 12	https://www.ncbi.nlm.nih.gov/pubmed/38530158
The Pore-Forming Protein Gasdermin D Regulates Interleukin-1 Secretion from Living Macrophages.	Evavold CL, Ruan J, Tan Y, Xia S, Wu H, Kagan JC	Immunity	29195811	Immunity	2018 Jan 16	https://www.ncbi.nlm.nih.gov/pubmed/29195811
Structures and gating mechanism of human TRPM2.	Wang L, Fu TM, Zhou Y, Xia S, Greka A, Wu H	Science (New York, N.Y.)	30467180	Science	2018 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/30467180
The Structure of the Necrosome RIPK1-RIPK3 Core, a Human Hetero-Amyloid Signaling Complex.	Mompeán M, Li W, Li J, Laage S, Siemer AB, Bozkurt G, Wu H, McDermott AE	Cell	29681455	Cell	2018 May 17	https://www.ncbi.nlm.nih.gov/pubmed/29681455
Assembly mechanism of the CARMA1-BCL10-MALT1-TRAF6 signalosome.	David L, Li Y, Ma J, Garner E, Zhang X, Wu H	Proceedings of the National Academy of Sciences of the United States of America	29382759	Proc Natl Acad Sci U S A	2018 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/29382759
HDAC6 mediates an aggresome-like mechanism for NLRP3 and pyrin inflammasome activation.	Magupalli VG, Negro R, Tian Y, Hauenstein AV, Di Caprio G, Skillern W, Deng Q, Orning P, Alam HB, Maliga Z, Sharif H, Hu JJ, Evavold CL, Kagan JC, Schmidt FI, Fitzgerald KA, Kirchhausen T, Li Y, Wu H	Science (New York, N.Y.)	32943500	Science	2020 Sep 18	https://www.ncbi.nlm.nih.gov/pubmed/32943500
Structural and mechanistic elucidation of inflammasome signaling by cryo-EM.	Shen C, Sharif H, Xia S, Wu H	Current opinion in structural biology	31128494	Curr Opin Struct Biol	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31128494
A single domain antibody fragment that recognizes the adaptor ASC defines the role of ASC domains in inflammasome assembly.	Schmidt FI, Lu A, Chen JW, Ruan J, Tang C, Wu H, Ploegh HL	The Journal of experimental medicine	27069117	J Exp Med	2016 May 2	https://www.ncbi.nlm.nih.gov/pubmed/27069117
Inflammasome-activated gasdermin D causes pyroptosis by forming membrane pores.	Liu X, Zhang Z, Ruan J, Pan Y, Magupalli VG, Wu H, Lieberman J	Nature	27383986	Nature	2016 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/27383986
An Acetylation Switch of the NLRP3 Inflammasome Regulates Aging-Associated Chronic Inflammation and Insulin Resistance.	He M, Chiang HH, Luo H, Zheng Z, Qiao Q, Wang L, Tan M, Ohkubo R, Mu WC, Zhao S, Wu H, Chen D	Cell metabolism	32032542	Cell Metab	2020 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/32032542
Molecular mechanism for NLRP6 inflammasome assembly and activation.	Shen C, Lu A, Xie WJ, Ruan J, Negro R, Egelman EH, Fu TM, Wu H	Proceedings of the National Academy of Sciences of the United States of America	30674671	Proc Natl Acad Sci U S A	2019 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/30674671
Monitoring gasdermin pore formation in vitro.	Xia S, Ruan J, Wu H	Methods in enzymology	31455540	Methods Enzymol	2019	https://www.ncbi.nlm.nih.gov/pubmed/31455540
Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.	Zhang L, Chen S, Ruan J, Wu J, Tong AB, Yin Q, Li Y, David L, Lu A, Wang WL, Marks C, Ouyang Q, Zhang X, Mao Y, Wu H	Science (New York, N.Y.)	26449474	Science	2015 Oct 23	https://www.ncbi.nlm.nih.gov/pubmed/26449474
Publisher Correction: SERPINB1-mediated checkpoint of inflammatory caspase activation.	Choi YJ, Kim S, Choi Y, Nielsen TB, Yan J, Lu A, Ruan J, Lee HR, Wu H, Spellberg B, Jung JU	Nature immunology	30846880	Nat Immunol	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/30846880
Gasdermin D pore structure reveals preferential release of mature interleukin-1.	Xia S, Zhang Z, Magupalli VG, Pablo JL, Dong Y, Vora SM, Wang L, Fu TM, Jacobson MP, Greka A, Lieberman J, Ruan J, Wu H	Nature	33883744	Nature	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/33883744
Structural principles of B cell antigen receptor assembly.	Dong Y, Pi X, Bartels-Burgahn F, Saltukoglu D, Liang Z, Yang J, Alt FW, Reth M, Wu H	Nature	36228656	Nature	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36228656
NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation.	Andreeva L, David L, Rawson S, Shen C, Pasricha T, Pelegrin P, Wu H	Cell	34861190	Cell	2021 Dec 22	https://www.ncbi.nlm.nih.gov/pubmed/34861190
A structural atlas of death domain fold proteins reveals their versatile roles in biology and function.	Wu EJ, Kandalkar AT, Ehrmann JF, Tong AB, Zhang J, Cong Q, Wu H	Proceedings of the National Academy of Sciences of the United States of America	39977327	Proc Natl Acad Sci U S A	2025 Feb 25	https://www.ncbi.nlm.nih.gov/pubmed/39977327
Prevalence and correlates of MRSA and MSSA nasal carriage at a Ugandan regional referral hospital.	Bebell LM, Ayebare A, Boum Y 2nd, Siedner MJ, Bazira J, Schiff SJ, Metlay JP, Bangsberg DR, Ttendo S, Firth PG	The Journal of antimicrobial chemotherapy	27999030	J Antimicrob Chemother	2017 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/27999030
Complete Genome Sequences of the Human Pathogen Paenibacillus thiaminolyticus Mbale and Type Strain P. thiaminolyticus NRRL B-4156.	Hehnly C, Zhang L, Paulson JN, Almeida M, von Bredow B, Wijetunge DSS, Galperin MY, Sheldon K, Schiff SJ, Broach JR	Microbiology resource announcements	32273361	Microbiol Resour Announc	2020 Apr 9	https://www.ncbi.nlm.nih.gov/pubmed/32273361
Economic burden of neonatal sepsis in sub-Saharan Africa.	Ranjeva SL, Warf BC, Schiff SJ	BMJ global health	29564153	BMJ Glob Health	2018	https://www.ncbi.nlm.nih.gov/pubmed/29564153
Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus.	Hehnly C, Shi A, Ssentongo P, Zhang L, Isaacs A, Morton SU, Streck N, Erdmann-Gilmore P, Tolstoy I, Townsend RR, Limbrick DD, Paulson JN, Ericson JE, Galperin MY, Schiff SJ, Broach JR	mBio	36374038	mBio	2022 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/36374038
Global, regional and national epidemiology and prevalence of child stunting, wasting and underweight in low- and middle-income countries, 2006-2018.	Ssentongo P, Ssentongo AE, Ba DM, Ericson JE, Na M, Gao X, Fronterre C, Chinchilli VM, Schiff SJ	Scientific reports	33664313	Sci Rep	2021 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/33664313
Design of a mobile, homogeneous, and efficient electromagnet with a large field of view for neonatal low-field MRI.	Lother S, Schiff SJ, Neuberger T, Jakob PM, Fidler F	Magma (New York, N.Y.)	26861046	MAGMA	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26861046
The Problem of Microbial Dark Matter in Neonatal Sepsis.	Sinnar SA, Schiff SJ	Emerging infectious diseases	33080169	Emerg Infect Dis	2020 Nov	https://www.ncbi.nlm.nih.gov/pubmed/33080169
Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda.	Ericson JE, Burgoine K, Kumbakumba E, Ochora M, Hehnly C, Bajunirwe F, Bazira J, Fronterre C, Hagmann C, Kulkarni AV, Kumar MS, Magombe J, Mbabazi-Kabachelor E, Morton SU, Movassagh M, Mugamba J, Mulondo R, Natukwatsa D, Kaaya BN, Olupot-Olupot P, Onen J, Sheldon K, Smith J, Ssentongo P, Ssenyonga P, Warf B, Wegoye E, Zhang L, Kiwanuka J, Paulson JN, Broach JR, Schiff SJ	Clinical infectious diseases : an official publication of the Infectious Diseases Society of America	37279589	Clin Infect Dis	2023 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/37279589
Vaginal microbiome topic modeling of laboring Ugandan women with and without fever.	Movassagh M, Bebell LM, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar SA, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga BK, Weeks AD, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts DJ, Meier FA, Irizarry RA, Broach JR, Schiff SJ, Paulson JN	NPJ biofilms and microbiomes	34508087	NPJ Biofilms Microbiomes	2021 Sep 10	https://www.ncbi.nlm.nih.gov/pubmed/34508087
Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants.	Paulson JN, Williams BL, Hehnly C, Mishra N, Sinnar SA, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge DSS, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell LM, Burgoine K, Couto-Rodriguez M, Ericson JE, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs AM, Kaaya BN, Kangere SM, Kulkarni AV, Kumbakumba E, Li X, Limbrick DD Jr, Magombe J, Morton SU, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson MR, Roy F, Sheldon K, Townsend R, Weeks AD, Whalen AJ, Quackenbush J, Ssenyonga P, Galperin MY, Almeida M, Atkins H, Warf BC, Lipkin WI, Broach JR, Schiff SJ	Science translational medicine	32998967	Sci Transl Med	2020 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/32998967
Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection.	Isaacs AM, Morton SU, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales DM, Sinnar SA, Ericson JE, Mbabazi-Kabachelor E, Ssenyonga P, Onen J, Mulondo R, Hornig M, Warf BC, Broach JR, Townsend RR, Limbrick DD Jr, Paulson JN, Schiff SJ	iScience	33912816	iScience	2021 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/33912816
Design of a sustainable prepolarizing magnetic resonance imaging system for infant hydrocephalus.	Obungoloch J, Harper JR, Consevage S, Savukov IM, Neuberger T, Tadigadapa S, Schiff SJ	Magma (New York, N.Y.)	29644479	MAGMA	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/29644479
Inflammation in acquired hydrocephalus: pathogenic mechanisms and therapeutic targets.	Karimy JK, Reeves BC, Damisah E, Duy PQ, Antwi P, David W, Wang K, Schiff SJ, Limbrick DD Jr, Alper SL, Warf BC, Nedergaard M, Simard JM, Kahle KT	Nature reviews. Neurology	32152460	Nat Rev Neurol	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/32152460
Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome.	Schiff SJ, Kiwanuka J, Riggio G, Nguyen L, Mu K, Sproul E, Bazira J, Mwanga-Amumpaire J, Tumusiime D, Nyesigire E, Lwanga N, Bogale KT, Kapur V, Broach JR, Morton SU, Warf BC, Poss M	Frontiers in medicine	27379237	Front Med (Lausanne)	2016	https://www.ncbi.nlm.nih.gov/pubmed/27379237
Changes in Ugandan Climate Rainfall at the Village and Forest Level.	Ssentongo P, Muwanguzi AJB, Eden U, Sauer T, Bwanga G, Kateregga G, Aribo L, Ojara M, Mugerwa WK, Schiff SJ	Scientific reports	29476058	Sci Rep	2018 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/29476058
Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus.	Jin SC, Dong W, Kundishora AJ, Panchagnula S, Moreno-De-Luca A, Furey CG, Allocco AA, Walker RL, Nelson-Williams C, Smith H, Dunbar A, Conine S, Lu Q, Zeng X, Sierant MC, Knight JR, Sullivan W, Duy PQ, DeSpenza T, Reeves BC, Karimy JK, Marlier A, Castaldi C, Tikhonova IR, Li B, Peña HP, Broach JR, Kabachelor EM, Ssenyonga P, Hehnly C, Ge L, Keren B, Timberlake AT, Goto J, Mangano FT, Johnston JM, Butler WE, Warf BC, Smith ER, Schiff SJ, Limbrick DD Jr, Heuer G, Jackson EM, Iskandar BJ, Mane S, Haider S, Guclu B, Bayri Y, Sahin Y, Duncan CC, Apuzzo MLJ, DiLuna ML, Hoffman EJ, Sestan N, Ment LR, Alper SL, Bilguvar K, Geschwind DH, Günel M, Lifton RP, Kahle KT	Nature medicine	33077954	Nat Med	2020 Nov	https://www.ncbi.nlm.nih.gov/pubmed/33077954
Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus.	Hehnly C, Ssentongo P, Bebell LM, Burgoine K, Bazira J, Fronterre C, Kumbakumba E, Mulondo R, Mbabazi-Kabachelor E, Morton SU, Ngonzi J, Ochora M, Olupot-Olupot P, Mugamba J, Onen J, Roberts DJ, Sheldon K, Sinnar SA, Smith J, Ssenyonga P, Kiwanuka J, Paulson JN, Meier FA, Ericson JE, Broach JR, Schiff SJ	International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases	35150915	Int J Infect Dis	2022 May	https://www.ncbi.nlm.nih.gov/pubmed/35150915
mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis.	Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN	BMC genomics	35698050	BMC Genomics	2022 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/35698050
Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study.	Morton SU, Hehnly C, Burgoine K, Ssentongo P, Ericson JE, Kumar MS, Hagmann C, Fronterre C, Smith J, Movassagh M, Streck N, Bebell LM, Bazira J, Kumbakumba E, Bajunirwe F, Mulondo R, Mbabazi-Kabachelor E, Nsubuga BK, Natukwatsa D, Nalule E, Magombe J, Erickson T, Ngonzi J, Ochora M, Olupot-Olupot P, Onen J, Ssenyonga P, Mugamba J, Warf BC, Kulkarni AV, Lane J, Whalen AJ, Zhang L, Sheldon K, Meier FA, Kiwanuka J, Broach JR, Paulson JN, Schiff SJ	The Lancet. Microbe	37348522	Lancet Microbe	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37348522
Correction to Lancet Microbe 2023; published online June 19. https://doi.org/10.1016/S2666-5247(23)00106-4.		The Lancet. Microbe	37414068	Lancet Microbe	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37414068
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.	Levine JH, Simonds EF, Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, Nolan GP	Cell	26095251	Cell	2015 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/26095251
Characterization of cell fate probabilities in single-cell data with Palantir.	Setty M, Kiseliovas V, Levine J, Gayoso A, Mazutis L, Pe'er D	Nature biotechnology	30899105	Nat Biotechnol	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30899105
Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States.	Wei SC, Sharma R, Anang NAS, Levine JH, Zhao Y, Mancuso JJ, Setty M, Sharma P, Wang J, Pe'er D, Allison JP	Immunity	30926234	Immunity	2019 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/30926234
An Immune Atlas of Clear Cell Renal Cell Carcinoma.	Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, Ries CH, Ailles L, Jewett MAS, Moch H, van den Broek M, Beisel C, Stadler MB, Gedye C, Reis B, Pe'er D, Bodenmiller B	Cell	28475899	Cell	2017 May 4	https://www.ncbi.nlm.nih.gov/pubmed/28475899
Distinct Cellular Mechanisms Underlie Anti-CTLA-4 and Anti-PD-1 Checkpoint Blockade.	Wei SC, Levine JH, Cogdill AP, Zhao Y, Anang NAS, Andrews MC, Sharma P, Wang J, Wargo JA, Pe'er D, Allison JP	Cell	28803728	Cell	2017 Sep 7	https://www.ncbi.nlm.nih.gov/pubmed/28803728
PhenoGraph and viSNE facilitate the identification of abnormal T-cell populations in routine clinical flow cytometric data.	DiGiuseppe JA, Cardinali JL, Rezuke WN, Pe'er D	Cytometry. Part B, Clinical cytometry	28865188	Cytometry B Clin Cytom	2018 Sep	https://www.ncbi.nlm.nih.gov/pubmed/28865188
Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.	van Dijk D, Sharma R, Nainys J, Yim K, Kathail P, Carr AJ, Burdziak C, Moon KR, Chaffer CL, Pattabiraman D, Bierie B, Mazutis L, Wolf G, Krishnaswamy S, Pe'er D	Cell	29961576	Cell	2018 Jul 26	https://www.ncbi.nlm.nih.gov/pubmed/29961576
Detection of minimal residual disease in B lymphoblastic leukemia using viSNE.	DiGiuseppe JA, Tadmor MD, Pe'er D	Cytometry. Part B, Clinical cytometry	25974871	Cytometry B Clin Cytom	2015 Sep-Oct	https://www.ncbi.nlm.nih.gov/pubmed/25974871
Regenerative lineages and immune-mediated pruning in lung cancer metastasis.	Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y, Masilionis I, Carr AJ, Kottapalli S, Allaj V, Mattar M, Rekhtman N, Xavier JB, Mazutis L, Poirier JT, Rudin CM, Pe'er D, Massagué J	Nature medicine	32042191	Nat Med	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/32042191
Learning time-varying information flow from single-cell epithelial to mesenchymal transition data.	Krishnaswamy S, Zivanovic N, Sharma R, Pe'er D, Bodenmiller B	PloS one	30372433	PLoS One	2018	https://www.ncbi.nlm.nih.gov/pubmed/30372433
Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.	Azizi E, Carr AJ, Plitas G, Cornish AE, Konopacki C, Prabhakaran S, Nainys J, Wu K, Kiseliovas V, Setty M, Choi K, Fromme RM, Dao P, McKenney PT, Wasti RC, Kadaveru K, Mazutis L, Rudensky AY, Pe'er D	Cell	29961579	Cell	2018 Aug 23	https://www.ncbi.nlm.nih.gov/pubmed/29961579
Scalable microfluidics for single-cell RNA printing and sequencing.	Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA	Genome biology	26047807	Genome Biol	2015 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/26047807
Wishbone identifies bifurcating developmental trajectories from single-cell data.	Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, Kathail P, Choi K, Bendall S, Friedman N, Pe'er D	Nature biotechnology	27136076	Nat Biotechnol	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27136076
Trajectories of cell-cycle progression from fixed cell populations.	Gut G, Tadmor MD, Pe'er D, Pelkmans L, Liberali P	Nature methods	26301842	Nat Methods	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26301842
Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses.	Lavin Y, Kobayashi S, Leader A, Amir ED, Elefant N, Bigenwald C, Remark R, Sweeney R, Becker CD, Levine JH, Meinhof K, Chow A, Kim-Shulze S, Wolf A, Medaglia C, Li H, Rytlewski JA, Emerson RO, Solovyov A, Greenbaum BD, Sanders C, Vignali M, Beasley MB, Flores R, Gnjatic S, Pe'er D, Rahman A, Amit I, Merad M	Cell	28475900	Cell	2017 May 4	https://www.ncbi.nlm.nih.gov/pubmed/28475900
The emergent landscape of the mouse gut endoderm at single-cell resolution.	Nowotschin S, Setty M, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK, Pe'er D	Nature	30959515	Nature	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/30959515
Notch3 signaling promotes tumor cell adhesion and progression in a murine epithelial ovarian cancer model.	Price JC, Azizi E, Naiche LA, Parvani JG, Shukla P, Kim S, Slack-Davis JK, Pe'er D, Kitajewski JK	PloS one	32525899	PLoS One	2020	https://www.ncbi.nlm.nih.gov/pubmed/32525899
Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data.	Prabhakaran S, Azizi E, Carr A, Pe'er D	JMLR workshop and conference proceedings	29928470	JMLR Workshop Conf Proc	2016	https://www.ncbi.nlm.nih.gov/pubmed/29928470
Engineering γδT cells limits tonic signaling associated with chimeric antigen receptors.	Fisher J, Sharma R, Don DW, Barisa M, Hurtado MO, Abramowski P, Porter L, Day W, Borea R, Inglott S, Anderson J, Pe'er D	Science signaling	31506382	Sci Signal	2019 Sep 10	https://www.ncbi.nlm.nih.gov/pubmed/31506382
Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis.	Burdziak C, Alonso-Curbelo D, Walle T, Reyes J, Barriga FM, Haviv D, Xie Y, Zhao Z, Zhao CJ, Chen HA, Chaudhary O, Masilionis I, Choo ZN, Gao V, Luan W, Wuest A, Ho YJ, Wei Y, Quail DF, Koche R, Mazutis L, Chaligné R, Nawy T, Lowe SW, Pe'er D	Science (New York, N.Y.)	37167403	Science	2023 May 12	https://www.ncbi.nlm.nih.gov/pubmed/37167403
Contrasting genetic architectures in different mouse reference populations used for studying complex traits.	Buchner DA, Nadeau JH	Genome research	25953951	Genome Res	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25953951
Do Gametes Woo? Evidence for Their Nonrandom Union at Fertilization.	Nadeau JH	Genetics	28978771	Genetics	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28978771
Genetics. Systems genetics.	Nadeau JH, Dudley AM	Science (New York, N.Y.)	21350153	Science	2011 Feb 25	https://www.ncbi.nlm.nih.gov/pubmed/21350153
Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias.	Carouge D, Blanc V, Knoblaugh SE, Hunter RJ, Davidson NO, Nadeau JH	Proceedings of the National Academy of Sciences of the United States of America	27582469	Proc Natl Acad Sci U S A	2016 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/27582469
The need for calcium imaging in nonhuman primates: New motor neuroscience and brain-machine interfaces.	O'Shea DJ, Trautmann E, Chandrasekaran C, Stavisky S, Kao JC, Sahani M, Ryu S, Deisseroth K, Shenoy KV	Experimental neurology	27511294	Exp Neurol	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27511294
Vacillation, indecision and hesitation in moment-by-moment decoding of monkey motor cortex.	Kaufman MT, Churchland MM, Ryu SI, Shenoy KV	eLife	25942352	Elife	2015 May 5	https://www.ncbi.nlm.nih.gov/pubmed/25942352
Inferring single-trial neural population dynamics using sequential auto-encoders.	Pandarinath C, O'Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann EM, Kaufman MT, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV, Abbott LF, Sussillo D	Nature methods	30224673	Nat Methods	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30224673
Leveraging neural dynamics to extend functional lifetime of brain-machine interfaces.	Kao JC, Ryu SI, Shenoy KV	Scientific reports	28784984	Sci Rep	2017 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/28784984
Discovering Precise Temporal Patterns in Large-Scale Neural Recordings through Robust and Interpretable Time Warping.	Williams AH, Poole B, Maheswaranathan N, Dhawale AK, Fisher T, Wilson CD, Brann DH, Trautmann EM, Ryu S, Shusterman R, Rinberg D, Ölveczky BP, Shenoy KV, Ganguli S	Neuron	31786013	Neuron	2020 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/31786013
Simultaneous motor preparation and execution in a last-moment reach correction task.	Ames KC, Ryu SI, Shenoy KV	Nature communications	31221968	Nat Commun	2019 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/31221968
An Open Resource for Non-human Primate Optogenetics.	Tremblay S, Acker L, Afraz A, Albaugh DL, Amita H, Andrei AR, Angelucci A, Aschner A, Balan PF, Basso MA, Benvenuti G, Bohlen MO, Caiola MJ, Calcedo R, Cavanaugh J, Chen Y, Chen S, Chernov MM, Clark AM, Dai J, Debes SR, Deisseroth K, Desimone R, Dragoi V, Egger SW, Eldridge MAG, El-Nahal HG, Fabbrini F, Federer F, Fetsch CR, Fortuna MG, Friedman RM, Fujii N, Gail A, Galvan A, Ghosh S, Gieselmann MA, Gulli RA, Hikosaka O, Hosseini EA, Hu X, Hüer J, Inoue KI, Janz R, Jazayeri M, Jiang R, Ju N, Kar K, Klein C, Kohn A, Komatsu M, Maeda K, Martinez-Trujillo JC, Matsumoto M, Maunsell JHR, Mendoza-Halliday D, Monosov IE, Muers RS, Nurminen L, Ortiz-Rios M, O'Shea DJ, Palfi S, Petkov CI, Pojoga S, Rajalingham R, Ramakrishnan C, Remington ED, Revsine C, Roe AW, Sabes PN, Saunders RC, Scherberger H, Schmid MC, Schultz W, Seidemann E, Senova YS, Shadlen MN, Sheinberg DL, Siu C, Smith Y, Solomon SS, Sommer MA, Spudich JL, Stauffer WR, Takada M, Tang S, Thiele A, Treue S, Vanduffel W, Vogels R, Whitmire MP, Wichmann T, Wurtz RH, Xu H, Yazdan-Shahmorad A, Shenoy KV, DiCarlo JJ, Platt ML	Neuron	33080229	Neuron	2020 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/33080229
Causal Role of Motor Preparation during Error-Driven Learning.	Vyas S, O'Shea DJ, Ryu SI, Shenoy KV	Neuron	32053768	Neuron	2020 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/32053768
Structure in Neural Activity during Observed and Executed Movements Is Shared at the Neural Population Level, Not in Single Neurons.	Jiang X, Saggar H, Ryu SI, Shenoy KV, Kao JC	Cell reports	32783934	Cell Rep	2020 Aug 11	https://www.ncbi.nlm.nih.gov/pubmed/32783934
Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface.	Trautmann EM, O'Shea DJ, Sun X, Marshel JH, Crow A, Hsueh B, Vesuna S, Cofer L, Bohner G, Allen W, Kauvar I, Quirin S, MacDougall M, Chen Y, Whitmire MP, Ramakrishnan C, Sahani M, Seidemann E, Ryu SI, Deisseroth K, Shenoy KV	Nature communications	34140486	Nat Commun	2021 Jun 17	https://www.ncbi.nlm.nih.gov/pubmed/34140486
Single-trial dynamics of motor cortex and their applications to brain-machine interfaces.	Kao JC, Nuyujukian P, Ryu SI, Churchland MM, Cunningham JP, Shenoy KV	Nature communications	26220660	Nat Commun	2015 Jul 29	https://www.ncbi.nlm.nih.gov/pubmed/26220660
A neural network that finds a naturalistic solution for the production of muscle activity.	Sussillo D, Churchland MM, Kaufman MT, Shenoy KV	Nature neuroscience	26075643	Nat Neurosci	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26075643
Decoding and perturbing decision states in real time.	Peixoto D, Verhein JR, Kiani R, Kao JC, Nuyujukian P, Chandrasekaran C, Brown J, Fong S, Ryu SI, Shenoy KV, Newsome WT	Nature	33473215	Nature	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33473215
Trial-by-Trial Motor Cortical Correlates of a Rapidly Adapting Visuomotor Internal Model.	Stavisky SD, Kao JC, Ryu SI, Shenoy KV	The Journal of neuroscience : the official journal of the Society for Neuroscience	28087767	J Neurosci	2017 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/28087767
The Importance of Planning in Motor Learning.	O'Shea DJ, Shenoy KV	Neuron	27883896	Neuron	2016 Nov 23	https://www.ncbi.nlm.nih.gov/pubmed/27883896
Brain-machine interface cursor position only weakly affects monkey and human motor cortical activity in the absence of arm movements.	Stavisky SD, Kao JC, Nuyujukian P, Pandarinath C, Blabe C, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV	Scientific reports	30397281	Sci Rep	2018 Nov 5	https://www.ncbi.nlm.nih.gov/pubmed/30397281
Neural Population Dynamics Underlying Motor Learning Transfer.	Vyas S, Even-Chen N, Stavisky SD, Ryu SI, Nuyujukian P, Shenoy KV	Neuron	29456026	Neuron	2018 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/29456026
Cortical preparatory activity indexes learned motor memories.	Sun X, O'Shea DJ, Golub MD, Trautmann EM, Vyas S, Ryu SI, Shenoy KV	Nature	35082444	Nature	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/35082444
A low-power band of neuronal spiking activity dominated by local single units improves the performance of brain-machine interfaces.	Nason SR, Vaskov AK, Willsey MS, Welle EJ, An H, Vu PP, Bullard AJ, Nu CS, Kao JC, Shenoy KV, Jang T, Kim HS, Blaauw D, Patil PG, Chestek CA	Nature biomedical engineering	32719512	Nat Biomed Eng	2020 Oct	https://www.ncbi.nlm.nih.gov/pubmed/32719512
Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis.	Williams AH, Kim TH, Wang F, Vyas S, Ryu SI, Shenoy KV, Schnitzer M, Kolda TG, Ganguli S	Neuron	29887338	Neuron	2018 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/29887338
A high performing brain-machine interface driven by low-frequency local field potentials alone and together with spikes.	Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV	Journal of neural engineering	25946198	J Neural Eng	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25946198
Comparison of spike sorting and thresholding of voltage waveforms for intracortical brain-machine interface performance.	Christie BP, Tat DM, Irwin ZT, Gilja V, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV, Thompson DE, Chestek CA	Journal of neural engineering	25504690	J Neural Eng	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25504690
Augmenting intracortical brain-machine interface with neurally driven error detectors.	Even-Chen N, Stavisky SD, Kao JC, Ryu SI, Shenoy KV	Journal of neural engineering	29130452	J Neural Eng	2017 Dec	https://www.ncbi.nlm.nih.gov/pubmed/29130452
Motor Cortical Visuomotor Feedback Activity Is Initially Isolated from Downstream Targets in Output-Null Neural State Space Dimensions.	Stavisky SD, Kao JC, Ryu SI, Shenoy KV	Neuron	28625485	Neuron	2017 Jul 5	https://www.ncbi.nlm.nih.gov/pubmed/28625485
Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1.	Seely JS, Kaufman MT, Ryu SI, Shenoy KV, Cunningham JP, Churchland MM	PLoS computational biology	27814353	PLoS Comput Biol	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/27814353
Design of an implantable artificial dural window for chronic two-photon optical imaging in non-human primates.	Trautmann E, O'Shea DJ, Shrestha S, Lin S, Ryu S, Shenoy K	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	26738040	Annu Int Conf IEEE Eng Med Biol Soc	2015	https://www.ncbi.nlm.nih.gov/pubmed/26738040
Non-linear dimensionality reduction on extracellular waveforms reveals cell type diversity in premotor cortex.	Lee EK, Balasubramanian H, Tsolias A, Anakwe SU, Medalla M, Shenoy KV, Chandrasekaran C	eLife	34355695	Elife	2021 Aug 6	https://www.ncbi.nlm.nih.gov/pubmed/34355695
Power-saving design opportunities for wireless intracortical brain-computer interfaces.	Even-Chen N, Muratore DG, Stavisky SD, Hochberg LR, Henderson JM, Murmann B, Shenoy KV	Nature biomedical engineering	32747834	Nat Biomed Eng	2020 Oct	https://www.ncbi.nlm.nih.gov/pubmed/32747834
Frequency Shifts and Depth Dependence of Premotor Beta Band Activity during Perceptual Decision-Making.	Chandrasekaran C, Bray IE, Shenoy KV	The Journal of neuroscience : the official journal of the Society for Neuroscience	30606756	J Neurosci	2019 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/30606756
Laminar differences in decision-related neural activity in dorsal premotor cortex.	Chandrasekaran C, Peixoto D, Newsome WT, Shenoy KV	Nature communications	28931803	Nat Commun	2017 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/28931803
Initial conditions combine with sensory evidence to induce decision-related dynamics in premotor cortex.	Boucher PO, Wang T, Carceroni L, Kane G, Shenoy KV, Chandrasekaran C	Nature communications	37845221	Nat Commun	2023 Oct 16	https://www.ncbi.nlm.nih.gov/pubmed/37845221
Optochemical dissection of T-box gene-dependent medial floor plate development.	Payumo AY, Walker WJ, McQuade LE, Yamazoe S, Chen JK	ACS chemical biology	25781211	ACS Chem Biol	2015 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/25781211
In vivo imaging of Hedgehog pathway activation with a nuclear fluorescent reporter.	Mich JK, Payumo AY, Rack PG, Chen JK	PloS one	25068273	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/25068273
Ultrasensitive optical imaging with lanthanide lumiphores.	Cho U, Riordan DP, Ciepla P, Kocherlakota KS, Chen JK, Harbury PB	Nature chemical biology	29106397	Nat Chem Biol	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29106397
trLRET microscopy: Ultrasensitive imaging of lanthanide luminophores.	Ciepla P, Cho U, Chen JK	Methods in enzymology	32560800	Methods Enzymol	2020	https://www.ncbi.nlm.nih.gov/pubmed/32560800
Functional inhibition of UQCRB suppresses angiogenesis in zebrafish.	Cho YS, Jung HJ, Seok SH, Payumo AY, Chen JK, Kwon HJ	Biochemical and biophysical research communications	23454382	Biochem Biophys Res Commun	2013 Apr 19	https://www.ncbi.nlm.nih.gov/pubmed/23454382
Arhgap36-dependent activation of Gli transcription factors.	Rack PG, Ni J, Payumo AY, Nguyen V, Crapster JA, Hovestadt V, Kool M, Jones DT, Mich JK, Firestone AJ, Pfister SM, Cho YJ, Chen JK	Proceedings of the National Academy of Sciences of the United States of America	25024229	Proc Natl Acad Sci U S A	2014 Jul 29	https://www.ncbi.nlm.nih.gov/pubmed/25024229
Sequential gene silencing using wavelength-selective caged morpholino oligonucleotides.	Yamazoe S, Liu Q, McQuade LE, Deiters A, Chen JK	Angewandte Chemie (International ed. in English)	25130695	Angew Chem Int Ed Engl	2014 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/25130695
Nitroreductase-activatable morpholino oligonucleotides for in vivo gene silencing.	Yamazoe S, McQuade LE, Chen JK	ACS chemical biology	25069083	ACS Chem Biol	2014 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/25069083
General method for regulating protein stability with light.	Bonger KM, Rakhit R, Payumo AY, Chen JK, Wandless TJ	ACS chemical biology	24180414	ACS Chem Biol	2014 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/24180414
An inducible long noncoding RNA amplifies DNA damage signaling.	Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY	Nature genetics	27668660	Nat Genet	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/27668660
Tbx16 regulates hox gene activation in mesodermal progenitor cells.	Payumo AY, McQuade LE, Walker WJ, Yamazoe S, Chen JK	Nature chemical biology	27376691	Nat Chem Biol	2016 Sep	https://www.ncbi.nlm.nih.gov/pubmed/27376691
A mechanism of lysosomal calcium entry.	Zajac M, Mukherjee S, Anees P, Oettinger D, Henn K, Srikumar J, Zou J, Saminathan A, Krishnan Y	Science advances	38354239	Sci Adv	2024 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/38354239
Passive endocytosis in model protocells.	Zhang SJ, Lowe LA, Anees P, Krishnan Y, Fai TG, Szostak JW, Wang A	Proceedings of the National Academy of Sciences of the United States of America	37276401	Proc Natl Acad Sci U S A	2023 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/37276401
The chemistry of next-generation sequencing.	Rodriguez R, Krishnan Y	Nature biotechnology	37845570	Nat Biotechnol	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37845570
Detecting organelle-specific activity of potassium channels with a DNA nanodevice.	Anees P, Saminathan A, Rozmus ER, Di A, Malik AB, Delisle BP, Krishnan Y	Nature biotechnology	37735264	Nat Biotechnol	2024 Jul	https://www.ncbi.nlm.nih.gov/pubmed/37735264
Quantitative Chemical Imaging of Organelles.	Tinker J, Anees P, Krishnan Y	Accounts of chemical research	38916405	Acc Chem Res	2024 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/38916405
A DNA nanodevice for mapping sodium at single-organelle resolution.	Zou J, Mitra K, Anees P, Oettinger D, Ramirez JR, Veetil AT, Gupta PD, Rao R, Smith JJ, Kratsios P, Krishnan Y	Nature biotechnology	37735265	Nat Biotechnol	2024 Jul	https://www.ncbi.nlm.nih.gov/pubmed/37735265
Fit for Purpose Approach To Evaluate Detection of Amino Acid Substitutions in Shotgun Proteomics.	Lundgren TJ, Clark PL, Champion MM	Journal of proteome research	38478054	J Proteome Res	2024 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/38478054
CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern.	Wright G, Rodriguez A, Li J, Milenkovic T, Emrich SJ, Clark PL	Protein science : a publication of the Protein Society	34738275	Protein Sci	2022 Jan	https://www.ncbi.nlm.nih.gov/pubmed/34738275
Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production.	Rodriguez A, Diehl JD, Wright GS, Bonar CD, Lundgren TJ, Moss MJ, Li J, Milenkovic T, Huber PW, Champion MM, Emrich SJ, Clark PL	Proceedings of the National Academy of Sciences of the United States of America	39190361	Proc Natl Acad Sci U S A	2024 Sep 3	https://www.ncbi.nlm.nih.gov/pubmed/39190361
Discovery of an on-pathway protein folding intermediate illuminates the kinetic competition between folding and misfolding.	Luan Q, Clark PL	bioRxiv : the preprint server for biology	39868219	bioRxiv	2024 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/39868219
How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins.	Baxa MC, Lin X, Mukinay CD, Chakravarthy S, Sachleben JR, Antilla S, Hartrampf N, Riback JA, Gagnon IA, Pentelute BL, Clark PL, Sosnick TR	Protein science : a publication of the Protein Society	38607226	Protein Sci	2024 May	https://www.ncbi.nlm.nih.gov/pubmed/38607226
The Effects of Codon Usage on Protein Structure and Folding.	Moss MJ, Chamness LM, Clark PL	Annual review of biophysics	38134335	Annu Rev Biophys	2024 Jul	https://www.ncbi.nlm.nih.gov/pubmed/38134335
A Versatile eIF3d in Translational Control of Stress Adaptation.	Jia L, Qian SB	Molecular cell	33417853	Mol Cell	2021 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/33417853
Bi-directional ribosome scanning controls the stringency of start codon selection.	Gu Y, Mao Y, Jia L, Dong L, Qian SB	Nature communications	34782646	Nat Commun	2021 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/34782646
Making sense of mRNA translational "noise".	Mao Y, Qian SB	Seminars in cell & developmental biology	36925447	Semin Cell Dev Biol	2024 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/36925447
A heat shock-responsive lncRNA Heat acts as a HSF1-directed transcriptional brake via m(6)A modification.	Ji Q, Zong X, Mao Y, Qian SB	Proceedings of the National Academy of Sciences of the United States of America	34131081	Proc Natl Acad Sci U S A	2021 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/34131081
Lysosomal cystine governs ferroptosis sensitivity in cancer via cysteine stress response.	Swanda RV, Ji Q, Wu X, Yan J, Dong L, Mao Y, Uematsu S, Dong Y, Qian SB	Molecular cell	37647899	Mol Cell	2023 Sep 21	https://www.ncbi.nlm.nih.gov/pubmed/37647899
Dynamic eIF3a O-GlcNAcylation controls translation reinitiation during nutrient stress.	Shu XE, Mao Y, Jia L, Qian SB	Nature chemical biology	34887587	Nat Chem Biol	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/34887587
De novo-designed translation-repressing riboregulators for multi-input cellular logic.	Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA	Nature chemical biology	31686032	Nat Chem Biol	2019 Dec	https://www.ncbi.nlm.nih.gov/pubmed/31686032
Functional analysis of rare genetic variants in complement factor I in advanced age-related macular degeneration.	Java A, Pozzi N, Schroeder MC, Hu Z, Huan T, Seddon JM, Atkinson J	Human molecular genetics	35531992	Hum Mol Genet	2022 Oct 28	https://www.ncbi.nlm.nih.gov/pubmed/35531992
Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels.	Hong F, Kishi JY, Delgado RN, Jeong J, Saka SK, Su H, Cepko CL, Yin P	Nature methods	38151595	Nat Methods	2024 Feb	https://www.ncbi.nlm.nih.gov/pubmed/38151595
Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.	Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CT	bioRxiv : the preprint server for biology	38370628	bioRxiv	2025 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/38370628
Scalable design of orthogonal DNA barcode libraries.	Gowri G, Sheng K, Yin P	Nature computational science	38849559	Nat Comput Sci	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/38849559
Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST.	Schaefer IM, Hemming ML, Lundberg MZ, Serrata MP, Goldaracena I, Liu N, Yin P, Paulo JA, Gygi SP, George S, Morgan JA, Bertagnolli MM, Sicinska ET, Chu C, Zheng S, Mariño-Enríquez A, Hornick JL, Raut CP, Ou WB, Demetri GD, Saka SK, Fletcher JA	British journal of cancer	36175617	Br J Cancer	2022 Nov	https://www.ncbi.nlm.nih.gov/pubmed/36175617
Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.	Kishi JY, Liu N, West ER, Sheng K, Jordanides JJ, Serrata M, Cepko CL, Saka SK, Yin P	Nature methods	36216958	Nat Methods	2022 Nov	https://www.ncbi.nlm.nih.gov/pubmed/36216958
The emerging landscape of single-molecule protein sequencing technologies.	Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C	Nature methods	34099939	Nat Methods	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/34099939
Single-strand RPA for rapid and sensitive detection of SARS-CoV-2 RNA.	Kim Y, Yaseen AB, Kishi JY, Hong F, Saka SK, Sheng K, Gopalkrishnan N, Schaus TE, Yin P	medRxiv : the preprint server for health sciences	32839783	medRxiv	2020 Oct 25	https://www.ncbi.nlm.nih.gov/pubmed/32839783
Super-resolution labelling with Action-PAINT.	Liu N, Dai M, Saka SK, Yin P	Nature chemistry	31527848	Nat Chem	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31527848
Enhancing Biocompatible Stability of DNA Nanostructures Using Dendritic Oligonucleotides and Brick Motifs.	Kim Y, Yin P	Angewandte Chemie (International ed. in English)	31595637	Angew Chem Int Ed Engl	2020 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/31595637
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues.	Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P	Nature biotechnology	31427819	Nat Biotechnol	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31427819
Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly.	Liu D, Thélot FA, Piccirilli JA, Liao M, Yin P	Nature methods	35501384	Nat Methods	2022 May	https://www.ncbi.nlm.nih.gov/pubmed/35501384
Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry.	Lun XK, Sheng K, Yu X, Lam CY, Gowri G, Serrata M, Zhai Y, Su H, Luan J, Kim Y, Ingber DE, Jackson HW, Yaffe MB, Yin P	Nature biotechnology	39075149	Nat Biotechnol	2024 Jul 29	https://www.ncbi.nlm.nih.gov/pubmed/39075149
Molecular robotic agents that survey molecular landscapes for information retrieval.	Woo S, Saka SK, Xuan F, Yin P	Nature communications	38632239	Nat Commun	2024 Apr 17	https://www.ncbi.nlm.nih.gov/pubmed/38632239
Cas9 Cleavage of Viral Genomes Primes the Acquisition of New Immunological Memories.	Nussenzweig PM, McGinn J, Marraffini LA	Cell host & microbe	31585845	Cell Host Microbe	2019 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/31585845
Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci.	Varble A, Meaden S, Barrangou R, Westra ER, Marraffini LA	Nature microbiology	30886355	Nat Microbiol	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/30886355
(Ph)ighting Phages: How Bacteria Resist Their Parasites.	Rostøl JT, Marraffini L	Cell host & microbe	30763533	Cell Host Microbe	2019 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/30763533
Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes.	Varble A, Campisi E, Euler CW, Maguin P, Kozlova A, Fyodorova J, Rostøl JT, Fischetti VA, Marraffini LA	Nature microbiology	34819640	Nat Microbiol	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34819640
Type III-A CRISPR immunity promotes mutagenesis of staphylococci.	Mo CY, Mathai J, Rostøl JT, Varble A, Banh DV, Marraffini LA	Nature	33828299	Nature	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/33828299
Non-specific degradation of transcripts promotes plasmid clearance during type III-A CRISPR-Cas immunity.	Rostøl JT, Marraffini LA	Nature microbiology	30692669	Nat Microbiol	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30692669
Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response.	Heler R, Wright AV, Vucelja M, Doudna JA, Marraffini LA	Cell host & microbe	30709780	Cell Host Microbe	2019 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/30709780
RNA Guide Complementarity Prevents Self-Targeting in Type VI CRISPR Systems.	Meeske AJ, Marraffini LA	Molecular cell	30122537	Mol Cell	2018 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/30122537
Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6.	Garcia-Doval C, Schwede F, Berk C, Rostøl JT, Niewoehner O, Tejero O, Hall J, Marraffini LA, Jinek M	Nature communications	32221291	Nat Commun	2020 Mar 27	https://www.ncbi.nlm.nih.gov/pubmed/32221291
Co-evolution within structured bacterial communities results in multiple expansion of CRISPR loci and enhanced immunity.	Pyenson NC, Marraffini LA	eLife	32223887	Elife	2020 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/32223887
Three New Cs for CRISPR: Collateral, Communicate, Cooperate.	Varble A, Marraffini LA	Trends in genetics : TIG	31036344	Trends Genet	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31036344
Viral recombination systems limit CRISPR-Cas targeting through the generation of escape mutations.	Hossain AA, McGinn J, Meeske AJ, Modell JW, Marraffini LA	Cell host & microbe	34582782	Cell Host Microbe	2021 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/34582782
Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response.	Maguin P, Varble A, Modell JW, Marraffini LA	Molecular cell	35134339	Mol Cell	2022 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/35134339
Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity.	Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ	Molecular cell	30503773	Mol Cell	2019 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/30503773
Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage.	Meeske AJ, Nakandakari-Higa S, Marraffini LA	Nature	31142834	Nature	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31142834
Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts.	Goldberg GW, McMillan EA, Varble A, Modell JW, Samai P, Jiang W, Marraffini LA	Nature communications	29302058	Nat Commun	2018 Jan 4	https://www.ncbi.nlm.nih.gov/pubmed/29302058
Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system.	Aviram N, Thornal AN, Zeevi D, Marraffini LA	Nucleic acids research	35048966	Nucleic Acids Res	2022 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/35048966
Rarely acquired type II-A CRISPR-Cas spacers mediate anti-viral immunity through the targeting of a non-canonical PAM sequence.	Kenney CT, Marraffini LA	Nucleic acids research	37293964	Nucleic Acids Res	2023 Aug 11	https://www.ncbi.nlm.nih.gov/pubmed/37293964
If You'd Like to Stop a Type III CRISPR Ribonuclease, Then You Should Put a Ring (Nuclease) on It.	Mo CY, Marraffini LA	Molecular cell	30444997	Mol Cell	2018 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/30444997
Dynamics of Cas10 Govern Discrimination between Self and Non-self in Type III CRISPR-Cas Immunity.	Wang L, Mo CY, Wasserman MR, Rostøl JT, Marraffini LA, Liu S	Molecular cell	30503774	Mol Cell	2019 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/30503774
Molecular mechanisms of CRISPR-Cas spacer acquisition.	McGinn J, Marraffini LA	Nature reviews. Microbiology	30171202	Nat Rev Microbiol	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30171202
The Card1 nuclease provides defence during type III CRISPR immunity.	Rostøl JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA	Nature	33461211	Nature	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33461211
A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity.	Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA	Science (New York, N.Y.)	32467331	Science	2020 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/32467331
The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity.	Aviram N, Shilton AK, Lyn NG, Reis BS, Brivanlou A, Marraffini LA	bioRxiv : the preprint server for biology	38405743	bioRxiv	2024 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/38405743
Regulation by 3'-Untranslated Regions.	Mayr C	Annual review of genetics	28853924	Annu Rev Genet	2017 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/28853924
Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia.	Lee SH, Singh I, Tisdale S, Abdel-Wahab O, Leslie CS, Mayr C	Nature	30150773	Nature	2018 Sep	https://www.ncbi.nlm.nih.gov/pubmed/30150773
Generation of 3'UTR knockout cell lines by CRISPR/Cas9-mediated genome editing.	Mitschka S, Fansler MM, Mayr C	Methods in enzymology	34183132	Methods Enzymol	2021	https://www.ncbi.nlm.nih.gov/pubmed/34183132
Subcytoplasmic location of translation controls protein output.	Horste EL, Fansler MM, Cai T, Chen X, Mitschka S, Zhen G, Lee FCY, Ule J, Mayr C	Molecular cell	38134885	Mol Cell	2023 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/38134885
Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression.	Fansler MM, Mitschka S, Mayr C	Nature communications	38744866	Nat Commun	2024 May 14	https://www.ncbi.nlm.nih.gov/pubmed/38744866
What Are 3' UTRs Doing?	Mayr C	Cold Spring Harbor perspectives in biology	30181377	Cold Spring Harb Perspect Biol	2019 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/30181377
3' UTRs Regulate Protein Functions by Providing a Nurturing Niche during Protein Synthesis.	Mayr C	Cold Spring Harbor symposia on quantitative biology	31900325	Cold Spring Harb Symp Quant Biol	2019	https://www.ncbi.nlm.nih.gov/pubmed/31900325
Endogenous p53 expression in human and mouse is not regulated by its 3'UTR.	Mitschka S, Mayr C	eLife	33955355	Elife	2021 May 6	https://www.ncbi.nlm.nih.gov/pubmed/33955355
The FXR1 network acts as signaling scaffold for actomyosin remodeling.	Chen X, Fansler MM, Janjoš U, Ule J, Mayr C	bioRxiv : the preprint server for biology	37961296	bioRxiv	2024 May 25	https://www.ncbi.nlm.nih.gov/pubmed/37961296
In vivo reconstitution finds multivalent RNA-RNA interactions as drivers of mesh-like condensates.	Ma W, Zhen G, Xie W, Mayr C	eLife	33650968	Elife	2021 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/33650968
A Membraneless Organelle Associated with the Endoplasmic Reticulum Enables 3'UTR-Mediated Protein-Protein Interactions.	Ma W, Mayr C	Cell	30449617	Cell	2018 Nov 29	https://www.ncbi.nlm.nih.gov/pubmed/30449617
Gain of Additional BIRC3 Protein Functions through 3'-UTR-Mediated Protein Complex Formation.	Lee SH, Mayr C	Molecular cell	30948266	Mol Cell	2019 May 16	https://www.ncbi.nlm.nih.gov/pubmed/30948266
Widespread intronic polyadenylation diversifies immune cell transcriptomes.	Singh I, Lee SH, Sperling AS, Samur MK, Tai YT, Fulciniti M, Munshi NC, Mayr C, Leslie CS	Nature communications	29712909	Nat Commun	2018 Apr 30	https://www.ncbi.nlm.nih.gov/pubmed/29712909
mRNA interactions with disordered regions control protein activity.	Luo Y, Pratihar S, Horste EH, Mitschka S, Mey ASJS, Al-Hashimi HM, Mayr C	bioRxiv : the preprint server for biology	36824771	bioRxiv	2023 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/36824771
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly.	Chen X, Mayr C	RNA (New York, N.Y.)	34706978	RNA	2022 Jan	https://www.ncbi.nlm.nih.gov/pubmed/34706978
Enhancers regulate 3' end processing activity to control expression of alternative 3'UTR isoforms.	Kwon B, Fansler MM, Patel ND, Lee J, Ma W, Mayr C	Nature communications	35581194	Nat Commun	2022 May 17	https://www.ncbi.nlm.nih.gov/pubmed/35581194
Context-specific regulation and function of mRNA alternative polyadenylation.	Mitschka S, Mayr C	Nature reviews. Molecular cell biology	35798852	Nat Rev Mol Cell Biol	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/35798852
The FXR1 network acts as a signaling scaffold for actomyosin remodeling.	Chen X, Fansler MM, Janjoš U, Ule J, Mayr C	Cell	39106863	Cell	2024 Sep 5	https://www.ncbi.nlm.nih.gov/pubmed/39106863
Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis.	Wang J, Kaletsky R, Silva M, Williams A, Haas LA, Androwski RJ, Landis JN, Patrick C, Rashid A, Santiago-Martinez D, Gravato-Nobre M, Hodgkin J, Hall DH, Murphy CT, Barr MM	Current biology : CB	26687621	Curr Biol	2015 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/26687621
Piwi/PRG-1 Argonaute and TGF-β Mediate Transgenerational Learned Pathogenic Avoidance.	Moore RS, Kaletsky R, Murphy CT	Cell	31178117	Cell	2019 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/31178117
Caenorhabditis elegans sperm carry a histone-based epigenetic memory of both spermatogenesis and oogenesis.	Tabuchi TM, Rechtsteiner A, Jeffers TE, Egelhofer TA, Murphy CT, Strome S	Nature communications	30333496	Nat Commun	2018 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/30333496
Regulation of reproduction and longevity by nutrient-sensing pathways.	Templeman NM, Murphy CT	The Journal of cell biology	29074705	J Cell Biol	2018 Jan 2	https://www.ncbi.nlm.nih.gov/pubmed/29074705
The role of the Cer1 transposon in horizontal transfer of transgenerational memory.	Moore RS, Kaletsky R, Lesnik C, Cota V, Blackman E, Parsons LR, Gitai Z, Murphy CT	Cell	34363756	Cell	2021 Sep 2	https://www.ncbi.nlm.nih.gov/pubmed/34363756
Mating and male pheromone kill Caenorhabditis males through distinct mechanisms.	Shi C, Runnels AM, Murphy CT	eLife	28290982	Elife	2017 Mar 14	https://www.ncbi.nlm.nih.gov/pubmed/28290982
High-throughput behavioral screen in C. elegans reveals Parkinson's disease drug candidates.	Sohrabi S, Mor DE, Kaletsky R, Keyes W, Murphy CT	Communications biology	33589689	Commun Biol	2021 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/33589689
Mitochondrial hyperactivity as a potential therapeutic target in Parkinson's disease.	Mor DE, Murphy CT	Translational medicine of aging	33178902	Transl Med Aging	2020	https://www.ncbi.nlm.nih.gov/pubmed/33178902
C. elegans interprets bacterial non-coding RNAs to learn pathogenic avoidance.	Kaletsky R, Moore RS, Vrla GD, Parsons LR, Gitai Z, Murphy CT	Nature	32908307	Nature	2020 Oct	https://www.ncbi.nlm.nih.gov/pubmed/32908307
piRNAs regulate a Hedgehog germline-to-soma pro-aging signal.	Shi C, Murphy CT	Nature aging	37118518	Nat Aging	2023 Jan	https://www.ncbi.nlm.nih.gov/pubmed/37118518
Metformin rescues Parkinson's disease phenotypes caused by hyperactive mitochondria.	Mor DE, Sohrabi S, Kaletsky R, Keyes W, Tartici A, Kalia V, Miller GW, Murphy CT	Proceedings of the National Academy of Sciences of the United States of America	33024014	Proc Natl Acad Sci U S A	2020 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/33024014
GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease.	McIntyre LM, Huertas F, Morse AM, Kaletsky R, Murphy CT, Kalia V, Miller GW, Moskalenko O, Conesa A, Mor DE	Scientific reports	35228596	Sci Rep	2022 Feb 28	https://www.ncbi.nlm.nih.gov/pubmed/35228596
Transcriptional Profiling of C. elegans Adult Cells and Tissues with Age.	Kaletsky R, Murphy CT	Methods in molecular biology (Clifton, N.J.)	32410035	Methods Mol Biol	2020	https://www.ncbi.nlm.nih.gov/pubmed/32410035
An integrative tissue-network approach to identify and test human disease genes.	Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG	Nature biotechnology	30346941	Nat Biotechnol	2018 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/30346941
Novel elasticity measurements reveal C. elegans cuticle stiffens with age and in a long-lived mutant.	Rahimi M, Sohrabi S, Murphy CT	Biophysical journal	35065051	Biophys J	2022 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/35065051
The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators.	Kaletsky R, Lakhina V, Arey R, Williams A, Landis J, Ashraf J, Murphy CT	Nature	26675724	Nature	2016 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/26675724
A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance.	Sengupta T, St Ange J, Moore R, Kaletsky R, Marogi J, Myhrvold C, Gitai Z, Murphy CT	bioRxiv : the preprint server for biology	37503135	bioRxiv	2023 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/37503135
Pseudomonas fluorescens 15 small RNA Pfs1 mediates transgenerational epigenetic inheritance of pathogen avoidance in C. elegans through the Ephrin receptor VAB-1.	Seto R, Brown R, Kaletsky R, Parsons LR, Moore RS, Murphy CT	bioRxiv : the preprint server for biology	38826453	bioRxiv	2024 May 23	https://www.ncbi.nlm.nih.gov/pubmed/38826453
A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance.	Sengupta T, St Ange J, Kaletsky R, Moore RS, Seto RJ, Marogi J, Myhrvold C, Gitai Z, Murphy CT	PLoS genetics	38547071	PLoS Genet	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38547071
Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.	Kaletsky R, Yao V, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT	PLoS genetics	30096138	PLoS Genet	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/30096138
The usual suspects, dopamine and alpha-synuclein, conspire to cause neurodegeneration.	Mor DE, Daniels MJ, Ischiropoulos H	Movement disorders : official journal of the Movement Disorder Society	30633814	Mov Disord	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30633814
Protocol for transgenerational learned pathogen avoidance behavior assays in Caenorhabditis elegans.	Moore RS, Kaletsky R, Murphy CT	STAR protocols	33748786	STAR Protoc	2021 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/33748786
Zinc transporters belonging to the Cation Diffusion Facilitator (CDF) family have complementary roles in transporting zinc out of the cytosol.	Choi S, Hu YM, Corkins ME, Palmer AE, Bird AJ	PLoS genetics	29529046	PLoS Genet	2018 Mar	https://www.ncbi.nlm.nih.gov/pubmed/29529046
Native and engineered sensors for Ca(2+) and Zn(2+): lessons from calmodulin and MTF1.	Carpenter MC, Palmer AE	Essays in biochemistry	28487400	Essays Biochem	2017 May 9	https://www.ncbi.nlm.nih.gov/pubmed/28487400
Superiority of SpiroZin2 Versus FluoZin-3 for monitoring vesicular Zn(2+) allows tracking of lysosomal Zn(2+) pools.	Han Y, Goldberg JM, Lippard SJ, Palmer AE	Scientific reports	30302024	Sci Rep	2018 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/30302024
A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells.	Braselmann E, Wierzba AJ, Polaski JT, Chromiński M, Holmes ZE, Hung ST, Batan D, Wheeler JR, Parker R, Jimenez R, Gryko D, Batey RT, Palmer AE	Nature chemical biology	30061719	Nat Chem Biol	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30061719
Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter.	Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo MN, Palmer AE, Jimenez R	Integrative biology : quantitative biosciences from nano to macro	30094420	Integr Biol (Camb)	2018 Sep 17	https://www.ncbi.nlm.nih.gov/pubmed/30094420
Systematic Comparison of Vesicular Targeting Signals Leads to the Development of Genetically Encoded Vesicular Fluorescent Zn(2+) and pH Sensors.	Pratt EPS, Anson KJ, Tapper JK, Simpson DM, Palmer AE	ACS sensors	33305939	ACS Sens	2020 Dec 24	https://www.ncbi.nlm.nih.gov/pubmed/33305939
A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells.	Braselmann E, Palmer AE	Methods in enzymology	32713529	Methods Enzymol	2020	https://www.ncbi.nlm.nih.gov/pubmed/32713529
The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins.	Rodriguez EA, Campbell RE, Lin JY, Lin MZ, Miyawaki A, Palmer AE, Shu X, Zhang J, Tsien RY	Trends in biochemical sciences	27814948	Trends Biochem Sci	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/27814948
Intracellular Zn(2+) transients modulate global gene expression in dissociated rat hippocampal neurons.	Sanford L, Carpenter MC, Palmer AE	Scientific reports	31253848	Sci Rep	2019 Jun 28	https://www.ncbi.nlm.nih.gov/pubmed/31253848
Engineering of a Brighter Variant of the FusionRed Fluorescent Protein Using Lifetime Flow Cytometry and Structure-Guided Mutations.	Mukherjee S, Hung ST, Douglas N, Manna P, Thomas C, Ekrem A, Palmer AE, Jimenez R	Biochemistry	32914619	Biochemistry	2020 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/32914619
Illuminating RNA Biology: Tools for Imaging RNA in Live Mammalian Cells.	Braselmann E, Rathbun C, Richards EM, Palmer AE	Cell chemical biology	32640188	Cell Chem Biol	2020 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/32640188
Single cell analysis reveals multiple requirements for zinc in the mammalian cell cycle.	Lo MN, Damon LJ, Wei Tay J, Jia S, Palmer AE	eLife	32014109	Elife	2020 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/32014109
Human cells experience a Zn(2+) pulse in early G1.	Rakshit A, Holtzen SE, Lo MN, Conway KA, Palmer AE	Cell reports	37330912	Cell Rep	2023 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/37330912
Dissociated Hippocampal Neurons Exhibit Distinct Zn(2+) Dynamics in a Stimulation-Method-Dependent Manner.	Sanford L, Palmer AE	ACS chemical neuroscience	32013397	ACS Chem Neurosci	2020 Feb 19	https://www.ncbi.nlm.nih.gov/pubmed/32013397
Erratum: Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter.	Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo M, Palmer AE, Jimenez R	Integrative biology : quantitative biosciences from nano to macro	31788687	Integr Biol (Camb)	2019 Dec 31	https://www.ncbi.nlm.nih.gov/pubmed/31788687
Tools and techniques for illuminating the cell biology of zinc.	Pratt EPS, Damon LJ, Anson KJ, Palmer AE	Biochimica et biophysica acta. Molecular cell research	32980354	Biochim Biophys Acta Mol Cell Res	2021 Jan	https://www.ncbi.nlm.nih.gov/pubmed/32980354
Zn(2+) influx activates ERK and Akt signaling pathways.	Anson KJ, Corbet GA, Palmer AE	Proceedings of the National Academy of Sciences of the United States of America	33712543	Proc Natl Acad Sci U S A	2021 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/33712543
Discovery of a ZIP7 inhibitor from a Notch pathway screen.	Nolin E, Gans S, Llamas L, Bandyopadhyay S, Brittain SM, Bernasconi-Elias P, Carter KP, Loureiro JJ, Thomas JR, Schirle M, Yang Y, Guo N, Roma G, Schuierer S, Beibel M, Lindeman A, Sigoillot F, Chen A, Xie KX, Ho S, Reece-Hoyes J, Weihofen WA, Tyskiewicz K, Hoepfner D, McDonald RI, Guthrie N, Dogra A, Guo H, Shao J, Ding J, Canham SM, Boynton G, George EL, Kang ZB, Antczak C, Porter JA, Wallace O, Tallarico JA, Palmer AE, Jenkins JL, Jain RK, Bushell SM, Fryer CJ	Nature chemical biology	30643281	Nat Chem Biol	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30643281
Intramolecular Fluorescent Protein Association in a Class of Zinc FRET Sensors Leads to Increased Dynamic Range.	Slocum JD, Palmer AE, Jimenez R	The journal of physical chemistry. B	30942588	J Phys Chem B	2019 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/30942588
Critical Comparison of FRET-Sensor Functionality in the Cytosol and Endoplasmic Reticulum and Implications for Quantification of Ions.	Carter KP, Carpenter MC, Fiedler B, Jimenez R, Palmer AE	Analytical chemistry	28758723	Anal Chem	2017 Sep 5	https://www.ncbi.nlm.nih.gov/pubmed/28758723
Droplet Microfluidic Flow Cytometer For Sorting On Transient Cellular Responses Of Genetically-Encoded Sensors.	Fiedler BL, Van Buskirk S, Carter KP, Qin Y, Carpenter MC, Palmer AE, Jimenez R	Analytical chemistry	27959493	Anal Chem	2017 Jan 3	https://www.ncbi.nlm.nih.gov/pubmed/27959493
Techniques for measuring cellular zinc.	Carpenter MC, Lo MN, Palmer AE	Archives of biochemistry and biophysics	27580940	Arch Biochem Biophys	2016 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/27580940
Characterization of Global Gene Expression, Regulation of Metal Ions, and Infection Outcomes in Immune-Competent 129S6 Mouse Macrophages.	Janiszewski LN, Minson M, Allen MA, Dowell RD, Palmer AE	Infection and immunity	34370511	Infect Immun	2021 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/34370511
A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging.	Specht EA, Braselmann E, Palmer AE	Annual review of physiology	27860833	Annu Rev Physiol	2017 Feb 10	https://www.ncbi.nlm.nih.gov/pubmed/27860833
Remodeling of Zn(2+) homeostasis upon differentiation of mammary epithelial cells.	Han Y, Sanford L, Simpson DM, Dowell RD, Palmer AE	Metallomics : integrated biometal science	31950952	Metallomics	2020 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/31950952
Single molecule microscopy to profile the effect of zinc status on transcription factor dynamics.	Damon LJ, Aaron J, Palmer AE	Scientific reports	36273101	Sci Rep	2022 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/36273101
Directed Evolution of a Bright Variant of mCherry: Suppression of Nonradiative Decay by Fluorescence Lifetime Selections.	Mukherjee S, Manna P, Hung ST, Vietmeyer F, Friis P, Palmer AE, Jimenez R	The journal of physical chemistry. B	35709514	J Phys Chem B	2022 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/35709514
Nucleoside Reverse Transcriptase Inhibitors Suppress Laser-Induced Choroidal Neovascularization in Mice.	Mizutani T, Fowler BJ, Kim Y, Yasuma R, Krueger LA, Gelfand BD, Ambati J	Investigative ophthalmology & visual science	26529046	Invest Ophthalmol Vis Sci	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26529046
A Revised Hemodynamic Theory of Age-Related Macular Degeneration.	Gelfand BD, Ambati J	Trends in molecular medicine	27423265	Trends Mol Med	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27423265
Dry Age-Related Macular Degeneration Pharmacology.	Wright CB, Ambati J	Handbook of experimental pharmacology	27900609	Handb Exp Pharmacol	2017	https://www.ncbi.nlm.nih.gov/pubmed/27900609
Voluntary Exercise Suppresses Choroidal Neovascularization in Mice.	Makin RD, Argyle D, Hirahara S, Nagasaka Y, Zhang M, Yan Z, Kerur N, Ambati J, Gelfand BD	Investigative ophthalmology & visual science	32460310	Invest Ophthalmol Vis Sci	2020 May 11	https://www.ncbi.nlm.nih.gov/pubmed/32460310
DDX17 is an essential mediator of sterile NLRC4 inflammasome activation by retrotransposon RNAs.	Wang SB, Narendran S, Hirahara S, Varshney A, Pereira F, Apicella I, Ambati M, Ambati VL, Yerramothu P, Ambati K, Nagasaka Y, Argyle D, Huang P, Baker KL, Marion KM, Gupta K, Liu B, Hinton DR, Canna SW, Sallam T, Sadda SR, Kerur N, Gelfand BD, Ambati J	Science immunology	34860583	Sci Immunol	2021 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/34860583
Human IgG1 antibodies suppress angiogenesis in a target-independent manner.	Bogdanovich S, Kim Y, Mizutani T, Yasuma R, Tudisco L, Cicatiello V, Bastos-Carvalho A, Kerur N, Hirano Y, Baffi JZ, Tarallo V, Li S, Yasuma T, Arpitha P, Fowler BJ, Wright CB, Apicella I, Greco A, Brunetti A, Ruvo M, Sandomenico A, Nozaki M, Ijima R, Kaneko H, Ogura Y, Terasaki H, Ambati BK, Leusen JH, Langdon WY, Clark MR, Armour KL, Bruhns P, Verbeek JS, Gelfand BD, De Falco S, Ambati J	Signal transduction and targeted therapy	26918197	Signal Transduct Target Ther	2016	https://www.ncbi.nlm.nih.gov/pubmed/26918197
Intravenous immune globulin suppresses angiogenesis in mice and humans.	Yasuma R, Cicatiello V, Mizutani T, Tudisco L, Kim Y, Tarallo V, Bogdanovich S, Hirano Y, Kerur N, Li S, Yasuma T, Fowler BJ, Wright CB, Apicella I, Greco A, Brunetti A, Ambati BK, Helmers SB, Lundberg IE, Viklicky O, Leusen JH, Verbeek JS, Gelfand BD, Bastos-Carvalho A, De Falco S, Ambati J	Signal transduction and targeted therapy	26925256	Signal Transduct Target Ther	2016	https://www.ncbi.nlm.nih.gov/pubmed/26925256
Nucleoside reverse transcriptase inhibitors possess intrinsic anti-inflammatory activity.	Fowler BJ, Gelfand BD, Kim Y, Kerur N, Tarallo V, Hirano Y, Amarnath S, Fowler DH, Radwan M, Young MT, Pittman K, Kubes P, Agarwal HK, Parang K, Hinton DR, Bastos-Carvalho A, Li S, Yasuma T, Mizutani T, Yasuma R, Wright C, Ambati J	Science (New York, N.Y.)	25414314	Science	2014 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/25414314
A non-canonical, interferon-independent signaling activity of cGAMP triggers DNA damage response signaling.	Banerjee D, Langberg K, Abbas S, Odermatt E, Yerramothu P, Volaric M, Reidenbach MA, Krentz KJ, Rubinstein CD, Brautigan DL, Abbas T, Gelfand BD, Ambati J, Kerur N	Nature communications	34707113	Nat Commun	2021 Oct 27	https://www.ncbi.nlm.nih.gov/pubmed/34707113
DICER1/Alu RNA dysmetabolism induces Caspase-8-mediated cell death in age-related macular degeneration.	Kim Y, Tarallo V, Kerur N, Yasuma T, Gelfand BD, Bastos-Carvalho A, Hirano Y, Yasuma R, Mizutani T, Fowler BJ, Li S, Kaneko H, Bogdanovich S, Ambati BK, Hinton DR, Hauswirth WW, Hakem R, Wright C, Ambati J	Proceedings of the National Academy of Sciences of the United States of America	25349431	Proc Natl Acad Sci U S A	2014 Nov 11	https://www.ncbi.nlm.nih.gov/pubmed/25349431
Cytoplasmic synthesis of endogenous Alu complementary DNA via reverse transcription and implications in age-related macular degeneration.	Fukuda S, Varshney A, Fowler BJ, Wang SB, Narendran S, Ambati K, Yasuma T, Magagnoli J, Leung H, Hirahara S, Nagasaka Y, Yasuma R, Apicella I, Pereira F, Makin RD, Magner E, Liu X, Sun J, Wang M, Baker K, Marion KM, Huang X, Baghdasaryan E, Ambati M, Ambati VL, Pandey A, Pandya L, Cummings T, Banerjee D, Huang P, Yerramothu P, Tolstonog GV, Held U, Erwin JA, Paquola ACM, Herdy JR, Ogura Y, Terasaki H, Oshika T, Darwish S, Singh RK, Mozaffari S, Bhattarai D, Kim KB, Hardin JW, Bennett CL, Hinton DR, Hanson TE, Röver C, Parang K, Kerur N, Liu J, Werner BC, Sutton SS, Sadda SR, Schumann GG, Gelfand BD, Gage FH, Ambati J	Proceedings of the National Academy of Sciences of the United States of America	33526699	Proc Natl Acad Sci U S A	2021 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/33526699
Powerful anti-tumor and anti-angiogenic activity of a new anti-vascular endothelial growth factor receptor 1 peptide in colorectal cancer models.	Cicatiello V, Apicella I, Tudisco L, Tarallo V, Formisano L, Sandomenico A, Kim Y, Bastos-Carvalho A, Orlandi A, Ambati J, Ruvo M, Bianco R, De Falco S	Oncotarget	25868854	Oncotarget	2015 Apr 30	https://www.ncbi.nlm.nih.gov/pubmed/25868854
IL-18 is not therapeutic for neovascular age-related macular degeneration.	Hirano Y, Yasuma T, Mizutani T, Fowler BJ, Tarallo V, Yasuma R, Kim Y, Bastos-Carvalho A, Kerur N, Gelfand BD, Bogdanovich S, He S, Zhang X, Nozaki M, Ijima R, Kaneko H, Ogura Y, Terasaki H, Nagai H, Haro I, Núñez G, Ambati BK, Hinton DR, Ambati J	Nature medicine	25473914	Nat Med	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25473914
RF/6A Chorioretinal Cells Do Not Display Key Endothelial Phenotypes.	Makin RD, Apicella I, Nagasaka Y, Kaneko H, Turner SD, Kerur N, Ambati J, Gelfand BD	Investigative ophthalmology & visual science	30508043	Invest Ophthalmol Vis Sci	2018 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/30508043
Zidovudine ameliorates pathology in the mouse model of Duchenne muscular dystrophy via P2RX7 purinoceptor antagonism.	Al-Khalidi R, Panicucci C, Cox P, Chira N, Róg J, Young CNJ, McGeehan RE, Ambati K, Ambati J, Zabłocki K, Gazzerro E, Arkle S, Bruno C, Górecki DC	Acta neuropathologica communications	29642926	Acta Neuropathol Commun	2018 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/29642926
L1 drives IFN in senescent cells and promotes age-associated inflammation.	De Cecco M, Ito T, Petrashen AP, Elias AE, Skvir NJ, Criscione SW, Caligiana A, Brocculi G, Adney EM, Boeke JD, Le O, Beauséjour C, Ambati J, Ambati K, Simon M, Seluanov A, Gorbunova V, Slagboom PE, Helfand SL, Neretti N, Sedivy JM	Nature	30728521	Nature	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30728521
Chronic Dicer1 deficiency promotes atrophic and neovascular outer retinal pathologies in mice.	Wright CB, Uehara H, Kim Y, Yasuma T, Yasuma R, Hirahara S, Makin RD, Apicella I, Pereira F, Nagasaka Y, Narendran S, Fukuda S, Albuquerque R, Fowler BJ, Bastos-Carvalho A, Georgel P, Hatada I, Chang B, Kerur N, Ambati BK, Ambati J, Gelfand BD	Proceedings of the National Academy of Sciences of the United States of America	31964819	Proc Natl Acad Sci U S A	2020 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/31964819
cGAS drives noncanonical-inflammasome activation in age-related macular degeneration.	Kerur N, Fukuda S, Banerjee D, Kim Y, Fu D, Apicella I, Varshney A, Yasuma R, Fowler BJ, Baghdasaryan E, Marion KM, Huang X, Yasuma T, Hirano Y, Serbulea V, Ambati M, Ambati VL, Kajiwara Y, Ambati K, Hirahara S, Bastos-Carvalho A, Ogura Y, Terasaki H, Oshika T, Kim KB, Hinton DR, Leitinger N, Cambier JC, Buxbaum JD, Kenney MC, Jazwinski SM, Nagai H, Hara I, West AP, Fitzgerald KA, Sadda SR, Gelfand BD, Ambati J	Nature medicine	29176737	Nat Med	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29176737
Iron Toxicity in the Retina Requires Alu RNA and the NLRP3 Inflammasome.	Gelfand BD, Wright CB, Kim Y, Yasuma T, Yasuma R, Li S, Fowler BJ, Bastos-Carvalho A, Kerur N, Uittenbogaard A, Han YS, Lou D, Kleinman ME, McDonald WH, Núñez G, Georgel P, Dunaief JL, Ambati J	Cell reports	26074074	Cell Rep	2015 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/26074074
Fluorescent indicators for simultaneous reporting of all four cell cycle phases.	Bajar BT, Lam AJ, Badiee RK, Oh YH, Chu J, Zhou XX, Kim N, Kim BB, Chung M, Yablonovitch AL, Cruz BF, Kulalert K, Tao JJ, Meyer T, Su XD, Lin MZ	Nature methods	27798610	Nat Methods	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27798610
Photoswitchable fluorescent proteins: ten years of colorful chemistry and exciting applications.	Zhou XX, Lin MZ	Current opinion in chemical biology	23876529	Curr Opin Chem Biol	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23876529
Optobiology: optical control of biological processes via protein engineering.	Kim B, Lin MZ	Biochemical Society transactions	24059506	Biochem Soc Trans	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24059506
Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments.	Welf ES, Driscoll MK, Dean KM, Schäfer C, Chu J, Davidson MW, Lin MZ, Danuser G, Fiolka R	Developmental cell	26906741	Dev Cell	2016 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/26906741
A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription.	Zhou XX, Zou X, Chung HK, Gao Y, Liu Y, Qi LS, Lin MZ	ACS chemical biology	28938067	ACS Chem Biol	2018 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/28938067
An orange calcium-modulated bioluminescent indicator for non-invasive activity imaging.	Oh Y, Park Y, Cho JH, Wu H, Paulk NK, Liu LX, Kim N, Kay MA, Wu JC, Lin MZ	Nature chemical biology	30936501	Nat Chem Biol	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/30936501
Optical control of biological processes by light-switchable proteins.	Fan LZ, Lin MZ	Wiley interdisciplinary reviews. Developmental biology	25858669	Wiley Interdiscip Rev Dev Biol	2015 Sep-Oct	https://www.ncbi.nlm.nih.gov/pubmed/25858669
Investigating neuronal function with optically controllable proteins.	Zhou XX, Pan M, Lin MZ	Frontiers in molecular neuroscience	26257603	Front Mol Neurosci	2015	https://www.ncbi.nlm.nih.gov/pubmed/26257603
Structure-guided wavelength tuning in far-red fluorescent proteins.	Ng HL, Lin MZ	Current opinion in structural biology	27468111	Curr Opin Struct Biol	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27468111
Genetically encoded indicators of neuronal activity.	Lin MZ, Schnitzer MJ	Nature neuroscience	27571193	Nat Neurosci	2016 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/27571193
Optical control of cell signaling by single-chain photoswitchable kinases.	Zhou XX, Fan LZ, Li P, Shen K, Lin MZ	Science (New York, N.Y.)	28232577	Science	2017 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/28232577
Optical regulation of endogenous RhoA reveals selection of cellular responses by signal amplitude.	Ju J, Lee HN, Ning L, Ryu H, Zhou XX, Chun H, Lee YW, Lee-Richerson AI, Jeong C, Lin MZ, Seong J	Cell reports	35830815	Cell Rep	2022 Jul 12	https://www.ncbi.nlm.nih.gov/pubmed/35830815
Generation of complexity in fungal terpene biosynthesis: discovery of a multifunctional cytochrome P450 in the fumagillin pathway.	Lin HC, Tsunematsu Y, Dhingra S, Xu W, Fukutomi M, Chooi YH, Cane DE, Calvo AM, Watanabe K, Tang Y	Journal of the American Chemical Society	24568283	J Am Chem Soc	2014 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/24568283
Short pathways to complexity generation: fungal peptidyl alkaloid multicyclic scaffolds from anthranilate building blocks.	Walsh CT, Haynes SW, Ames BD, Gao X, Tang Y	ACS chemical biology	23659680	ACS Chem Biol	2013 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/23659680
A cytochrome P450 serves as an unexpected terpene cyclase during fungal meroterpenoid biosynthesis.	Chooi YH, Hong YJ, Cacho RA, Tantillo DJ, Tang Y	Journal of the American Chemical Society	24161266	J Am Chem Soc	2013 Nov 13	https://www.ncbi.nlm.nih.gov/pubmed/24161266
Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent.	Cochrane RV, Sanichar R, Lambkin GR, Reiz B, Xu W, Tang Y, Vederas JC	Angewandte Chemie (International ed. in English)	26783060	Angew Chem Int Ed Engl	2016 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/26783060
A carbonate-forming Baeyer-Villiger monooxygenase.	Hu Y, Dietrich D, Xu W, Patel A, Thuss JA, Wang J, Yin WB, Qiao K, Houk KN, Vederas JC, Tang Y	Nature chemical biology	24838010	Nat Chem Biol	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24838010
Structural basis of nonribosomal peptide macrocyclization in fungi.	Zhang J, Liu N, Cacho RA, Gong Z, Liu Z, Qin W, Tang C, Tang Y, Zhou J	Nature chemical biology	27748753	Nat Chem Biol	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27748753
Genome Mining and Assembly-Line Biosynthesis of the UCS1025A Pyrrolizidinone Family of Fungal Alkaloids.	Li L, Tang MC, Tang S, Gao S, Soliman S, Hang L, Xu W, Ye T, Watanabe K, Tang Y	Journal of the American Chemical Society	29373009	J Am Chem Soc	2018 Feb 14	https://www.ncbi.nlm.nih.gov/pubmed/29373009
Enzymatic one-step ring contraction for quinolone biosynthesis.	Kishimoto S, Hara K, Hashimoto H, Hirayama Y, Champagne PA, Houk KN, Tang Y, Watanabe K	Nature communications	30026518	Nat Commun	2018 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/30026518
Discovery of cryptic polyketide metabolites from dermatophytes using heterologous expression in Aspergillus nidulans.	Yin WB, Chooi YH, Smith AR, Cacho RA, Hu Y, White TC, Tang Y	ACS synthetic biology	23758576	ACS Synth Biol	2013 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/23758576
The fumagillin gene cluster, an example of hundreds of genes under veA control in Aspergillus fumigatus.	Dhingra S, Lind AL, Lin HC, Tang Y, Rokas A, Calvo AM	PloS one	24116213	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/24116213
Identification and characterization of the echinocandin B biosynthetic gene cluster from Emericella rugulosa NRRL 11440.	Cacho RA, Jiang W, Chooi YH, Walsh CT, Tang Y	Journal of the American Chemical Society	22998630	J Am Chem Soc	2012 Oct 10	https://www.ncbi.nlm.nih.gov/pubmed/22998630
Cyclization of fungal nonribosomal peptides by a terminal condensation-like domain.	Gao X, Haynes SW, Ames BD, Wang P, Vien LP, Walsh CT, Tang Y	Nature chemical biology	22902615	Nat Chem Biol	2012 Oct	https://www.ncbi.nlm.nih.gov/pubmed/22902615
Discovery of Unclustered Fungal Indole Diterpene Biosynthetic Pathways through Combinatorial Pathway Reassembly in Engineered Yeast.	Tang MC, Lin HC, Li D, Zou Y, Li J, Xu W, Cacho RA, Hillenmeyer ME, Garg NK, Tang Y	Journal of the American Chemical Society	26469304	J Am Chem Soc	2015 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/26469304
Enzyme-Catalyzed Intramolecular Enantioselective Hydroalkoxylation.	Gao SS, Garcia-Borràs M, Barber JS, Hai Y, Duan A, Garg NK, Houk KN, Tang Y	Journal of the American Chemical Society	28240554	J Am Chem Soc	2017 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/28240554
P450-Mediated Coupling of Indole Fragments To Forge Communesin and Unnatural Isomers.	Lin HC, McMahon TC, Patel A, Corsello M, Simon A, Xu W, Zhao M, Houk KN, Garg NK, Tang Y	Journal of the American Chemical Society	26963294	J Am Chem Soc	2016 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/26963294
Phenalenone Polyketide Cyclization Catalyzed by Fungal Polyketide Synthase and Flavin-Dependent Monooxygenase.	Gao SS, Duan A, Xu W, Yu P, Hang L, Houk KN, Tang Y	Journal of the American Chemical Society	26978228	J Am Chem Soc	2016 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/26978228
Understanding Programming of Fungal Iterative Polyketide Synthases: The Biochemical Basis for Regioselectivity by the Methyltransferase Domain in the Lovastatin Megasynthase.	Cacho RA, Thuss J, Xu W, Sanichar R, Gao Z, Nguyen A, Vederas JC, Tang Y	Journal of the American Chemical Society	26630357	J Am Chem Soc	2015 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/26630357
Thioesterase-Catalyzed Aminoacylation and Thiolation of Polyketides in Fungi.	Tang MC, Fischer CR, Chari JV, Tan D, Suresh S, Chu A, Miranda M, Smith J, Zhang Z, Garg NK, St Onge RP, Tang Y	Journal of the American Chemical Society	31051070	J Am Chem Soc	2019 May 22	https://www.ncbi.nlm.nih.gov/pubmed/31051070
Methylation-dependent acyl transfer between polyketide synthase and nonribosomal peptide synthetase modules in fungal natural product biosynthesis.	Zou Y, Xu W, Tsunematsu Y, Tang M, Watanabe K, Tang Y	Organic letters	25494235	Org Lett	2014 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/25494235
Mechanism of the P450-Catalyzed Oxidative Cyclization in the Biosynthesis of Griseofulvin.	Grandner JM, Cacho RA, Tang Y, Houk KN	ACS catalysis	28503354	ACS Catal	2016 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/28503354
SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis.	Ohashi M, Liu F, Hai Y, Chen M, Tang MC, Yang Z, Sato M, Watanabe K, Houk KN, Tang Y	Nature	28902839	Nature	2017 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/28902839
Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi.	Cacho RA, Tang Y, Chooi YH	Frontiers in microbiology	25642215	Front Microbiol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25642215
Genome mining of a prenylated and immunosuppressive polyketide from pathogenic fungi.	Chooi YH, Fang J, Liu H, Filler SG, Wang P, Tang Y	Organic letters	23368997	Org Lett	2013 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/23368997
Identification and characterization of the chaetoviridin and chaetomugilin gene cluster in Chaetomium globosum reveal dual functions of an iterative highly-reducing polyketide synthase.	Winter JM, Sato M, Sugimoto S, Chiou G, Garg NK, Tang Y, Watanabe K	Journal of the American Chemical Society	23072467	J Am Chem Soc	2012 Oct 31	https://www.ncbi.nlm.nih.gov/pubmed/23072467
Complexity generation in fungal polyketide biosynthesis: a spirocycle-forming P450 in the concise pathway to the antifungal drug griseofulvin.	Cacho RA, Chooi YH, Zhou H, Tang Y	ACS chemical biology	23978092	ACS Chem Biol	2013 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/23978092
Elucidation of pseurotin biosynthetic pathway points to trans-acting C-methyltransferase: generation of chemical diversity.	Tsunematsu Y, Fukutomi M, Saruwatari T, Noguchi H, Hotta K, Tang Y, Watanabe K	Angewandte Chemie (International ed. in English)	24939566	Angew Chem Int Ed Engl	2014 Aug 4	https://www.ncbi.nlm.nih.gov/pubmed/24939566
Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action.	Yan Y, Liu Q, Zang X, Yuan S, Bat-Erdene U, Nguyen C, Gan J, Zhou J, Jacobsen SE, Tang Y	Nature	29995859	Nature	2018 Jul	https://www.ncbi.nlm.nih.gov/pubmed/29995859
Identification and Heterologous Production of a Benzoyl-Primed Tricarboxylic Acid Polyketide Intermediate from the Zaragozic Acid A Biosynthetic Pathway.	Liu N, Hung YS, Gao SS, Hang L, Zou Y, Chooi YH, Tang Y	Organic letters	28605916	Org Lett	2017 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/28605916
Coordinated and Iterative Enzyme Catalysis in Fungal Polyketide Biosynthesis.	Hang L, Liu N, Tang Y	ACS catalysis	28529817	ACS Catal	2016 Sep 2	https://www.ncbi.nlm.nih.gov/pubmed/28529817
EcdGHK are three tailoring iron oxygenases for amino acid building blocks of the echinocandin scaffold.	Jiang W, Cacho RA, Chiou G, Garg NK, Tang Y, Walsh CT	Journal of the American Chemical Society	23451921	J Am Chem Soc	2013 Mar 20	https://www.ncbi.nlm.nih.gov/pubmed/23451921
Tandem prenyltransferases catalyze isoprenoid elongation and complexity generation in biosynthesis of quinolone alkaloids.	Zou Y, Zhan Z, Li D, Tang M, Cacho RA, Watanabe K, Tang Y	Journal of the American Chemical Society	25859931	J Am Chem Soc	2015 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/25859931
Involvement of Lipocalin-like CghA in Decalin-Forming Stereoselective Intramolecular [4+2] Cycloaddition.	Sato M, Yagishita F, Mino T, Uchiyama N, Patel A, Chooi YH, Goda Y, Xu W, Noguchi H, Yamamoto T, Hotta K, Houk KN, Tang Y, Watanabe K	Chembiochem : a European journal of chemical biology	26360642	Chembiochem	2015 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/26360642
Comparison of 10,11-Dehydrocurvularin Polyketide Synthases from Alternaria cinerariae and Aspergillus terreus Highlights Key Structural Motifs.	Cochrane RV, Gao Z, Lambkin GR, Xu W, Winter JM, Marcus SL, Tang Y, Vederas JC	Chembiochem : a European journal of chemical biology	26493380	Chembiochem	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26493380
Fungal polyketide synthase product chain-length control by partnering thiohydrolase.	Zabala AO, Chooi YH, Choi MS, Lin HC, Tang Y	ACS chemical biology	24845309	ACS Chem Biol	2014 Jul 18	https://www.ncbi.nlm.nih.gov/pubmed/24845309
Biochemical and Structural Basis for Controlling Chemical Modularity in Fungal Polyketide Biosynthesis.	Winter JM, Cascio D, Dietrich D, Sato M, Watanabe K, Sawaya MR, Vederas JC, Tang Y	Journal of the American Chemical Society	26172141	J Am Chem Soc	2015 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/26172141
Biosynthesis of the α-nitro-containing cyclic tripeptide psychrophilin.	Zhao M, Lin HC, Tang Y	The Journal of antibiotics	26956794	J Antibiot (Tokyo)	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26956794
Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis.	Yamamoto T, Tsunematsu Y, Hara K, Suzuki T, Kishimoto S, Kawagishi H, Noguchi H, Hashimoto H, Tang Y, Hotta K, Watanabe K	Angewandte Chemie (International ed. in English)	27072782	Angew Chem Int Ed Engl	2016 May 17	https://www.ncbi.nlm.nih.gov/pubmed/27072782
Biosynthesis of fungal indole alkaloids.	Xu W, Gavia DJ, Tang Y	Natural product reports	25180619	Nat Prod Rep	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25180619
Saccharomyces cerevisiae as a tool for mining, studying and engineering fungal polyketide synthases.	Bond C, Tang Y, Li L	Fungal genetics and biology : FG & B	26850128	Fungal Genet Biol	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/26850128
Investigation of fungal iterative polyketide synthase functions using partially assembled intermediates.	Gao Z, Wang J, Norquay AK, Qiao K, Tang Y, Vederas JC	Journal of the American Chemical Society	23356934	J Am Chem Soc	2013 Feb 6	https://www.ncbi.nlm.nih.gov/pubmed/23356934
Elucidation of the concise biosynthetic pathway of the communesin indole alkaloids.	Lin HC, Chiou G, Chooi YH, McMahon TC, Xu W, Garg NK, Tang Y	Angewandte Chemie (International ed. in English)	25571861	Angew Chem Int Ed Engl	2015 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/25571861
The fumagillin biosynthetic gene cluster in Aspergillus fumigatus encodes a cryptic terpene cyclase involved in the formation of β-trans-bergamotene.	Lin HC, Chooi YH, Dhingra S, Xu W, Calvo AM, Tang Y	Journal of the American Chemical Society	23488861	J Am Chem Soc	2013 Mar 27	https://www.ncbi.nlm.nih.gov/pubmed/23488861
Collaborative Biosynthesis of Maleimide- and Succinimide-Containing Natural Products by Fungal Polyketide Megasynthases.	Sato M, Dander JE, Sato C, Hung YS, Gao SS, Tang MC, Hang L, Winter JM, Garg NK, Watanabe K, Tang Y	Journal of the American Chemical Society	28365998	J Am Chem Soc	2017 Apr 19	https://www.ncbi.nlm.nih.gov/pubmed/28365998
Expanding the structural diversity of polyketides by exploring the cofactor tolerance of an inline methyltransferase domain.	Winter JM, Chiou G, Bothwell IR, Xu W, Garg NK, Luo M, Tang Y	Organic letters	23837609	Org Lett	2013 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/23837609
Enzyme-catalyzed cationic epoxide rearrangements in quinolone alkaloid biosynthesis.	Zou Y, Garcia-Borràs M, Tang MC, Hirayama Y, Li DH, Li L, Watanabe K, Houk KN, Tang Y	Nature chemical biology	28114276	Nat Chem Biol	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28114276
Biochemical Characterization of a Eukaryotic Decalin-Forming Diels-Alderase.	Li L, Yu P, Tang MC, Zou Y, Gao SS, Hung YS, Zhao M, Watanabe K, Houk KN, Tang Y	Journal of the American Chemical Society	27960349	J Am Chem Soc	2016 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/27960349
Combinatorial Generation of Chemical Diversity by Redox Enzymes in Chaetoviridin Biosynthesis.	Sato M, Winter JM, Kishimoto S, Noguchi H, Tang Y, Watanabe K	Organic letters	26959241	Org Lett	2016 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/26959241
Biosynthesis of Strained Piperazine Alkaloids: Uncovering the Concise Pathway of Herquline A.	Yu X, Liu F, Zou Y, Tang MC, Hang L, Houk KN, Tang Y	Journal of the American Chemical Society	27690412	J Am Chem Soc	2016 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/27690412
Efficient Biosynthesis of Fungal Polyketides Containing the Dioxabicyclo-octane Ring System.	Mao XM, Zhan ZJ, Grayson MN, Tang MC, Xu W, Li YQ, Yin WB, Lin HC, Chooi YH, Houk KN, Tang Y	Journal of the American Chemical Society	26340065	J Am Chem Soc	2015 Sep 23	https://www.ncbi.nlm.nih.gov/pubmed/26340065
Epigenetic genome mining of an endophytic fungus leads to the pleiotropic biosynthesis of natural products.	Mao XM, Xu W, Li D, Yin WB, Chooi YH, Li YQ, Tang Y, Hu Y	Angewandte Chemie (International ed. in English)	26013262	Angew Chem Int Ed Engl	2015 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/26013262
Identification of the Pyranonigrin A Biosynthetic Gene Cluster by Genome Mining in Penicillium thymicola IBT 5891.	Tang MC, Zou Y, Yee D, Tang Y	AIChE journal. American Institute of Chemical Engineers	31588145	AIChE J	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/31588145
Reversible Product Release and Recapture by a Fungal Polyketide Synthase Using a Carnitine Acyltransferase Domain.	Hang L, Tang MC, Harvey CJB, Page CG, Li J, Hung YS, Liu N, Hillenmeyer ME, Tang Y	Angewandte Chemie (International ed. in English)	28679030	Angew Chem Int Ed Engl	2017 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/28679030
Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries.	Schmidt TL, Beliveau BJ, Uca YO, Theilmann M, Da Cruz F, Wu CT, Shih WM	Nature communications	26567534	Nat Commun	2015 Nov 16	https://www.ncbi.nlm.nih.gov/pubmed/26567534
Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.	Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT	Proceedings of the National Academy of Sciences of the United States of America	23236188	Proc Natl Acad Sci U S A	2012 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/23236188
Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries.	Murgha Y, Beliveau B, Semrau K, Schwartz D, Wu CT, Gulari E, Rouillard JM	BioTechniques	26054766	Biotechniques	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/26054766
Visualizing genomes with Oligopaint FISH probes.	Beliveau BJ, Apostolopoulos N, Wu CT	Current protocols in molecular biology	24510436	Curr Protoc Mol Biol	2014 Jan 6	https://www.ncbi.nlm.nih.gov/pubmed/24510436
Germline progenitors escape the widespread phenomenon of homolog pairing during Drosophila development.	Joyce EF, Apostolopoulos N, Beliveau BJ, Wu CT	PLoS genetics	24385920	PLoS Genet	2013	https://www.ncbi.nlm.nih.gov/pubmed/24385920
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.	Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT	PLoS genetics	30586358	PLoS Genet	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30586358
Genes with monoallelic expression contribute disproportionately to genetic diversity in humans.	Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA	Nature genetics	26808112	Nat Genet	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26808112
An Unexpected Regulatory Cascade Governs a Core Function of the Drosophila PRC1 Chromatin Protein Su(z)2.	Nguyen SC, Yu S, Oberlick E, Wu CT	Genetics	27881472	Genetics	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/27881472
Islands of retroelements are major components of Drosophila centromeres.	Chang CH, Chavan A, Palladino J, Wei X, Martins NMC, Santinello B, Chen CC, Erceg J, Beliveau BJ, Wu CT, Larracuente AM, Mellone BG	PLoS biology	31086362	PLoS Biol	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/31086362
Highly structured homolog pairing reflects functional organization of the Drosophila genome.	AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT	Nature communications	31582763	Nat Commun	2019 Oct 3	https://www.ncbi.nlm.nih.gov/pubmed/31582763
In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT.	Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu CT	Methods in molecular biology (Clifton, N.J.)	28924672	Methods Mol Biol	2017	https://www.ncbi.nlm.nih.gov/pubmed/28924672
Pairing and anti-pairing: a balancing act in the diploid genome.	Joyce EF, Erceg J, Wu CT	Current opinion in genetics & development	27065367	Curr Opin Genet Dev	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/27065367
Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.	McCole RB, Erceg J, Saylor W, Wu CT	Cell reports	29996107	Cell Rep	2018 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/29996107
Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin.	Lee YCG, Ogiyama Y, Martins NMC, Beliveau BJ, Acevedo D, Wu CT, Cavalli G, Karpen GH	PLoS genetics	32203508	PLoS Genet	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/32203508
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.	Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu CT, Yin P	Proceedings of the National Academy of Sciences of the United States of America	29463736	Proc Natl Acad Sci U S A	2018 Mar 6	https://www.ncbi.nlm.nih.gov/pubmed/29463736
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes.	Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT	Nature communications	25962338	Nat Commun	2015 May 12	https://www.ncbi.nlm.nih.gov/pubmed/25962338
Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei.	Senaratne TN, Joyce EF, Nguyen SC, Wu CT	PLoS genetics	27541002	PLoS Genet	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27541002
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.	Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X	Nature	26760202	Nature	2016 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/26760202
3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.	Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Lioutas A, Hershberg EA, Martins NMC, Reginato PL, Hannan M, Beliveau BJ, Church GM, Daugharthy ER, Marti-Renom MA, Wu CT	Nature methods	32719531	Nat Methods	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32719531
Spatial organization of chromatin domains and compartments in single chromosomes.	Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang X	Science (New York, N.Y.)	27445307	Science	2016 Aug 5	https://www.ncbi.nlm.nih.gov/pubmed/27445307
A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans.	Fields BD, Nguyen SC, Nir G, Kennedy S	eLife	31084706	Elife	2019 May 14	https://www.ncbi.nlm.nih.gov/pubmed/31084706
Allosteric activation of apicomplexan calcium-dependent protein kinases.	Ingram JR, Knockenhauer KE, Markus BM, Mandelbaum J, Ramek A, Shan Y, Shaw DE, Schwartz TU, Ploegh HL, Lourido S	Proceedings of the National Academy of Sciences of the United States of America	26305940	Proc Natl Acad Sci U S A	2015 Sep 8	https://www.ncbi.nlm.nih.gov/pubmed/26305940
Durable antitumor responses to CD47 blockade require adaptive immune stimulation.	Sockolosky JT, Dougan M, Ingram JR, Ho CC, Kauke MJ, Almo SC, Ploegh HL, Garcia KC	Proceedings of the National Academy of Sciences of the United States of America	27091975	Proc Natl Acad Sci U S A	2016 May 10	https://www.ncbi.nlm.nih.gov/pubmed/27091975
Noninvasive imaging of immune responses.	Rashidian M, Keliher EJ, Bilate AM, Duarte JN, Wojtkiewicz GR, Jacobsen JT, Cragnolini J, Swee LK, Victora GD, Weissleder R, Ploegh HL	Proceedings of the National Academy of Sciences of the United States of America	25902531	Proc Natl Acad Sci U S A	2015 May 12	https://www.ncbi.nlm.nih.gov/pubmed/25902531
How lamina-associated polypeptide 1 (LAP1) activates Torsin.	Sosa BA, Demircioglu FE, Chen JZ, Ingram J, Ploegh HL, Schwartz TU	eLife	25149450	Elife	2014 Aug 22	https://www.ncbi.nlm.nih.gov/pubmed/25149450
Intracellular expression of camelid single-domain antibodies specific for influenza virus nucleoprotein uncovers distinct features of its nuclear localization.	Ashour J, Schmidt FI, Hanke L, Cragnolini J, Cavallari M, Altenburg A, Brewer R, Ingram J, Shoemaker C, Ploegh HL	Journal of virology	25540369	J Virol	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25540369
Structurally Defined αMHC-II Nanobody-Drug Conjugates: A Therapeutic and Imaging System for B-Cell Lymphoma.	Fang T, Duarte JN, Ling J, Li Z, Guzman JS, Ploegh HL	Angewandte Chemie (International ed. in English)	26840214	Angew Chem Int Ed Engl	2016 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/26840214
Generation of Immunity against Pathogens via Single-Domain Antibody-Antigen Constructs.	Duarte JN, Cragnolini JJ, Swee LK, Bilate AM, Bader J, Ingram JR, Rashidfarrokhi A, Fang T, Schiepers A, Hanke L, Ploegh HL	Journal of immunology (Baltimore, Md. : 1950)	27821668	J Immunol	2016 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/27821668
In vitro AMPylation Assays Using Purified, Recombinant Proteins.	Truttmann MC, Ploegh HL	Bio-protocol	29170749	Bio Protoc	2017 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/29170749
Predicting the response to CTLA-4 blockade by longitudinal noninvasive monitoring of CD8 T cells.	Rashidian M, Ingram JR, Dougan M, Dongre A, Whang KA, LeGall C, Cragnolini JJ, Bierie B, Gostissa M, Gorman J, Grotenbreg GM, Bhan A, Weinberg RA, Ploegh HL	The Journal of experimental medicine	28666979	J Exp Med	2017 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/28666979
Anti-CTLA-4 therapy requires an Fc domain for efficacy.	Ingram JR, Blomberg OS, Rashidian M, Ali L, Garforth S, Fedorov E, Fedorov AA, Bonanno JB, Le Gall C, Crowley S, Espinosa C, Biary T, Keliher EJ, Weissleder R, Almo SC, Dougan SK, Ploegh HL, Dougan M	Proceedings of the National Academy of Sciences of the United States of America	29581255	Proc Natl Acad Sci U S A	2018 Apr 10	https://www.ncbi.nlm.nih.gov/pubmed/29581255
Targeted antigen delivery by an anti-class II MHC VHH elicits focused αMUC1(Tn) immunity.	Fang T, Van Elssen CHMJ, Duarte JN, Guzman JS, Chahal JS, Ling J, Ploegh HL	Chemical science	28970938	Chem Sci	2017 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/28970938
Antigen-specific B-cell receptor sensitizes B cells to infection by influenza virus.	Dougan SK, Ashour J, Karssemeijer RA, Popp MW, Avalos AM, Barisa M, Altenburg AF, Ingram JR, Cragnolini JJ, Guo C, Alt FW, Jaenisch R, Ploegh HL	Nature	24141948	Nature	2013 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/24141948
Crystal structure of a substrate-engaged SecY protein-translocation channel.	Li L, Park E, Ling J, Ingram J, Ploegh H, Rapoport TA	Nature	26950603	Nature	2016 Mar 17	https://www.ncbi.nlm.nih.gov/pubmed/26950603
HypE-specific nanobodies as tools to modulate HypE-mediated target AMPylation.	Truttmann MC, Wu Q, Stiegeler S, Duarte JN, Ingram J, Ploegh HL	The Journal of biological chemistry	25678711	J Biol Chem	2015 Apr 3	https://www.ncbi.nlm.nih.gov/pubmed/25678711
Phenotypic lentivirus screens to identify functional single domain antibodies.	Schmidt FI, Hanke L, Morin B, Brewer R, Brusic V, Whelan SP, Ploegh HL	Nature microbiology	27573105	Nat Microbiol	2016 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/27573105
Noninvasive Imaging of Human Immune Responses in a Human Xenograft Model of Graft-Versus-Host Disease.	Van Elssen CHMJ, Rashidian M, Vrbanac V, Wucherpfennig KW, Habre ZE, Sticht J, Freund C, Jacobsen JT, Cragnolini J, Ingram J, Plaisier L, Spierings E, Tager AM, Ploegh HL	Journal of nuclear medicine : official publication, Society of Nuclear Medicine	28209904	J Nucl Med	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28209904
One-step enzymatic modification of the cell surface redirects cellular cytotoxicity and parasite tropism.	Swee LK, Lourido S, Bell GW, Ingram JR, Ploegh HL	ACS chemical biology	25360987	ACS Chem Biol	2015 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/25360987
Rapid and Direct VHH and Target Identification by Staphylococcal Surface Display Libraries.	Cavallari M	International journal of molecular sciences	28704956	Int J Mol Sci	2017 Jul 12	https://www.ncbi.nlm.nih.gov/pubmed/28704956
PD-L1 is an activation-independent marker of brown adipocytes.	Ingram JR, Dougan M, Rashidian M, Knoll M, Keliher EJ, Garrett S, Garforth S, Blomberg OS, Espinosa C, Bhan A, Almo SC, Weissleder R, Lodish H, Dougan SK, Ploegh HL	Nature communications	28935898	Nat Commun	2017 Sep 21	https://www.ncbi.nlm.nih.gov/pubmed/28935898
rAMPing Up Stress Signaling: Protein AMPylation in Metazoans.	Truttmann MC, Ploegh HL	Trends in cell biology	28433487	Trends Cell Biol	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28433487
Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication.	Hanke L, Schmidt FI, Knockenhauer KE, Morin B, Whelan SP, Schwartz TU, Ploegh HL	EMBO reports	28396572	EMBO Rep	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28396572
Fluorophore-Conjugated Holliday Junctions for Generating Super-Bright Antibodies and Antibody Fragments.	Li Z, Theile CS, Chen GY, Bilate AM, Duarte JN, Avalos AM, Fang T, Barberena R, Sato S, Ploegh HL	Angewandte Chemie (International ed. in English)	26252716	Angew Chem Int Ed Engl	2015 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/26252716
Posttranscriptional Regulation of Glycoprotein Quality Control in the Endoplasmic Reticulum Is Controlled by the E2 Ub-Conjugating Enzyme UBC6e.	Hagiwara M, Ling J, Koenig PA, Ploegh HL	Molecular cell	27570074	Mol Cell	2016 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/27570074
The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment.	Hanke L, Knockenhauer KE, Brewer RC, van Diest E, Schmidt FI, Schwartz TU, Ploegh HL	mBio	27965447	mBio	2016 Dec 13	https://www.ncbi.nlm.nih.gov/pubmed/27965447
Rapid capture and labeling of cells on single domain antibodies-functionalized flow cell.	Chen GY, Li Z, Duarte JN, Esteban A, Cheloha RW, Theile CS, Fink GR, Ploegh HL	Biosensors & bioelectronics	27816596	Biosens Bioelectron	2017 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/27816596
Engineered red blood cells as carriers for systemic delivery of a wide array of functional probes.	Shi J, Kundrat L, Pishesha N, Bilate A, Theile C, Maruyama T, Dougan SK, Ploegh HL, Lodish HF	Proceedings of the National Academy of Sciences of the United States of America	24982154	Proc Natl Acad Sci U S A	2014 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/24982154
Enhanced Cell Capture on Functionalized Graphene Oxide Nanosheets through Oxygen Clustering.	Bardhan NM, Kumar PV, Li Z, Ploegh HL, Grossman JC, Belcher AM, Chen GY	ACS nano	28085249	ACS Nano	2017 Feb 28	https://www.ncbi.nlm.nih.gov/pubmed/28085249
Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.	Burg JS, Ingram JR, Venkatakrishnan AJ, Jude KM, Dukkipati A, Feinberg EN, Angelini A, Waghray D, Dror RO, Ploegh HL, Garcia KC	Science (New York, N.Y.)	25745166	Science	2015 Mar 6	https://www.ncbi.nlm.nih.gov/pubmed/25745166
Production of unnaturally linked chimeric proteins using a combination of sortase-catalyzed transpeptidation and click chemistry.	Witte MD, Theile CS, Wu T, Guimaraes CP, Blom AE, Ploegh HL	Nature protocols	23989675	Nat Protoc	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23989675
The use of (18)F-2-fluorodeoxyglucose (FDG) to label antibody fragments for immuno-PET of pancreatic cancer.	Rashidian M, Keliher E, Dougan M, Juras PK, Cavallari M, Wojtkiewicz GR, Jacobsen J, Edens JG, Tas JM, Victora G, Weissleder R, Ploegh H	ACS central science	26955657	ACS Cent Sci	2015 Jun 24	https://www.ncbi.nlm.nih.gov/pubmed/26955657
Enzyme-Mediated Modification of Single-Domain Antibodies for Imaging Modalities with Different Characteristics.	Rashidian M, Wang L, Edens JG, Jacobsen JT, Hossain I, Wang Q, Victora GD, Vasdev N, Ploegh H, Liang SH	Angewandte Chemie (International ed. in English)	26630549	Angew Chem Int Ed Engl	2016 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/26630549
Structures of TorsinA and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia.	Demircioglu FE, Sosa BA, Ingram J, Ploegh HL, Schwartz TU	eLife	27490483	Elife	2016 Aug 4	https://www.ncbi.nlm.nih.gov/pubmed/27490483
Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas.	Dongre A, Rashidian M, Reinhardt F, Bagnato A, Keckesova Z, Ploegh HL, Weinberg RA	Cancer research	28428275	Cancer Res	2017 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/28428275
Localized CD47 blockade enhances immunotherapy for murine melanoma.	Ingram JR, Blomberg OS, Sockolosky JT, Ali L, Schmidt FI, Pishesha N, Espinosa C, Dougan SK, Garcia KC, Ploegh HL, Dougan M	Proceedings of the National Academy of Sciences of the United States of America	28874561	Proc Natl Acad Sci U S A	2017 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/28874561
Tissue-specific emergence of regulatory and intraepithelial T cells from a clonal T cell precursor.	Bilate AM, Bousbaine D, Mesin L, Agudelo M, Leube J, Kratzert A, Dougan SK, Victora GD, Ploegh HL	Science immunology	28783695	Sci Immunol	2016 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/28783695
Graphene Oxide Nanosheets Modified with Single-Domain Antibodies for Rapid and Efficient Capture of Cells.	Chen GY, Li Z, Theile CS, Bardhan NM, Kumar PV, Duarte JN, Maruyama T, Rashidfarrokh A, Belcher AM, Ploegh HL	Chemistry (Weinheim an der Bergstrasse, Germany)	26472062	Chemistry	2015 Nov 23	https://www.ncbi.nlm.nih.gov/pubmed/26472062
Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa.	Murray JL, Kwon T, Marcotte EM, Whiteley M	mBio	26507235	mBio	2015 Oct 27	https://www.ncbi.nlm.nih.gov/pubmed/26507235
UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry.	Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS	Analytical chemistry	26938041	Anal Chem	2016 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/26938041
Modes of interaction between individuals dominate the topologies of real world networks.	Lee I, Kim E, Marcotte EM	PloS one	25793969	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/25793969
Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains.	Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM	Journal of proteome research	24742327	J Proteome Res	2014 May 2	https://www.ncbi.nlm.nih.gov/pubmed/24742327
A self-assembling lanthanide molecular nanoparticle for optical imaging.	Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, Jones RA	Dalton transactions (Cambridge, England : 2003)	25512085	Dalton Trans	2015 Feb 14	https://www.ncbi.nlm.nih.gov/pubmed/25512085
Towards Consensus Gene Ages.	Liebeskind BJ, McWhite CD, Marcotte EM	Genome biology and evolution	27259914	Genome Biol Evol	2016 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/27259914
Efforts to make and apply humanized yeast.	Laurent JM, Young JH, Kachroo AH, Marcotte EM	Briefings in functional genomics	26462863	Brief Funct Genomics	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26462863
Systematic comparison of variant calling pipelines using gold standard personal exome variants.	Hwang S, Kim E, Lee I, Marcotte EM	Scientific reports	26639839	Sci Rep	2015 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/26639839
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness.	Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE	Nature chemical biology	24487692	Nat Chem Biol	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24487692
2,2'-Bipyridine and hydrazide containing peptides for cyclization and complex quaternary structural control.	Hernandez ET, Rogelio Escamilla P, Kwon SY, Partridge J, McVeigh M, Rivera S, Reuther JF, Anslyn EV	New journal of chemistry = Nouveau journal de chimie	30386131	New J Chem	2018 Jun 7	https://www.ncbi.nlm.nih.gov/pubmed/30386131
Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer.	Young JH, Peyton M, Seok Kim H, McMillan E, Minna JD, White MA, Marcotte EM	Bioinformatics (Oxford, England)	26755624	Bioinformatics	2016 May 1	https://www.ncbi.nlm.nih.gov/pubmed/26755624
Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing.	Hernandez ET, Swaminathan J, Marcotte EM, Anslyn EV	New journal of chemistry = Nouveau journal de chimie	28983186	New J Chem	2017 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/28983186
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses.	Vogel C, Marcotte EM	Nature reviews. Genetics	22411467	Nat Rev Genet	2012 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/22411467
Statistical approach to protein quantification.	Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Bühlmann P	Molecular & cellular proteomics : MCP	24255132	Mol Cell Proteomics	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24255132
The proteomic response to mutants of the Escherichia coli RNA degradosome.	Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C	Molecular bioSystems	23403814	Mol Biosyst	2013 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/23403814
A census of human soluble protein complexes.	Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A	Cell	22939629	Cell	2012 Aug 31	https://www.ncbi.nlm.nih.gov/pubmed/22939629
The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot.	Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW	PLoS biology	25710520	PLoS Biol	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25710520
A theoretical justification for single molecule peptide sequencing.	Swaminathan J, Boulgakov AA, Marcotte EM	PLoS computational biology	25714988	PLoS Comput Biol	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25714988
Improved Xanthone Synthesis, Stepwise Chemical Redox Cycling.	Bachman JL, Escamilla PR, Boley AJ, Pavlich CI, Anslyn EV	Organic letters	30582707	Org Lett	2019 Jan 4	https://www.ncbi.nlm.nih.gov/pubmed/30582707
Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications.	Jones RA, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Yang X, Schipper D, Hall JW, DePue LJ, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, Brown KA	Faraday discussions	25284181	Faraday Discuss	2014	https://www.ncbi.nlm.nih.gov/pubmed/25284181
Proteomic identification of monoclonal antibodies from serum.	Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM	Analytical chemistry	24684310	Anal Chem	2014 May 20	https://www.ncbi.nlm.nih.gov/pubmed/24684310
Long-term neural and physiological phenotyping of a single human.	Poldrack RA, Laumann TO, Koyejo O, Gregory B, Hover A, Chen MY, Gorgolewski KJ, Luci J, Joo SJ, Boyd RL, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, Gordon E, Snyder AZ, Adeyemo B, Petersen SE, Glahn DC, Reese Mckay D, Curran JE, Göring HH, Carless MA, Blangero J, Dougherty R, Leemans A, Handwerker DA, Frick L, Marcotte EM, Mumford JA	Nature communications	26648521	Nat Commun	2015 Dec 9	https://www.ncbi.nlm.nih.gov/pubmed/26648521
Sperm is epigenetically programmed to regulate gene transcription in embryos.	Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen GE, Erkek S, Kwon T, Marcotte EM, Zegerman P, Bradshaw CR, Peters AH, Gurdon JB, Jullien J	Genome research	27034506	Genome Res	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27034506
The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.	Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, University of Washington Center for Mendelian Genomics, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB	Nature genetics	27158779	Nat Genet	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27158779
Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access.	Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV	Organic letters	31825225	Org Lett	2020 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/31825225
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway.	Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM	eLife	28661399	Elife	2017 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/28661399
Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development.	Mallam AL, Marcotte EM	Cell systems	28544880	Cell Syst	2017 May 24	https://www.ncbi.nlm.nih.gov/pubmed/28544880
A proteomic survey of widespread protein aggregation in yeast.	O'Connell JD, Tsechansky M, Royal A, Boutz DR, Ellington AD, Marcotte EM	Molecular bioSystems	24488121	Mol Biosyst	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24488121
A highly parallel strategy for storage of digital information in living cells.	Akhmetov A, Ellington AD, Marcotte EM	BMC biotechnology	30333005	BMC Biotechnol	2018 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/30333005
Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9.	Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM	Bio-protocol	29770349	Bio Protoc	2018 Mar 20	https://www.ncbi.nlm.nih.gov/pubmed/29770349
Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus.	Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R	Nature	29320479	Nature	2018 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/29320479
Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.	Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO	PLoS computational biology	26275208	PLoS Comput Biol	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26275208
Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function.	Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB	Journal of cell science	29180514	J Cell Sci	2018 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/29180514
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity.	Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM	Science (New York, N.Y.)	25999509	Science	2015 May 22	https://www.ncbi.nlm.nih.gov/pubmed/25999509
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates.	Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I	Nucleic acids research	26527726	Nucleic Acids Res	2016 Jan 4	https://www.ncbi.nlm.nih.gov/pubmed/26527726
Classification of Single Particles from Human Cell Extract Reveals Distinct Structures.	Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW	Cell reports	29972786	Cell Rep	2018 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/29972786
Photography Coupled with Self-Propagating Chemical Cascades: Differentiation and Quantitation of G- and V-Nerve Agent Mimics via Chromaticity.	Sun X, Boulgakov AA, Smith LN, Metola P, Marcotte EM, Anslyn EV	ACS central science	30062113	ACS Cent Sci	2018 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/30062113
Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.	Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A	Data in brief	26870755	Data Brief	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26870755
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes.	Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K	Cell reports	31665645	Cell Rep	2019 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/31665645
A liquid-like organelle at the root of motile ciliopathy.	Huizar RL, Lee C, Boulgakov AA, Horani A, Tu F, Marcotte EM, Brody SL, Wallingford JB	eLife	30561330	Elife	2018 Dec 18	https://www.ncbi.nlm.nih.gov/pubmed/30561330
Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures.	Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM	Nature biotechnology	30346938	Nat Biotechnol	2018 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/30346938
HumanNet v2: human gene networks for disease research.	Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I	Nucleic acids research	30418591	Nucleic Acids Res	2019 Jan 8	https://www.ncbi.nlm.nih.gov/pubmed/30418591
The Many Nuanced Evolutionary Consequences of Duplicated Genes.	Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO	Molecular biology and evolution	30428072	Mol Biol Evol	2019 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/30428072
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.	Drew K, Müller CL, Bonneau R, Marcotte EM	PLoS computational biology	29023445	PLoS Comput Biol	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/29023445
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes.	Drew K, Lee C, Huizar RL, Tu F, Borgeson B, McWhite CD, Ma Y, Wallingford JB, Marcotte EM	Molecular systems biology	28596423	Mol Syst Biol	2017 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/28596423
An efficient methodology to introduce o-(aminomethyl)phenyl-boronic acids into peptides: alkylation of secondary amines.	Hernandez ET, Kolesnichenko IV, Reuther JF, Anslyn EV	New journal of chemistry = Nouveau journal de chimie	28649175	New J Chem	2017 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/28649175
Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection.	Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ	Nature microbiology	28924191	Nat Microbiol	2017 Nov	https://www.ncbi.nlm.nih.gov/pubmed/28924191
Applications of comparative evolution to human disease genetics.	McWhite CD, Liebeskind BJ, Marcotte EM	Current opinion in genetics & development	26338499	Curr Opin Genet Dev	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26338499
Panorama of ancient metazoan macromolecular complexes.	Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A	Nature	26344197	Nature	2015 Sep 17	https://www.ncbi.nlm.nih.gov/pubmed/26344197
Bringing Microscopy-By-Sequencing into View.	Boulgakov AA, Ellington AD, Marcotte EM	Trends in biotechnology	31416630	Trends Biotechnol	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/31416630
Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities.	Wang X, Pan T	PLoS genetics	26709516	PLoS Genet	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26709516
Modifications and functional genomics of human transfer RNA.	Pan T	Cell research	29463900	Cell Res	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29463900
Adaptive translation as a mechanism of stress response and adaptation.	Pan T	Annual review of genetics	23988117	Annu Rev Genet	2013	https://www.ncbi.nlm.nih.gov/pubmed/23988117
Codon optimality controls differential mRNA translation during amino acid starvation.	Saikia M, Wang X, Mao Y, Wan J, Pan T, Qian SB	RNA (New York, N.Y.)	27613579	RNA	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/27613579
Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures.	Schwartz MH, Pan T	Nucleic acids research	26657639	Nucleic Acids Res	2016 Jan 8	https://www.ncbi.nlm.nih.gov/pubmed/26657639
Determining the fidelity of tRNA aminoacylation via microarrays.	Schwartz MH, Pan T	Methods (San Diego, Calif.)	27639882	Methods	2017 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/27639882
N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding.	Zhou KI, Parisien M, Dai Q, Liu N, Diatchenko L, Sachleben JR, Pan T	Journal of molecular biology	26343757	J Mol Biol	2016 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/26343757
Selective Enzymatic Demethylation of N(2) ,N(2) -Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing.	Dai Q, Zheng G, Schwartz MH, Clark WC, Pan T	Angewandte Chemie (International ed. in English)	28371071	Angew Chem Int Ed Engl	2017 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/28371071
Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis.	Wang X, Pan T	Advances in nutrition (Bethesda, Md.)	27422514	Adv Nutr	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/27422514
Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli.	Schwartz MH, Waldbauer JR, Zhang L, Pan T	Nucleic acids research	27672035	Nucleic Acids Res	2016 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/27672035
tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ.	Schwartz MH, Pan T	Microbial ecology	28070678	Microb Ecol	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28070678
tRNA base methylation identification and quantification via high-throughput sequencing.	Clark WC, Evans ME, Dominissini D, Zheng G, Pan T	RNA (New York, N.Y.)	27613580	RNA	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/27613580
Efficient and quantitative high-throughput tRNA sequencing.	Zheng G, Qin Y, Clark WC, Dai Q, Yi C, He C, Lambowitz AM, Pan T	Nature methods	26214130	Nat Methods	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/26214130
Misacylation of tRNA with methionine in Saccharomyces cerevisiae.	Wiltrout E, Goodenbour JM, Fréchin M, Pan T	Nucleic acids research	22941646	Nucleic Acids Res	2012 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/22941646
Diversity of human tRNA genes from the 1000-genomes project.	Parisien M, Wang X, Pan T	RNA biology	24448271	RNA Biol	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24448271
Function and origin of mistranslation in distinct cellular contexts.	Schwartz MH, Pan T	Critical reviews in biochemistry and molecular biology	28075177	Crit Rev Biochem Mol Biol	2017 Apr	https://www.ncbi.nlm.nih.gov/pubmed/28075177
Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair.	Sun L, Gomes AC, He W, Zhou H, Wang X, Pan DW, Schimmel P, Pan T, Yang XL	Journal of the American Chemical Society	27622773	J Am Chem Soc	2016 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/27622773
A dual fluorescent reporter for the investigation of methionine mistranslation in live cells.	Gomes AC, Kordala AJ, Strack R, Wang X, Geslain R, Delaney K, Clark WC, Keenan R, Pan T	RNA (New York, N.Y.)	26729921	RNA	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26729921
Interaction of tRNA with MEK2 in pancreatic cancer cells.	Wang X, Chow CR, Ebine K, Lee J, Rosner MR, Pan T, Munshi HG	Scientific reports	27301426	Sci Rep	2016 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/27301426
My adventure in tRNA biology, so far.	Pan T	RNA (New York, N.Y.)	25780201	RNA	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25780201
The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove.	Fry MY, Saladi SM, Clemons WM Jr	Protein science : a publication of the Protein Society	33620121	Protein Sci	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/33620121
Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes.	Fry MY, Saladi SM, Cunha A, Clemons WM Jr	Traffic (Copenhagen, Denmark)	34288289	Traffic	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/34288289
Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni.	Jang KS, Sweredoski MJ, Graham RL, Hess S, Clemons WM Jr	Journal of proteomics	24382552	J Proteomics	2014 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/24382552
Improving membrane protein expression by optimizing integration efficiency.	Niesen MJM, Marshall SS, Miller TF 3rd, Clemons WM Jr	The Journal of biological chemistry	28918393	J Biol Chem	2017 Nov 24	https://www.ncbi.nlm.nih.gov/pubmed/28918393
Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3.	Fry MY, Najdrová V, Maggiolo AO, Saladi SM, Doležal P, Clemons WM Jr	Nature structural & molecular biology	35851188	Nat Struct Mol Biol	2022 Aug	https://www.ncbi.nlm.nih.gov/pubmed/35851188
Chemoenzymatic syntheses of water-soluble lipid I fluorescent probes.	Mitachi K, Siricilla S, Klaic L, Clemons WM Jr, Kurosu M	Tetrahedron letters	26190869	Tetrahedron Lett	2015 Jun 3	https://www.ncbi.nlm.nih.gov/pubmed/26190869
Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2.	Lin KF, Fry MY, Saladi SM, Clemons WM Jr	The Journal of biological chemistry	33610544	J Biol Chem	2021 Jan-Jun	https://www.ncbi.nlm.nih.gov/pubmed/33610544
A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency.	Marshall SS, Niesen MJM, Müller A, Tiemann K, Saladi SM, Galimidi RP, Zhang B, Clemons WM Jr, Miller TF 3rd	Cell reports	27524616	Cell Rep	2016 Aug 23	https://www.ncbi.nlm.nih.gov/pubmed/27524616
A statistical model for improved membrane protein expression using sequence-derived features.	Saladi SM, Javed N, Müller A, Clemons WM Jr	The Journal of biological chemistry	29378850	J Biol Chem	2018 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/29378850
A cationic cysteine-hydrazide as an enrichment tool for the mass spectrometric characterization of bacterial free oligosaccharides.	Jang KS, Nani RR, Kalli A, Levin S, Müller A, Hess S, Reisman SE, Clemons WM Jr	Analytical and bioanalytical chemistry	26100547	Anal Bioanal Chem	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26100547
Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis.	Barlow AN, Manu MS, Saladi SM, Tarr PT, Yadav Y, Thinn AMM, Zhu Y, Laganowsky AD, Clemons WM Jr, Ramasamy S	The Journal of biological chemistry	37100288	J Biol Chem	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/37100288
Negative selection of self-reactive chicken B cells requires B cell receptor signaling and is independent of the bursal microenvironment.	Davani D, Pancer Z, Cheroutre H, Ratcliffe MJ	Journal of immunology (Baltimore, Md. : 1950)	24516196	J Immunol	2014 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/24516196
Following the fate of one insulin-reactive CD4 T cell: conversion into Teffs and Tregs in the periphery controls diabetes in NOD mice.	Fousteri G, Jasinski J, Dave A, Nakayama M, Pagni P, Lambolez F, Juntti T, Sarikonda G, Cheng Y, Croft M, Cheroutre H, Eisenbarth G, von Herrath M	Diabetes	22403296	Diabetes	2012 May	https://www.ncbi.nlm.nih.gov/pubmed/22403296
The checkpoint for agonist selection precedes conventional selection in human thymus.	Verstichel G, Vermijlen D, Martens L, Goetgeluk G, Brouwer M, Thiault N, Van Caeneghem Y, De Munter S, Weening K, Bonte S, Leclercq G, Taghon T, Kerre T, Saeys Y, Van Dorpe J, Cheroutre H, Vandekerckhove B	Science immunology	28783686	Sci Immunol	2017 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/28783686
Reverse-correlation analysis of navigation dynamics in Drosophila larva using optogenetics.	Hernandez-Nunez L, Belina J, Klein M, Si G, Claus L, Carlson JR, Samuel AD	eLife	25942453	Elife	2015 May 5	https://www.ncbi.nlm.nih.gov/pubmed/25942453
Integration of Plasticity Mechanisms within a Single Sensory Neuron of C. elegans Actuates a Memory.	Hawk JD, Calvo AC, Liu P, Almoril-Porras A, Aljobeh A, Torruella-Suárez ML, Ren I, Cook N, Greenwood J, Luo L, Wang ZW, Samuel ADT, Colón-Ramos DA	Neuron	29307713	Neuron	2018 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/29307713
Structured Odorant Response Patterns across a Complete Olfactory Receptor Neuron Population.	Si G, Kanwal JK, Hu Y, Tabone CJ, Baron J, Berck M, Vignoud G, Samuel ADT	Neuron	30683545	Neuron	2019 Mar 6	https://www.ncbi.nlm.nih.gov/pubmed/30683545
An extrasynaptic GABAergic signal modulates a pattern of forward movement in Caenorhabditis elegans.	Shen Y, Wen Q, Liu H, Zhong C, Qin Y, Harris G, Kawano T, Wu M, Xu T, Samuel AD, Zhang Y	eLife	27138642	Elife	2016 May 3	https://www.ncbi.nlm.nih.gov/pubmed/27138642
The wiring diagram of a glomerular olfactory system.	Berck ME, Khandelwal A, Claus L, Hernandez-Nunez L, Si G, Tabone CJ, Li F, Truman JW, Fetter RD, Louis M, Samuel AD, Cardona A	eLife	27177418	Elife	2016 May 13	https://www.ncbi.nlm.nih.gov/pubmed/27177418
Two alternating motor programs drive navigation in Drosophila larva.	Lahiri S, Shen K, Klein M, Tang A, Kane E, Gershow M, Garrity P, Samuel AD	PloS one	21858019	PLoS One	2011	https://www.ncbi.nlm.nih.gov/pubmed/21858019
Sensorimotor structure of Drosophila larva phototaxis.	Kane EA, Gershow M, Afonso B, Larderet I, Klein M, Carter AR, de Bivort BL, Sprecher SG, Samuel AD	Proceedings of the National Academy of Sciences of the United States of America	24043822	Proc Natl Acad Sci U S A	2013 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/24043822
Contrasting responses within a single neuron class enable sex-specific attraction in Caenorhabditis elegans.	Narayan A, Venkatachalam V, Durak O, Reilly DK, Bose N, Schroeder FC, Samuel AD, Srinivasan J, Sternberg PW	Proceedings of the National Academy of Sciences of the United States of America	26903633	Proc Natl Acad Sci U S A	2016 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/26903633
Controlling airborne cues to study small animal navigation.	Gershow M, Berck M, Mathew D, Luo L, Kane EA, Carlson JR, Samuel AD	Nature methods	22245808	Nat Methods	2012 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/22245808
The Ionotropic Receptors IR21a and IR25a mediate cool sensing in Drosophila.	Ni L, Klein M, Svec KV, Budelli G, Chang EC, Ferrer AJ, Benton R, Samuel AD, Garrity PA	eLife	27126188	Elife	2016 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/27126188
Distinct combinations of variant ionotropic glutamate receptors mediate thermosensation and hygrosensation in Drosophila.	Knecht ZA, Silbering AF, Ni L, Klein M, Budelli G, Bell R, Abuin L, Ferrer AJ, Samuel AD, Benton R, Garrity PA	eLife	27656904	Elife	2016 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/27656904
Pan-neuronal imaging in roaming Caenorhabditis elegans.	Venkatachalam V, Ji N, Wang X, Clark C, Mitchell JK, Klein M, Tabone CJ, Florman J, Ji H, Greenwood J, Chisholm AD, Srinivasan J, Alkema M, Zhen M, Samuel AD	Proceedings of the National Academy of Sciences of the United States of America	26711989	Proc Natl Acad Sci U S A	2016 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/26711989
Functional diversity among sensory receptors in a Drosophila olfactory circuit.	Mathew D, Martelli C, Kelley-Swift E, Brusalis C, Gershow M, Samuel AD, Emonet T, Carlson JR	Proceedings of the National Academy of Sciences of the United States of America	23690583	Proc Natl Acad Sci U S A	2013 Jun 4	https://www.ncbi.nlm.nih.gov/pubmed/23690583
Imaging whole nervous systems: insights into behavior from worms to fish.	Calarco JA, Samuel ADT	Nature methods	30573822	Nat Methods	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30573822
The power and promise of applying genomics to honey bee health.	Grozinger CM, Robinson GE	Current opinion in insect science	26273565	Curr Opin Insect Sci	2015 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/26273565
General strategy for biodetection in high ionic strength solutions using transistor-based nanoelectronic sensors.	Gao N, Zhou W, Jiang X, Hong G, Fu TM, Lieber CM	Nano letters	25664395	Nano Lett	2015 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/25664395
Long term stability of nanowire nanoelectronics in physiological environments.	Zhou W, Dai X, Fu TM, Xie C, Liu J, Lieber CM	Nano letters	24479700	Nano Lett	2014 Mar 12	https://www.ncbi.nlm.nih.gov/pubmed/24479700
Multifunctional three-dimensional macroporous nanoelectronic networks for smart materials.	Liu J, Xie C, Dai X, Jin L, Zhou W, Lieber CM	Proceedings of the National Academy of Sciences of the United States of America	23569270	Proc Natl Acad Sci U S A	2013 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/23569270
Nano-Bioelectronics.	Zhang A, Lieber CM	Chemical reviews	26691648	Chem Rev	2016 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/26691648
Flexible electrical recording from cells using nanowire transistor arrays.	Cohen-Karni T, Timko BP, Weiss LE, Lieber CM	Proceedings of the National Academy of Sciences of the United States of America	19365078	Proc Natl Acad Sci U S A	2009 May 5	https://www.ncbi.nlm.nih.gov/pubmed/19365078
Syringe-injectable electronics.	Liu J, Fu TM, Cheng Z, Hong G, Zhou T, Jin L, Duvvuri M, Jiang Z, Kruskal P, Xie C, Suo Z, Fang Y, Lieber CM	Nature nanotechnology	26053995	Nat Nanotechnol	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26053995
Three-dimensional mapping and regulation of action potential propagation in nanoelectronics-innervated tissues.	Dai X, Zhou W, Gao T, Liu J, Lieber CM	Nature nanotechnology	27347837	Nat Nanotechnol	2016 Sep	https://www.ncbi.nlm.nih.gov/pubmed/27347837
Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.	Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK	Nature biotechnology	27347757	Nat Biotechnol	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27347757
Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.	Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK	Nature biotechnology	24108092	Nat Biotechnol	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24108092
Improving CRISPR-Cas nuclease specificity using truncated guide RNAs.	Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK	Nature biotechnology	24463574	Nat Biotechnol	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24463574
Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.	Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R	Cell	24360274	Cell	2013 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/24360274
Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma.	Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N	Cancer discovery	27231123	Cancer Discov	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/27231123
Hypoxia drives transient site-specific copy gain and drug-resistant gene expression.	Black JC, Atabakhsh E, Kim J, Biette KM, Van Rechem C, Ladd B, Burrowes PD, Donado C, Mattoo H, Kleinstiver BP, Song B, Andriani G, Joung JK, Iliopoulos O, Montagna C, Pillai S, Getz G, Whetstine JR	Genes & development	25995187	Genes Dev	2015 May 15	https://www.ncbi.nlm.nih.gov/pubmed/25995187
Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq.	Lazzarotto CR, Nguyen NT, Tang X, Malagon-Lopez J, Guo JA, Aryee MJ, Joung JK, Tsai SQ	Nature protocols	30341435	Nat Protoc	2018 Nov	https://www.ncbi.nlm.nih.gov/pubmed/30341435
Nodal patterning without Lefty inhibitory feedback is functional but fragile.	Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC, Reyon D, Tsai SQ, Joung JK, Schier AF	eLife	29215332	Elife	2017 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/29215332
Functional analysis of Collagen 17a1: A genetic modifier of junctional epidermolysis bullosa in mice.	Sproule TJ, Wilpan RY, Low BE, Silva KA, Reyon D, Joung JK, Wiles MV, Roopenian DC, Sundberg JP	PloS one	37796769	PLoS One	2023	https://www.ncbi.nlm.nih.gov/pubmed/37796769
In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.	Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK	Nucleic acids research	23945932	Nucleic Acids Res	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23945932
Locus-specific editing of histone modifications at endogenous enhancers.	Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE	Nature biotechnology	24013198	Nat Biotechnol	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/24013198
Zinc-finger nucleases for somatic gene therapy: the next frontier.	Rahman SH, Maeder ML, Joung JK, Cathomen T	Human gene therapy	21631241	Hum Gene Ther	2011 Aug	https://www.ncbi.nlm.nih.gov/pubmed/21631241
Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition.	Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, Joung JK	Nature biotechnology	26524662	Nat Biotechnol	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26524662
Genome Editing in Human Cells Using CRISPR/Cas Nucleases.	Wyvekens N, Tsai SQ, Joung JK	Current protocols in molecular biology	26423589	Curr Protoc Mol Biol	2015 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/26423589
CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.	Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK	Nature methods	28459458	Nat Methods	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28459458
Efficient CRISPR/Cas9-mediated editing of trinucleotide repeat expansion in myotonic dystrophy patient-derived iPS and myogenic cells.	Dastidar S, Ardui S, Singh K, Majumdar D, Nair N, Fu Y, Reyon D, Samara E, Gerli MFM, Klein AF, De Schrijver W, Tipanee J, Seneca S, Tulalamba W, Wang H, Chai YC, In't Veld P, Furling D, Tedesco FS, Vermeesch JR, Joung JK, Chuah MK, VandenDriessche T	Nucleic acids research	29947794	Nucleic Acids Res	2018 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/29947794
Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.	Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A	Nature genetics	25822089	Nat Genet	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25822089
CRISPR-Cas systems for editing, regulating and targeting genomes.	Sander JD, Joung JK	Nature biotechnology	24584096	Nat Biotechnol	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24584096
Continuous directed evolution of DNA-binding proteins to improve TALEN specificity.	Hubbard BP, Badran AH, Zuris JA, Guilinger JP, Davis KM, Chen L, Tsai SQ, Sander JD, Joung JK, Liu DR	Nature methods	26258293	Nat Methods	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26258293
TALENs: a widely applicable technology for targeted genome editing.	Joung JK, Sander JD	Nature reviews. Molecular cell biology	23169466	Nat Rev Mol Cell Biol	2013 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23169466
High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.	Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD	Nature biotechnology	23792628	Nat Biotechnol	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23792628
Induction of stable drug resistance in human breast cancer cells using a combinatorial zinc finger transcription factor library.	Lee J, Hirsh AS, Wittner BS, Maeder ML, Singavarapu R, Lang M, Janarthanan S, McDermott U, Yajnik V, Ramaswamy S, Joung JK, Sgroi DC	PloS one	21818254	PLoS One	2011	https://www.ncbi.nlm.nih.gov/pubmed/21818254
Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing.	Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK	Nature biotechnology	24770325	Nat Biotechnol	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24770325
Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq.	Malinin NL, Lee G, Lazzarotto CR, Li Y, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Iafrate AJ, Le LP, Aryee MJ, Joung JK, Tsai SQ	Nature protocols	34773119	Nat Protoc	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34773119
IκB kinase β (IKBKB) mutations in lymphomas that constitutively activate canonical nuclear factor κB (NFκB) signaling.	Kai X, Chellappa V, Donado C, Reyon D, Sekigami Y, Ataca D, Louissaint A, Mattoo H, Joung JK, Pillai S	The Journal of biological chemistry	25107905	J Biol Chem	2014 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/25107905
Context influences on TALE-DNA binding revealed by quantitative profiling.	Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML	Nature communications	26067805	Nat Commun	2015 Jun 11	https://www.ncbi.nlm.nih.gov/pubmed/26067805
Engineered CRISPR-Cas9 nucleases with altered PAM specificities.	Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK	Nature	26098369	Nature	2015 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/26098369
High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects.	Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK	Nature	26735016	Nature	2016 Jan 28	https://www.ncbi.nlm.nih.gov/pubmed/26735016
Efficient genome editing in zebrafish using a CRISPR-Cas system.	Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK	Nature biotechnology	23360964	Nat Biotechnol	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23360964
Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage.	Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM	Genes & development	25184681	Genes Dev	2014 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/25184681
Camptothecin resistance is determined by the regulation of topoisomerase I degradation mediated by ubiquitin proteasome pathway.	Ando K, Shah AK, Sachdev V, Kleinstiver BP, Taylor-Parker J, Welch MM, Hu Y, Salgia R, White FM, Parvin JD, Ozonoff A, Rameh LE, Joung JK, Bharti AK	Oncotarget	28415827	Oncotarget	2017 Jul 4	https://www.ncbi.nlm.nih.gov/pubmed/28415827
Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases.	Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, Sander JD, Reyon D, Joung JK, Voytas DF	G3 (Bethesda, Md.)	23979943	G3 (Bethesda)	2013 Oct 3	https://www.ncbi.nlm.nih.gov/pubmed/23979943
Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity.	Guilinger JP, Pattanayak V, Reyon D, Tsai SQ, Sander JD, Joung JK, Liu DR	Nature methods	24531420	Nat Methods	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24531420
piggyBac transposase tools for genome engineering.	Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB Jr, Bushman FD, Sinn PL, Craig NL	Proceedings of the National Academy of Sciences of the United States of America	23723351	Proc Natl Acad Sci U S A	2013 Jun 18	https://www.ncbi.nlm.nih.gov/pubmed/23723351
CRISPR RNA-guided activation of endogenous human genes.	Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK	Nature methods	23892898	Nat Methods	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23892898
Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.	Tsai SQ, Joung JK	Nature reviews. Genetics	27087594	Nat Rev Genet	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/27087594
A zebrafish model of myelodysplastic syndrome produced through tet2 genomic editing.	Gjini E, Mansour MR, Sander JD, Moritz N, Nguyen AT, Kesarsing M, Gans E, He S, Chen S, Ko M, Kuang YY, Yang S, Zhou Y, Rodig S, Zon LI, Joung JK, Rao A, Look AT	Molecular and cellular biology	25512612	Mol Cell Biol	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25512612
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.	Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK	Nature biotechnology	25513782	Nat Biotechnol	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25513782
Novel synthetic Medea selfish genetic elements drive population replacement in Drosophila; a theoretical exploration of Medea-dependent population suppression.	Akbari OS, Chen CH, Marshall JM, Huang H, Antoshechkin I, Hay BA	ACS synthetic biology	23654248	ACS Synth Biol	2014 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/23654248
Inertial imaging with nanomechanical systems.	Hanay MS, Kelber SI, O'Connell CD, Mulvaney P, Sader JE, Roukes ML	Nature nanotechnology	25822931	Nat Nanotechnol	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25822931
Nanotools for neuroscience and brain activity mapping.	Alivisatos AP, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X	ACS nano	23514423	ACS Nano	2013 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/23514423
Vapor sensing characteristics of nanoelectromechanical chemical sensors functionalized using surface-initiated polymerization.	McCaig HC, Myers E, Lewis NS, Roukes ML	Nano letters	24922358	Nano Lett	2014 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/24922358
Single-protein nanomechanical mass spectrometry in real time.	Hanay MS, Kelber S, Naik AK, Chi D, Hentz S, Bullard EC, Colinet E, Duraffourg L, Roukes ML	Nature nanotechnology	22922541	Nat Nanotechnol	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22922541
Neutral particle mass spectrometry with nanomechanical systems.	Sage E, Brenac A, Alava T, Morel R, Dupré C, Hanay MS, Roukes ML, Duraffourg L, Masselon C, Hentz S	Nature communications	25753929	Nat Commun	2015 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/25753929
A National Network of Neurotechnology Centers for the BRAIN Initiative.	Alivisatos AP, Chun M, Church GM, Greenspan RJ, Roukes ML, Yuste R	Neuron	26481036	Neuron	2015 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/26481036
Frequency fluctuations in silicon nanoresonators.	Sansa M, Sage E, Bullard EC, Gély M, Alava T, Colinet E, Naik AK, Villanueva LG, Duraffourg L, Roukes ML, Jourdan G, Hentz S	Nature nanotechnology	26925826	Nat Nanotechnol	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/26925826
Neuroscience. The brain activity map.	Alivisatos AP, Chun M, Church GM, Deisseroth K, Donoghue JP, Greenspan RJ, McEuen PL, Roukes ML, Sejnowski TJ, Weiss PS, Yuste R	Science (New York, N.Y.)	23470729	Science	2013 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/23470729
The brain activity map project and the challenge of functional connectomics.	Alivisatos AP, Chun M, Church GM, Greenspan RJ, Roukes ML, Yuste R	Neuron	22726828	Neuron	2012 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/22726828
Patterned photostimulation via visible-wavelength photonic probes for deep brain optogenetics.	Segev E, Reimer J, Moreaux LC, Fowler TM, Chi D, Sacher WD, Lo M, Deisseroth K, Tolias AS, Faraon A, Roukes ML	Neurophotonics	27990451	Neurophotonics	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27990451
Spatiotemporal dynamics in large-scale cortical networks.	Higley MJ, Cardin JA	Current opinion in neurobiology	36115252	Curr Opin Neurobiol	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36115252
Spatiotemporally heterogeneous coordination of cholinergic and neocortical activity.	Lohani S, Moberly AH, Benisty H, Landa B, Jing M, Li Y, Higley MJ, Cardin JA	Nature neuroscience	36443609	Nat Neurosci	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36443609
Retrosplenial inputs drive diverse visual representations in the medial entorhinal cortex.	Dubanet O, Higley MJ	bioRxiv : the preprint server for biology	37873152	bioRxiv	2023 Oct 4	https://www.ncbi.nlm.nih.gov/pubmed/37873152
Developmental trajectory of cortical somatostatin interneuron function.	Wang A, Ferguson KA, Gupta J, Higley MJ, Cardin JA	bioRxiv : the preprint server for biology	38496673	bioRxiv	2024 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/38496673
Retrosplenial inputs drive visual representations in the medial entorhinal cortex.	Dubanet O, Higley MJ	Cell reports	38985682	Cell Rep	2024 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/38985682
The Cousa objective: a long-working distance air objective for multiphoton imaging in vivo.	Yu CH, Yu Y, Adsit LM, Chang JT, Barchini J, Moberly AH, Benisty H, Kim J, Young BK, Heng K, Farinella DM, Leikvoll A, Pavan R, Vistein R, Nanfito BR, Hildebrand DGC, Otero-Coronel S, Vaziri A, Goldberg JL, Ricci AJ, Fitzpatrick D, Cardin JA, Higley MJ, Smith GB, Kara P, Nielsen KJ, Smith IT, Smith SL	Nature methods	38129618	Nat Methods	2024 Jan	https://www.ncbi.nlm.nih.gov/pubmed/38129618
Rapid fluctuations in functional connectivity of cortical networks encode spontaneous behavior.	Benisty H, Barson D, Moberly AH, Lohani S, Tang L, Coifman RR, Crair MC, Mishne G, Cardin JA, Higley MJ	Nature neuroscience	38036743	Nat Neurosci	2024 Jan	https://www.ncbi.nlm.nih.gov/pubmed/38036743
Neuroscience thinks big (and collaboratively).	Kandel ER, Markram H, Matthews PM, Yuste R, Koch C	Nature reviews. Neuroscience	23958663	Nat Rev Neurosci	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23958663
Simultaneous imaging of neural activity in three dimensions.	Quirin S, Jackson J, Peterka DS, Yuste R	Frontiers in neural circuits	24772066	Front Neural Circuits	2014	https://www.ncbi.nlm.nih.gov/pubmed/24772066
Two-photon neuronal and astrocytic stimulation with azobenzene-based photoswitches.	Izquierdo-Serra M, Gascón-Moya M, Hirtz JJ, Pittolo S, Poskanzer KE, Ferrer È, Alibés R, Busqué F, Yuste R, Hernando J, Gorostiza P	Journal of the American Chemical Society	24857186	J Am Chem Soc	2014 Jun 18	https://www.ncbi.nlm.nih.gov/pubmed/24857186
Glial Calcium Waves are Triggered by Seizure Activity and Not Essential for Initiating Ictal Onset or Neurovascular Coupling.	Baird-Daniel E, Daniel AGS, Wenzel M, Li D, Liou JY, Laffont P, Zhao M, Yuste R, Ma H, Schwartz TH	Cerebral cortex (New York, N.Y. : 1991)	28369176	Cereb Cortex	2017 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/28369176
Acute Focal Seizures Start As Local Synchronizations of Neuronal Ensembles.	Wenzel M, Hamm JP, Peterka DS, Yuste R	The Journal of neuroscience : the official journal of the Society for Neuroscience	31427393	J Neurosci	2019 Oct 23	https://www.ncbi.nlm.nih.gov/pubmed/31427393
Genetic voltage indicators.	Bando Y, Grimm C, Cornejo VH, Yuste R	BMC biology	31514747	BMC Biol	2019 Sep 12	https://www.ncbi.nlm.nih.gov/pubmed/31514747
Role of inhibitory control in modulating focal seizure spread.	Liou JY, Ma H, Wenzel M, Zhao M, Baird-Daniel E, Smith EH, Daniel A, Emerson R, Yuste R, Schwartz TH, Schevon CA	Brain : a journal of neurology	29757347	Brain	2018 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/29757347
Holographic imaging and photostimulation of neural activity.	Yang W, Yuste R	Current opinion in neurobiology	29660600	Curr Opin Neurobiol	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29660600
Comparative Evaluation of Genetically Encoded Voltage Indicators.	Bando Y, Sakamoto M, Kim S, Ayzenshtat I, Yuste R	Cell reports	30650368	Cell Rep	2019 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/30650368
In vivo imaging of neural activity.	Yang W, Yuste R	Nature methods	28362436	Nat Methods	2017 Apr	https://www.ncbi.nlm.nih.gov/pubmed/28362436
Two-Color Volumetric Imaging of Neuronal Activity of Cortical Columns.	Han S, Yang W, Yuste R	Cell reports	31091458	Cell Rep	2019 May 14	https://www.ncbi.nlm.nih.gov/pubmed/31091458
VIP+ interneurons control neocortical activity across brain states.	Jackson J, Ayzenshtat I, Karnani MM, Yuste R	Journal of neurophysiology	26961109	J Neurophysiol	2016 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/26961109
Imprinting and recalling cortical ensembles.	Carrillo-Reid L, Yang W, Bando Y, Peterka DS, Yuste R	Science (New York, N.Y.)	27516599	Science	2016 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/27516599
Orientation Tuning Depends on Spatial Frequency in Mouse Visual Cortex.	Ayzenshtat I, Jackson J, Yuste R	eNeuro	27699210	eNeuro	2016 Sep-Oct	https://www.ncbi.nlm.nih.gov/pubmed/27699210
moco: Fast Motion Correction for Calcium Imaging.	Dubbs A, Guevara J, Yuste R	Frontiers in neuroinformatics	26909035	Front Neuroinform	2016	https://www.ncbi.nlm.nih.gov/pubmed/26909035
Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data.	Pnevmatikakis EA, Soudry D, Gao Y, Machado TA, Merel J, Pfau D, Reardon T, Mu Y, Lacefield C, Yang W, Ahrens M, Bruno R, Jessell TM, Peterka DS, Yuste R, Paninski L	Neuron	26774160	Neuron	2016 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/26774160
Controlling Visually Guided Behavior by Holographic Recalling of Cortical Ensembles.	Carrillo-Reid L, Han S, Yang W, Akrouh A, Yuste R	Cell	31257030	Cell	2019 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/31257030
The new century of the brain.	Yuste R, Church GM	Scientific American	24660326	Sci Am	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24660326
From the neuron doctrine to neural networks.	Yuste R	Nature reviews. Neuroscience	26152865	Nat Rev Neurosci	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26152865
Non-overlapping Neural Networks in Hydra vulgaris.	Dupre C, Yuste R	Current biology : CB	28366745	Curr Biol	2017 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/28366745
Reliable and Elastic Propagation of Cortical Seizures In Vivo.	Wenzel M, Hamm JP, Peterka DS, Yuste R	Cell reports	28658617	Cell Rep	2017 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/28658617
Light sheet theta microscopy for rapid high-resolution imaging of large biological samples.	Migliori B, Datta MS, Dupre C, Apak MC, Asano S, Gao R, Boyden ES, Hermanson O, Yuste R, Tomer R	BMC biology	29843722	BMC Biol	2018 May 29	https://www.ncbi.nlm.nih.gov/pubmed/29843722
Engineering a genetically-encoded SHG chromophore by electrostatic targeting to the membrane.	Jinno Y, Shoda K, Rial-Verde E, Yuste R, Miyawaki A, Tsutsui H	Frontiers in molecular neuroscience	25505870	Front Mol Neurosci	2014	https://www.ncbi.nlm.nih.gov/pubmed/25505870
Opening Holes in the Blanket of Inhibition: Localized Lateral Disinhibition by VIP Interneurons.	Karnani MM, Jackson J, Ayzenshtat I, Hamzehei Sichani A, Manoocheri K, Kim S, Yuste R	The Journal of neuroscience : the official journal of the Society for Neuroscience	27013676	J Neurosci	2016 Mar 23	https://www.ncbi.nlm.nih.gov/pubmed/27013676
Instantaneous three-dimensional sensing using spatial light modulator illumination with extended depth of field imaging.	Quirin S, Peterka DS, Yuste R	Optics express	23842387	Opt Express	2013 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/23842387
Altered Cortical Ensembles in Mouse Models of Schizophrenia.	Hamm JP, Peterka DS, Gogos JA, Yuste R	Neuron	28384469	Neuron	2017 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/28384469
A miniaturized multi-clamp CMOS amplifier for intracellular neural recording.	Shekar S, Jayant K, Rabadan MA, Tomer R, Yuste R, Shepard KL	Nature electronics	31850397	Nat Electron	2019 Aug	https://www.ncbi.nlm.nih.gov/pubmed/31850397
A blanket of inhibition: functional inferences from dense inhibitory connectivity.	Karnani MM, Agetsuma M, Yuste R	Current opinion in neurobiology	24440415	Curr Opin Neurobiol	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24440415
Overproduction of Neurons Is Correlated with Enhanced Cortical Ensembles and Increased Perceptual Discrimination.	Fang WQ, Yuste R	Cell reports	29020625	Cell Rep	2017 Oct 10	https://www.ncbi.nlm.nih.gov/pubmed/29020625
Neuronal photoactivation through second-harmonic near-infrared absorption by gold nanoparticles.	de Boer WDAM, Hirtz JJ, Capretti A, Gregorkiewicz T, Izquierdo-Serra M, Han S, Dupre C, Shymkiv Y, Yuste R	Light, science & applications	30534369	Light Sci Appl	2018	https://www.ncbi.nlm.nih.gov/pubmed/30534369
Spatial distribution of neurons innervated by chandelier cells.	Blazquez-Llorca L, Woodruff A, Inan M, Anderson SA, Yuste R, DeFelipe J, Merchan-Perez A	Brain structure & function	25056931	Brain Struct Funct	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25056931
Temporal dynamics in fMRI resting-state activity.	Yuste R, Fairhall AL	Proceedings of the National Academy of Sciences of the United States of America	25902550	Proc Natl Acad Sci U S A	2015 Apr 28	https://www.ncbi.nlm.nih.gov/pubmed/25902550
Parvalbumin-Positive Interneurons Regulate Neuronal Ensembles in Visual Cortex.	Agetsuma M, Hamm JP, Tao K, Fujisawa S, Yuste R	Cerebral cortex (New York, N.Y. : 1991)	29106504	Cereb Cortex	2018 May 1	https://www.ncbi.nlm.nih.gov/pubmed/29106504
Multi-scale approaches for high-speed imaging and analysis of large neural populations.	Friedrich J, Yang W, Soudry D, Mu Y, Ahrens MB, Yuste R, Peterka DS, Paninski L	PLoS computational biology	28771570	PLoS Comput Biol	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28771570
Imaging and Optically Manipulating Neuronal Ensembles.	Carrillo-Reid L, Yang W, Kang Miller JE, Peterka DS, Yuste R	Annual review of biophysics	28301770	Annu Rev Biophys	2017 May 22	https://www.ncbi.nlm.nih.gov/pubmed/28301770
Cortical Control of Spatial Resolution by VIP+ Interneurons.	Ayzenshtat I, Karnani MM, Jackson J, Yuste R	The Journal of neuroscience : the official journal of the Society for Neuroscience	27911754	J Neurosci	2016 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/27911754
Cooperative Subnetworks of Molecularly Similar Interneurons in Mouse Neocortex.	Karnani MM, Jackson J, Ayzenshtat I, Tucciarone J, Manoocheri K, Snider WG, Yuste R	Neuron	27021171	Neuron	2016 Apr 6	https://www.ncbi.nlm.nih.gov/pubmed/27021171
Simultaneous Multi-plane Imaging of Neural Circuits.	Yang W, Miller JE, Carrillo-Reid L, Pnevmatikakis E, Paninski L, Yuste R, Peterka DS	Neuron	26774159	Neuron	2016 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/26774159
Optical triggered seizures using a caged 4-Aminopyridine.	Zhao M, McGarry LM, Ma H, Harris S, Berwick J, Yuste R, Schwartz TH	Frontiers in neuroscience	25698919	Front Neurosci	2015	https://www.ncbi.nlm.nih.gov/pubmed/25698919
Neocortical activity is stimulus- and scale-invariant.	Karimipanah Y, Ma Z, Miller JK, Yuste R, Wessel R	PloS one	28489906	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28489906
Super-multiplex vibrational imaging.	Wei L, Chen Z, Shi L, Long R, Anzalone AV, Zhang L, Hu F, Yuste R, Cornish VW, Min W	Nature	28424513	Nature	2017 Apr 27	https://www.ncbi.nlm.nih.gov/pubmed/28424513
Simultaneous two-photon imaging and two-photon optogenetics of cortical circuits in three dimensions.	Yang W, Carrillo-Reid L, Bando Y, Peterka DS, Yuste R	eLife	29412138	Elife	2018 Feb 7	https://www.ncbi.nlm.nih.gov/pubmed/29412138
Two-Photon Optogenetic Mapping of Excitatory Synaptic Connectivity and Strength.	Izquierdo-Serra M, Hirtz JJ, Shababo B, Yuste R	iScience	30268510	iScience	2018 Oct 26	https://www.ncbi.nlm.nih.gov/pubmed/30268510
Brain maps at the nanoscale.	Yang W, Yuste R	Nature biotechnology	30872818	Nat Biotechnol	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30872818
Back to the Basics: Cnidarians Start to Fire.	Bosch TCG, Klimovich A, Domazet-Lošo T, Gründer S, Holstein TW, Jékely G, Miller DJ, Murillo-Rincon AP, Rentzsch F, Richards GS, Schröder K, Technau U, Yuste R	Trends in neurosciences	28041633	Trends Neurosci	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/28041633
Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy.	Quirin S, Vladimirov N, Yang CT, Peterka DS, Yuste R, Ahrens MB	Optics letters	26974063	Opt Lett	2016 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/26974063
Somatostatin Interneurons Control a Key Component of Mismatch Negativity in Mouse Visual Cortex.	Hamm JP, Yuste R	Cell reports	27396334	Cell Rep	2016 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/27396334
Reduced Repertoire of Cortical Microstates and Neuronal Ensembles in Medically Induced Loss of Consciousness.	Wenzel M, Han S, Smith EH, Hoel E, Greger B, House PA, Yuste R	Cell systems	31054810	Cell Syst	2019 May 22	https://www.ncbi.nlm.nih.gov/pubmed/31054810
Flexible Nanopipettes for Minimally Invasive Intracellular Electrophysiology In Vivo.	Jayant K, Wenzel M, Bando Y, Hamm JP, Mandriota N, Rabinowitz JH, Plante IJ, Owen JS, Sahin O, Shepard KL, Yuste R	Cell reports	30605681	Cell Rep	2019 Jan 2	https://www.ncbi.nlm.nih.gov/pubmed/30605681
Endogenous sequential cortical activity evoked by visual stimuli.	Carrillo-Reid L, Miller JE, Hamm JP, Jackson J, Yuste R	The Journal of neuroscience : the official journal of the Society for Neuroscience	26063915	J Neurosci	2015 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/26063915
Exploiting metabolic and antioxidant pathways to maintain vision in blinding disease.	Ramachandran PS, Song JY, Bennett J	The Journal of clinical investigation	25798615	J Clin Invest	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25798615
Plasticity of the human visual system after retinal gene therapy in patients with Leber's congenital amaurosis.	Ashtari M, Zhang H, Cook PA, Cyckowski LL, Shindler KS, Marshall KA, Aravand P, Vossough A, Gee JC, Maguire AM, Baker CI, Bennett J	Science translational medicine	26180100	Sci Transl Med	2015 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/26180100
Synthetic Adeno-Associated Viral Vector Efficiently Targets Mouse and Nonhuman Primate Retina In Vivo.	Carvalho LS, Xiao R, Wassmer SJ, Langsdorf A, Zinn E, Pacouret S, Shah S, Comander JI, Kim LA, Lim L, Vandenberghe LH	Human gene therapy	29325457	Hum Gene Ther	2018 Jul	https://www.ncbi.nlm.nih.gov/pubmed/29325457
Evaluation of Dose and Safety of AAV7m8 and AAV8BP2 in the Non-Human Primate Retina.	Ramachandran PS, Lee V, Wei Z, Song JY, Casal G, Cronin T, Willett K, Huckfeldt R, Morgan JI, Aleman TS, Maguire AM, Bennett J	Human gene therapy	27750461	Hum Gene Ther	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/27750461
Safety and durability of effect of contralateral-eye administration of AAV2 gene therapy in patients with childhood-onset blindness caused by RPE65 mutations: a follow-on phase 1 trial.	Bennett J, Wellman J, Marshall KA, McCague S, Ashtari M, DiStefano-Pappas J, Elci OU, Chung DC, Sun J, Wright JF, Cross DR, Aravand P, Cyckowski LL, Bennicelli JL, Mingozzi F, Auricchio A, Pierce EA, Ruggiero J, Leroy BP, Simonelli F, High KA, Maguire AM	Lancet (London, England)	27375040	Lancet	2016 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/27375040
Amelioration of Neurosensory Structure and Function in Animal and Cellular Models of a Congenital Blindness.	Song JY, Aravand P, Nikonov S, Leo L, Lyubarsky A, Bennicelli JL, Pan J, Wei Z, Shpylchak I, Herrera P, Bennett DJ, Commins N, Maguire AM, Pham J, den Hollander AI, Cremers FPM, Koenekoop RK, Roepman R, Nishina P, Zhou S, Pan W, Ying GS, Aleman TS, de Melo J, McNamara I, Sun J, Mills J, Bennett J	Molecular therapy : the journal of the American Society of Gene Therapy	29673930	Mol Ther	2018 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/29673930
Single stranded adeno-associated virus achieves efficient gene transfer to anterior segment in the mouse eye.	Wang L, Xiao R, Andres-Mateos E, Vandenberghe LH	PloS one	28763501	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28763501
Refining surgical techniques for efficient posterior semicircular canal gene delivery in the adult mammalian inner ear with minimal hearing loss.	Zhu J, Choi JW, Ishibashi Y, Isgrig K, Grati M, Bennett J, Chien W	Scientific reports	34552193	Sci Rep	2021 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/34552193
Immunology of AAV-Mediated Gene Transfer in the Eye.	Willett K, Bennett J	Frontiers in immunology	24009613	Front Immunol	2013	https://www.ncbi.nlm.nih.gov/pubmed/24009613
Progress in gene therapy for neurological disorders.	Simonato M, Bennett J, Boulis NM, Castro MG, Fink DJ, Goins WF, Gray SJ, Lowenstein PR, Vandenberghe LH, Wilson TJ, Wolfe JH, Glorioso JC	Nature reviews. Neurology	23609618	Nat Rev Neurol	2013 May	https://www.ncbi.nlm.nih.gov/pubmed/23609618
Disruption of CEP290 microtubule/membrane-binding domains causes retinal degeneration.	Drivas TG, Holzbaur EL, Bennett J	The Journal of clinical investigation	24051377	J Clin Invest	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24051377
Gene therapy restores auditory and vestibular function in a mouse model of Usher syndrome type 1c.	Pan B, Askew C, Galvin A, Heman-Ackah S, Asai Y, Indzhykulian AA, Jodelka FM, Hastings ML, Lentz JJ, Vandenberghe LH, Holt JR, Géléoc GS	Nature biotechnology	28165476	Nat Biotechnol	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28165476
Institutional Conflict of Interest.	Bennett J	JAMA ophthalmology	27583791	JAMA Ophthalmol	2016 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/27583791
Taking Stock of Retinal Gene Therapy: Looking Back and Moving Forward.	Bennett J	Molecular therapy : the journal of the American Society of Gene Therapy	28391961	Mol Ther	2017 May 3	https://www.ncbi.nlm.nih.gov/pubmed/28391961
Evaluating Efficiencies of Dual AAV Approaches for Retinal Targeting.	Carvalho LS, Turunen HT, Wassmer SJ, Luna-Velez MV, Xiao R, Bennett J, Vandenberghe LH	Frontiers in neuroscience	28943836	Front Neurosci	2017	https://www.ncbi.nlm.nih.gov/pubmed/28943836
Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65-mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial.	Russell S, Bennett J, Wellman JA, Chung DC, Yu ZF, Tillman A, Wittes J, Pappas J, Elci O, McCague S, Cross D, Marshall KA, Walshire J, Kehoe TL, Reichert H, Davis M, Raffini L, George LA, Hudson FP, Dingfield L, Zhu X, Haller JA, Sohn EH, Mahajan VB, Pfeifer W, Weckmann M, Johnson C, Gewaily D, Drack A, Stone E, Wachtel K, Simonelli F, Leroy BP, Wright JF, High KA, Maguire AM	Lancet (London, England)	28712537	Lancet	2017 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/28712537
Gene Therapy and Stem Cell Transplantation in Retinal Disease: The New Frontier.	MacLaren RE, Bennett J, Schwartz SD	Ophthalmology	27664291	Ophthalmology	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27664291
AAV8BP2 and AAV8 transduce the mammalian cochlear lateral wall and endolymphatic sac with high efficiency.	Isgrig K, Ishibashi Y, Lee HJ, Zhu J, Grati M, Bennett J, Griffith AJ, Roux I, Chien WW	Molecular therapy. Methods & clinical development	36034771	Mol Ther Methods Clin Dev	2022 Sep 8	https://www.ncbi.nlm.nih.gov/pubmed/36034771
Differential targeting of feline photoreceptors by recombinant adeno-associated viral vectors: implications for preclinical gene therapy trials.	Minella AL, Mowat FM, Willett KL, Sledge D, Bartoe JT, Bennett J, Petersen-Jones SM	Gene therapy	25056608	Gene Ther	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25056608
An Autogenously Regulated Expression System for Gene Therapeutic Ocular Applications.	Sochor MA, Vasireddy V, Drivas TG, Wojno A, Doung T, Shpylchak I, Bennicelli J, Chung D, Bennett J, Lewis M	Scientific reports	26597678	Sci Rep	2015 Nov 24	https://www.ncbi.nlm.nih.gov/pubmed/26597678
fMRI of retina-originated phosphenes experienced by patients with Leber congenital amaurosis.	Ashtari M, Cyckowski L, Yazdi A, Viands A, Marshall K, Bókkon I, Maguire A, Bennett J	PloS one	24465873	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24465873
AAV2.7m8 is a powerful viral vector for inner ear gene therapy.	Isgrig K, McDougald DS, Zhu J, Wang HJ, Bennett J, Chien WW	Nature communications	30683875	Nat Commun	2019 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/30683875
Exosome-associated AAV2 vector mediates robust gene delivery into the murine retina upon intravitreal injection.	Wassmer SJ, Carvalho LS, György B, Vandenberghe LH, Maguire CA	Scientific reports	28361998	Sci Rep	2017 Mar 31	https://www.ncbi.nlm.nih.gov/pubmed/28361998
Novel mobility test to assess functional vision in patients with inherited retinal dystrophies.	Chung DC, McCague S, Yu ZF, Thill S, DiStefano-Pappas J, Bennett J, Cross D, Marshall K, Wellman J, High KA	Clinical & experimental ophthalmology	28697537	Clin Exp Ophthalmol	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/28697537
The effect of noise correlations in populations of diversely tuned neurons.	Ecker AS, Berens P, Tolias AS, Bethge M	The Journal of neuroscience : the official journal of the Society for Neuroscience	21976512	J Neurosci	2011 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/21976512
Spike sorting for large, dense electrode arrays.	Rossant C, Kadir SN, Goodman DFM, Schulman J, Hunter MLD, Saleem AB, Grosmark A, Belluscio M, Denfield GH, Ecker AS, Tolias AS, Solomon S, Buzsaki G, Carandini M, Harris KD	Nature neuroscience	26974951	Nat Neurosci	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/26974951
State dependence of noise correlations in macaque primary visual cortex.	Ecker AS, Berens P, Cotton RJ, Subramaniyan M, Denfield GH, Cadwell CR, Smirnakis SM, Bethge M, Tolias AS	Neuron	24698278	Neuron	2014 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/24698278
Macaque monkeys perceive the flash lag illusion.	Subramaniyan M, Ecker AS, Berens P, Tolias AS	PloS one	23527024	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23527024
Three-dimensional mapping of microcircuit correlation structure.	Cotton RJ, Froudarakis E, Storer P, Saggau P, Tolias AS	Frontiers in neural circuits	24133414	Front Neural Circuits	2013	https://www.ncbi.nlm.nih.gov/pubmed/24133414
A neural basis of probabilistic computation in visual cortex.	Walker EY, Cotton RJ, Ma WJ, Tolias AS	Nature neuroscience	31873286	Nat Neurosci	2020 Jan	https://www.ncbi.nlm.nih.gov/pubmed/31873286
Developmental broadening of inhibitory sensory maps.	Quast KB, Ung K, Froudarakis E, Huang L, Herman I, Addison AP, Ortiz-Guzman J, Cordiner K, Saggau P, Tolias AS, Arenkiel BR	Nature neuroscience	28024159	Nat Neurosci	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/28024159
Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.	Berens P, Freeman J, Deneux T, Chenkov N, McColgan T, Speiser A, Macke JH, Turaga SC, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, Stone J, Rogerson LE, Sofroniew NJ, Reimer J, Froudarakis E, Euler T, Román Rosón M, Theis L, Tolias AS, Bethge M	PLoS computational biology	29782491	PLoS Comput Biol	2018 May	https://www.ncbi.nlm.nih.gov/pubmed/29782491
Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity-at Depth and in Real Time.	Moreaux LC, Yatsenko D, Sacher WD, Choi J, Lee C, Kubat NJ, Cotton RJ, Boyden ES, Lin MZ, Tian L, Tolias AS, Poon JKS, Shepard KL, Roukes ML	Neuron	33058767	Neuron	2020 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/33058767
Evaluating Public Health Interventions: 1. Examples, Definitions, and a Personal Note.	Spiegelman D	American journal of public health	26562122	Am J Public Health	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26562122
Evaluating Public Health Interventions: 3. The Two-Stage Design for Confounding Bias Reduction-Having Your Cake and Eating It Two.	Spiegelman D, Rivera-Rodriguez CL, Haneuse S	American journal of public health	27285260	Am J Public Health	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/27285260
Service readiness of health facilities in Bangladesh, Haiti, Kenya, Malawi, Namibia, Nepal, Rwanda, Senegal, Uganda and the United Republic of Tanzania.	Leslie HH, Spiegelman D, Zhou X, Kruk ME	Bulletin of the World Health Organization	29147054	Bull World Health Organ	2017 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/29147054
On the Analysis of Case-Control Studies in Cluster-correlated Data Settings.	Haneuse S, Rivera-Rodriguez C	Epidemiology (Cambridge, Mass.)	29068840	Epidemiology	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29068840
The effect of risk factor misclassification on the partial population attributable risk.	Wong BHW, Peskoe SB, Spiegelman D	Statistics in medicine	29333614	Stat Med	2018 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/29333614
Inverse probability weighted estimation of risk under representative interventions in observational studies.	Young JG, Logan RW, Robins JM, Hernán MA	Journal of the American Statistical Association	31564760	J Am Stat Assoc	2019	https://www.ncbi.nlm.nih.gov/pubmed/31564760
Coaching Intensity, Adherence to Essential Birth Practices, and Health Outcomes in the BetterBirth Trial in Uttar Pradesh, India.	Barnhart DA, Spiegelman D, Zigler CM, Kara N, Delaney MM, Kalita T, Maji P, Hirschhorn LR, Semrau KEA	Global health, science and practice	32127359	Glob Health Sci Pract	2020 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/32127359
The fidelity of implementation of recommended care for children with malaria by community health workers in Nigeria.	Adeoti O, Spiegelman D, Afonne C, Falade CO, Jegede AS, Oshiname FO, Gomes M, Ajayi IO	Implementation science : IS	32131852	Implement Sci	2020 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/32131852
Estimation in the Cox survival regression model with covariate measurement error and a changepoint.	Agami S, Zucker DM, Spiegelman D	Biometrical journal. Biometrische Zeitschrift	32003495	Biom J	2020 Sep	https://www.ncbi.nlm.nih.gov/pubmed/32003495
There is no impact of exposure measurement error on latency estimation in linear models.	Peskoe SB, Spiegelman D, Wang M	Statistics in medicine	30515870	Stat Med	2019 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/30515870
Multiple robust estimation of marginal structural mean models for unconstrained outcomes.	Babino L, Rotnitzky A, Robins J	Biometrics	30004573	Biometrics	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30004573
Spiegelman Responds.	Spiegelman D	American journal of public health	27153027	Am J Public Health	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27153027
Assessing Individual and Disseminated Effects in Network-Randomized Studies.	Buchanan AL, Vermund SH, Friedman SR, Spiegelman D	American journal of epidemiology	30052722	Am J Epidemiol	2018 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/30052722
A maximum likelihood approach to power calculations for stepped wedge designs of binary outcomes.	Zhou X, Liao X, Kunz LM, Normand ST, Wang M, Spiegelman D	Biostatistics (Oxford, England)	30084949	Biostatistics	2020 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/30084949
Optimizing the development and evaluation of complex interventions: lessons learned from the BetterBirth Program and associated trial.	Barnhart DA, Semrau KEA, Zigler CM, Molina RL, Delaney MM, Hirschhorn LR, Spiegelman D	Implementation science communications	32885188	Implement Sci Commun	2020	https://www.ncbi.nlm.nih.gov/pubmed/32885188
Structural, interpersonal, psychosocial, and behavioral risk factors for HIV acquisition among female bar workers in Dar es Salaam, Tanzania.	Barnhart DA, Harling G, Muya A, Ortblad KF, Mashasi I, Dambach P, Ulenga N, Mboggo E, Oldenburg CE, Bärnighausen TW, Spiegelman D	AIDS care	31079476	AIDS Care	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31079476
Exposure misclassification in propensity score-based time-to-event data analysis.	Yang Y, Wang M	Statistical methods in medical research	33826453	Stat Methods Med Res	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/33826453
Impact of the Affordable Care Act on Colorectal Cancer Outcomes: A Systematic Review.	Xu MR, Kelly AMB, Kushi LH, Reed ME, Koh HK, Spiegelman D	American journal of preventive medicine	32008799	Am J Prev Med	2020 Apr	https://www.ncbi.nlm.nih.gov/pubmed/32008799
Assessing the quality of tuberculosis care using routine surveillance data: a process evaluation employing the Zero TB Indicator Framework in Mongolia.	Saranjav A, Parisi C, Zhou X, Dorjnamjil K, Samdan T, Erdenebaatar S, Chuluun A, Dalkh T, Ganbaatar G, Brooks MB, Spiegelman D, Ganmaa D, Davis JL	BMJ open	35973702	BMJ Open	2022 Aug 16	https://www.ncbi.nlm.nih.gov/pubmed/35973702
How are qualitative methods used in implementation science research? A scoping review protocol.	Hagaman A, Rhodes EC, Nyhan K, Katague M, Schwartz A, Spiegelman D	JBI evidence synthesis	33323772	JBI Evid Synth	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33323772
"Cross-sectional" stepped wedge designs always reduce the required sample size when there is no time effect.	Zhou X, Liao X, Spiegelman D	Journal of clinical epidemiology	28093263	J Clin Epidemiol	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28093263
Evaluating Public Health Interventions: 4. The Nurses' Health Study and Methods for Eliminating Bias Attributable to Measurement Error and Misclassification.	Spiegelman D	American journal of public health	27509282	Am J Public Health	2016 Sep	https://www.ncbi.nlm.nih.gov/pubmed/27509282
Evaluating Public Health Interventions: 5. Causal Inference in Public Health Research-Do Sex, Race, and Biological Factors Cause Health Outcomes?	Glymour MM, Spiegelman D	American journal of public health	27854526	Am J Public Health	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27854526
Evaluating Public Health Interventions: 2. Stepping Up to Routine Public Health Evaluation With the Stepped Wedge Design.	Spiegelman D	American journal of public health	26885961	Am J Public Health	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26885961
Evaluating Public Health Interventions: 7. Let the Subject Matter Choose the Effect Measure: Ratio, Difference, or Something Else Entirely.	Spiegelman D, Khudyakov P, Wang M, Vanderweele TJ	American journal of public health	29161073	Am J Public Health	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29161073
Nepal Pioneer Worksite Intervention Study to lower cardio-metabolic risk factors: design and protocol.	Shrestha A, Tamrakar D, Karmacharya BM, Shrestha A, Shrestha R, Bhatta RD, Pyakurel P, Khudyakov P, Malik V, Mattei J, Spiegelman D	BMC cardiovascular disorders	30819098	BMC Cardiovasc Disord	2019 Feb 28	https://www.ncbi.nlm.nih.gov/pubmed/30819098
Augmented pseudo-likelihood estimation for two-phase studies.	Rivera-Rodriguez C, Haneuse S, Wang M, Spiegelman D	Statistical methods in medical research	30834815	Stat Methods Med Res	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30834815
On the analysis of two-phase designs in cluster-correlated data settings.	Rivera-Rodriguez C, Spiegelman D, Haneuse S	Statistics in medicine	31359448	Stat Med	2019 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/31359448
The Association of Cooking Fuel Use, Dietary Intake, and Blood Pressure among Rural Women in China.	Bellows AL, Spiegelman D, Du S, Jaacks LM	International journal of environmental research and public health	32751678	Int J Environ Res Public Health	2020 Jul 30	https://www.ncbi.nlm.nih.gov/pubmed/32751678
Worksite intervention study to prevent diabetes in Nepal: a randomised trial protocol.	Pyakurel P, Shrestha A, Karmacharya BM, Budhathoki SS, Chaudhari RK, Tamrakar D, Shrestha A, Karmacharya RM, Shrestha A, Sharma S, Sharma SK, Spiegelman D	Open heart	32847993	Open Heart	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32847993
Access of choice-disabled young women in Botswana to government structural support programmes: a cross-sectional study.	Cockcroft A, Marokoane N, Kgakole L, Tswetla N, Andersson N	AIDS care	29848044	AIDS Care	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29848044
Association of the US President's Emergency Plan for AIDS Relief's Funding With Prevention of Mother-to-Child Transmission of HIV in Kenya.	Barnhart DA, Tsikhutsu I, Kirui D, Sawe F, Muli J, Sugut W, Abboud N, Birx D, Hamm T, Coakley P, Hickey PW, Wolfman V, Lee E, Spiegelman D	JAMA network open	31517966	JAMA Netw Open	2019 Sep 4	https://www.ncbi.nlm.nih.gov/pubmed/31517966
Diet and Health - What Should We Eat ?	Shrestha A, Spiegelman D	Kathmandu University medical journal (KUMJ)	30353891	Kathmandu Univ Med J (KUMJ)	2017 Jul-Sept.	https://www.ncbi.nlm.nih.gov/pubmed/30353891
Comparison of HPV-16 and HPV-18 Genotyping and Cytological Testing as Triage Testing Within Human Papillomavirus-Based Screening in Mexico.	Torres-Ibarra L, Cuzick J, Lorincz AT, Spiegelman D, Lazcano-Ponce E, Franco EL, Moscicki AB, Mahmud SM, Wheeler CM, Rivera-Paredez B, Hernández-López R, León-Maldonado L, Salmerón J, FRIDA Study Group.	JAMA network open	31747033	JAMA Netw Open	2019 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/31747033
swdpwr: A SAS macro and an R package for power calculations in stepped wedge cluster randomized trials.	Chen J, Zhou X, Li F, Spiegelman D	Computer methods and programs in biomedicine	34818620	Comput Methods Programs Biomed	2022 Jan	https://www.ncbi.nlm.nih.gov/pubmed/34818620
Facilitators and barriers to healthy eating in a worksite cafeteria: a qualitative study.	Stern D, Blanco I, Olmos LA, Valdivia JJ, Shrestha A, Mattei J, Spiegelman D	BMC public health	34022846	BMC Public Health	2021 May 22	https://www.ncbi.nlm.nih.gov/pubmed/34022846
Drivers of healthy eating in a workplace in Nepal: a qualitative study.	Tamrakar D, Shrestha A, Rai A, Karmacharya BM, Malik V, Mattei J, Spiegelman D	BMJ open	32102804	BMJ Open	2020 Feb 25	https://www.ncbi.nlm.nih.gov/pubmed/32102804
Health system measurement: Harnessing machine learning to advance global health.	Leslie HH, Zhou X, Spiegelman D, Kruk ME	PloS one	30289935	PLoS One	2018	https://www.ncbi.nlm.nih.gov/pubmed/30289935
Partial Identification of the Average Treatment Effect Using Instrumental Variables: Review of Methods for Binary Instruments, Treatments, and Outcomes.	Swanson SA, Hernán MA, Miller M, Robins JM, Richardson TS	Journal of the American Statistical Association	31537952	J Am Stat Assoc	2018	https://www.ncbi.nlm.nih.gov/pubmed/31537952
Estimating the natural indirect effect and the mediation proportion via the product method.	Cheng C, Spiegelman D, Li F	BMC medical research methodology	34800985	BMC Med Res Methodol	2021 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/34800985
ANALYSIS OF "LEARN-AS-YOU-GO" (LAGO) STUDIES.	Nevo D, Lok JJ, Spiegelman D	Annals of statistics	35510045	Ann Stat	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/35510045
Impact of the Affordable Care Act on Colorectal Cancer Incidence and Mortality.	Lee C, Kushi LH, Reed ME, Eldridge EH, Lee JK, Zhang J, Spiegelman D	American journal of preventive medicine	34763959	Am J Prev Med	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/34763959
Facilitators and barriers to healthy eating in a worksite cafeteria: a qualitative study from Nepal.	Shrestha A, Pyakurel P, Shrestha A, Gautam R, Manandhar N, Rhodes E, Tamrakar D, Karmacharya BM, Malik V, Mattei J, Spiegelman D	Heart Asia	29225703	Heart Asia	2017	https://www.ncbi.nlm.nih.gov/pubmed/29225703
Prevalence estimation when disease status is verified only among test positives: Applications in HIV screening programs.	G Thomas E, B Peskoe S, Spiegelman D	Statistics in medicine	29230839	Stat Med	2018 Mar 30	https://www.ncbi.nlm.nih.gov/pubmed/29230839
Survival analysis with functions of mismeasured covariate histories: the case of chronic air pollution exposure in relation to mortality in the nurses' health study.	Liao X, Zhou X, Wang M, Hart JE, Laden F, Spiegelman D	Journal of the Royal Statistical Society. Series C, Applied statistics	29430064	J R Stat Soc Ser C Appl Stat	2018 Feb	https://www.ncbi.nlm.nih.gov/pubmed/29430064
Evaluating Public Health Interventions: 6. Modeling Ratios or Differences? Let the Data Tell Us.	Spiegelman D, VanderWeele TJ	American journal of public health	28590865	Am J Public Health	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28590865
Intra-Cluster Correlation Estimates for HIV-related Outcomes from Care and Treatment Clinics in Dar es Salaam, Tanzania.	Barnhart D, Hertzmark E, Liu E, Mungure E, Muya AN, Sando D, Chalamilla G, Ulenga N, Bärnighausen T, Fawzi W, Spiegelman D	Contemporary clinical trials communications	27766318	Contemp Clin Trials Commun	2016 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/27766318
Mediation analysis in the presence of continuous exposure measurement error.	Cheng C, Spiegelman D, Li F	Statistics in medicine	36869626	Stat Med	2023 May 20	https://www.ncbi.nlm.nih.gov/pubmed/36869626
Assessing Direct and Spillover Effects of Intervention Packages in Network-randomized Studies.	Buchanan AL, Hernández-Ramírez RU, Lok JJ, Vermund SH, Friedman SR, Forastiere L, Spiegelman D	Epidemiology (Cambridge, Mass.)	38709023	Epidemiology	2024 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/38709023
Overall, Direct, Spillover, and Composite Effects of Components of a Peer-Driven Intervention Package on Injection Risk Behavior Among People Who Inject Drugs in the HPTN 037 Study.	Hernández-Ramírez RU, Spiegelman D, Lok JJ, Forastiere L, Friedman SR, Latkin CA, Vermund SH, Buchanan AL	AIDS and behavior	37932493	AIDS Behav	2024 Jan	https://www.ncbi.nlm.nih.gov/pubmed/37932493
Dietary interventions to prevent and manage diabetes in worksite settings: a meta-analysis.	Shrestha A, Karmacharya BM, Khudyakov P, Weber MB, Spiegelman D	Journal of occupational health	29187673	J Occup Health	2018 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/29187673
Evaluating Public Health Interventions: 8. Causal Inference for Time-Invariant Interventions.	Spiegelman D, Zhou X	American journal of public health	30024804	Am J Public Health	2018 Sep	https://www.ncbi.nlm.nih.gov/pubmed/30024804
Interpretation of the Individual Effect Under Treatment Spillover.	Crawford FW, Morozova O, Buchanan AL, Spiegelman D	American journal of epidemiology	31094425	Am J Epidemiol	2019 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/31094425
Spiegelman and Zhou Respond.	Spiegelman D, Zhou X	American journal of public health	30726133	Am J Public Health	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30726133
Estimation and Inference for the Mediation Proportion.	Nevo D, Liao X, Spiegelman D	The international journal of biostatistics	28930628	Int J Biostat	2017 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/28930628
A note on "Design and analysis of stepped wedge cluster randomized trials".	Liao X, Zhou X, Spiegelman D	Contemporary clinical trials	26394003	Contemp Clin Trials	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26394003
Assessing Direct and Spillover Effects of Intervention Packages in Network-Randomized Studies.	Buchanan AL, Hernández-Ramírez RU, Lok JJ, Vermund SH, Friedman SR, Forastiere L, Spiegelman D	medRxiv : the preprint server for health sciences	38352598	medRxiv	2024 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/38352598
Father-son chats: inheriting stress through sperm RNA.	Sharma U, Rando OJ	Cell metabolism	24896534	Cell Metab	2014 Jun 3	https://www.ncbi.nlm.nih.gov/pubmed/24896534
Regulation of X-linked gene expression during early mouse development by Rlim.	Wang F, Shin J, Shea JM, Yu J, Bošković A, Byron M, Zhu X, Shalek AK, Regev A, Lawrence JB, Torres EM, Zhu LJ, Rando OJ, Bach I	eLife	27642011	Elife	2016 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/27642011
Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome.	Shea JM, Serra RW, Carone BR, Shulha HP, Kucukural A, Ziller MJ, Vallaster MP, Gu H, Tapper AR, Gardner PD, Meissner A, Garber M, Rando OJ	Developmental cell	26702833	Dev Cell	2015 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/26702833
Deficient spermiogenesis in mice lacking Rlim.	Wang F, Gervasi MG, Bošković A, Sun F, Rinaldi VD, Yu J, Wallingford MC, Tourzani DA, Mager J, Zhu LJ, Rando OJ, Visconti PE, Strittmatter L, Bach I	eLife	33620316	Elife	2021 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/33620316
Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm.	Sharma U, Sun F, Conine CC, Reichholf B, Kukreja S, Herzog VA, Ameres SL, Rando OJ	Developmental cell	30057273	Dev Cell	2018 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/30057273
Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs.	Wang F, McCannell KN, Bošković A, Zhu X, Shin J, Yu J, Gallant J, Byron M, Lawrence JB, Zhu LJ, Jones SN, Rando OJ, Fazzio TG, Bach I	Cell reports	29281819	Cell Rep	2017 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/29281819
Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation.	Chou HJ, Donnard E, Gustafsson HT, Garber M, Rando OJ	Molecular cell	29198561	Mol Cell	2017 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/29198561
I'm eating for two: parental dietary effects on offspring metabolism.	Rando OJ, Simmons RA	Cell	25815988	Cell	2015 Mar 26	https://www.ncbi.nlm.nih.gov/pubmed/25815988
Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.	Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, Song L, Carone BR, Ricci EP, Li XZ, Fauquier L, Moore MJ, Sullivan R, Mello CC, Garber M, Rando OJ	Science (New York, N.Y.)	26721685	Science	2016 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/26721685
Small RNAs Gained during Epididymal Transit of Sperm Are Essential for Embryonic Development in Mice.	Conine CC, Sun F, Song L, Rivera-Pérez JA, Rando OJ	Developmental cell	30057276	Dev Cell	2018 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/30057276
Identification of chemicals that mimic transcriptional changes associated with autism, brain aging and neurodegeneration.	Pearson BL, Simon JM, McCoy ES, Salazar G, Fragola G, Zylka MJ	Nature communications	27029645	Nat Commun	2016 Mar 31	https://www.ncbi.nlm.nih.gov/pubmed/27029645
Single-cell transcriptomic analysis of mouse neocortical development.	Loo L, Simon JM, Xing L, McCoy ES, Niehaus JK, Guo J, Anton ES, Zylka MJ	Nature communications	30635555	Nat Commun	2019 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/30635555
High-throughput screening and classification of chemicals and their effects on neuronal gene expression using RASL-seq.	Simon JM, Paranjape SR, Wolter JM, Salazar G, Zylka MJ	Scientific reports	30872602	Sci Rep	2019 Mar 14	https://www.ncbi.nlm.nih.gov/pubmed/30872602
Toward a conceptual framework for early brain and behavior development in autism.	Piven J, Elison JT, Zylka MJ	Molecular psychiatry	28937691	Mol Psychiatry	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28937691
Chd8 haploinsufficiency impairs early brain development and protein homeostasis later in life.	Jiménez JA, Ptacek TS, Tuttle AH, Schmid RS, Moy SS, Simon JM, Zylka MJ	Molecular autism	33023670	Mol Autism	2020 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/33023670
An Autism-Linked Mutation Disables Phosphorylation Control of UBE3A.	Yi JJ, Berrios J, Newbern JM, Snider WD, Philpot BD, Hahn KM, Zylka MJ	Cell	26255772	Cell	2015 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/26255772
The Troubled Touch of Autism.	Tuttle AH, Bartsch VB, Zylka MJ	Cell	27419865	Cell	2016 Jul 14	https://www.ncbi.nlm.nih.gov/pubmed/27419865
Choice of vehicle affects pyraclostrobin toxicity in mice.	Tuttle AH, Salazar G, Cooper EM, Stapleton HM, Zylka MJ	Chemosphere	30497033	Chemosphere	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30497033
Enhanced Nociception in Angelman Syndrome Model Mice.	McCoy ES, Taylor-Blake B, Aita M, Simon JM, Philpot BD, Zylka MJ	The Journal of neuroscience : the official journal of the Society for Neuroscience	28931574	J Neurosci	2017 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/28931574
Deletion of Topoisomerase 1 in excitatory neurons causes genomic instability and early onset neurodegeneration.	Fragola G, Mabb AM, Taylor-Blake B, Niehaus JK, Chronister WD, Mao H, Simon JM, Yuan H, Li Z, McConnell MJ, Zylka MJ	Nature communications	32327659	Nat Commun	2020 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/32327659
A deep neural network to assess spontaneous pain from mouse facial expressions.	Tuttle AH, Molinaro MJ, Jethwa JF, Sotocinal SG, Prieto JC, Styner MA, Mogil JS, Zylka MJ	Molecular pain	29546805	Mol Pain	2018 Jan-Dec	https://www.ncbi.nlm.nih.gov/pubmed/29546805
Gene length matters in neurons.	Zylka MJ, Simon JM, Philpot BD	Neuron	25905808	Neuron	2015 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/25905808
Maternal Ube3a Loss Disrupts Sleep Homeostasis But Leaves Circadian Rhythmicity Largely Intact.	Ehlen JC, Jones KA, Pinckney L, Gray CL, Burette S, Weinberg RJ, Evans JA, Brager AJ, Zylka MJ, Paul KN, Philpot BD, DeBruyne JP	The Journal of neuroscience : the official journal of the Society for Neuroscience	26446213	J Neurosci	2015 Oct 7	https://www.ncbi.nlm.nih.gov/pubmed/26446213
Topoisomerase 1 inhibition reversibly impairs synaptic function.	Mabb AM, Kullmann PH, Twomey MA, Miriyala J, Philpot BD, Zylka MJ	Proceedings of the National Academy of Sciences of the United States of America	25404338	Proc Natl Acad Sci U S A	2014 Dec 2	https://www.ncbi.nlm.nih.gov/pubmed/25404338
Zylka et al. reply.	Zylka MJ, Philpot BD, King IF	Nature	25100485	Nature	2014 Aug 7	https://www.ncbi.nlm.nih.gov/pubmed/25100485
The autism-linked UBE3A T485A mutant E3 ubiquitin ligase activates the Wnt/β-catenin pathway by inhibiting the proteasome.	Yi JJ, Paranjape SR, Walker MP, Choudhury R, Wolter JM, Fragola G, Emanuele MJ, Major MB, Zylka MJ	The Journal of biological chemistry	28559284	J Biol Chem	2017 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/28559284
lncRNA-Induced Spread of Polycomb Controlled by Genome Architecture, RNA Abundance, and CpG Island DNA.	Schertzer MD, Braceros KCA, Starmer J, Cherney RE, Lee DM, Salazar G, Justice M, Bischoff SR, Cowley DO, Ariel P, Zylka MJ, Dowen JM, Magnuson T, Calabrese JM	Molecular cell	31256989	Mol Cell	2019 Aug 8	https://www.ncbi.nlm.nih.gov/pubmed/31256989
Topoisomerase 1 Regulates Gene Expression in Neurons through Cleavage Complex-Dependent and -Independent Mechanisms.	Mabb AM, Simon JM, King IF, Lee HM, An LK, Philpot BD, Zylka MJ	PloS one	27231886	PLoS One	2016	https://www.ncbi.nlm.nih.gov/pubmed/27231886
Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes.	Multhaup ML, Seldin MM, Jaffe AE, Lei X, Kirchner H, Mondal P, Li Y, Rodriguez V, Drong A, Hussain M, Lindgren C, McCarthy M, Näslund E, Zierath JR, Wong GW, Feinberg AP	Cell metabolism	25565211	Cell Metab	2015 Jan 6	https://www.ncbi.nlm.nih.gov/pubmed/25565211
Improving Metabolic Health Through Precision Dietetics in Mice.	Barrington WT, Wulfridge P, Wells AE, Rojas CM, Howe SYF, Perry A, Hua K, Pellizzon MA, Hansen KD, Voy BH, Bennett BJ, Pomp D, Feinberg AP, Threadgill DW	Genetics	29158425	Genetics	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29158425
Potential energy landscapes identify the information-theoretic nature of the epigenome.	Jenkinson G, Pujadas E, Goutsias J, Feinberg AP	Nature genetics	28346445	Nat Genet	2017 May	https://www.ncbi.nlm.nih.gov/pubmed/28346445
DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis.	Kular L, Liu Y, Ruhrmann S, Zheleznyakova G, Marabita F, Gomez-Cabrero D, James T, Ewing E, Lindén M, Górnikiewicz B, Aeinehband S, Stridh P, Link J, Andlauer TFM, Gasperi C, Wiendl H, Zipp F, Gold R, Tackenberg B, Weber F, Hemmer B, Strauch K, Heilmann-Heimbach S, Rawal R, Schminke U, Schmidt CO, Kacprowski T, Franke A, Laudes M, Dilthey AT, Celius EG, Søndergaard HB, Tegnér J, Harbo HF, Oturai AB, Olafsson S, Eggertsson HP, Halldorsson BV, Hjaltason H, Olafsson E, Jonsdottir I, Stefansson K, Olsson T, Piehl F, Ekström TJ, Kockum I, Feinberg AP, Jagodic M	Nature communications	29921915	Nat Commun	2018 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/29921915
Determinants of Adiposity Rebound Timing in Children.	Ip EH, Marshall SA, Saldana S, Skelton JA, Suerken CK, Arcury TA, Quandt SA	The Journal of pediatrics	28242030	J Pediatr	2017 May	https://www.ncbi.nlm.nih.gov/pubmed/28242030
The dawn of virtual cell biology.	Freddolino PL, Tavazoie S	Cell	22817888	Cell	2012 Jul 20	https://www.ncbi.nlm.nih.gov/pubmed/22817888
Bacterial adaptation through loss of function.	Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S	PLoS genetics	23874220	PLoS Genet	2013	https://www.ncbi.nlm.nih.gov/pubmed/23874220
Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry.	Freddolino L, Yang J, Momen-Roknabadi A, Tavazoie S	eLife	29620524	Elife	2018 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/29620524
Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.	Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S	Genome biology	22182234	Genome Biol	2011 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/22182234
Principles of Systems Biology, No. 29.		Cell systems	29792823	Cell Syst	2018 May 23	https://www.ncbi.nlm.nih.gov/pubmed/29792823
Genetic origins of lactase persistence and the spread of pastoralism in Africa.	Ranciaro A, Campbell MC, Hirbo JB, Ko WY, Froment A, Anagnostou P, Kotze MJ, Ibrahim M, Nyambo T, Omar SA, Tishkoff SA	American journal of human genetics	24630847	Am J Hum Genet	2014 Apr 3	https://www.ncbi.nlm.nih.gov/pubmed/24630847
The genetic prehistory of southern Africa.	Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, Güldemann T, Kure B, Mpoloka SW, Nakagawa H, Naumann C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante CD, Berger B, Tishkoff SA, Henn BM, Stoneking M, Reich D, Pakendorf B	Nature communications	23072811	Nat Commun	2012	https://www.ncbi.nlm.nih.gov/pubmed/23072811
Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.	Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF	Genome research	26888264	Genome Res	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26888264
Regulation of amyloid-β dynamics and pathology by the circadian clock.	Kress GJ, Liao F, Dimitry J, Cedeno MR, FitzGerald GA, Holtzman DM, Musiek ES	The Journal of experimental medicine	29382695	J Exp Med	2018 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/29382695
Extraction and Analysis of Pan-metabolome Polar Metabolites by Ultra Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS).	Malik DM, Rhoades S, Weljie A	Bio-protocol	29623284	Bio Protoc	2018 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/29623284
Structural diversity and African origin of the 17q21.31 inversion polymorphism.	Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE	Nature genetics	22751100	Nat Genet	2012 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/22751100
SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it.	Lachance J, Tishkoff SA	BioEssays : news and reviews in molecular, cellular and developmental biology	23836388	Bioessays	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23836388
Genome-wide patterns of population structure and admixture in West Africans and African Americans.	Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM, Wambebe C, Tishkoff SA, Bustamante CD	Proceedings of the National Academy of Sciences of the United States of America	20080753	Proc Natl Acad Sci U S A	2010 Jan 12	https://www.ncbi.nlm.nih.gov/pubmed/20080753
Shorter telomere length in Europeans than in Africans due to polygenetic adaptation.	Hansen ME, Hunt SC, Stone RC, Horvath K, Herbig U, Ranciaro A, Hirbo J, Beggs W, Reiner AP, Wilson JG, Kimura M, De Vivo I, Chen MM, Kark JD, Levy D, Nyambo T, Tishkoff SA, Aviv A	Human molecular genetics	26936823	Hum Mol Genet	2016 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/26936823
A Locus at 5q33.3 Confers Resistance to Tuberculosis in Highly Susceptible Individuals.	Sobota RS, Stein CM, Kodaman N, Scheinfeldt LB, Maro I, Wieland-Alter W, Igo RP Jr, Magohe A, Malone LL, Chervenak K, Hall NB, Modongo C, Zetola N, Matee M, Joloba M, Froment A, Nyambo TB, Moore JH, Scott WK, Lahey T, Boom WH, von Reyn CF, Tishkoff SA, Sirugo G, Williams SM	American journal of human genetics	26942285	Am J Hum Genet	2016 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/26942285
Going global by adapting local: A review of recent human adaptation.	Fan S, Hansen ME, Lo Y, Tishkoff SA	Science (New York, N.Y.)	27846491	Science	2016 Oct 7	https://www.ncbi.nlm.nih.gov/pubmed/27846491
Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.	Hsieh P, Veeramah KR, Lachance J, Tishkoff SA, Wall JD, Hammer MF, Gutenkunst RN	Genome research	26888263	Genome Res	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26888263
Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.	Lachance J, Tishkoff SA	American journal of human genetics	25279983	Am J Hum Genet	2014 Oct 2	https://www.ncbi.nlm.nih.gov/pubmed/25279983
The peopling of the African continent and the diaspora into the new world.	Campbell MC, Hirbo JB, Townsend JP, Tishkoff SA	Current opinion in genetics & development	25461616	Curr Opin Genet Dev	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25461616
Global diversity, population stratification, and selection of human copy-number variation.	Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer MF, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE	Science (New York, N.Y.)	26249230	Science	2015 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/26249230
The Sustained Impact of Model Organisms-in Genetics and Epigenetics.	Bonini NM, Berger SL	Genetics	28049700	Genetics	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/28049700
Genetic Hitchhiking and Population Bottlenecks Contribute to Prostate Cancer Disparities in Men of African Descent.	Lachance J, Berens AJ, Hansen MEB, Teng AK, Tishkoff SA, Rebbeck TR	Cancer research	29438991	Cancer Res	2018 May 1	https://www.ncbi.nlm.nih.gov/pubmed/29438991
Genetically Determined Later Puberty Impacts Lowered Bone Mineral Density in Childhood and Adulthood.	Cousminer DL, Mitchell JA, Chesi A, Roy SM, Kalkwarf HJ, Lappe JM, Gilsanz V, Oberfield SE, Shepherd JA, Kelly A, McCormack SE, Voight BF, Zemel BS, Grant SF	Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research	29068475	J Bone Miner Res	2018 Mar	https://www.ncbi.nlm.nih.gov/pubmed/29068475
Limited evidence for adaptive evolution and functional effect of allelic variation at rs702424 in the promoter of the TAS2R16 bitter taste receptor gene in Africa.	Campbell MC, Ranciaro A, Zinshteyn D, Rawlings-Goss R, Hirbo J, Thompson S, Woldemeskel D, Froment A, Omar SA, Bodo JM, Nyambo T, Belay G, Drayna D, Breslin PA, Tishkoff SA	Journal of human genetics	24785689	J Hum Genet	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24785689
Specific inactivation of two immunomodulatory SIGLEC genes during human evolution.	Wang X, Mitra N, Secundino I, Banda K, Cruz P, Padler-Karavani V, Verhagen A, Reid C, Lari M, Rizzi E, Balsamo C, Corti G, De Bellis G, Longo L, NISC Comparative Sequencing Program, Beggs W, Caramelli D, Tishkoff SA, Hayakawa T, Green ED, Mullikin JC, Nizet V, Bui J, Varki A	Proceedings of the National Academy of Sciences of the United States of America	22665810	Proc Natl Acad Sci U S A	2012 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/22665810
Higher frequency of genetic variants conferring increased risk for ADRs for commonly used drugs treating cancer, AIDS and tuberculosis in persons of African descent.	Aminkeng F, Ross CJ, Rassekh SR, Brunham LR, Sistonen J, Dube MP, Ibrahim M, Nyambo TB, Omar SA, Froment A, Bodo JM, Tishkoff S, Carleton BC, Hayden MR, Canadian Pharmacogenomics Network for Drug Safety Consortium	The pharmacogenomics journal	23588107	Pharmacogenomics J	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/23588107
Apparent variation in Neanderthal admixture among African populations is consistent with gene flow from Non-African populations.	Wang S, Lachance J, Tishkoff SA, Hey J, Xing J	Genome biology and evolution	24162011	Genome Biol Evol	2013	https://www.ncbi.nlm.nih.gov/pubmed/24162011
Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity.	Ferreira Z, Hurle B, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson WJ, NISC Comparative Sequencing Program, Green ED, Clark AG, Seixas S	Genome biology and evolution	24356879	Genome Biol Evol	2013	https://www.ncbi.nlm.nih.gov/pubmed/24356879
Genetic adaptation to high altitude in the Ethiopian highlands.	Scheinfeldt LB, Soi S, Thompson S, Ranciaro A, Woldemeskel D, Beggs W, Lambert C, Jarvis JP, Abate D, Belay G, Tishkoff SA	Genome biology	22264333	Genome Biol	2012 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/22264333
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana.	Hansen MEB, Rubel MA, Bailey AG, Ranciaro A, Thompson SR, Campbell MC, Beggs W, Dave JR, Mokone GG, Mpoloka SW, Nyambo T, Abnet C, Chanock SJ, Bushman FD, Tishkoff SA	Genome biology	30665461	Genome Biol	2019 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/30665461
Population Genomics of Human Adaptation.	Lachance J, Tishkoff SA	Annual review of ecology, evolution, and systematics	25383060	Annu Rev Ecol Evol Syst	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/25383060
Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.	Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo TB, Rebbeck TR, Zhang K, Akey JM, Tishkoff SA	Cell	22840920	Cell	2012 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/22840920
Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation.	Scheinfeldt LB, Soi S, Lambert C, Ko WY, Coulibaly A, Ranciaro A, Thompson S, Hirbo J, Beggs W, Ibrahim M, Nyambo T, Omar S, Woldemeskel D, Belay G, Froment A, Kim J, Tishkoff SA	Proceedings of the National Academy of Sciences of the United States of America	30782801	Proc Natl Acad Sci U S A	2019 Mar 5	https://www.ncbi.nlm.nih.gov/pubmed/30782801
Origin and differential selection of allelic variation at TAS2R16 associated with salicin bitter taste sensitivity in Africa.	Campbell MC, Ranciaro A, Zinshteyn D, Rawlings-Goss R, Hirbo J, Thompson S, Woldemeskel D, Froment A, Rucker JB, Omar SA, Bodo JM, Nyambo T, Belay G, Drayna D, Breslin PA, Tishkoff SA	Molecular biology and evolution	24177185	Mol Biol Evol	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24177185
Great ape genetic diversity and population history.	Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T	Nature	23823723	Nature	2013 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/23823723
Identifying Darwinian selection acting on different human APOL1 variants among diverse African populations.	Ko WY, Rajan P, Gomez F, Scheinfeldt L, An P, Winkler CA, Froment A, Nyambo TB, Omar SA, Wambebe C, Ranciaro A, Hirbo JB, Tishkoff SA	American journal of human genetics	23768513	Am J Hum Genet	2013 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/23768513
Genomic analyses inform on migration events during the peopling of Eurasia.	Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M	Nature	27654910	Nature	2016 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/27654910
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.	Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JT, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D	Nature	27654912	Nature	2016 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/27654912
Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis.	Nagel ZD, Margulies CM, Chaim IA, McRee SK, Mazzucato P, Ahmad A, Abo RP, Butty VL, Forget AL, Samson LD	Proceedings of the National Academy of Sciences of the United States of America	24757057	Proc Natl Acad Sci U S A	2014 May 6	https://www.ncbi.nlm.nih.gov/pubmed/24757057
DNA Repair Capacity in Multiple Pathways Predicts Chemoresistance in Glioblastoma Multiforme.	Nagel ZD, Kitange GJ, Gupta SK, Joughin BA, Chaim IA, Mazzucato P, Lauffenburger DA, Sarkaria JN, Samson LD	Cancer research	27793847	Cancer Res	2017 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/27793847
Microcolony Size Distribution Assay Enables High-Throughput Cell Survival Quantitation.	Ngo LP, Chan TK, Ge J, Samson LD, Engelward BP	Cell reports	30726746	Cell Rep	2019 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/30726746
CometChip analysis of human primary lymphocytes enables quantification of inter-individual differences in the kinetics of repair of oxidative DNA damage.	Ngo LP, Kaushal S, Chaim IA, Mazzucato P, Ricciardi C, Samson LD, Nagel ZD, Engelward BP	Free radical biology & medicine	34324980	Free Radic Biol Med	2021 Oct	https://www.ncbi.nlm.nih.gov/pubmed/34324980
In vivo measurements of interindividual differences in DNA glycosylases and APE1 activities.	Chaim IA, Nagel ZD, Jordan JJ, Mazzucato P, Ngo LP, Samson LD	Proceedings of the National Academy of Sciences of the United States of America	29122935	Proc Natl Acad Sci U S A	2017 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/29122935
Single-cell analysis of ribonucleotide reductase transcriptional and translational response to DNA damage.	Mazumder A, Tummler K, Bathe M, Samson LD	Molecular and cellular biology	23184665	Mol Cell Biol	2013 Feb	https://www.ncbi.nlm.nih.gov/pubmed/23184665
Towards precision prevention: Technologies for identifying healthy individuals with high risk of disease.	Nagel ZD, Engelward BP, Brenner DJ, Begley TJ, Sobol RW, Bielas JH, Stambrook PJ, Wei Q, Hu JJ, Terry MB, Dilworth C, McAllister KA, Reinlib L, Worth L, Shaughnessy DT	Mutation research	28458064	Mutat Res	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28458064
Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research.	Nagel ZD, Chaim IA, Samson LD	DNA repair	24780560	DNA Repair (Amst)	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24780560
Fluorogenic Real-Time Reporters of DNA Repair by MGMT, a Clinical Predictor of Antitumor Drug Response.	Beharry AA, Nagel ZD, Samson LD, Kool ET	PloS one	27035132	PLoS One	2016	https://www.ncbi.nlm.nih.gov/pubmed/27035132
Minor Changes in Expression of the Mismatch Repair Protein MSH2 Exert a Major Impact on Glioblastoma Response to Temozolomide.	McFaline-Figueroa JL, Braun CJ, Stanciu M, Nagel ZD, Mazzucato P, Sangaraju D, Cerniauskas E, Barford K, Vargas A, Chen Y, Tretyakova N, Lees JA, Hemann MT, White FM, Samson LD	Cancer research	26025730	Cancer Res	2015 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/26025730
Biomolecular actuators for genetically selective acoustic manipulation of cells.	Wu D, Baresch D, Cook C, Ma Z, Duan M, Malounda D, Maresca D, Abundo MP, Lee J, Shivaei S, Mittelstein DR, Qiu T, Fischer P, Shapiro MG	Science advances	36812320	Sci Adv	2023 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/36812320
Bioorthogonal Labeling Enables In Situ Fluorescence Imaging of Expressed Gas Vesicle Nanostructures.	Schrunk E, Dutka P, Hurt RC, Wu D, Shapiro MG	Bioconjugate chemistry	38346316	Bioconjug Chem	2024 Mar 20	https://www.ncbi.nlm.nih.gov/pubmed/38346316
Tissue-like Neural Probes for Understanding and Modulating the Brain.	Hong G, Viveros RD, Zwang TJ, Yang X, Lieber CM	Biochemistry	29529359	Biochemistry	2018 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/29529359
Novel electrode technologies for neural recordings.	Hong G, Lieber CM	Nature reviews. Neuroscience	30833706	Nat Rev Neurosci	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/30833706
Nanowired Bioelectric Interfaces.	Tian B, Lieber CM	Chemical reviews	30995019	Chem Rev	2019 Aug 14	https://www.ncbi.nlm.nih.gov/pubmed/30995019
Syringe-injectable Mesh Electronics for Stable Chronic Rodent Electrophysiology.	Schuhmann TG Jr, Zhou T, Hong G, Lee JM, Fu TM, Park HG, Lieber CM	Journal of visualized experiments : JoVE	30080192	J Vis Exp	2018 Jul 21	https://www.ncbi.nlm.nih.gov/pubmed/30080192
A method for single-neuron chronic recording from the retina in awake mice.	Hong G, Fu TM, Qiao M, Viveros RD, Yang X, Zhou T, Lee JM, Park HG, Sanes JR, Lieber CM	Science (New York, N.Y.)	29954976	Science	2018 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/29954976
Nanowire-Enabled Bioelectronics.	Zhang A, Lee JH, Lieber CM	Nano today	36970717	Nano Today	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/36970717
Mesh Nanoelectronics: Seamless Integration of Electronics with Tissues.	Dai X, Hong G, Gao T, Lieber CM	Accounts of chemical research	29381054	Acc Chem Res	2018 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/29381054
Nanoenabled Direct Contact Interfacing of Syringe-Injectable Mesh Electronics.	Lee JM, Hong G, Lin D, Schuhmann TG Jr, Sullivan AT, Viveros RD, Park HG, Lieber CM	Nano letters	31361503	Nano Lett	2019 Aug 14	https://www.ncbi.nlm.nih.gov/pubmed/31361503
Mesh electronics: a new paradigm for tissue-like brain probes.	Hong G, Yang X, Zhou T, Lieber CM	Current opinion in neurobiology	29202327	Curr Opin Neurobiol	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29202327
Bioinspired neuron-like electronics.	Yang X, Zhou T, Zwang TJ, Hong G, Zhao Y, Viveros RD, Fu TM, Gao T, Lieber CM	Nature materials	30804509	Nat Mater	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/30804509
Advanced One- and Two-Dimensional Mesh Designs for Injectable Electronics.	Viveros RD, Zhou T, Hong G, Fu TM, Lin HG, Lieber CM	Nano letters	31075202	Nano Lett	2019 Jun 12	https://www.ncbi.nlm.nih.gov/pubmed/31075202
Precision electronic medicine in the brain.	Patel SR, Lieber CM	Nature biotechnology	31477925	Nat Biotechnol	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31477925
Spectral reading of optical resonance-encoded cells in microfluidics.	Humar M, Upadhya A, Yun SH	Lab on a chip	28686280	Lab Chip	2017 Aug 8	https://www.ncbi.nlm.nih.gov/pubmed/28686280
Wavelength-encoded laser particles for massively multiplexed cell tagging.	Martino N, Kwok SJJ, Liapis AC, Forward S, Jang H, Kim HM, Wu SJ, Wu J, Dannenberg PH, Jang SJ, Lee YH, Yun SH	Nature photonics	32231707	Nat Photonics	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/32231707
High-dimensional multi-pass flow cytometry via spectrally encoded cellular barcoding.	Kwok SJJ, Forward S, Fahlberg MD, Assita ER, Cosgriff S, Lee SH, Abbott GR, Zhu H, Minasian NH, Vote AS, Martino N, Yun SH	Nature biomedical engineering	38036616	Nat Biomed Eng	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38036616
Non-destructive mapping of stress and strain in soft thin films through sound waves.	Li GY, Gower AL, Destrade M, Yun SH	Communications physics	37744302	Commun Phys	2022	https://www.ncbi.nlm.nih.gov/pubmed/37744302
Supershear surface waves reveal prestress and anisotropy of soft materials.	Li GY, Feng X, Ramier A, Yun SH	Journal of the mechanics and physics of solids	37828998	J Mech Phys Solids	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37828998
Precise photoelectrochemical tuning of semiconductor microdisk lasers.	Sarkar D, Dannenberg PH, Martino N, Kim KH, Yun SH	Advanced photonics	38993283	Adv Photonics	2023 Sep	https://www.ncbi.nlm.nih.gov/pubmed/38993283
Laser particles with omnidirectional emission for cell tracking.	Tang SJ, Dannenberg PH, Liapis AC, Martino N, Zhuo Y, Xiao YF, Yun SH	Light, science & applications	33495436	Light Sci Appl	2021 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/33495436
Submicrometer perovskite plasmonic lasers at room temperature.	Cho S, Yang Y, Soljačić M, Yun SH	Science advances	34433555	Sci Adv	2021 Aug	https://www.ncbi.nlm.nih.gov/pubmed/34433555
Laser particle activated cell sorting in microfluidics.	Dannenberg PH, Kang J, Martino N, Kashiparekh A, Forward S, Wu J, Liapis AC, Wang J, Yun SH	Lab on a chip	35621381	Lab Chip	2022 Jun 14	https://www.ncbi.nlm.nih.gov/pubmed/35621381
Ultrasmall InGa(As)P Dielectric and Plasmonic Nanolasers.	Sarkar D, Cho S, Yan H, Martino N, Dannenberg PH, Yun SH	ACS nano	37523588	ACS Nano	2023 Aug 22	https://www.ncbi.nlm.nih.gov/pubmed/37523588
Facile layer-by-layer fabrication of semiconductor microdisk laser particles.	Dannenberg PH, Liapis AC, Martino N, Sarkar D, Kim KH, Yun SH	APL photonics	38031595	APL Photonics	2023 Feb	https://www.ncbi.nlm.nih.gov/pubmed/38031595
Droplet microfluidic generation of a million optical microparticle barcodes.	Dannenberg PH, Wang J, Zhuo Y, Cho S, Kim KH, Yun SH	Optics express	34808870	Opt Express	2021 Nov 8	https://www.ncbi.nlm.nih.gov/pubmed/34808870
Conformal Coating of Freestanding Particles by Vapor-Phase Infiltration.	Liapis AC, Subramanian A, Cho S, Kisslinger K, Nam CY, Yun SH	Advanced materials interfaces	33708471	Adv Mater Interfaces	2020 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/33708471
Label-free histological imaging of tissues using Brillouin light scattering contrast.	Ryu S, Martino N, Kwok SJJ, Bernstein L, Yun SH	Biomedical optics express	33796364	Biomed Opt Express	2021 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/33796364
Whispering-gallery-mode emission from biological luminescent protein microcavity assemblies.	Humar M, Yun SH	Optica	29046889	Optica	2017	https://www.ncbi.nlm.nih.gov/pubmed/29046889
Multiplexed laser particles for spatially resolved single-cell analysis.	Kwok SJJ, Martino N, Dannenberg PH, Yun SH	Light, science & applications	31645920	Light Sci Appl	2019	https://www.ncbi.nlm.nih.gov/pubmed/31645920
Laser Particle Stimulated Emission Microscopy.	Cho S, Humar M, Martino N, Yun SH	Physical review letters	27858427	Phys Rev Lett	2016 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/27858427
Biomaterial microlasers implantable in the cornea, skin, and blood.	Humar M, Dobravec A, Zhao X, Yun SH	Optica	30333986	Optica	2017 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/30333986
Author Correction: Laser particles with omnidirectional emission for cell tracking.	Tang SJ, Dannenberg PH, Liapis AC, Martino N, Zhuo Y, Xiao YF, Yun SH	Light, science & applications	33637671	Light Sci Appl	2021 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/33637671
Light in diagnosis, therapy and surgery.	Yun SH, Kwok SJJ	Nature biomedical engineering	28649464	Nat Biomed Eng	2017	https://www.ncbi.nlm.nih.gov/pubmed/28649464
Poly(catecholamine) coated CsPbBr(3) perovskite microlasers: lasing in water and biofunctionalization.	Cho S, Yun SH	Advanced functional materials	34539305	Adv Funct Mater	2021 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/34539305
Compact Quantum-Dot Microbeads with Sub-Nanometer Emission Linewidth.	Kim KH, Dannenberg PH, Yan H, Cho S, Yun SH	Advanced functional materials	35418816	Adv Funct Mater	2021 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/35418816
Encrypted Three-dimensional Dynamic Imaging using Snapshot Time-of-flight Compressed Ultrafast Photography.	Liang J, Gao L, Hai P, Li C, Wang LV	Scientific reports	26503834	Sci Rep	2015 Oct 27	https://www.ncbi.nlm.nih.gov/pubmed/26503834
Dual-Modality Photoacoustic and Ultrasound Imaging System for Noninvasive Sentinel Lymph Node Detection in Patients with Breast Cancer.	Garcia-Uribe A, Erpelding TN, Krumholz A, Ke H, Maslov K, Appleton C, Margenthaler JA, Wang LV	Scientific reports	26510774	Sci Rep	2015 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/26510774
Three-dimensional photoacoustic endoscopic imaging of the rabbit esophagus.	Yang JM, Favazza C, Yao J, Chen R, Zhou Q, Shung KK, Wang LV	PloS one	25874640	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/25874640
Handheld photoacoustic microscopy to detect melanoma depth in vivo.	Zhou Y, Xing W, Maslov KI, Cornelius LA, Wang LV	Optics letters	25121860	Opt Lett	2014 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/25121860
Microcirculatory changes identified by photoacoustic microscopy in patients with complex regional pain syndrome type I after stellate ganglion blocks.	Zhou Y, Yi X, Xing W, Hu S, Maslov KI, Wang LV	Journal of biomedical optics	25144451	J Biomed Opt	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/25144451
Photoacoustic microscopy and computed tomography: from bench to bedside.	Wang LV, Gao L	Annual review of biomedical engineering	24905877	Annu Rev Biomed Eng	2014 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/24905877
Urogenital photoacoustic endoscope.	Li C, Yang JM, Chen R, Yeh CH, Zhu L, Maslov K, Zhou Q, Shung KK, Wang LV	Optics letters	24690816	Opt Lett	2014 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/24690816
Time-reversed adapted-perturbation (TRAP) optical focusing onto dynamic objects inside scattering media.	Ma C, Xu X, Liu Y, Wang LV	Nature photonics	25530797	Nat Photonics	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25530797
Optical drug monitoring: photoacoustic imaging of nanosensors to monitor therapeutic lithium in vivo.	Cash KJ, Li C, Xia J, Wang LV, Clark HA	ACS nano	25588028	ACS Nano	2015 Feb 24	https://www.ncbi.nlm.nih.gov/pubmed/25588028
Photoacoustic tomography: principles and advances.	Xia J, Yao J, Wang LV	Electromagnetic waves (Cambridge, Mass.)	25642127	Electromagn Waves (Camb)	2014	https://www.ncbi.nlm.nih.gov/pubmed/25642127
Multi-view optical resolution photoacoustic microscopy.	Zhu L, Li L, Gao L, Wang LV	Optica	25558469	Optica	2014	https://www.ncbi.nlm.nih.gov/pubmed/25558469
Focusing light through biological tissue and tissue-mimicking phantoms up to 9.6 cm in thickness with digital optical phase conjugation.	Shen Y, Liu Y, Ma C, Wang LV	Journal of biomedical optics	27533439	J Biomed Opt	2016 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/27533439
Structured-illumination photoacoustic Doppler flowmetry of axial flow in homogeneous scattering media.	Zhang R, Yao J, Maslov KI, Wang LV	Applied physics letters	24065864	Appl Phys Lett	2013 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/24065864
Photoacoustic recovery after photothermal bleaching in living cells.	Li C, Zhang C, Gao L, Garcia-Uribe A, Wang LV	Journal of biomedical optics	24089253	J Biomed Opt	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/24089253
Cross-correlation-based transverse flow measurements using optical resolution photoacoustic microscopy with a digital micromirror device.	Liang J, Zhou Y, Maslov KI, Wang LV	Journal of biomedical optics	24002191	J Biomed Opt	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/24002191
In vivo optically encoded photoacoustic flowgraphy.	Zhang R, Wang L, Yao J, Yeh CH, Wang LV	Optics letters	24978744	Opt Lett	2014 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/24978744
Photoacoustic microscopy of arteriovenous shunts and blood diffusion in early-stage tumors.	Yeh C, Liang J, Zhou Y, Hu S, Sohn RE, Arbeit JM, Wang LV	Journal of biomedical optics	26882446	J Biomed Opt	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/26882446
Breakthrough in Photonics 2013: Photoacoustic Tomography in Biomedicine.	Yao J, Wang LV	IEEE photonics journal	25383143	IEEE Photonics J	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25383143
Optical sectioning by wide-field photobleaching imprinting microscopy.	Li C, Gao L, Liu Y, Wang LV	Applied physics letters	24273331	Appl Phys Lett	2013 Oct 28	https://www.ncbi.nlm.nih.gov/pubmed/24273331
In vivo photoacoustic flowmetry at depths of the diffusive regime based on saline injection.	Zhou Y, Poudel J, Li G, Wang LV	Journal of biomedical optics	26267364	J Biomed Opt	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26267364
Multicontrast photoacoustic in vivo imaging using near-infrared fluorescent proteins.	Krumholz A, Shcherbakova DM, Xia J, Wang LV, Verkhusha VV	Scientific reports	24487319	Sci Rep	2014 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/24487319
Absolute photoacoustic thermometry in deep tissue.	Yao J, Ke H, Tai S, Zhou Y, Wang LV	Optics letters	24322224	Opt Lett	2013 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/24322224
Label-free photoacoustic microscopy of peripheral nerves.	Matthews TP, Zhang C, Yao DK, Maslov K, Wang LV	Journal of biomedical optics	24395587	J Biomed Opt	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24395587
Focusing light through scattering media by polarization modulation based generalized digital optical phase conjugation.	Yang J, Shen Y, Liu Y, Hemphill AS, Wang LV	Applied physics letters	29203931	Appl Phys Lett	2017 Nov 13	https://www.ncbi.nlm.nih.gov/pubmed/29203931
Single-impulse Panoramic Photoacoustic Computed Tomography of Small-animal Whole-body Dynamics at High Spatiotemporal Resolution.	Li L, Zhu L, Ma C, Lin L, Yao J, Wang L, Maslov K, Zhang R, Chen W, Shi J, Wang LV	Nature biomedical engineering	29333331	Nat Biomed Eng	2017	https://www.ncbi.nlm.nih.gov/pubmed/29333331
Label-free cell nuclear imaging by Grüneisen relaxation photoacoustic microscopy.	Liu X, Wong TTW, Shi J, Ma J, Yang Q, Wang LV	Optics letters	29444034	Opt Lett	2018 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/29444034
In vivo label-free photoacoustic flow cytography and on-the-spot laser killing of single circulating melanoma cells.	He Y, Wang L, Shi J, Yao J, Li L, Zhang R, Huang CH, Zou J, Wang LV	Scientific reports	28000788	Sci Rep	2016 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/28000788
Handheld optical-resolution photoacoustic microscopy.	Lin L, Zhang P, Xu S, Shi J, Li L, Yao J, Wang L, Zou J, Wang LV	Journal of biomedical optics	27775746	J Biomed Opt	2017 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/27775746
Optical-resolution photoacoustic endomicroscopy in vivo.	Yang JM, Li C, Chen R, Rao B, Yao J, Yeh CH, Danielli A, Maslov K, Zhou Q, Shung KK, Wang LV	Biomedical optics express	25798315	Biomed Opt Express	2015 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/25798315
Single-exposure optical focusing inside scattering media using binarized time-reversed adapted perturbation.	Ma C, Zhou F, Liu Y, Wang LV	Optica	30221184	Optica	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30221184
Multiview Hilbert transformation in full-ring transducer array-based photoacoustic computed tomography.	Li L, Zhu L, Shen Y, Wang LV	Journal of biomedical optics	28745385	J Biomed Opt	2017 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/28745385
Label-free high-throughput photoacoustic tomography of suspected circulating melanoma tumor cells in patients in vivo.	Hai P, Qu Y, Li Y, Zhu L, Shmuylovich L, Cornelius LA, Wang LV	Journal of biomedical optics	32170857	J Biomed Opt	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/32170857
Picosecond-resolution phase-sensitive imaging of transparent objects in a single shot.	Kim T, Liang J, Zhu L, Wang LV	Science advances	32010772	Sci Adv	2020 Jan	https://www.ncbi.nlm.nih.gov/pubmed/32010772
Synthetic Bessel light needle for extended depth-of-field microscopy.	Yang J, Gong L, Shen Y, Wang LV	Applied physics letters	30449893	Appl Phys Lett	2018 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/30449893
In vivo characterization of connective tissue remodeling using infrared photoacoustic spectra.	Qu Y, Hu P, Shi J, Maslov K, Zhao P, Li C, Ma J, Garcia-Uribe A, Meyers K, Diveley E, Pizzella S, Muench L, Punyamurthy N, Goldstein N, Onwumere O, Alisio M, Meyenburg K, Maynard J, Helm K, Altieri E, Slaughter J, Barber S, Burger T, Kramer C, Chubiz J, Anderson M, McCarthy R, England SK, Macones GA, Stout MJ, Tuuli M, Wang LV	Journal of biomedical optics	30520275	J Biomed Opt	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30520275
Dual-view photoacoustic microscopy for quantitative cell nuclear imaging.	Cai D, Wong TTW, Zhu L, Shi J, Chen SL, Wang LV	Optics letters	30320772	Opt Lett	2018 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/30320772
Motionless volumetric photoacoustic microscopy with spatially invariant resolution.	Yang J, Gong L, Xu X, Hai P, Shen Y, Suzuki Y, Wang LV	Nature communications	28974681	Nat Commun	2017 Oct 3	https://www.ncbi.nlm.nih.gov/pubmed/28974681
Multifocal photoacoustic microscopy using a single-element ultrasonic transducer through an ergodic relay.	Li Y, Wong TTW, Shi J, Hsu HC, Wang LV	Light, science & applications	32793336	Light Sci Appl	2020	https://www.ncbi.nlm.nih.gov/pubmed/32793336
Delivery of AAV for Expression of Fluorescent Biosensors in Juvenile Mouse Hippocampus.	Díaz-García CM, Nathwani N, Martínez-François JR, Yellen G	Bio-protocol	35087918	Bio Protoc	2021 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/35087918
Single-shot photoacoustic imaging with single-element transducer through a spatiotemporal encoder.	Zhao Y, Wang LV	Journal of biomedical optics	37065647	J Biomed Opt	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/37065647
Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting.	Gao L, Zhu L, Li C, Wang LV	Journal of the Royal Society, Interface	24478278	J R Soc Interface	2014 Apr 6	https://www.ncbi.nlm.nih.gov/pubmed/24478278
Deep-tissue photoacoustic tomography of Förster resonance energy transfer.	Wang Y, Xia J, Wang LV	Journal of biomedical optics	23884608	J Biomed Opt	2013 Oct	https://www.ncbi.nlm.nih.gov/pubmed/23884608
Intracellular temperature mapping with fluorescence-assisted photoacoustic-thermometry.	Gao L, Zhang C, Li C, Wang LV	Applied physics letters	23825801	Appl Phys Lett	2013 May 13	https://www.ncbi.nlm.nih.gov/pubmed/23825801
Enhancement of photoacoustic tomography by ultrasonic computed tomography based on optical excitation of elements of a full-ring transducer array.	Xia J, Huang C, Maslov K, Anastasio MA, Wang LV	Optics letters	24104670	Opt Lett	2013 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/24104670
Optical clearing-aided photoacoustic microscopy with enhanced resolution and imaging depth.	Zhou Y, Yao J, Wang LV	Optics letters	23939121	Opt Lett	2013 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/23939121
Photoacoustic thermography of tissue.	Ke H, Tai S, Wang LV	Journal of biomedical optics	24522803	J Biomed Opt	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/24522803
Ultrasonically encoded photoacoustic flowgraphy in biological tissue.	Wang L, Xia J, Yao J, Maslov KI, Wang LV	Physical review letters	24289689	Phys Rev Lett	2013 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/24289689
Retrospective respiration-gated whole-body photoacoustic computed tomography of mice.	Xia J, Chen W, Maslov K, Anastasio MA, Wang LV	Journal of biomedical optics	24395586	J Biomed Opt	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24395586
Photoacoustic and optical coherence tomography of epilepsy with high temporal and spatial resolution and dual optical contrasts.	Tsytsarev V, Rao B, Maslov KI, Li L, Wang LV	Journal of neuroscience methods	23603664	J Neurosci Methods	2013 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/23603664
High-sensitivity ultrasound-modulated optical tomography with a photorefractive polymer.	Suzuki Y, Lai P, Xu X, Wang L	Optics letters	23503253	Opt Lett	2013 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/23503253
Bit-efficient, sub-millisecond wavefront measurement using a lock-in camera for time-reversal based optical focusing inside scattering media.	Liu Y, Ma C, Shen Y, Wang LV	Optics letters	27192226	Opt Lett	2016 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/27192226
Integration of Multitargeted Polymer-Based Contrast Agents with Photoacoustic Computed Tomography: An Imaging Technique to Visualize Breast Cancer Intratumor Heterogeneity.	Li L, Patil D, Petruncio G, Harnden KK, Somasekharan JV, Paige M, Wang LV, Salvador-Morales C	ACS nano	33464827	ACS Nano	2021 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/33464827
Real-time observation and control of optical chaos.	Fan L, Yan X, Wang H, Wang LV	Science advances	33523874	Sci Adv	2021 Jan	https://www.ncbi.nlm.nih.gov/pubmed/33523874
Noninvasive Determination of Melanoma Depth using a Handheld Photoacoustic Probe.	Zhou Y, Tripathi SV, Rosman I, Ma J, Hai P, Linette GP, Council ML, Fields RC, Wang LV, Cornelius LA	The Journal of investigative dermatology	28163070	J Invest Dermatol	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28163070
Focusing light through scattering media by full-polarization digital optical phase conjugation.	Shen Y, Liu Y, Ma C, Wang LV	Optics letters	26977651	Opt Lett	2016 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/26977651
Lock-in camera based heterodyne holography for ultrasound-modulated optical tomography inside dynamic scattering media.	Liu Y, Shen Y, Ma C, Shi J, Wang LV	Applied physics letters	27493275	Appl Phys Lett	2016 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/27493275
Dichroism-sensitive photoacoustic computed tomography.	Qu Y, Li L, Shen Y, Wei X, Wong TTW, Hu P, Yao J, Maslov K, Wang LV	Optica	30820444	Optica	2018 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/30820444
High-throughput, label-free, single-cell photoacoustic microscopy of intratumoral metabolic heterogeneity.	Hai P, Imai T, Xu S, Zhang R, Aft RL, Zou J, Wang LV	Nature biomedical engineering	30936431	Nat Biomed Eng	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/30936431
Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo.	Li L, Shemetov AA, Baloban M, Hu P, Zhu L, Shcherbakova DM, Zhang R, Shi J, Yao J, Wang LV, Verkhusha VV	Nature communications	30013153	Nat Commun	2018 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/30013153
Microvascular quantification based on contour-scanning photoacoustic microscopy.	Yeh C, Soetikno B, Hu S, Maslov KI, Wang LV	Journal of biomedical optics	25223708	J Biomed Opt	2014 Sep	https://www.ncbi.nlm.nih.gov/pubmed/25223708
Calibration-free structured-illumination photoacoustic flowgraphy of transverse flow in scattering media.	Yao J, Gilson RC, Maslov KI, Wang L, Wang LV	Journal of biomedical optics	24718385	J Biomed Opt	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24718385
Nonlinear photoacoustic spectroscopy of hemoglobin.	Danielli A, Maslov K, Favazza CP, Xia J, Wang LV	Applied physics letters	26045627	Appl Phys Lett	2015 May 18	https://www.ncbi.nlm.nih.gov/pubmed/26045627
Fast label-free multilayered histology-like imaging of human breast cancer by photoacoustic microscopy.	Wong TTW, Zhang R, Hai P, Zhang C, Pleitez MA, Aft RL, Novack DV, Wang LV	Science advances	28560329	Sci Adv	2017 May	https://www.ncbi.nlm.nih.gov/pubmed/28560329
Sub-Nyquist sampling boosts targeted light transport through opaque scattering media.	Shen Y, Liu Y, Ma C, Wang LV	Optica	28670607	Optica	2017 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/28670607
Focusing light inside dynamic scattering media with millisecond digital optical phase conjugation.	Liu Y, Ma C, Shen Y, Shi J, Wang LV	Optica	28815194	Optica	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/28815194
In vivo photoacoustic tomography of myoglobin oxygen saturation.	Lin L, Yao J, Li L, Wang LV	Journal of biomedical optics	26719943	J Biomed Opt	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/26719943
High-resolution deep functional imaging of the whole mouse brain by photoacoustic computed tomography in vivo.	Zhang P, Li L, Lin L, Hu P, Shi J, He Y, Zhu L, Zhou Y, Wang LV	Journal of biophotonics	28635056	J Biophotonics	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/28635056
Label-free automated three-dimensional imaging of whole organs by microtomy-assisted photoacoustic microscopy.	Wong TTW, Zhang R, Zhang C, Hsu HC, Maslov KI, Wang L, Shi J, Chen R, Shung KK, Zhou Q, Wang LV	Nature communications	29123109	Nat Commun	2017 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/29123109
alphaVbeta3-targeted copper nanoparticles incorporating an Sn 2 lipase-labile fumagillin prodrug for photoacoustic neovascular imaging and treatment.	Zhang R, Pan D, Cai X, Yang X, Senpan A, Allen JS, Lanza GM, Wang LV	Theranostics	25553103	Theranostics	2015	https://www.ncbi.nlm.nih.gov/pubmed/25553103
Catheter-based photoacoustic endoscope.	Yang JM, Li C, Chen R, Zhou Q, Shung KK, Wang LV	Journal of biomedical optics	24887743	J Biomed Opt	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24887743
Photoacoustic microscopy: superdepth, superresolution, and superb contrast.	Yao J, Song L, Wang LV	IEEE pulse	25974913	IEEE Pulse	2015 May-Jun	https://www.ncbi.nlm.nih.gov/pubmed/25974913
Calibration-free absolute quantification of particle concentration by statistical analyses of photoacoustic signals in vivo.	Zhou Y, Yao J, Maslov KI, Wang LV	Journal of biomedical optics	24589987	J Biomed Opt	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24589987
Single-shot ultrafast optical imaging.	Liang J, Wang LV	Optica	30820445	Optica	2018 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/30820445
Optical-resolution photoacoustic microscopy: auscultation of biological systems at the cellular level.	Hu S, Wang LV	Biophysical journal	23972836	Biophys J	2013 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/23972836
Small-animal whole-body photoacoustic tomography: a review.	Xia J, Wang LV	IEEE transactions on bio-medical engineering	24108456	IEEE Trans Biomed Eng	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24108456
Continuous scanning of a time-reversed ultrasonically encoded optical focus by reflection-mode digital phase conjugation.	Suzuki Y, Tay JW, Yang Q, Wang LV	Optics letters	24978506	Opt Lett	2014 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/24978506
Amplitude-masked photoacoustic wavefront shaping and application in flowmetry.	Tay JW, Liang J, Wang LV	Optics letters	25360912	Opt Lett	2014 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/25360912
Photoacoustic lymphatic imaging with high spatial-temporal resolution.	Martel C, Yao J, Huang CH, Zou J, Randolph GJ, Wang LV	Journal of biomedical optics	25408958	J Biomed Opt	2014 Nov	https://www.ncbi.nlm.nih.gov/pubmed/25408958
Frequency-swept time-reversed ultrasonically encoded optical focusing.	Suzuki Y, Wang LV	Applied physics letters	25425744	Appl Phys Lett	2014 Nov 10	https://www.ncbi.nlm.nih.gov/pubmed/25425744
Micromachined Silicon Parallel Acoustic Delay Lines as Time Delayed Ultrasound Detector Array for Real-Time Photoacoustic Tomography.	Cho Y, Chang CC, Wang LV, Zou J	Journal of optics (2010)	31998470	J Opt	2016	https://www.ncbi.nlm.nih.gov/pubmed/31998470
Angular-spectrum modeling of focusing light inside scattering media by optical phase conjugation.	Yang J, Li J, He S, Wang LV	Optica	32025534	Optica	2019 Mar 20	https://www.ncbi.nlm.nih.gov/pubmed/32025534
High-resolution, high-contrast mid-infrared imaging of fresh biological samples with ultraviolet-localized photoacoustic microscopy.	Shi J, Wong TTW, He Y, Li L, Zhang R, Yung CS, Hwang J, Maslov K, Wang LV	Nature photonics	31440304	Nat Photonics	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31440304
Photoacoustic measurement of the Grüneisen parameter of tissue.	Yao DK, Zhang C, Maslov K, Wang LV	Journal of biomedical optics	24474512	J Biomed Opt	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/24474512
Photoimprint photoacoustic microscopy for three-dimensional label-free subdiffraction imaging.	Yao J, Wang L, Li C, Zhang C, Wang LV	Physical review letters	24483902	Phys Rev Lett	2014 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/24483902
Improving limited-view photoacoustic tomography with an acoustic reflector.	Huang B, Xia J, Maslov K, Wang LV	Journal of biomedical optics	24285421	J Biomed Opt	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24285421
Reflection-mode multifocal optical-resolution photoacoustic microscopy.	Li G, Maslov KI, Wang LV	Journal of biomedical optics	23446704	J Biomed Opt	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23446704
Calibration-free quantification of absolute oxygen saturation based on the dynamics of photoacoustic signals.	Xia J, Danielli A, Liu Y, Wang L, Maslov K, Wang LV	Optics letters	23903146	Opt Lett	2013 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/23903146
Slow-sound photoacoustic microscopy.	Zhang C, Zhou Y, Li C, Wang LV	Applied physics letters	23696693	Appl Phys Lett	2013 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/23696693
Single-shot stereo-polarimetric compressed ultrafast photography for light-speed observation of high-dimensional optical transients with picosecond resolution.	Liang J, Wang P, Zhu L, Wang LV	Nature communications	33067438	Nat Commun	2020 Oct 16	https://www.ncbi.nlm.nih.gov/pubmed/33067438
The distinct roles of calcium in rapid control of neuronal glycolysis and the tricarboxylic acid cycle.	Díaz-García CM, Meyer DJ, Nathwani N, Rahman M, Martínez-François JR, Yellen G	eLife	33555254	Elife	2021 Feb 8	https://www.ncbi.nlm.nih.gov/pubmed/33555254
Single-shot real-time femtosecond imaging of temporal focusing.	Liang J, Zhu L, Wang LV	Light, science & applications	30839588	Light Sci Appl	2018	https://www.ncbi.nlm.nih.gov/pubmed/30839588
Single-breath-hold photoacoustic computed tomography of the breast.	Lin L, Hu P, Shi J, Appleton CM, Maslov K, Li L, Zhang R, Wang LV	Nature communications	29907740	Nat Commun	2018 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/29907740
Recent progress in photoacoustic molecular imaging.	Yao J, Wang LV	Current opinion in chemical biology	29631120	Curr Opin Chem Biol	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29631120
Photoacoustically guided wavefront shaping for enhanced optical focusing in scattering media.	Lai P, Wang L, Tay JW, Wang LV	Nature photonics	25914725	Nat Photonics	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25914725
Analog time-reversed ultrasonically encoded light focusing inside scattering media with a 33,000× optical power gain.	Ma C, Xu X, Wang LV	Scientific reports	25753905	Sci Rep	2015 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/25753905
Noninvasive photoacoustic microscopy of methemoglobin in vivo.	Tang M, Zhou Y, Zhang R, Wang LV	Journal of biomedical optics	25760655	J Biomed Opt	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25760655
Three-dimensional arbitrary trajectory scanning photoacoustic microscopy.	Yeh C, Soetikno B, Hu S, Maslov KI, Wang LV	Journal of biophotonics	25077689	J Biophotonics	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25077689
Label-free photoacoustic nanoscopy.	Danielli A, Maslov K, Garcia-Uribe A, Winkler AM, Li C, Wang L, Chen Y, Dorn GW 2nd, Wang LV	Journal of biomedical optics	25104412	J Biomed Opt	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/25104412
Single-shot compressed ultrafast photography at one hundred billion frames per second.	Gao L, Liang J, Li C, Wang LV	Nature	25471883	Nature	2014 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/25471883
Handheld photoacoustic probe to detect both melanoma depth and volume at high speed in vivo.	Zhou Y, Li G, Zhu L, Li C, Cornelius LA, Wang LV	Journal of biophotonics	25676898	J Biophotonics	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/25676898
Label-free photoacoustic tomography of whole mouse brain structures ex vivo.	Li L, Xia J, Li G, Garcia-Uribe A, Sheng Q, Anastasio MA, Wang LV	Neurophotonics	29181425	Neurophotonics	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/29181425
Space- and intensity-constrained reconstruction for compressed ultrafast photography.	Zhu L, Chen Y, Liang J, Xu Q, Gao L, Ma C, Wang LV	Optica	28775997	Optica	2016 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28775997
A review of snapshot multidimensional optical imaging: measuring photon tags in parallel.	Gao L, Wang LV	Physics reports	27134340	Phys Rep	2016 Feb 29	https://www.ncbi.nlm.nih.gov/pubmed/27134340
Reversibly switchable fluorescence microscopy with enhanced resolution and image contrast.	Yao J, Shcherbakova DM, Li C, Krumholz A, Lorca RA, Reinl E, England SK, Verkhusha VV, Wang LV	Journal of biomedical optics	25144452	J Biomed Opt	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/25144452
Integrated photoacoustic, confocal, and two-photon microscope.	Rao B, Soto F, Kerschensteiner D, Wang LV	Journal of biomedical optics	24589986	J Biomed Opt	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24589986
Dependence of optical scattering from Intralipid in gelatin-gel based tissue-mimicking phantoms on mixing temperature and time.	Lai P, Xu X, Wang LV	Journal of biomedical optics	24604534	J Biomed Opt	2014 Mar	https://www.ncbi.nlm.nih.gov/pubmed/24604534
Bessel-beam Grueneisen relaxation photoacoustic microscopy with extended depth of field.	Shi J, Wang L, Noordam C, Wang LV	Journal of biomedical optics	26524679	J Biomed Opt	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26524679
Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse.	Liang J, Ma C, Zhu L, Chen Y, Gao L, Wang LV	Science advances	28116357	Sci Adv	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/28116357
Tutorial on photoacoustic tomography.	Zhou Y, Yao J, Wang LV	Journal of biomedical optics	27086868	J Biomed Opt	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27086868
Optical focusing deep inside dynamic scattering media with near-infrared time-reversed ultrasonically encoded (TRUE) light.	Liu Y, Lai P, Ma C, Xu X, Grabar AA, Wang LV	Nature communications	25556918	Nat Commun	2015 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/25556918
In vivo deep brain imaging of rats using oral-cavity illuminated photoacoustic computed tomography.	Lin L, Xia J, Wong TT, Li L, Wang LV	Journal of biomedical optics	25611865	J Biomed Opt	2015 Jan	https://www.ncbi.nlm.nih.gov/pubmed/25611865
Tripling the detection view of high-frequency linear-array-based photoacoustic computed tomography by using two planar acoustic reflectors.	Li G, Xia J, Wang K, Maslov K, Anastasio MA, Wang LV	Quantitative imaging in medicine and surgery	25694954	Quant Imaging Med Surg	2015 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25694954
Near-infrared optical-resolution photoacoustic microscopy.	Hai P, Yao J, Maslov KI, Zhou Y, Wang LV	Optics letters	25166107	Opt Lett	2014 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/25166107
Hybridized wavefront shaping for high-speed, high-efficiency focusing through dynamic diffusive media.	Hemphill AS, Tay JW, Wang LV	Journal of biomedical optics	27626770	J Biomed Opt	2016 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/27626770
Grueneisen relaxation photoacoustic microscopy.	Wang L, Zhang C, Wang LV	Physical review letters	25379919	Phys Rev Lett	2014 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/25379919
Photoacoustic Brain Imaging: from Microscopic to Macroscopic Scales.	Yao J, Wang LV	Neurophotonics	25401121	Neurophotonics	2014 May 28	https://www.ncbi.nlm.nih.gov/pubmed/25401121
Fully motorized optical-resolution photoacoustic microscopy.	Li L, Yeh C, Hu S, Wang L, Soetikno BT, Chen R, Zhou Q, Shung KK, Maslov KI, Wang LV	Optics letters	24686689	Opt Lett	2014 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/24686689
Plasmonics-enhanced and optically modulated delivery of gold nanostars into brain tumor.	Yuan H, Wilson CM, Xia J, Doyle SL, Li S, Fales AM, Liu Y, Ozaki E, Mulfaul K, Hanna G, Palmer GM, Wang LV, Grant GA, Vo-Dinh T	Nanoscale	24619405	Nanoscale	2014 Apr 21	https://www.ncbi.nlm.nih.gov/pubmed/24619405
Sensitivity of photoacoustic microscopy.	Yao J, Wang LV	Photoacoustics	25302158	Photoacoustics	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25302158
High-resolution photoacoustic tomography of resting-state functional connectivity in the mouse brain.	Nasiriavanaki M, Xia J, Wan H, Bauer AQ, Culver JP, Wang LV	Proceedings of the National Academy of Sciences of the United States of America	24367107	Proc Natl Acad Sci U S A	2014 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/24367107
Wide-field two-dimensional multifocal optical-resolution photoacoustic-computed microscopy.	Xia J, Li G, Wang L, Nasiriavanaki M, Maslov K, Engelbach JA, Garbow JR, Wang LV	Optics letters	24322226	Opt Lett	2013 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/24322226
High-speed alignment optimization of digital optical phase conjugation systems based on autocovariance analysis in conjunction with orthonormal rectangular polynomials.	Hemphill AS, Shen Y, Hwang J, Wang LV	Journal of biomedical optics	30156064	J Biomed Opt	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/30156064
Dual-axis illumination for virtually augmenting the detection view of optical-resolution photoacoustic microscopy.	Hsu HC, Li L, Yao J, Wong TTW, Shi J, Chen R, Zhou Q, Wang L	Journal of biomedical optics	29981225	J Biomed Opt	2018 Jul	https://www.ncbi.nlm.nih.gov/pubmed/29981225
A practical guide to photoacoustic tomography in the life sciences.	Wang LV, Yao J	Nature methods	27467726	Nat Methods	2016 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/27467726
Time-reversed ultrasonically encoded optical focusing through highly scattering ex vivo human cataractous lenses.	Liu Y, Shen Y, Ruan H, Brodie FL, Wong TTW, Yang C, Wang LV	Journal of biomedical optics	29322749	J Biomed Opt	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29322749
Transvaginal fast-scanning optical-resolution photoacoustic endoscopy.	Qu Y, Li C, Shi J, Chen R, Xu S, Rafsanjani H, Maslov K, Krigman H, Garvey L, Hu P, Zhao P, Meyers K, Diveley E, Pizzella S, Muench L, Punyamurthy N, Goldstein N, Onwumere O, Alisio M, Meyenburg K, Maynard J, Helm K, Slaughter J, Barber S, Burger T, Kramer C, Chubiz J, Anderson M, McCarthy R, England SK, Macones GA, Zhou Q, Shung KK, Zou J, Stout MJ, Tuuli M, Wang LV	Journal of biomedical optics	30520276	J Biomed Opt	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30520276
Multiscale Functional and Molecular Photoacoustic Tomography.	Yao J, Xia J, Wang LV	Ultrasonic imaging	25933617	Ultrason Imaging	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/25933617
Photoacoustic computed tomography of human extremities.	Wray P, Lin L, Hu P, Wang LV	Journal of biomedical optics	30784244	J Biomed Opt	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30784244
In vivo superresolution photoacoustic computed tomography by localization of single dyed droplets.	Zhang P, Li L, Lin L, Shi J, Wang LV	Light, science & applications	30962922	Light Sci Appl	2019	https://www.ncbi.nlm.nih.gov/pubmed/30962922
Real-time frequency-encoded spatiotemporal focusing through scattering media using a programmable 2D ultrafine optical frequency comb.	Wei X, Shen Y, Jing JC, Hemphill AS, Yang C, Xu S, Yang Z, Wang LV	Science advances	32128401	Sci Adv	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/32128401
Snapshot Photoacoustic Topography Through an Ergodic Relay for High-throughput Imaging of Optical Absorption.	Li Y, Li L, Zhu L, Maslov K, Shi J, Hu P, Bo E, Yao J, Liang J, Wang L, Wang LV	Nature photonics	34178097	Nat Photonics	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/34178097
Time-reversed ultrasonically encoded optical focusing using two ultrasonic transducers for improved ultrasonic axial resolution.	Yang Q, Xu X, Lai P, Xu D, Wang LV	Journal of biomedical optics	24194060	J Biomed Opt	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24194060
Ultrasound-heated photoacoustic flowmetry.	Wang L, Yao J, Maslov KI, Xing W, Wang LV	Journal of biomedical optics	24194064	J Biomed Opt	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24194064
Noise-equivalent sensitivity of photoacoustics.	Winkler AM, Maslov K, Wang LV	Journal of biomedical optics	24026425	J Biomed Opt	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/24026425
Focused fluorescence excitation with time-reversed ultrasonically encoded light and imaging in thick scattering media.	Lai P, Suzuki Y, Xu X, Wang LV	Laser physics letters	24465244	Laser Phys Lett	2013	https://www.ncbi.nlm.nih.gov/pubmed/24465244
Ultrasonically encoded wavefront shaping for focusing into random media.	Tay JW, Lai P, Suzuki Y, Wang LV	Scientific reports	24472822	Sci Rep	2014 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/24472822
Spatially Fourier-encoded photoacoustic microscopy using a digital micromirror device.	Liang J, Gao L, Li C, Wang LV	Optics letters	24487832	Opt Lett	2014 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/24487832
Graphene-based contrast agents for photoacoustic and thermoacoustic tomography.	Lalwani G, Cai X, Nie L, Wang LV, Sitharaman B	Photoacoustics	24490141	Photoacoustics	2013 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/24490141
Photobleaching imprinting microscopy: seeing clearer and deeper.	Gao L, Garcia-Uribe A, Liu Y, Li C, Wang LV	Journal of cell science	24317295	J Cell Sci	2014 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/24317295
Random-access optical-resolution photoacoustic microscopy using a digital micromirror device.	Liang J, Zhou Y, Winkler AW, Wang L, Maslov KI, Li C, Wang LV	Optics letters	23903111	Opt Lett	2013 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/23903111
Calibration-free in vivo transverse blood flowmetry based on cross correlation of slow time profiles from photoacoustic microscopy.	Zhou Y, Liang J, Maslov KI, Wang LV	Optics letters	24081077	Opt Lett	2013 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/24081077
Dry coupling for whole-body small-animal photoacoustic computed tomography.	Yeh C, Li L, Zhu L, Xia J, Li C, Chen W, Garcia-Uribe A, Maslov KI, Wang LV	Journal of biomedical optics	28241305	J Biomed Opt	2017 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/28241305
Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe.	Yao J, Kaberniuk AA, Li L, Shcherbakova DM, Zhang R, Wang L, Li G, Verkhusha VV, Wang LV	Nature methods	26550774	Nat Methods	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26550774
Photoacoustic elastography.	Hai P, Yao J, Li G, Li C, Wang LV	Optics letters	26872173	Opt Lett	2016 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/26872173
Photoacoustic tomography imaging and estimation of oxygen saturation of hemoglobin in ocular tissue of rabbits.	Hennen SN, Xing W, Shui YB, Zhou Y, Kalishman J, Andrews-Kaminsky LB, Kass MA, Beebe DC, Maslov KI, Wang LV	Experimental eye research	26048477	Exp Eye Res	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/26048477
Grueneisen relaxation photoacoustic microscopy in vivo.	Ma J, Shi J, Hai P, Zhou Y, Wang LV	Journal of biomedical optics	27272096	J Biomed Opt	2016 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/27272096
Photoacoustic tomography of vascular compliance in humans.	Hai P, Zhou Y, Liang J, Li C, Wang LV	Journal of biomedical optics	26720875	J Biomed Opt	2015	https://www.ncbi.nlm.nih.gov/pubmed/26720875
Quantitative photoacoustic elastography in humans.	Hai P, Zhou Y, Gong L, Wang LV	Journal of biomedical optics	27304419	J Biomed Opt	2016 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/27304419
Multiview Hilbert transformation for full-view photoacoustic computed tomography using a linear array.	Li G, Li L, Zhu L, Xia J, Wang LV	Journal of biomedical optics	26112369	J Biomed Opt	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/26112369
Cuffing-based photoacoustic flowmetry in humans in the optical diffusive regime.	Zhou Y, Liang J, Wang LV	Journal of biophotonics	26515158	J Biophotonics	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26515158
A microrobotic system guided by photoacoustic computed tomography for targeted navigation in intestines in vivo.	Wu Z, Li L, Yang Y, Hu P, Li Y, Yang SY, Wang LV, Gao W	Science robotics	32632399	Sci Robot	2019 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/32632399
Focusing light inside live tissue using reversibly switchable bacterial phytochrome as a genetically encoded photochromic guide star.	Yang J, Li L, Shemetov AA, Lee S, Zhao Y, Liu Y, Shen Y, Li J, Oka Y, Verkhusha VV, Wang LV	Science advances	31844671	Sci Adv	2019 Dec	https://www.ncbi.nlm.nih.gov/pubmed/31844671
High-speed single-shot optical focusing through dynamic scattering media with full-phase wavefront shaping.	Hemphill AS, Shen Y, Liu Y, Wang LV	Applied physics letters	29249832	Appl Phys Lett	2017 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/29249832
High-speed label-free functional photoacoustic microscopy of mouse brain in action.	Yao J, Wang L, Yang JM, Maslov KI, Wong TT, Li L, Huang CH, Zou J, Wang LV	Nature methods	25822799	Nat Methods	2015 May	https://www.ncbi.nlm.nih.gov/pubmed/25822799
Ultrasonic-heating-encoded photoacoustic tomography with virtually augmented detection view.	Wang L, Li G, Xia J, Wang LV	Optica	25984555	Optica	2015	https://www.ncbi.nlm.nih.gov/pubmed/25984555
Use of a single xenon flash lamp for photoacoustic computed tomography of multiple-centimeter-thick biological tissue ex vivo and a whole mouse body in vivo.	Wong TT, Zhou Y, Garcia-Uribe A, Li L, Maslov K, Lin L, Wang LV	Journal of biomedical optics	27775747	J Biomed Opt	2017 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/27775747
In vivo photoacoustic microscopy of human cuticle microvasculature with single-cell resolution.	Hsu HC, Wang L, Wang LV	Journal of biomedical optics	27207113	J Biomed Opt	2016 May 1	https://www.ncbi.nlm.nih.gov/pubmed/27207113
Imaging changes in the cytosolic ATP-to-ADP ratio.	Tantama M, Yellen G	Methods in enzymology	25416365	Methods Enzymol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25416365
BAD knockout provides metabolic seizure resistance in a genetic model of epilepsy with sudden unexplained death in epilepsy.	Foley J, Burnham V, Tedoldi M, Danial NN, Yellen G	Epilepsia	29171006	Epilepsia	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29171006
Hepatic NADH reductive stress underlies common variation in metabolic traits.	Goodman RP, Markhard AL, Shah H, Sharma R, Skinner OS, Clish CB, Deik A, Patgiri A, Hsu YH, Masia R, Noh HL, Suk S, Goldberger O, Hirschhorn JN, Yellen G, Kim JK, Mootha VK	Nature	32461692	Nature	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32461692
Akt regulation of glycolysis mediates bioenergetic stability in epithelial cells.	Hung YP, Teragawa C, Kosaisawe N, Gillies TE, Pargett M, Minguet M, Distor K, Rocha-Gregg BL, Coloff JL, Keibler MA, Stephanopoulos G, Yellen G, Brugge JS, Albeck JG	eLife	29239720	Elife	2017 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/29239720
Imaging energy status in live cells with a fluorescent biosensor of the intracellular ATP-to-ADP ratio.	Tantama M, Martínez-François JR, Mongeon R, Yellen G	Nature communications	24096541	Nat Commun	2013	https://www.ncbi.nlm.nih.gov/pubmed/24096541
Quantitative two-photon imaging of fluorescent biosensors.	Yellen G, Mongeon R	Current opinion in chemical biology	26079046	Curr Opin Chem Biol	2015 Aug	https://www.ncbi.nlm.nih.gov/pubmed/26079046
Live-cell imaging of cytosolic NADH-NAD+ redox state using a genetically encoded fluorescent biosensor.	Hung YP, Yellen G	Methods in molecular biology (Clifton, N.J.)	24052382	Methods Mol Biol	2014	https://www.ncbi.nlm.nih.gov/pubmed/24052382
Fueling thought: Management of glycolysis and oxidative phosphorylation in neuronal metabolism.	Yellen G	The Journal of cell biology	29752396	J Cell Biol	2018 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/29752396
BAD and K(ATP) channels regulate neuron excitability and epileptiform activity.	Martínez-François JR, Fernández-Agüera MC, Nathwani N, Lahmann C, Burnham VL, Danial NN, Yellen G	eLife	29368690	Elife	2018 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/29368690
Neuronal Stimulation Triggers Neuronal Glycolysis and Not Lactate Uptake.	Díaz-García CM, Mongeon R, Lahmann C, Koveal D, Zucker H, Yellen G	Cell metabolism	28768175	Cell Metab	2017 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/28768175
Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step.	Shestov AA, Liu X, Ser Z, Cluntun AA, Hung YP, Huang L, Kim D, Le A, Yellen G, Albeck JG, Locasale JW	eLife	25009227	Elife	2014 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/25009227
Quantitative in vivo imaging of neuronal glucose concentrations with a genetically encoded fluorescence lifetime sensor.	Díaz-García CM, Lahmann C, Martínez-François JR, Li B, Koveal D, Nathwani N, Rahman M, Keller JP, Marvin JS, Looger LL, Yellen G	Journal of neuroscience research	31106909	J Neurosci Res	2019 Aug	https://www.ncbi.nlm.nih.gov/pubmed/31106909
A PKA activity sensor for quantitative analysis of endogenous GPCR signaling via 2-photon FRET-FLIM imaging.	Chen Y, Saulnier JL, Yellen G, Sabatini BL	Frontiers in pharmacology	24765076	Front Pharmacol	2014	https://www.ncbi.nlm.nih.gov/pubmed/24765076
Cytosolic NADH-NAD(+) Redox Visualized in Brain Slices by Two-Photon Fluorescence Lifetime Biosensor Imaging.	Mongeon R, Venkatachalam V, Yellen G	Antioxidants & redox signaling	26857245	Antioxid Redox Signal	2016 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/26857245
The leak channel NALCN controls tonic firing and glycolytic sensitivity of substantia nigra pars reticulata neurons.	Lutas A, Lahmann C, Soumillon M, Yellen G	eLife	27177420	Elife	2016 May 13	https://www.ncbi.nlm.nih.gov/pubmed/27177420
Live cell imaging of cytosolic NADH/NAD(+) ratio in hepatocytes and liver slices.	Masia R, McCarty WJ, Lahmann C, Luther J, Chung RT, Yarmush ML, Yellen G	American journal of physiology. Gastrointestinal and liver physiology	29025729	Am J Physiol Gastrointest Liver Physiol	2018 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/29025729
Pretreatment of Asian elephant (Elephas maximus) spermatozoa with cholesterol-loaded cyclodextrins and glycerol addition at 4°C improves cryosurvival.	Kiso WK, Asano A, Travis AJ, Schmitt DL, Brown JL, Pukazhenthi BS	Reproduction, fertility, and development	22954260	Reprod Fertil Dev	2012	https://www.ncbi.nlm.nih.gov/pubmed/22954260
Biomimicry enhances sequential reactions of tethered glycolytic enzymes, TPI and GAPDHS.	Mukai C, Gao L, Bergkvist M, Nelson JL, Hinchman MM, Travis AJ	PloS one	23626684	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23626684
Biomimicry Promotes the Efficiency of a 10-Step Sequential Enzymatic Reaction on Nanoparticles, Converting Glucose to Lactate.	Mukai C, Gao L, Nelson JL, Lata JP, Cohen R, Wu L, Hinchman MM, Bergkvist M, Sherwood RW, Zhang S, Travis AJ	Angewandte Chemie (International ed. in English)	27901298	Angew Chem Int Ed Engl	2017 Jan 2	https://www.ncbi.nlm.nih.gov/pubmed/27901298
The role of MATER in endoplasmic reticulum distribution and calcium homeostasis in mouse oocytes.	Kim B, Zhang X, Kan R, Cohen R, Mukai C, Travis AJ, Coonrod SA	Developmental biology	24374158	Dev Biol	2014 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/24374158
Ferromagnetic nanoparticles with peroxidase-like activity enhance the cleavage of biological macromolecules for biofilm elimination.	Gao L, Giglio KM, Nelson JL, Sondermann H, Travis AJ	Nanoscale	24468900	Nanoscale	2014 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/24468900
Live Births from Domestic Dog (Canis familiaris) Embryos Produced by In Vitro Fertilization.	Nagashima JB, Sylvester SR, Nelson JL, Cheong SH, Mukai C, Lambo C, Flanders JA, Meyers-Wallen VN, Songsasen N, Travis AJ	PloS one	26650234	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26650234
Subwavelength lattice optics by evolutionary design.	Huntington MD, Lauhon LJ, Odom TW	Nano letters	25380062	Nano Lett	2014 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/25380062
Tunable loading of oligonucleotides with secondary structure on gold nanoparticles through a pH-driven method.	Dam DH, Lee H, Lee RC, Kim KH, Kelleher NL, Odom TW	Bioconjugate chemistry	25564799	Bioconjug Chem	2015 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/25564799
Enhanced Human Epidermal Growth Factor Receptor 2 Degradation in Breast Cancer Cells by Lysosome-Targeting Gold Nanoconstructs.	Lee H, Dam DH, Ha JW, Yue J, Odom TW	ACS nano	26335372	ACS Nano	2015 Oct 27	https://www.ncbi.nlm.nih.gov/pubmed/26335372
Challenges and Opportunities for Small-Molecule Fluorescent Probes in Redox Biology Applications.	Jiang X, Wang L, Carroll SL, Chen J, Wang MC, Wang J	Antioxidants & redox signaling	29320869	Antioxid Redox Signal	2018 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/29320869
'Inside Out'- a dialogue between mitochondria and bacteria.	Han B, Lin CJ, Hu G, Wang MC	The FEBS journal	30390412	FEBS J	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30390412
Does Autophagy Promote Longevity? It Depends.	Savini M, Wang MC	Cell	30951663	Cell	2019 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/30951663
Neuronal regulation of longevity by staying cool.	Lin CJ, Neve IAA, Wang MC	Genes & development	29491133	Genes Dev	2018 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/29491133
Escherichia coli Metabolite Profiling Leads to the Development of an RNA Interference Strain for Caenorhabditis elegans.	Neve IAA, Sowa JN, Lin CJ, Sivaramakrishnan P, Herman C, Ye Y, Han L, Wang MC	G3 (Bethesda, Md.)	31712257	G3 (Bethesda)	2020 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/31712257
Targeting calcium-mediated inter-organellar crosstalk in cardiac diseases.	Hulsurkar MM, Lahiri SK, Karch J, Wang MC, Wehrens XHT	Expert opinion on therapeutic targets	35426759	Expert Opin Ther Targets	2022 Apr	https://www.ncbi.nlm.nih.gov/pubmed/35426759
3D genomics across the tree of life reveals condensin II as a determinant of architecture type.	Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD	Science (New York, N.Y.)	34045355	Science	2021 May 28	https://www.ncbi.nlm.nih.gov/pubmed/34045355
Mitochondrial GTP metabolism controls reproductive aging in C. elegans.	Lee YT, Savini M, Chen T, Yang J, Zhao Q, Ding L, Gao SM, Senturk M, Sowa JN, Wang JD, Wang MC	Developmental cell	37708895	Dev Cell	2023 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/37708895
Optogenetic control of gut bacterial metabolism to promote longevity.	Hartsough LA, Park M, Kotlajich MV, Lazar JT, Han B, Lin CJ, Musteata E, Gambill L, Wang MC, Tabor JJ	eLife	33325823	Elife	2020 Dec 16	https://www.ncbi.nlm.nih.gov/pubmed/33325823
High-throughput screens using photo-highlighting discover BMP signaling in mitochondrial lipid oxidation.	Yu Y, Mutlu AS, Liu H, Wang MC	Nature communications	29021566	Nat Commun	2017 Oct 11	https://www.ncbi.nlm.nih.gov/pubmed/29021566
Lysosomal Signaling Promotes Longevity by Adjusting Mitochondrial Activity.	Ramachandran PV, Savini M, Folick AK, Hu K, Masand R, Graham BH, Wang MC	Developmental cell	30713071	Dev Cell	2019 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/30713071
Methyl-Sensing Nuclear Receptor Liver Receptor Homolog-1 Regulates Mitochondrial Function in Mouse Hepatocytes.	Choi S, Dong B, Lin CJ, Heo MJ, Kim KH, Sun Z, Wagner M, Putluri N, Suh JM, Wang MC, Moore DD	Hepatology (Baltimore, Md.)	31355949	Hepatology	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/31355949
Molecular Mechanisms of Lysosome and Nucleus Communication.	Zhao Q, Gao SM, Wang MC	Trends in biochemical sciences	32624271	Trends Biochem Sci	2020 Nov	https://www.ncbi.nlm.nih.gov/pubmed/32624271
Olfactory specificity regulates lipid metabolism through neuroendocrine signaling in Caenorhabditis elegans.	Mutlu AS, Gao SM, Zhang H, Wang MC	Nature communications	32193370	Nat Commun	2020 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/32193370
Lipid droplets and peroxisomes are co-regulated to drive lifespan extension in response to mono-unsaturated fatty acids.	Papsdorf K, Miklas JW, Hosseini A, Cabruja M, Morrow CS, Savini M, Yu Y, Silva-García CG, Haseley NR, Murphy LM, Yao P, de Launoit E, Dixon SJ, Snyder MP, Wang MC, Mair WB, Brunet A	Nature cell biology	37127715	Nat Cell Biol	2023 May	https://www.ncbi.nlm.nih.gov/pubmed/37127715
Localized glucose import, glycolytic processing, and mitochondria generate a focused ATP burst to power basement-membrane invasion.	Garde A, Kenny IW, Kelley LC, Chi Q, Mutlu AS, Wang MC, Sherwood DR	Developmental cell	35316617	Dev Cell	2022 Mar 28	https://www.ncbi.nlm.nih.gov/pubmed/35316617
Dissecting lipid droplet biology with coherent Raman scattering microscopy.	Chen T, Yavuz A, Wang MC	Journal of cell science	33975358	J Cell Sci	2022 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/33975358
The Bacterivore's Solution: Fight and Flight to Promote Survival.	Lee YT, Wang MC	Developmental cell	30965036	Dev Cell	2019 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/30965036
Structural characterization of life-extending Caenorhabditis elegans Lipid Binding Protein 8.	Tillman MC, Khadka M, Duffy J, Wang MC, Ortlund EA	Scientific reports	31292465	Sci Rep	2019 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/31292465
Fingerprint Stimulated Raman Scattering Imaging Reveals Retinoid Coupling Lipid Metabolism and Survival.	Chen AJ, Li J, Jannasch A, Mutlu AS, Wang MC, Cheng JX	Chemphyschem : a European journal of chemical physics and physical chemistry	29911339	Chemphyschem	2018 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/29911339
Microbial Genetic Composition Tunes Host Longevity.	Han B, Sivaramakrishnan P, Lin CJ, Neve IAA, He J, Tay LWR, Sowa JN, Sizovs A, Du G, Wang J, Herman C, Wang MC	Cell	29727664	Cell	2018 May 3	https://www.ncbi.nlm.nih.gov/pubmed/29727664
Lysosome lipid signalling from the periphery to neurons regulates longevity.	Savini M, Folick A, Lee YT, Jin F, Cuevas A, Tillman MC, Duffy JD, Zhao Q, Neve IA, Hu PW, Yu Y, Zhang Q, Ye Y, Mair WB, Wang J, Han L, Ortlund EA, Wang MC	Nature cell biology	35681008	Nat Cell Biol	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35681008
Aging: Antagonistic Pleiotropy Supported by Gut Eating.	Park M, Wang MC	Current biology : CB	30130513	Curr Biol	2018 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/30130513
Building multidisciplinary research.	Wang MC	Molecular biology of the cell	29084905	Mol Biol Cell	2017 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/29084905
Microbial Genetic Composition Tunes Host Longevity.	Han B, Sivaramakrishnan P, Lin CJ, Neve IAA, He J, Tay LWR, Sowa JN, Sizovs A, Du G, Wang J, Herman C, Wang MC	Cell	28622510	Cell	2017 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/28622510
Quantitative Real-Time Imaging of Glutathione with Subcellular Resolution.	Jiang X, Zhang C, Chen J, Choi S, Zhou Y, Zhao M, Song X, Chen X, Maletić-Savatić M, Palzkill T, Moore D, Wang MC, Wang J	Antioxidants & redox signaling	30358421	Antioxid Redox Signal	2019 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/30358421
Label-Free Imaging of Lipid Storage Dynamics in Caenorhabditis elegans using Stimulated Raman Scattering Microscopy.	Mutlu AS, Chen T, Deng D, Wang MC	Journal of visualized experiments : JoVE	34125101	J Vis Exp	2021 May 28	https://www.ncbi.nlm.nih.gov/pubmed/34125101
Microbial metabolites regulate host lipid metabolism through NR5A-Hedgehog signalling.	Lin CJ, Wang MC	Nature cell biology	28436966	Nat Cell Biol	2017 May	https://www.ncbi.nlm.nih.gov/pubmed/28436966
Reversible Reaction-Based Fluorescent Probe for Real-Time Imaging of Glutathione Dynamics in Mitochondria.	Chen J, Jiang X, Zhang C, MacKenzie KR, Stossi F, Palzkill T, Wang MC, Wang J	ACS sensors	28809477	ACS Sens	2017 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/28809477
Quantitative real-time imaging of glutathione.	Jiang X, Chen J, Bajić A, Zhang C, Song X, Carroll SL, Cai ZL, Tang M, Xue M, Cheng N, Schaaf CP, Li F, MacKenzie KR, Ferreon ACM, Xia F, Wang MC, Maletić-Savatić M, Wang J	Nature communications	28703127	Nat Commun	2017 Jul 13	https://www.ncbi.nlm.nih.gov/pubmed/28703127
Lysosomes: Signaling Hubs for Metabolic Sensing and Longevity.	Savini M, Zhao Q, Wang MC	Trends in cell biology	31611045	Trends Cell Biol	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31611045
Lipid metabolism and lipid signals in aging and longevity.	Mutlu AS, Duffy J, Wang MC	Developmental cell	33891896	Dev Cell	2021 May 17	https://www.ncbi.nlm.nih.gov/pubmed/33891896
Host and microbiota metabolic signals in aging and longevity.	Zhou Y, Hu G, Wang MC	Nature chemical biology	34552221	Nat Chem Biol	2021 Oct	https://www.ncbi.nlm.nih.gov/pubmed/34552221
Mediterranean mechanisms of longevity.	Mendenhall AR	Nature cell biology	37127713	Nat Cell Biol	2023 May	https://www.ncbi.nlm.nih.gov/pubmed/37127713
Aging atlas reveals cell-type-specific effects of pro-longevity strategies.	Gao SM, Qi Y, Zhang Q, Guan Y, Lee YT, Ding L, Wang L, Mohammed AS, Li H, Fu Y, Wang MC	Nature aging	38816550	Nat Aging	2024 Jul	https://www.ncbi.nlm.nih.gov/pubmed/38816550
Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain.	McKee SE, Zhang S, Chen L, Rabinowitz JD, Reyes TM	Journal of neurochemistry	29423909	J Neurochem	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29423909
Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors.	Lu W, Wang L, Chen L, Hui S, Rabinowitz JD	Antioxidants & redox signaling	28497978	Antioxid Redox Signal	2018 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/28497978
Chemical Basis for Deuterium Labeling of Fat and NADPH.	Zhang Z, Chen L, Liu L, Su X, Rabinowitz JD	Journal of the American Chemical Society	28911221	J Am Chem Soc	2017 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/28911221
mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein.	Nofal M, Zhang K, Han S, Rabinowitz JD	Molecular cell	28918901	Mol Cell	2017 Sep 21	https://www.ncbi.nlm.nih.gov/pubmed/28918901
Serine Catabolism Feeds NADH when Respiration Is Impaired.	Yang L, Garcia Canaveras JC, Chen Z, Wang L, Liang L, Jang C, Mayr JA, Zhang Z, Ghergurovich JM, Zhan L, Joshi S, Hu Z, McReynolds MR, Su X, White E, Morscher RJ, Rabinowitz JD	Cell metabolism	32187526	Cell Metab	2020 Apr 7	https://www.ncbi.nlm.nih.gov/pubmed/32187526
Novel Pyrrolo[3,2-d]pyrimidine Compounds Target Mitochondrial and Cytosolic One-carbon Metabolism with Broad-spectrum Antitumor Efficacy.	Dekhne AS, Shah K, Ducker GS, Katinas JM, Wong-Roushar J, Nayeen MJ, Doshi A, Ning C, Bao X, Frühauf J, Liu J, Wallace-Povirk A, O'Connor C, Dzinic SH, White K, Kushner J, Kim S, Hüttemann M, Polin L, Rabinowitz JD, Li J, Hou Z, Dann CE 3rd, Gangjee A, Matherly LH	Molecular cancer therapeutics	31289137	Mol Cancer Ther	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31289137
The metabolites NADP(+) and NADPH are the targets of the circadian protein Nocturnin (Curled).	Estrella MA, Du J, Chen L, Rath S, Prangley E, Chitrakar A, Aoki T, Schedl P, Rabinowitz J, Korennykh A	Nature communications	31147539	Nat Commun	2019 May 30	https://www.ncbi.nlm.nih.gov/pubmed/31147539
Quantitative flux analysis in mammals.	Bartman CR, TeSlaa T, Rabinowitz JD	Nature metabolism	34211182	Nat Metab	2021 Jul	https://www.ncbi.nlm.nih.gov/pubmed/34211182
The Source of Glycolytic Intermediates in Mammalian Tissues.	TeSlaa T, Bartman CR, Jankowski CSR, Zhang Z, Xu X, Xing X, Wang L, Lu W, Hui S, Rabinowitz JD	Cell metabolism	33472024	Cell Metab	2021 Feb 2	https://www.ncbi.nlm.nih.gov/pubmed/33472024
GCN2 adapts protein synthesis to scavenging-dependent growth.	Nofal M, Wang T, Yang L, Jankowski CSR, Hsin-Jung Li S, Han S, Parsons L, Frese AN, Gitai Z, Anthony TG, Wühr M, Sabatini DM, Rabinowitz JD	Cell systems	34706266	Cell Syst	2022 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/34706266
Spatially resolved isotope tracing reveals tissue metabolic activity.	Wang L, Xing X, Zeng X, Jackson SR, TeSlaa T, Al-Dalahmah O, Samarah LZ, Goodwin K, Yang L, McReynolds MR, Li X, Wolff JJ, Rabinowitz JD, Davidson SM	Nature methods	35132243	Nat Methods	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/35132243
Monitoring mammalian mitochondrial translation with MitoRiboSeq.	Li SH, Nofal M, Parsons LR, Rabinowitz JD, Gitai Z	Nature protocols	33953394	Nat Protoc	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33953394
Gut bacterial nutrient preferences quantified in vivo.	Zeng X, Xing X, Gupta M, Keber FC, Lopez JG, Lee YJ, Roichman A, Wang L, Neinast MD, Donia MS, Wühr M, Jang C, Rabinowitz JD	Cell	36055202	Cell	2022 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/36055202
Metabolite Exchange between Mammalian Organs Quantified in Pigs.	Jang C, Hui S, Zeng X, Cowan AJ, Wang L, Chen L, Morscher RJ, Reyes J, Frezza C, Hwang HY, Imai A, Saito Y, Okamoto K, Vaspoli C, Kasprenski L, Zsido GA 2nd, Gorman JH 3rd, Gorman RC, Rabinowitz JD	Cell metabolism	36070684	Cell Metab	2022 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/36070684
NAD precursors cycle between host tissues and the gut microbiome.	Chellappa K, McReynolds MR, Lu W, Zeng X, Makarov M, Hayat F, Mukherjee S, Bhat YR, Lingala SR, Shima RT, Descamps HC, Cox T, Ji L, Jankowski C, Chu Q, Davidson SM, Thaiss CA, Migaud ME, Rabinowitz JD, Baur JA	Cell metabolism	36476934	Cell Metab	2022 Dec 6	https://www.ncbi.nlm.nih.gov/pubmed/36476934
Glycine homeostasis requires reverse SHMT flux.	McBride MJ, Hunter CJ, Zhang Z, TeSlaa T, Xu X, Ducker GS, Rabinowitz JD	Cell metabolism	38171330	Cell Metab	2024 Jan 2	https://www.ncbi.nlm.nih.gov/pubmed/38171330
Serine Metabolism Supports Macrophage IL-1β Production.	Rodriguez AE, Ducker GS, Billingham LK, Martinez CA, Mainolfi N, Suri V, Friedman A, Manfredi MG, Weinberg SE, Rabinowitz JD, Chandel NS	Cell metabolism	30773464	Cell Metab	2019 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/30773464
Lactate: the ugly duckling of energy metabolism.	Rabinowitz JD, Enerbäck S	Nature metabolism	32694798	Nat Metab	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32694798
Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity.	Lu W, Xing X, Wang L, Chen L, Zhang S, McReynolds MR, Rabinowitz JD	Analytical chemistry	32614575	Anal Chem	2020 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/32614575
Quantitative Fluxomics of Circulating Metabolites.	Hui S, Cowan AJ, Zeng X, Yang L, TeSlaa T, Li X, Bartman C, Zhang Z, Jang C, Wang L, Lu W, Rojas J, Baur J, Rabinowitz JD	Cell metabolism	32791100	Cell Metab	2020 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/32791100
Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate.	Zhao S, Jang C, Liu J, Uehara K, Gilbert M, Izzo L, Zeng X, Trefely S, Fernandez S, Carrer A, Miller KD, Schug ZT, Snyder NW, Gade TP, Titchenell PM, Rabinowitz JD, Wellen KE	Nature	32214246	Nature	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/32214246
Four Key Steps Control Glycolytic Flux in Mammalian Cells.	Tanner LB, Goglia AG, Wei MH, Sehgal T, Parsons LR, Park JO, White E, Toettcher JE, Rabinowitz JD	Cell systems	29960885	Cell Syst	2018 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/29960885
Mitochondrial translation requires folate-dependent tRNA methylation.	Morscher RJ, Ducker GS, Li SH, Mayer JA, Gitai Z, Sperl W, Rabinowitz JD	Nature	29364879	Nature	2018 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/29364879
mTORC1 promotes cell growth via m(6)A-dependent mRNA degradation.	Cho S, Lee G, Pickering BF, Jang C, Park JH, He L, Mathur L, Kim SS, Jung S, Tang HW, Monette S, Rabinowitz JD, Perrimon N, Jaffrey SR, Blenis J	Molecular cell	33756105	Mol Cell	2021 May 20	https://www.ncbi.nlm.nih.gov/pubmed/33756105
Local production of lactate, ribose phosphate, and amino acids within human triple-negative breast cancer.	Ghergurovich JM, Lang JD, Levin MK, Briones N, Facista SJ, Mueller C, Cowan AJ, McBride MJ, Rodriguez ESR, Killian A, Dao T, Lamont J, Barron A, Su X, Hendricks WPD, Espina V, Von Hoff DD, O'Shaughnessy J, Rabinowitz JD	Med (New York, N.Y.)	34223403	Med	2021 Jun 11	https://www.ncbi.nlm.nih.gov/pubmed/34223403
NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism.	Chen L, Zhang Z, Hoshino A, Zheng HD, Morley M, Arany Z, Rabinowitz JD	Nature metabolism	31058257	Nat Metab	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/31058257
Impact of acute stress on murine metabolomics and metabolic flux.	Lee WD, Liang L, AbuSalim J, Jankowski CSR, Samarah LZ, Neinast MD, Rabinowitz JD	Proceedings of the National Academy of Sciences of the United States of America	37186827	Proc Natl Acad Sci U S A	2023 May 23	https://www.ncbi.nlm.nih.gov/pubmed/37186827
Myeloid-derived itaconate suppresses cytotoxic CD8(+) T cells and promotes tumour growth.	Zhao H, Teng D, Yang L, Xu X, Chen J, Jiang T, Feng AY, Zhang Y, Frederick DT, Gu L, Cai L, Asara JM, Pasca di Magliano M, Boland GM, Flaherty KT, Swanson KD, Liu D, Rabinowitz JD, Zheng B	Nature metabolism	36376563	Nat Metab	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36376563
Serine catabolism generates liver NADPH and supports hepatic lipogenesis.	Zhang Z, TeSlaa T, Xu X, Zeng X, Yang L, Xing G, Tesz GJ, Clasquin MF, Rabinowitz JD	Nature metabolism	34845393	Nat Metab	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/34845393
Slow TCA flux and ATP production in primary solid tumours but not metastases.	Bartman CR, Weilandt DR, Shen Y, Lee WD, Han Y, TeSlaa T, Jankowski CSR, Samarah L, Park NR, da Silva-Diz V, Aleksandrova M, Gultekin Y, Marishta A, Wang L, Yang L, Roichman A, Bhatt V, Lan T, Hu Z, Xing X, Lu W, Davidson S, Wühr M, Vander Heiden MG, Herranz D, Guo JY, Kang Y, Rabinowitz JD	Nature	36725930	Nature	2023 Feb	https://www.ncbi.nlm.nih.gov/pubmed/36725930
NAD(+) flux is maintained in aged mice despite lower tissue concentrations.	McReynolds MR, Chellappa K, Chiles E, Jankowski C, Shen Y, Chen L, Descamps HC, Mukherjee S, Bhat YR, Lingala SR, Chu Q, Botolin P, Hayat F, Doke T, Susztak K, Thaiss CA, Lu W, Migaud ME, Su X, Rabinowitz JD, Baur JA	Cell systems	34559996	Cell Syst	2021 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/34559996
Sex and genetic background define the metabolic, physiologic, and molecular response to protein restriction.	Green CL, Pak HH, Richardson NE, Flores V, Yu D, Tomasiewicz JL, Dumas SN, Kredell K, Fan JW, Kirsh C, Chaiyakul K, Murphy ME, Babygirija R, Barrett-Wilt GA, Rabinowitz J, Ong IM, Jang C, Simcox J, Lamming DW	Cell metabolism	35108511	Cell Metab	2022 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/35108511
Methionine synthase supports tumour tetrahydrofolate pools.	Ghergurovich JM, Xu X, Wang JZ, Yang L, Ryseck RP, Wang L, Rabinowitz JD	Nature metabolism	34799699	Nat Metab	2021 Nov	https://www.ncbi.nlm.nih.gov/pubmed/34799699
5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination.	Rodan LH, Qi W, Ducker GS, Demirbas D, Laine R, Yang E, Walker MA, Eichler F, Rabinowitz JD, Anselm I, Berry GT, Undiagnosed Diseases Network (UDN)	Molecular genetics and metabolism	30031689	Mol Genet Metab	2018 Sep	https://www.ncbi.nlm.nih.gov/pubmed/30031689
Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8(+) T cell stemness and antitumor immunity.	Hermans D, Gautam S, García-Cañaveras JC, Gromer D, Mitra S, Spolski R, Li P, Christensen S, Nguyen R, Lin JX, Oh J, Du N, Veenbergen S, Fioravanti J, Ebina-Shibuya R, Bleck C, Neckers LM, Rabinowitz JD, Gattinoni L, Leonard WJ	Proceedings of the National Academy of Sciences of the United States of America	32123114	Proc Natl Acad Sci U S A	2020 Mar 17	https://www.ncbi.nlm.nih.gov/pubmed/32123114
The adverse metabolic effects of branched-chain amino acids are mediated by isoleucine and valine.	Yu D, Richardson NE, Green CL, Spicer AB, Murphy ME, Flores V, Jang C, Kasza I, Nikodemova M, Wakai MH, Tomasiewicz JL, Yang SE, Miller BR, Pak HH, Brinkman JA, Rojas JM, Quinn WJ 3rd, Cheng EP, Konon EN, Haider LR, Finke M, Sonsalla M, Alexander CM, Rabinowitz JD, Baur JA, Malecki KC, Lamming DW	Cell metabolism	33887198	Cell Metab	2021 May 4	https://www.ncbi.nlm.nih.gov/pubmed/33887198
SHMT inhibition is effective and synergizes with methotrexate in T-cell acute lymphoblastic leukemia.	García-Cañaveras JC, Lancho O, Ducker GS, Ghergurovich JM, Xu X, da Silva-Diz V, Minuzzo S, Indraccolo S, Kim H, Herranz D, Rabinowitz JD	Leukemia	32382081	Leukemia	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/32382081
Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids.	Neinast MD, Jang C, Hui S, Murashige DS, Chu Q, Morscher RJ, Li X, Zhan L, White E, Anthony TG, Rabinowitz JD, Arany Z	Cell metabolism	30449684	Cell Metab	2019 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/30449684
Macrophage de novo NAD(+) synthesis specifies immune function in aging and inflammation.	Minhas PS, Liu L, Moon PK, Joshi AU, Dove C, Mhatre S, Contrepois K, Wang Q, Lee BA, Coronado M, Bernstein D, Snyder MP, Migaud M, Majeti R, Mochly-Rosen D, Rabinowitz JD, Andreasson KI	Nature immunology	30478397	Nat Immunol	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30478397
Metabolomics and Isotope Tracing.	Jang C, Chen L, Rabinowitz JD	Cell	29727671	Cell	2018 May 3	https://www.ncbi.nlm.nih.gov/pubmed/29727671
Circulating metabolite homeostasis achieved through mass action.	Li X, Hui S, Mirek ET, Jonsson WO, Anthony TG, Lee WD, Zeng X, Jang C, Rabinowitz JD	Nature metabolism	35058631	Nat Metab	2022 Jan	https://www.ncbi.nlm.nih.gov/pubmed/35058631
Lactate homeostasis is maintained through regulation of glycolysis and lipolysis.	Lee WD, Weilandt DR, Liang L, MacArthur MR, Jaiswal N, Ong O, Mann CG, Chu Q, Hunter CJ, Ryseck RP, Lu W, Oschmann AM, Cowan AJ, TeSlaa TA, Bartman CR, Jang C, Baur JA, Titchenell PM, Rabinowitz JD	Cell metabolism	39889702	Cell Metab	2025 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/39889702
Quantitative Analysis of NAD Synthesis-Breakdown Fluxes.	Liu L, Su X, Quinn WJ 3rd, Hui S, Krukenberg K, Frederick DW, Redpath P, Zhan L, Chellappa K, White E, Migaud M, Mitchison TJ, Baur JA, Rabinowitz JD	Cell metabolism	29685734	Cell Metab	2018 May 1	https://www.ncbi.nlm.nih.gov/pubmed/29685734
The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.	Jang C, Hui S, Lu W, Cowan AJ, Morscher RJ, Lee G, Liu W, Tesz GJ, Birnbaum MJ, Rabinowitz JD	Cell metabolism	29414685	Cell Metab	2018 Feb 6	https://www.ncbi.nlm.nih.gov/pubmed/29414685
Restoring metabolism of myeloid cells reverses cognitive decline in ageing.	Minhas PS, Latif-Hernandez A, McReynolds MR, Durairaj AS, Wang Q, Rubin A, Joshi AU, He JQ, Gauba E, Liu L, Wang C, Linde M, Sugiura Y, Moon PK, Majeti R, Suematsu M, Mochly-Rosen D, Weissman IL, Longo FM, Rabinowitz JD, Andreasson KI	Nature	33473210	Nature	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33473210
The small intestine shields the liver from fructose-induced steatosis.	Jang C, Wada S, Yang S, Gosis B, Zeng X, Zhang Z, Shen Y, Lee G, Arany Z, Rabinowitz JD	Nature metabolism	32694791	Nat Metab	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32694791
Comprehensive quantification of fuel use by the failing and nonfailing human heart.	Murashige D, Jang C, Neinast M, Edwards JJ, Cowan A, Hyman MC, Rabinowitz JD, Frankel DS, Arany Z	Science (New York, N.Y.)	33060364	Science	2020 Oct 16	https://www.ncbi.nlm.nih.gov/pubmed/33060364
Metabolite Exchange between Mammalian Organs Quantified in Pigs.	Jang C, Hui S, Zeng X, Cowan AJ, Wang L, Chen L, Morscher RJ, Reyes J, Frezza C, Hwang HY, Imai A, Saito Y, Okamoto K, Vaspoli C, Kasprenski L, Zsido GA 2nd, Gorman JH 3rd, Gorman RC, Rabinowitz JD	Cell metabolism	31257152	Cell Metab	2019 Sep 3	https://www.ncbi.nlm.nih.gov/pubmed/31257152
A small molecule G6PD inhibitor reveals immune dependence on pentose phosphate pathway.	Ghergurovich JM, García-Cañaveras JC, Wang J, Schmidt E, Zhang Z, TeSlaa T, Patel H, Chen L, Britt EC, Piqueras-Nebot M, Gomez-Cabrera MC, Lahoz A, Fan J, Beier UH, Kim H, Rabinowitz JD	Nature chemical biology	32393898	Nat Chem Biol	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32393898
Glucose-6-Phosphate Dehydrogenase Is Not Essential for K-Ras-Driven Tumor Growth or Metastasis.	Ghergurovich JM, Esposito M, Chen Z, Wang JZ, Bhatt V, Lan T, White E, Kang Y, Guo JY, Rabinowitz JD	Cancer research	32661137	Cancer Res	2020 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/32661137
Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics.	Wang L, Xing X, Chen L, Yang L, Su X, Rabitz H, Lu W, Rabinowitz JD	Analytical chemistry	30586294	Anal Chem	2019 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/30586294
Metabolite Measurement: Pitfalls to Avoid and Practices to Follow.	Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD	Annual review of biochemistry	28654323	Annu Rev Biochem	2017 Jun 20	https://www.ncbi.nlm.nih.gov/pubmed/28654323
Glucose feeds the TCA cycle via circulating lactate.	Hui S, Ghergurovich JM, Morscher RJ, Jang C, Teng X, Lu W, Esparza LA, Reya T, Le Zhan, Yanxiang Guo J, White E, Rabinowitz JD	Nature	29045397	Nature	2017 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/29045397
Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth.	Yang L, TeSlaa T, Ng S, Nofal M, Wang L, Lan T, Zeng X, Cowan A, McBride M, Lu W, Davidson S, Liang G, Oh TG, Downes M, Evans R, Von Hoff D, Guo JY, Han H, Rabinowitz JD	Med (New York, N.Y.)	35425930	Med	2022 Feb 11	https://www.ncbi.nlm.nih.gov/pubmed/35425930
The pentose phosphate pathway in health and disease.	TeSlaa T, Ralser M, Fan J, Rabinowitz JD	Nature metabolism	37612403	Nat Metab	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37612403
One-carbon unit supplementation fuels tumor-infiltrating T cells and augments checkpoint blockade.	Xu X, Chen Z, Bartman CR, Xing X, Olszewski K, Rabinowitz JD	bioRxiv : the preprint server for biology	37961420	bioRxiv	2023 Nov 3	https://www.ncbi.nlm.nih.gov/pubmed/37961420
Reprogramming neuroblastoma by diet-enhanced polyamine depletion.	Cherkaoui S, Yang L, McBride M, Turn CS, Lu W, Eigenmann C, Allen GE, Panasenko OO, Zhang L, Vu A, Liu K, Li Y, Gandhi OH, Surrey L, Wierer M, White E, Rabinowitz JD, Hogarty MD, Morscher RJ	bioRxiv : the preprint server for biology	38260457	bioRxiv	2024 Jan 8	https://www.ncbi.nlm.nih.gov/pubmed/38260457
CRISPR-Cas9 mediated one-step disabling of pancreatogenesis in pigs.	Wu J, Vilarino M, Suzuki K, Okamura D, Bogliotti YS, Park I, Rowe J, McNabb B, Ross PJ, Belmonte JCI	Scientific reports	28874671	Sci Rep	2017 Sep 5	https://www.ncbi.nlm.nih.gov/pubmed/28874671
Precise in vivo genome editing via single homology arm donor mediated intron-targeting gene integration for genetic disease correction.	Suzuki K, Yamamoto M, Hernandez-Benitez R, Li Z, Wei C, Soligalla RD, Aizawa E, Hatanaka F, Kurita M, Reddy P, Ocampo A, Hishida T, Sakurai M, Nemeth AN, Nuñez Delicado E, Campistol JM, Magistretti P, Guillen P, Rodriguez Esteban C, Gong J, Yuan Y, Gu Y, Liu GH, López-Otín C, Wu J, Zhang K, Izpisua Belmonte JC	Cell research	31444470	Cell Res	2019 Oct	https://www.ncbi.nlm.nih.gov/pubmed/31444470
Deconstructing the pluripotency gene regulatory network.	Li M, Izpisua Belmonte JC	Nature cell biology	29593328	Nat Cell Biol	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29593328
Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts.	Bogliotti YS, Wu J, Vilarino M, Okamura D, Soto DA, Zhong C, Sakurai M, Sampaio RV, Suzuki K, Izpisua Belmonte JC, Ross PJ	Proceedings of the National Academy of Sciences of the United States of America	29440377	Proc Natl Acad Sci U S A	2018 Feb 27	https://www.ncbi.nlm.nih.gov/pubmed/29440377
Generation of Blastocyst-like Structures from Mouse Embryonic and Adult Cell Cultures.	Li R, Zhong C, Yu Y, Liu H, Sakurai M, Yu L, Min Z, Shi L, Wei Y, Takahashi Y, Liao HK, Qiao J, Deng H, Nuñez-Delicado E, Rodriguez Esteban C, Wu J, Izpisua Belmonte JC	Cell	31626770	Cell	2019 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/31626770
Functional sensory circuits built from neurons of two species.	Throesch BT, Bin Imtiaz MK, Muñoz-Castañeda R, Sakurai M, Hartzell AL, James KN, Rodriguez AR, Martin G, Lippi G, Kupriyanov S, Wu Z, Osten P, Izpisua Belmonte JC, Wu J, Baldwin KK	Cell	38670072	Cell	2024 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/38670072
Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential.	Skye SM, Zhu W, Romano KA, Guo CJ, Wang Z, Jia X, Kirsop J, Haag B, Lang JM, DiDonato JA, Tang WHW, Lusis AJ, Rey FE, Fischbach MA, Hazen SL	Circulation research	30359185	Circ Res	2018 Oct 26	https://www.ncbi.nlm.nih.gov/pubmed/30359185
A metabolic pathway for bile acid dehydroxylation by the gut microbiome.	Funabashi M, Grove TL, Wang M, Varma Y, McFadden ME, Brown LC, Guo C, Higginbottom S, Almo SC, Fischbach MA	Nature	32555455	Nature	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/32555455
A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles.	Claesen J, Spagnolo JB, Ramos SF, Kurita KL, Byrd AL, Aksenov AA, Melnik AV, Wong WR, Wang S, Hernandez RD, Donia MS, Dorrestein PC, Kong HH, Segre JA, Linington RG, Fischbach MA, Lemon KP	Science translational medicine	33208503	Sci Transl Med	2020 Nov 18	https://www.ncbi.nlm.nih.gov/pubmed/33208503
Microbiome: Focus on Causation and Mechanism.	Fischbach MA	Cell	30096310	Cell	2018 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/30096310
Skin microbiota-host interactions.	Chen YE, Fischbach MA, Belkaid Y	Nature	29364286	Nature	2018 Jan 24	https://www.ncbi.nlm.nih.gov/pubmed/29364286
Depletion of microbiome-derived molecules in the host using Clostridium genetics.	Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, Nagashima K, Fischer CR, Sonnenburg JL, Spitzer MH, Fischbach MA	Science (New York, N.Y.)	31831639	Science	2019 Dec 13	https://www.ncbi.nlm.nih.gov/pubmed/31831639
Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA	Cell	36070752	Cell	2022 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/36070752
Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota.	Lima-Junior DS, Krishnamurthy SR, Bouladoux N, Collins N, Han SJ, Chen EY, Constantinides MG, Link VM, Lim AI, Enamorado M, Cataisson C, Gil L, Rao I, Farley TK, Koroleva G, Attig J, Yuspa SH, Fischbach MA, Kassiotis G, Belkaid Y	Cell	34166614	Cell	2021 Jul 8	https://www.ncbi.nlm.nih.gov/pubmed/34166614
Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA	Cell	37352836	Cell	2023 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/37352836
gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.	Pascal Andreu V, Augustijn HE, Chen L, Zhernakova A, Fu J, Fischbach MA, Dodd D, Medema MH	Nature biotechnology	36782070	Nat Biotechnol	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36782070
Mapping the Genetic Landscape of Human Cells.	Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA	Cell	30033366	Cell	2018 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/30033366
Bile acids profile, histopathological indices and genetic variants for non-alcoholic fatty liver disease progression.	Nimer N, Choucair I, Wang Z, Nemet I, Li L, Gukasyan J, Weeks TL, Alkhouri N, Zein N, Tang WHW, Fischbach MA, Brown JM, Allayee H, Dasarathy S, Gogonea V, Hazen SL	Metabolism: clinical and experimental	33275980	Metabolism	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33275980
Contextual control of skin immunity and inflammation by Corynebacterium.	Ridaura VK, Bouladoux N, Claesen J, Chen YE, Byrd AL, Constantinides MG, Merrill ED, Tamoutounour S, Fischbach MA, Belkaid Y	The Journal of experimental medicine	29382696	J Exp Med	2018 Mar 5	https://www.ncbi.nlm.nih.gov/pubmed/29382696
A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites.	Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL	Nature	29168502	Nature	2017 Nov 30	https://www.ncbi.nlm.nih.gov/pubmed/29168502
Comprehensive Clinical and Genetic Analyses of Circulating Bile Acids and Their Associations With Diabetes and Its Indices.	Choucair I, Mallela DP, Hilser JR, Hartiala JA, Nemet I, Gogonea V, Li L, Lusis AJ, Fischbach MA, Tang WHW, Allayee H, Hazen SL	Diabetes	38701355	Diabetes	2024 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/38701355
The Biosynthesis of Lipooligosaccharide from Bacteroides thetaiotaomicron.	Jacobson AN, Choudhury BP, Fischbach MA	mBio	29535205	mBio	2018 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/29535205
A metabolomics pipeline for the mechanistic interrogation of the gut microbiome.	Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL	Nature	34262212	Nature	2021 Jul	https://www.ncbi.nlm.nih.gov/pubmed/34262212
MAIT cells are imprinted by the microbiota in early life and promote tissue repair.	Constantinides MG, Link VM, Tamoutounour S, Wong AC, Perez-Chaparro PJ, Han SJ, Chen YE, Li K, Farhat S, Weckel A, Krishnamurthy SR, Vujkovic-Cvijin I, Linehan JL, Bouladoux N, Merrill ED, Roy S, Cua DJ, Adams EJ, Bhandoola A, Scharschmidt TC, Aubé J, Fischbach MA, Belkaid Y	Science (New York, N.Y.)	31649166	Science	2019 Oct 25	https://www.ncbi.nlm.nih.gov/pubmed/31649166
CRISPR-based functional genomics in human dendritic cells.	Jost M, Jacobson AN, Hussmann JA, Cirolia G, Fischbach MA, Weissman JS	eLife	33904395	Elife	2021 Apr 27	https://www.ncbi.nlm.nih.gov/pubmed/33904395
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota.	Pascal Andreu V, Roel-Touris J, Dodd D, Fischbach MA, Medema MH	Nucleic acids research	34019648	Nucleic Acids Res	2021 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/34019648
MHC II+ resident peritoneal and pleural macrophages rely on IRF4 for development from circulating monocytes.	Kim KW, Williams JW, Wang YT, Ivanov S, Gilfillan S, Colonna M, Virgin HW, Gautier EL, Randolph GJ	The Journal of experimental medicine	27551152	J Exp Med	2016 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/27551152
CD36 deficiency impairs the small intestinal barrier and induces subclinical inflammation in mice.	Cifarelli V, Ivanov S, Xie Y, Son NH, Saunders BT, Pietka TA, Shew TM, Yoshino J, Sundaresan S, Davidson NO, Goldberg IJ, Gelman AE, Zinselmeyer BH, Randolph GJ, Abumrad NA	Cellular and molecular gastroenterology and hepatology	28066800	Cell Mol Gastroenterol Hepatol	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/28066800
The Lymphatic System: Integral Roles in Immunity.	Randolph GJ, Ivanov S, Zinselmeyer BH, Scallan JP	Annual review of immunology	27860528	Annu Rev Immunol	2017 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/27860528
Tissue-Resident Macrophages in Pancreatic Ductal Adenocarcinoma Originate from Embryonic Hematopoiesis and Promote Tumor Progression.	Zhu Y, Herndon JM, Sojka DK, Kim KW, Knolhoff BL, Zuo C, Cullinan DR, Luo J, Bearden AR, Lavine KJ, Yokoyama WM, Hawkins WG, Fields RC, Randolph GJ, DeNardo DG	Immunity	28813661	Immunity	2017 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/28813661
Cytokine Circuits in Cardiovascular Disease.	Williams JW, Huang LH, Randolph GJ	Immunity	30995508	Immunity	2019 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/30995508
Limited proliferation capacity of aortic intima resident macrophages requires monocyte recruitment for atherosclerotic plaque progression.	Williams JW, Zaitsev K, Kim KW, Ivanov S, Saunders BT, Schrank PR, Kim K, Elvington A, Kim SH, Tucker CG, Wohltmann M, Fife BT, Epelman S, Artyomov MN, Lavine KJ, Zinselmeyer BH, Choi JH, Randolph GJ	Nature immunology	32895539	Nat Immunol	2020 Oct	https://www.ncbi.nlm.nih.gov/pubmed/32895539
Liver injury after small bowel resection is prevented in obesity-resistant 129S1/SvImJ mice.	Onufer EJ, Han YH, Courtney C, Steinberger A, Tecos M, Sutton S, Sescleifer A, Ou J, Sanguinetti Czepielewski R, Randolph GJ, Warner BW	American journal of physiology. Gastrointestinal and liver physiology	33729834	Am J Physiol Gastrointest Liver Physiol	2021 May 1	https://www.ncbi.nlm.nih.gov/pubmed/33729834
CXCR4-Binding Positron Emission Tomography Tracers Link Monocyte Recruitment and Endothelial Injury in Murine Atherosclerosis.	Baba O, Huang LH, Elvington A, Szpakowska M, Sultan D, Heo GS, Zhang X, Luehmann H, Detering L, Chevigne A, Liu Y, Randolph GJ	Arteriosclerosis, thrombosis, and vascular biology	33327748	Arterioscler Thromb Vasc Biol	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33327748
Myeloid-specific Asxl2 deletion limits diet-induced obesity by regulating energy expenditure.	Zou W, Rohatgi N, Brestoff JR, Moley JR, Li Y, Williams JW, Alippe Y, Pan H, Pietka TA, Mbalaviele G, Newberry EP, Davidson NO, Dey A, Shoghi KI, Head RD, Wickline SA, Randolph GJ, Abumrad NA, Teitelbaum SL	The Journal of clinical investigation	32310225	J Clin Invest	2020 May 1	https://www.ncbi.nlm.nih.gov/pubmed/32310225
Ileitis-associated tertiary lymphoid organs arise at lymphatic valves and impede mesenteric lymph flow in response to tumor necrosis factor.	Czepielewski RS, Erlich EC, Onufer EJ, Young S, Saunders BT, Han YH, Wohltmann M, Wang PL, Kim KW, Kumar S, Hsieh CS, Scallan JP, Yang Y, Zinselmeyer BH, Davis MJ, Randolph GJ	Immunity	34788601	Immunity	2021 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/34788601
Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity.	Fonseca DM, Hand TW, Han SJ, Gerner MY, Glatman Zaretsky A, Byrd AL, Harrison OJ, Ortiz AM, Quinones M, Trinchieri G, Brenchley JM, Brodsky IE, Germain RN, Randolph GJ, Belkaid Y	Cell	26451485	Cell	2015 Oct 8	https://www.ncbi.nlm.nih.gov/pubmed/26451485
Myeloid cells pave the way for lymphatic system development and maintenance.	Ivanov S, Randolph GJ	Pflugers Archiv : European journal of physiology	28220247	Pflugers Arch	2017 Apr	https://www.ncbi.nlm.nih.gov/pubmed/28220247
Lymphoid Aggregates Remodel Lymphatic Collecting Vessels that Serve Mesenteric Lymph Nodes in Crohn Disease.	Randolph GJ, Bala S, Rahier JF, Johnson MW, Wang PL, Nalbantoglu I, Dubuquoy L, Chau A, Pariente B, Kartheuser A, Zinselmeyer BH, Colombel JF	The American journal of pathology	27746181	Am J Pathol	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27746181
Mafb lineage tracing to distinguish macrophages from other immune lineages reveals dual identity of Langerhans cells.	Wu X, Briseño CG, Durai V, Albring JC, Haldar M, Bagadia P, Kim KW, Randolph GJ, Murphy TL, Murphy KM	The Journal of experimental medicine	27810926	J Exp Med	2016 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/27810926
A Stromal Niche Defined by Expression of the Transcription Factor WT1 Mediates Programming and Homeostasis of Cavity-Resident Macrophages.	Buechler MB, Kim KW, Onufer EJ, Williams JW, Little CC, Dominguez CX, Li Q, Sandoval W, Cooper JE, Harris CA, Junttila MR, Randolph GJ, Turley SJ	Immunity	31231034	Immunity	2019 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/31231034
Interleukin-17 Drives Interstitial Entrapment of Tissue Lipoproteins in Experimental Psoriasis.	Huang LH, Zinselmeyer BH, Chang CH, Saunders BT, Elvington A, Baba O, Broekelmann TJ, Qi L, Rueve JS, Swartz MA, Kim BS, Mecham RP, Wiig H, Thomas MJ, Sorci-Thomas MG, Randolph GJ	Cell metabolism	30415924	Cell Metab	2019 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/30415924
The Lymphatic Vasculature in the 21(st) Century: Novel Functional Roles in Homeostasis and Disease.	Oliver G, Kipnis J, Randolph GJ, Harvey NL	Cell	32707093	Cell	2020 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/32707093
A Polecat's View of Patrolling Monocytes.	Williams JW, Randolph GJ, Zinselmeyer BH	Circulation research	28546349	Circ Res	2017 May 26	https://www.ncbi.nlm.nih.gov/pubmed/28546349
Cholesterol Accumulation in Dendritic Cells Links the Inflammasome to Acquired Immunity.	Westerterp M, Gautier EL, Ganda A, Molusky MM, Wang W, Fotakis P, Wang N, Randolph GJ, D'Agati VD, Yvan-Charvet L, Tall AR	Cell metabolism	28479366	Cell Metab	2017 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/28479366
Enterically derived high-density lipoprotein restrains liver injury through the portal vein.	Han YH, Onufer EJ, Huang LH, Sprung RW, Davidson WS, Czepielewski RS, Wohltmann M, Sorci-Thomas MG, Warner BW, Randolph GJ	Science (New York, N.Y.)	34437091	Science	2021 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/34437091
Lymph nodes go with the flow.	Czepielewski RS, Randolph GJ	The Journal of experimental medicine	30355618	J Exp Med	2018 Nov 5	https://www.ncbi.nlm.nih.gov/pubmed/30355618
Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models.	Kim K, Shim D, Lee JS, Zaitsev K, Williams JW, Kim KW, Jang MY, Seok Jang H, Yun TJ, Lee SH, Yoon WK, Prat A, Seidah NG, Choi J, Lee SP, Yoon SH, Nam JW, Seong JK, Oh GT, Randolph GJ, Artyomov MN, Cheong C, Choi JH	Circulation research	30359200	Circ Res	2018 Oct 26	https://www.ncbi.nlm.nih.gov/pubmed/30359200
Peripheral nerve resident macrophages share tissue-specific programming and features of activated microglia.	Wang PL, Yim AKY, Kim KW, Avey D, Czepielewski RS, Colonna M, Milbrandt J, Randolph GJ	Nature communications	32439942	Nat Commun	2020 May 21	https://www.ncbi.nlm.nih.gov/pubmed/32439942
Expression of factor V by resident macrophages boosts host defense in the peritoneal cavity.	Zhang N, Czepielewski RS, Jarjour NN, Erlich EC, Esaulova E, Saunders BT, Grover SP, Cleuren AC, Broze GJ, Edelson BT, Mackman N, Zinselmeyer BH, Randolph GJ	The Journal of experimental medicine	31048328	J Exp Med	2019 Jun 3	https://www.ncbi.nlm.nih.gov/pubmed/31048328
Macrophage Biology, Classification, and Phenotype in Cardiovascular Disease: JACC Macrophage in CVD Series (Part 1).	Williams JW, Giannarelli C, Rahman A, Randolph GJ, Kovacic JC	Journal of the American College of Cardiology	30360826	J Am Coll Cardiol	2018 Oct 30	https://www.ncbi.nlm.nih.gov/pubmed/30360826
Limited Macrophage Positional Dynamics in Progressing or Regressing Murine Atherosclerotic Plaques-Brief Report.	Williams JW, Martel C, Potteaux S, Esaulova E, Ingersoll MA, Elvington A, Saunders BT, Huang LH, Habenicht AJ, Zinselmeyer BH, Randolph GJ	Arteriosclerosis, thrombosis, and vascular biology	29903736	Arterioscler Thromb Vasc Biol	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29903736
CCR7 and IRF4-dependent dendritic cells regulate lymphatic collecting vessel permeability.	Ivanov S, Scallan JP, Kim KW, Werth K, Johnson MW, Saunders BT, Wang PL, Kuan EL, Straub AC, Ouhachi M, Weinstein EG, Williams JW, Briseño C, Colonna M, Isakson BE, Gautier EL, Förster R, Davis MJ, Zinselmeyer BH, Randolph GJ	The Journal of clinical investigation	26999610	J Clin Invest	2016 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/26999610
Postprandial Chylomicron Output and Transport Through Intestinal Lymphatics Are Not Impaired in Active Crohn's Disease.	Huang LH, Deepak P, Ciorba MA, Mittendorfer B, Patterson BW, Randolph GJ	Gastroenterology	32681923	Gastroenterology	2020 Nov	https://www.ncbi.nlm.nih.gov/pubmed/32681923
Thermoneutrality but Not UCP1 Deficiency Suppresses Monocyte Mobilization Into Blood.	Williams JW, Elvington A, Ivanov S, Kessler S, Luehmann H, Baba O, Saunders BT, Kim KW, Johnson MW, Craft CS, Choi JH, Sorci-Thomas MG, Zinselmeyer BH, Brestoff JR, Liu Y, Randolph GJ	Circulation research	28696252	Circ Res	2017 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/28696252
B Cell-Mediated Antigen Presentation through MHC Class II Is Dispensable for Atherosclerosis Progression.	Williams JW, Elvington A, Kessler S, Wohltmann M, Wu GF, Randolph GJ	ImmunoHorizons	31356175	Immunohorizons	2019 Jan 21	https://www.ncbi.nlm.nih.gov/pubmed/31356175
Lymphatic network remodeling after small bowel resection.	Onufer EJ, Czepielewski R, Seiler KM, Erlich E, Courtney CM, Bustos A, Randolph GJ, Warner BW	Journal of pediatric surgery	30879758	J Pediatr Surg	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/30879758
LYVE1+ macrophages of murine peritoneal mesothelium promote omentum-independent ovarian tumor growth.	Zhang N, Kim SH, Gainullina A, Erlich EC, Onufer EJ, Kim J, Czepielewski RS, Helmink BA, Dominguez JR, Saunders BT, Ding J, Williams JW, Jiang JX, Segal BH, Zinselmeyer BH, Randolph GJ, Kim KW	The Journal of experimental medicine	34714329	J Exp Med	2021 Dec 6	https://www.ncbi.nlm.nih.gov/pubmed/34714329
Targeted DNA methylation in human cells using engineered dCas9-methyltransferases.	Xiong T, Meister GE, Workman RE, Kato NC, Spellberg MJ, Turker F, Timp W, Ostermeier M, Novina CD	Scientific reports	28751638	Sci Rep	2017 Jul 27	https://www.ncbi.nlm.nih.gov/pubmed/28751638
Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria.	Xiong T, Rohm D, Workman RE, Roundtree L, Novina CD, Timp W, Ostermeier M	PloS one	30562388	PLoS One	2018	https://www.ncbi.nlm.nih.gov/pubmed/30562388
Clutch Control: Changing the Speed and Direction of CAR-T Cell Therapy.	Nobili A, Kobayashi A, Gedeon PC, Novina CD	Journal of cancer immunology	36531912	J Cancer Immunol (Wilmington)	2022	https://www.ncbi.nlm.nih.gov/pubmed/36531912
Nuclear Localization of Mitochondrial TCA Cycle Enzymes as a Critical Step in Mammalian Zygotic Genome Activation.	Nagaraj R, Sharpley MS, Chi F, Braas D, Zhou Y, Kim R, Clark AT, Banerjee U	Cell	28086092	Cell	2017 Jan 12	https://www.ncbi.nlm.nih.gov/pubmed/28086092
Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice.	Isganaitis E, Jimenez-Chillaron J, Woo M, Chow A, DeCoste J, Vokes M, Liu M, Kasif S, Zavacki AM, Leshan RL, Myers MG, Patti ME	Diabetes	19208909	Diabetes	2009 May	https://www.ncbi.nlm.nih.gov/pubmed/19208909
Loss of autophagy in pro-opiomelanocortin neurons perturbs axon growth and causes metabolic dysregulation.	Coupé B, Ishii Y, Dietrich MO, Komatsu M, Horvath TL, Bouret SG	Cell metabolism	22285542	Cell Metab	2012 Feb 8	https://www.ncbi.nlm.nih.gov/pubmed/22285542
A marriage made to last in drug design.	Dietrich MO, Horvath TL	Nature medicine	23223057	Nat Med	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23223057
Leptin signaling in astrocytes regulates hypothalamic neuronal circuits and feeding.	Kim JG, Suyama S, Koch M, Jin S, Argente-Arizon P, Argente J, Liu ZW, Zimmer MR, Jeong JK, Szigeti-Buck K, Gao Y, Garcia-Caceres C, Yi CX, Salmaso N, Vaccarino FM, Chowen J, Diano S, Dietrich MO, Tschöp MH, Horvath TL	Nature neuroscience	24880214	Nat Neurosci	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24880214
Phosphoribosomes for fingerprinting neurons.	Dietrich MO, Horvath TL	Cell	23178116	Cell	2012 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/23178116
Neonatal insulin action impairs hypothalamic neurocircuit formation in response to maternal high-fat feeding.	Vogt MC, Paeger L, Hess S, Steculorum SM, Awazawa M, Hampel B, Neupert S, Nicholls HT, Mauer J, Hausen AC, Predel R, Kloppenburg P, Horvath TL, Brüning JC	Cell	24462248	Cell	2014 Jan 30	https://www.ncbi.nlm.nih.gov/pubmed/24462248
Obesity is associated with hypothalamic injury in rodents and humans.	Thaler JP, Yi CX, Schur EA, Guyenet SJ, Hwang BH, Dietrich MO, Zhao X, Sarruf DA, Izgur V, Maravilla KR, Nguyen HT, Fischer JD, Matsen ME, Wisse BE, Morton GJ, Horvath TL, Baskin DG, Tschöp MH, Schwartz MW	The Journal of clinical investigation	22201683	J Clin Invest	2012 Jan	https://www.ncbi.nlm.nih.gov/pubmed/22201683
Leptin regulates glutamate and glucose transporters in hypothalamic astrocytes.	Fuente-Martín E, García-Cáceres C, Granado M, de Ceballos ML, Sánchez-Garrido MÁ, Sarman B, Liu ZW, Dietrich MO, Tena-Sempere M, Argente-Arizón P, Díaz F, Argente J, Horvath TL, Chowen JA	The Journal of clinical investigation	23064363	J Clin Invest	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23064363
AgRP neurons: a switch between peripheral carbohydrate and lipid utilization.	Varela L, Horvath TL	The EMBO journal	23085989	EMBO J	2012 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/23085989
Modeling human cortical development in vitro using induced pluripotent stem cells.	Mariani J, Simonini MV, Palejev D, Tomasini L, Coppola G, Szekely AM, Horvath TL, Vaccarino FM	Proceedings of the National Academy of Sciences of the United States of America	22761314	Proc Natl Acad Sci U S A	2012 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/22761314
Sirtuin 1 and sirtuin 3: physiological modulators of metabolism.	Nogueiras R, Habegger KM, Chaudhary N, Finan B, Banks AS, Dietrich MO, Horvath TL, Sinclair DA, Pfluger PT, Tschöp MH	Physiological reviews	22811431	Physiol Rev	2012 Jul	https://www.ncbi.nlm.nih.gov/pubmed/22811431
Hunger-promoting hypothalamic neurons modulate effector and regulatory T-cell responses.	Matarese G, Procaccini C, Menale C, Kim JG, Kim JD, Diano S, Diano N, De Rosa V, Dietrich MO, Horvath TL	Proceedings of the National Academy of Sciences of the United States of America	23530205	Proc Natl Acad Sci U S A	2013 Apr 9	https://www.ncbi.nlm.nih.gov/pubmed/23530205
Limitations in anti-obesity drug development: the critical role of hunger-promoting neurons.	Dietrich MO, Horvath TL	Nature reviews. Drug discovery	22858652	Nat Rev Drug Discov	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22858652
Mitochondrial dynamics controlled by mitofusins regulate Agrp neuronal activity and diet-induced obesity.	Dietrich MO, Liu ZW, Horvath TL	Cell	24074868	Cell	2013 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/24074868
Maternal and offspring pools of osteocalcin influence brain development and functions.	Oury F, Khrimian L, Denny CA, Gardin A, Chamouni A, Goeden N, Huang YY, Lee H, Srinivas P, Gao XB, Suyama S, Langer T, Mann JJ, Horvath TL, Bonnin A, Karsenty G	Cell	24074871	Cell	2013 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/24074871
Minireview: Metabolism of female reproduction: regulatory mechanisms and clinical implications.	Seli E, Babayev E, Collins SC, Nemeth G, Horvath TL	Molecular endocrinology (Baltimore, Md.)	24678733	Mol Endocrinol	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/24678733
AgRP Neurons Regulate Bone Mass.	Kim JG, Sun BH, Dietrich MO, Koch M, Yao GQ, Diano S, Insogna K, Horvath TL	Cell reports	26411686	Cell Rep	2015 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/26411686
Leptin and insulin pathways in POMC and AgRP neurons that modulate energy balance and glucose homeostasis.	Varela L, Horvath TL	EMBO reports	23146889	EMBO Rep	2012 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23146889
Hypothalamic control of energy balance: insights into the role of synaptic plasticity.	Dietrich MO, Horvath TL	Trends in neurosciences	23318157	Trends Neurosci	2013 Feb	https://www.ncbi.nlm.nih.gov/pubmed/23318157
AgRP neurons regulate development of dopamine neuronal plasticity and nonfood-associated behaviors.	Dietrich MO, Bober J, Ferreira JG, Tellez LA, Mineur YS, Souza DO, Gao XB, Picciotto MR, Araújo I, Liu ZW, Horvath TL	Nature neuroscience	22729177	Nat Neurosci	2012 Jun 24	https://www.ncbi.nlm.nih.gov/pubmed/22729177
Hypothalamic POMC neurons promote cannabinoid-induced feeding.	Koch M, Varela L, Kim JG, Kim JD, Hernández-Nuño F, Simonds SE, Castorena CM, Vianna CR, Elmquist JK, Morozov YM, Rakic P, Bechmann I, Cowley MA, Szigeti-Buck K, Dietrich MO, Gao XB, Diano S, Horvath TL	Nature	25707796	Nature	2015 Mar 5	https://www.ncbi.nlm.nih.gov/pubmed/25707796
A minimal fate-selection switch.	Weinberger LS	Current opinion in cell biology	26611210	Curr Opin Cell Biol	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26611210
Spatial tuning of acoustofluidic pressure nodes by altering net sonic velocity enables high-throughput, efficient cell sorting.	Jung SY, Notton T, Fong E, Shusteff M, Weinberger LS	Lab on a chip	25563937	Lab Chip	2015 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/25563937
Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability.	Hansen MMK, Desai RV, Simpson ML, Weinberger LS	Cell systems	30243562	Cell Syst	2018 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/30243562
Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals.	Rast LI, Rouzine IM, Rozhnova G, Bishop L, Weinberger AD, Weinberger LS	PLoS computational biology	27152856	PLoS Comput Biol	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/27152856
Attacking Latent HIV with convertibleCAR-T Cells, a Highly Adaptable Killing Platform.	Herzig E, Kim KC, Packard TA, Vardi N, Schwarzer R, Gramatica A, Deeks SG, Williams SR, Landgraf K, Killeen N, Martin DW, Weinberger LS, Greene WC	Cell	31668804	Cell	2019 Oct 31	https://www.ncbi.nlm.nih.gov/pubmed/31668804
Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean.	Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS	PLoS biology	29045398	PLoS Biol	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/29045398
A Bioreactor Method to Generate High-titer, Genetically Stable, Clinical-isolate Human Cytomegalovirus.	Saykally VR, Rast LI, Sasaki J, Jung SY, Bolovan-Fritts C, Weinberger LS	Bio-protocol	29226181	Bio Protoc	2017 Nov 5	https://www.ncbi.nlm.nih.gov/pubmed/29226181
Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch.	Aull KH, Tanner EJ, Thomson M, Weinberger LS	Biophysical journal	28591615	Biophys J	2017 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/28591615
Feedback-mediated signal conversion promotes viral fitness.	Vardi N, Chaturvedi S, Weinberger LS	Proceedings of the National Academy of Sciences of the United States of America	30150412	Proc Natl Acad Sci U S A	2018 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/30150412
A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization.	Hansen MMK, Wen WY, Ingerman E, Razooky BS, Thompson CE, Dar RD, Chin CW, Simpson ML, Weinberger LS	Cell	29754821	Cell	2018 Jun 14	https://www.ncbi.nlm.nih.gov/pubmed/29754821
An evolutionary role for HIV latency in enhancing viral transmission.	Rouzine IM, Weinberger AD, Weinberger LS	Cell	25723173	Cell	2015 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/25723173
Post-Transcriptional Noise Control.	Hansen MMK, Weinberger LS	BioEssays : news and reviews in molecular, cellular and developmental biology	31222776	Bioessays	2019 Jul	https://www.ncbi.nlm.nih.gov/pubmed/31222776
Fate-Regulating Circuits in Viruses: From Discovery to New Therapy Targets.	Pai A, Weinberger LS	Annual review of virology	28800289	Annu Rev Virol	2017 Sep 29	https://www.ncbi.nlm.nih.gov/pubmed/28800289
Origin and Function of Stress-Induced IL-6 in Murine Models.	Qing H, Desrouleaux R, Israni-Winger K, Mineur YS, Fogelman N, Zhang C, Rashed S, Palm NW, Sinha R, Picciotto MR, Perry RJ, Wang A	Cell	32610084	Cell	2020 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/32610084
microRNA-33 maintains adaptive thermogenesis via enhanced sympathetic nerve activity.	Horie T, Nakao T, Miyasaka Y, Nishino T, Matsumura S, Nakazeki F, Ide Y, Kimura M, Tsuji S, Rodriguez RR, Watanabe T, Yamasaki T, Xu S, Otani C, Miyagawa S, Matsushita K, Sowa N, Omori A, Tanaka J, Nishimura C, Nishiga M, Kuwabara Y, Baba O, Watanabe S, Nishi H, Nakashima Y, Picciotto MR, Inoue H, Watanabe D, Nakamura K, Sasaki T, Kimura T, Ono K	Nature communications	33594062	Nat Commun	2021 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/33594062
Cumulative Effects of Social Stress on Reward-Guided Actions and Prefrontal Cortical Activity.	Barthas F, Hu MY, Siniscalchi MJ, Ali F, Mineur YS, Picciotto MR, Kwan AC	Biological psychiatry	32276717	Biol Psychiatry	2020 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/32276717
Acetylcholine is released in the basolateral amygdala in response to predictors of reward and enhances the learning of cue-reward contingency.	Crouse RB, Kim K, Batchelor HM, Girardi EM, Kamaletdinova R, Chan J, Rajebhosale P, Pittenger ST, Role LW, Talmage DA, Jing M, Li Y, Gao XB, Mineur YS, Picciotto MR	eLife	32945260	Elife	2020 Sep 18	https://www.ncbi.nlm.nih.gov/pubmed/32945260
Sex differences in stress-induced alcohol intake: a review of preclinical studies focused on amygdala and inflammatory pathways.	Mineur YS, Garcia-Rivas V, Thomas MA, Soares AR, McKee SA, Picciotto MR	Psychopharmacology	35359158	Psychopharmacology (Berl)	2022 Jul	https://www.ncbi.nlm.nih.gov/pubmed/35359158
ACh signaling modulates activity of the GABAergic signaling network in the basolateral amygdala and behavior in stress-relevant paradigms.	Mineur YS, Mose TN, Maibom KL, Pittenger ST, Soares AR, Wu H, Taylor SR, Huang Y, Picciotto MR	Molecular psychiatry	36050437	Mol Psychiatry	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36050437
Variability in nicotine conditioned place preference and stress-induced reinstatement in mice: Effects of sex, initial chamber preference, and guanfacine.	Lee AM, Calarco CA, McKee SA, Mineur YS, Picciotto MR	Genes, brain, and behavior	31364813	Genes Brain Behav	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/31364813
The role of acetylcholine in negative encoding bias: Too much of a good thing?	Mineur YS, Picciotto MR	The European journal of neuroscience	31821620	Eur J Neurosci	2021 Jan	https://www.ncbi.nlm.nih.gov/pubmed/31821620
Impaired hypocretin/orexin system alters responses to salient stimuli in obese male mice.	Tan Y, Hang F, Liu ZW, Stoiljkovic M, Wu M, Tu Y, Han W, Lee AM, Kelley C, Hajós M, Lu L, de Lecea L, De Araujo I, Picciotto MR, Horvath TL, Gao XB	The Journal of clinical investigation	32516139	J Clin Invest	2020 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/32516139
Sex Differences in the Ventral Tegmental Area and Nucleus Accumbens Proteome at Baseline and Following Nicotine Exposure.	Lee AM, Mansuri MS, Wilson RS, Lam TT, Nairn AC, Picciotto MR	Frontiers in molecular neuroscience	34335180	Front Mol Neurosci	2021	https://www.ncbi.nlm.nih.gov/pubmed/34335180
Muscarinic antagonists impair multiple aspects of operant discrimination learning and performance.	Yousuf H, Girardi EM, Crouse RB, Picciotto MR	Neuroscience letters	36529388	Neurosci Lett	2023 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/36529388
Effects of nicotine on DARPP-32 and CaMKII signaling relevant to addiction.	Lee AM, Picciotto MR	Advances in pharmacology (San Diego, Calif.)	33706940	Adv Pharmacol	2021	https://www.ncbi.nlm.nih.gov/pubmed/33706940
Activity of a direct VTA to ventral pallidum GABA pathway encodes unconditioned reward value and sustains motivation for reward.	Zhou WL, Kim K, Ali F, Pittenger ST, Calarco CA, Mineur YS, Ramakrishnan C, Deisseroth K, Kwan AC, Picciotto MR	Science advances	36260661	Sci Adv	2022 Oct 21	https://www.ncbi.nlm.nih.gov/pubmed/36260661
Nicotine addiction: More than just dopamine.	Kim K, Picciotto MR	Current opinion in neurobiology	37832393	Curr Opin Neurobiol	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37832393
Hippocampal knockdown of α2 nicotinic or M1 muscarinic acetylcholine receptors in C57BL/6J male mice impairs cued fear conditioning.	Mineur YS, Ernstsen C, Islam A, Lefoli Maibom K, Picciotto MR	Genes, brain, and behavior	32447811	Genes Brain Behav	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32447811
Hippocampal acetylcholine modulates stress-related behaviors independent of specific cholinergic inputs.	Mineur YS, Mose TN, Vanopdenbosch L, Etherington IM, Ogbejesi C, Islam A, Pineda CM, Crouse RB, Zhou W, Thompson DC, Bentham MP, Picciotto MR	Molecular psychiatry	34997190	Mol Psychiatry	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/34997190
How can I measure brain acetylcholine levels in vivo? Advantages and caveats of commonly used approaches.	Mineur YS, Picciotto MR	Journal of neurochemistry	37621094	J Neurochem	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37621094
Functionally refined encoding of threat memory by distinct populations of basal forebrain cholinergic projection neurons.	Rajebhosale P, Ananth MR, Kim R, Crouse R, Jiang L, López-Hernández G, Zhong C, Arty C, Wang S, Jone A, Desai NS, Li Y, Picciotto MR, Role LW, Talmage DA	eLife	38363713	Elife	2024 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/38363713
The following article for this Special Issue was previously published and can be found in its respective issue online: "How can I measure brain acetylcholine levels in vivo? Advantages and caveats of commonly used approaches".		Journal of neurochemistry	38607971	J Neurochem	2024 Apr	https://www.ncbi.nlm.nih.gov/pubmed/38607971
Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells.	Shalek AK, Robinson JT, Karp ES, Lee JS, Ahn DR, Yoon MH, Sutton A, Jorgolli M, Gertner RS, Gujral TS, MacBeath G, Yang EG, Park H	Proceedings of the National Academy of Sciences of the United States of America	20080678	Proc Natl Acad Sci U S A	2010 Feb 2	https://www.ncbi.nlm.nih.gov/pubmed/20080678
Structural basis for enhanced HIV-1 neutralization by a dimeric immunoglobulin G form of the glycan-recognizing antibody 2G12.	Wu Y, West AP Jr, Kim HJ, Thornton ME, Ward AB, Bjorkman PJ	Cell reports	24316082	Cell Rep	2013 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/24316082
Impact of delay in asthma diagnosis on health care service use.	Lynch BA, Van Norman CA, Jacobson RM, Weaver AL, Juhn YJ	Allergy and asthma proceedings	20819315	Allergy Asthma Proc	2010 Jul-Aug	https://www.ncbi.nlm.nih.gov/pubmed/20819315
PHM is required for normal developmental transitions and for biosynthesis of secretory peptides in Drosophila.	Jiang N, Kolhekar AS, Jacobs PS, Mains RE, Eipper BA, Taghert PH	Developmental biology	10993678	Dev Biol	2000 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/10993678
Interaction of Drosophila melanogaster prohormone convertase 2 and 7B2. Insect cell-specific processing and secretion.	Hwang JR, Siekhaus DE, Fuller RS, Taghert PH, Lindberg I	The Journal of biological chemistry	10749852	J Biol Chem	2000 Jun 9	https://www.ncbi.nlm.nih.gov/pubmed/10749852
Genetic analysis of the Drosophila ellipsoid body neuropil: organization and development of the central complex.	Renn SC, Armstrong JD, Yang M, Wang Z, An X, Kaiser K, Taghert PH	Journal of neurobiology	10512977	J Neurobiol	1999 Nov 5	https://www.ncbi.nlm.nih.gov/pubmed/10512977
Cell type-specific transcriptional regulation of the Drosophila FMRFamide neuropeptide gene.	Schneider LE, Roberts MS, Taghert PH	Neuron	8439413	Neuron	1993 Feb	https://www.ncbi.nlm.nih.gov/pubmed/8439413
Molecular genetic analysis of the FMRFamide-related neuropeptides in Drosophila.	Taghert PH, O'Brien MA, Schneider LE, Roberts MS	Progress in brain research	1302876	Prog Brain Res	1992	https://www.ncbi.nlm.nih.gov/pubmed/1302876
Development of the enteric nervous system in the moth. I. Diversity of cell types and the embryonic expression of FMRFamide-related neuropeptides.	Copenhaver PF, Taghert PH	Developmental biology	2909410	Dev Biol	1989 Jan	https://www.ncbi.nlm.nih.gov/pubmed/2909410
The genetic analysis of neuropeptide signaling systems.	O'Brien MA, Taghert PH	Zoological science	7765852	Zoolog Sci	1994 Oct	https://www.ncbi.nlm.nih.gov/pubmed/7765852
An immunocytochemical study of the FMRFamide neuropeptide gene products in Drosophila.	Schneider LE, Sun ET, Garland DJ, Taghert PH	The Journal of comparative neurology	8282851	J Comp Neurol	1993 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/8282851
Identification of Drosophila neuropeptide receptors by G protein-coupled receptors-beta-arrestin2 interactions.	Johnson EC, Bohn LM, Barak LS, Birse RT, Nässel DR, Caron MG, Taghert PH	The Journal of biological chemistry	14555656	J Biol Chem	2003 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/14555656
Ap-let neurons--a peptidergic circuit potentially controlling ecdysial behavior in Drosophila.	Park D, Han M, Kim YC, Han KA, Taghert PH	Developmental biology	15081360	Dev Biol	2004 May 1	https://www.ncbi.nlm.nih.gov/pubmed/15081360
Drosophila MEF2, a transcription factor that is essential for myogenesis.	Bour BA, O'Brien MA, Lockwood WL, Goldstein ES, Bodmer R, Taghert PH, Abmayr SM, Nguyen HT	Genes & development	7729689	Genes Dev	1995 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/7729689
Segment-specific modifications of a neuropeptide phenotype in embryonic neurons of the moth, Manduca sexta.	Wall JB, Taghert PH	The Journal of comparative neurology	1918442	J Comp Neurol	1991 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/1918442
Widely distributed Drosophila G-protein-coupled receptor (CG7887) is activated by endogenous tachykinin-related peptides.	Birse RT, Johnson EC, Taghert PH, Nässel DR	Journal of neurobiology	16193493	J Neurobiol	2006 Jan	https://www.ncbi.nlm.nih.gov/pubmed/16193493
Drosophila CG8422 encodes a functional diuretic hormone receptor.	Johnson EC, Bohn LM, Taghert PH	The Journal of experimental biology	14747406	J Exp Biol	2004 Feb	https://www.ncbi.nlm.nih.gov/pubmed/14747406
PDF receptor signaling in Drosophila contributes to both circadian and geotactic behaviors.	Mertens I, Vandingenen A, Johnson EC, Shafer OT, Li W, Trigg JS, De Loof A, Schoofs L, Taghert PH	Neuron	16242402	Neuron	2005 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/16242402
A novel diuretic hormone receptor in Drosophila: evidence for conservation of CGRP signaling.	Johnson EC, Shafer OT, Trigg JS, Park J, Schooley DA, Dow JA, Taghert PH	The Journal of experimental biology	15781884	J Exp Biol	2005 Apr	https://www.ncbi.nlm.nih.gov/pubmed/15781884
In situ hybridization analysis of the FMRFamide neuropeptide gene in Drosophila. II. Constancy in the cellular pattern of expression during metamorphosis.	O'Brien MA, Schneider LE, Taghert PH	The Journal of comparative neurology	1672877	J Comp Neurol	1991 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/1672877
Developmental neurobiology. Axon outgrowth in vertebrates.	Taghert PH, Lichtman JW	Nature	3960104	Nature	1986 Mar 20-26	https://www.ncbi.nlm.nih.gov/pubmed/3960104
Circadian pacemaker neurons display cophasic rhythms in basal calcium level and in fast calcium fluctuations.	Liang X, Holy TE, Taghert PH	Proceedings of the National Academy of Sciences of the United States of America	35446620	Proc Natl Acad Sci U S A	2022 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/35446620
Transcriptomic landscape of mammalian ventral pallidum at single-cell resolution.	Yang L, Fang LZ, Lynch MR, Xu CS, Hahm H, Zhang Y, Heitmeier MR, Costa V, Samineni VK, Creed MC	bioRxiv : the preprint server for biology	38826431	bioRxiv	2024 Sep 28	https://www.ncbi.nlm.nih.gov/pubmed/38826431
Cell type-specific regulation of the Drosophila FMRF-NH2 neuropeptide gene by Apterous, a LIM homeodomain transcription factor.	Benveniste RJ, Thor S, Thomas JB, Taghert PH	Development (Cambridge, England)	9806924	Development	1998 Dec	https://www.ncbi.nlm.nih.gov/pubmed/9806924
Origins of the insect enteric nervous system: differentiation of the enteric ganglia from a neurogenic epithelium.	Copenhaver PF, Taghert PH	Development (Cambridge, England)	1811931	Development	1991 Dec	https://www.ncbi.nlm.nih.gov/pubmed/1811931
Neurogenesis in the insect enteric nervous system: generation of premigratory neurons from an epithelial placode.	Copenhaver PF, Taghert PH	Development (Cambridge, England)	2209463	Development	1990 May	https://www.ncbi.nlm.nih.gov/pubmed/2209463
Development of the enteric nervous system in the moth. II. Stereotyped cell migration precedes the differentiation of embryonic neurons.	Copenhaver PF, Taghert PH	Developmental biology	2909411	Dev Biol	1989 Jan	https://www.ncbi.nlm.nih.gov/pubmed/2909411
Pair-rule expression of a cell surface molecule during gastrulation of the moth embryo.	Carr JN, Taghert PH	Development (Cambridge, England)	2627891	Development	1989 Sep	https://www.ncbi.nlm.nih.gov/pubmed/2627891
Developmental neurobiology. Trophic factor theory matures.	Lichtman JW, Taghert PH	Nature	3031503	Nature	1987 Mar 26-Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/3031503
Guidance of pioneer growth cones: filopodial contacts and coupling revealed with an antibody to Lucifer Yellow.	Taghert PH, Bastiani MJ, Ho RK, Goodman CS	Developmental biology	7152111	Dev Biol	1982 Dec	https://www.ncbi.nlm.nih.gov/pubmed/7152111
Lithium- and valproate-induced alterations in circadian locomotor behavior in Drosophila.	Dokucu ME, Yu L, Taghert PH	Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology	15956996	Neuropsychopharmacology	2005 Dec	https://www.ncbi.nlm.nih.gov/pubmed/15956996
Organization of the Drosophila circadian control circuit.	Nitabach MN, Taghert PH	Current biology : CB	18211849	Curr Biol	2008 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/18211849
Drosophila neuropeptide signaling.	Taghert PH, Veenstra JA	Advances in genetics	12779250	Adv Genet	2003	https://www.ncbi.nlm.nih.gov/pubmed/12779250
Regulators acting in combinatorial codes also act independently in single differentiating neurons.	Allan DW, Park D, St Pierre SE, Taghert PH, Thor S	Neuron	15748845	Neuron	2005 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/15748845
Peptidergic neurosecretory cells in insects: organization and control by the bHLH protein DIMMED.	Park D, Taghert PH	General and comparative endocrinology	19135054	Gen Comp Endocrinol	2009 May 15	https://www.ncbi.nlm.nih.gov/pubmed/19135054
A Series of Suppressive Signals within the Drosophila Circadian Neural Circuit Generates Sequential Daily Outputs.	Liang X, Holy TE, Taghert PH	Neuron	28552314	Neuron	2017 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/28552314
Polyphasic circadian neural circuits drive differential activities in multiple downstream rhythmic centers.	Liang X, Holy TE, Taghert PH	Current biology : CB	36610393	Curr Biol	2023 Jan 23	https://www.ncbi.nlm.nih.gov/pubmed/36610393
The timing of initial neuropeptide expression by an identified insect neuron does not depend on interactions with its normal peripheral target.	Wall JB, Taghert PH	Journal of neurobiology	1795159	J Neurobiol	1991 Dec	https://www.ncbi.nlm.nih.gov/pubmed/1795159
Metamorphosis of tangential visual system neurons in Drosophila.	Taghert PH, Roberts ME, Renn SC, Jacobs PS	Developmental biology	10837134	Dev Biol	2000 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/10837134
A pdf neuropeptide gene mutation and ablation of PDF neurons each cause severe abnormalities of behavioral circadian rhythms in Drosophila.	Renn SC, Park JH, Rosbash M, Hall JC, Taghert PH	Cell	10619432	Cell	1999 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/10619432
Characterization and cloning of tripeptidyl peptidase II from the fruit fly, Drosophila melanogaster.	Renn SC, Tomkinson B, Taghert PH	The Journal of biological chemistry	9668104	J Biol Chem	1998 Jul 24	https://www.ncbi.nlm.nih.gov/pubmed/9668104
Organization and expression of the Drosophila Phe-Met-Arg-Phe-NH2 neuropeptide gene.	Schneider LE, Taghert PH	The Journal of biological chemistry	2324103	J Biol Chem	1990 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/2324103
Drosophila uses two distinct neuropeptide amidating enzymes, dPAL1 and dPAL2.	Han M, Park D, Vanderzalm PJ, Mains RE, Eipper BA, Taghert PH	Journal of neurochemistry	15198673	J Neurochem	2004 Jul	https://www.ncbi.nlm.nih.gov/pubmed/15198673
Circadian biology: a neuropeptide is bound to activate its receptor.	Taghert PH	Current biology : CB	19706280	Curr Biol	2009 Aug 25	https://www.ncbi.nlm.nih.gov/pubmed/19706280
Morning and Evening Circadian Pacemakers Independently Drive Premotor Centers via a Specific Dopamine Relay.	Liang X, Ho MCW, Zhang Y, Li Y, Wu MN, Holy TE, Taghert PH	Neuron	30981533	Neuron	2019 May 22	https://www.ncbi.nlm.nih.gov/pubmed/30981533
The bHLH protein Dimmed controls neuroendocrine cell differentiation in Drosophila.	Hewes RS, Park D, Gauthier SA, Schaefer AM, Taghert PH	Development (Cambridge, England)	12642483	Development	2003 May	https://www.ncbi.nlm.nih.gov/pubmed/12642483
How does the circadian clock send timing information to the brain?	Taghert PH	Seminars in cell & developmental biology	11463217	Semin Cell Dev Biol	2001 Aug	https://www.ncbi.nlm.nih.gov/pubmed/11463217
Formation of the transverse nerve in moth embryos. I. A scaffold of nonneuronal cells prefigures the nerve.	Carr JN, Taghert PH	Developmental biology	3058542	Dev Biol	1988 Dec	https://www.ncbi.nlm.nih.gov/pubmed/3058542
Formation of the transverse nerve in moth embryos. II. Stereotyped growth by the axons of identified neuroendocrine neurons.	Carr JN, Taghert PH	Developmental biology	3197922	Dev Biol	1988 Dec	https://www.ncbi.nlm.nih.gov/pubmed/3197922
Circadian rhythms: in the loop at last.	Van Gelder RN, Herzog ED, Schwartz WJ, Taghert PH	Science (New York, N.Y.)	12791982	Science	2003 Jun 6	https://www.ncbi.nlm.nih.gov/pubmed/12791982
Cell determination and regulation during development of neuroblasts and neurones in grasshopper embryo.	Taghert PH, Doe CQ, Goodman CS	Nature	6690996	Nature	1984 Jan 12-18	https://www.ncbi.nlm.nih.gov/pubmed/6690996
FMRFamide neuropeptides and neuropeptide-associated enzymes in Drosophila.	Taghert PH	Microscopy research and technique	10332726	Microsc Res Tech	1999 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/10332726
Cell type-specific regulatory sequences control expression of the Drosophila FMRF-NH2 neuropeptide gene.	Benveniste RJ, Taghert PH	Journal of neurobiology	10084686	J Neurobiol	1999 Mar	https://www.ncbi.nlm.nih.gov/pubmed/10084686
In situ hybridization analysis of the FMRFamide neuropeptide gene in Drosophila. I. Restricted expression in embryonic and larval stages.	Schneider LE, O'Brien MA, Taghert PH	The Journal of comparative neurology	1672876	J Comp Neurol	1991 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/1672876
Neuroscience. A CRY to rise.	Im SH, Taghert PH	Science (New York, N.Y.)	21415342	Science	2011 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/21415342
Circadian rhythms: biological clocks work in phospho-time.	Duvall LB, Taghert PH	Current biology : CB	21549947	Curr Biol	2011 May 10	https://www.ncbi.nlm.nih.gov/pubmed/21549947
Mechanisms of clock output in the Drosophila circadian pacemaker system.	Taghert PH, Shafer OT	Journal of biological rhythms	17107935	J Biol Rhythms	2006 Dec	https://www.ncbi.nlm.nih.gov/pubmed/17107935
A peritracheal neuropeptide system in insects: release of myomodulin-like peptides at ecdysis.	O'Brien MA, Taghert PH	The Journal of experimental biology	9405303	J Exp Biol	1998 Jan	https://www.ncbi.nlm.nih.gov/pubmed/9405303
Synchronous Drosophila circadian pacemakers display nonsynchronous Ca²⁺ rhythms in vivo.	Liang X, Holy TE, Taghert PH	Science (New York, N.Y.)	26917772	Science	2016 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/26917772
NRAP-1 Is a Presynaptically Released NMDA Receptor Auxiliary Protein that Modifies Synaptic Strength.	Lei N, Mellem JE, Brockie PJ, Madsen DM, Maricq AV	Neuron	29224722	Neuron	2017 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/29224722
Mobile AMPARs are required for synaptic plasticity.	Hoerndli FJ, Kallarackal AJ, Maricq AV	Channels (Austin, Tex.)	26359683	Channels (Austin)	2015	https://www.ncbi.nlm.nih.gov/pubmed/26359683
MAPK signaling and a mobile scaffold complex regulate AMPA receptor transport to modulate synaptic strength.	Hoerndli FJ, Brockie PJ, Wang R, Mellem JE, Kallarackal A, Doser RL, Pierce DM, Madsen DM, Maricq AV	Cell reports	35354038	Cell Rep	2022 Mar 29	https://www.ncbi.nlm.nih.gov/pubmed/35354038
Neuronal Activity and CaMKII Regulate Kinesin-Mediated Transport of Synaptic AMPARs.	Hoerndli FJ, Wang R, Mellem JE, Kallarackal A, Brockie PJ, Thacker C, Madsen DM, Maricq AV	Neuron	25843407	Neuron	2015 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/25843407
Kinesin-1 regulates synaptic strength by mediating the delivery, removal, and redistribution of AMPA receptors.	Hoerndli FJ, Maxfield DA, Brockie PJ, Mellem JE, Jensen E, Wang R, Madsen DM, Maricq AV	Neuron	24360545	Neuron	2013 Dec 18	https://www.ncbi.nlm.nih.gov/pubmed/24360545
CD47 prevents Rac-mediated phagocytosis through Vav1 dephosphorylation.	Miller WD, Mishra AK, Sheedy CJ, Bond A, Gardner BM, Montell DJ, Morrissey MA	bioRxiv : the preprint server for biology	39990418	bioRxiv	2025 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/39990418
AND-gated protease-activated nanosensors for programmable detection of anti-tumour immunity.	Sivakumar A, Phuengkham H, Rajesh H, Mac QD, Rogers LC, Silva Trenkle AD, Bawage SS, Hincapie R, Li Z, Vainikos S, Lee I, Xue M, Qiu P, Finn MG, Kwong GA	Nature nanotechnology	39753733	Nat Nanotechnol	2025 Mar	https://www.ncbi.nlm.nih.gov/pubmed/39753733
Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity.	Houlahan KE, Khan A, Greenwald NF, West RB, Angelo M, Curtis C	bioRxiv : the preprint server for biology	36993286	bioRxiv	2023 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/36993286
A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids.	Sockell A, Wong W, Longwell S, Vu T, Karlsson K, Mokhtari D, Schaepe J, Lo YH, Cornelius V, Kuo C, Van Valen D, Curtis C, Fordyce PM	Cell systems	37734323	Cell Syst	2023 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/37734323
Cancers adapt to their mutational load by buffering protein misfolding stress.	Tilk S, Frydman J, Curtis C, Petrov DA	eLife	39585785	Elife	2024 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/39585785
Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity.	Houlahan KE, Khan A, Greenwald NF, Vivas CS, West RB, Angelo M, Curtis C	Science (New York, N.Y.)	38815010	Science	2024 May 31	https://www.ncbi.nlm.nih.gov/pubmed/38815010
A High-Dimensional Window into the Micro-Environment of Triple Negative Breast Cancer.	Nederlof I, Horlings HM, Curtis C, Kok M	Cancers	33467084	Cancers (Basel)	2021 Jan 16	https://www.ncbi.nlm.nih.gov/pubmed/33467084
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases.	Hu Z, Li Z, Ma Z, Curtis C	Nature genetics	32424352	Nat Genet	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32424352
Most cancers carry a substantial deleterious load due to Hill-Robertson interference.	Tilk S, Tkachenko S, Curtis C, Petrov DA, McFarland CD	eLife	36047771	Elife	2022 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/36047771
Functional screening of amplification outlier oncogenes in organoid models of early tumorigenesis.	Salahudeen AA, Seoane JA, Yuki K, Mah AT, Smith AR, Kolahi K, De la O SM, Hart DJ, Ding J, Ma Z, Barkal SA, Shukla ND, Zhang CH, Cantrell MA, Batish A, Usui T, Root DE, Hahn WC, Curtis C, Kuo CJ	Cell reports	37922313	Cell Rep	2023 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/37922313
The Mettl3 epitranscriptomic writer amplifies p53 stress responses.	Raj N, Wang M, Seoane JA, Zhao RL, Kaiser AM, Moonie NA, Demeter J, Boutelle AM, Kerr CH, Mulligan AS, Moffatt C, Zeng SX, Lu H, Barna M, Curtis C, Chang HY, Jackson PK, Attardi LD	Molecular cell	35512709	Mol Cell	2022 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/35512709
A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation.	Lo YH, Kolahi KS, Du Y, Chang CY, Krokhotin A, Nair A, Sobba WD, Karlsson K, Jones SJ, Longacre TA, Mah AT, Tercan B, Sockell A, Xu H, Seoane JA, Chen J, Shmulevich I, Weissman JS, Curtis C, Califano A, Fu H, Crabtree GR, Kuo CJ	Cancer discovery	33451982	Cancer Discov	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33451982
Quantitative evidence for early metastatic seeding in colorectal cancer.	Hu Z, Ding J, Ma Z, Sun R, Seoane JA, Scott Shaffer J, Suarez CJ, Berghoff AS, Cremolini C, Falcone A, Loupakis F, Birner P, Preusser M, Lenz HJ, Curtis C	Nature genetics	31209394	Nat Genet	2019 Jul	https://www.ncbi.nlm.nih.gov/pubmed/31209394
Deterministic evolution and stringent selection during preneoplasia.	Karlsson K, Przybilla MJ, Kotler E, Khan A, Xu H, Karagyozova K, Sockell A, Wong WH, Liu K, Mah A, Lo YH, Lu B, Houlahan KE, Ma Z, Suarez CJ, Barnes CP, Kuo CJ, Curtis C	Nature	37258665	Nature	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/37258665
Characterizing the ecological and evolutionary dynamics of cancer.	Zahir N, Sun R, Gallahan D, Gatenby RA, Curtis C	Nature genetics	32719518	Nat Genet	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32719518
Cell of Origin Influences Pancreatic Cancer Subtype.	Flowers BM, Xu H, Mulligan AS, Hanson KJ, Seoane JA, Vogel H, Curtis C, Wood LD, Attardi LD	Cancer discovery	34009137	Cancer Discov	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/34009137
Looking backward in time to define the chronology of metastasis.	Hu Z, Curtis C	Nature communications	32587245	Nat Commun	2020 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/32587245
Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups.	Rueda OM, Sammut SJ, Seoane JA, Chin SF, Caswell-Jin JL, Callari M, Batra R, Pereira B, Bruna A, Ali HR, Provenzano E, Liu B, Parisien M, Gillett C, McKinney S, Green AR, Murphy L, Purushotham A, Ellis IO, Pharoah PD, Rueda C, Aparicio S, Caldas C, Curtis C	Nature	30867590	Nature	2019 Mar	https://www.ncbi.nlm.nih.gov/pubmed/30867590
PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes.	Wang K, Hou L, Wang X, Zhai X, Lu Z, Zi Z, Zhai W, He X, Curtis C, Zhou D, Hu Z	Nature biotechnology	37524958	Nat Biotechnol	2024 May	https://www.ncbi.nlm.nih.gov/pubmed/37524958
The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts.	Beckedorff F, Blumenthal E, daSilva LF, Aoi Y, Cingaram PR, Yue J, Zhang A, Dokaneheifard S, Valencia MG, Gaidosh G, Shilatifard A, Shiekhattar R	Cell reports	32697989	Cell Rep	2020 Jul 21	https://www.ncbi.nlm.nih.gov/pubmed/32697989
It's a DoG-eat-DoG world-altered transcriptional mechanisms drive downstream-of-gene (DoG) transcript production.	Morgan M, Shiekhattar R, Shilatifard A, Lauberth SM	Molecular cell	35487209	Mol Cell	2022 Jun 2	https://www.ncbi.nlm.nih.gov/pubmed/35487209
Targeted chemotherapy overcomes drug resistance in melanoma.	Yue J, Vendramin R, Liu F, Lopez O, Valencia MG, Gomes Dos Santos H, Gaidosh G, Beckedorff F, Blumenthal E, Speroni L, Nimer SD, Marine JC, Shiekhattar R	Genes & development	32241802	Genes Dev	2020 May 1	https://www.ncbi.nlm.nih.gov/pubmed/32241802
NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release.	Aoi Y, Smith ER, Shah AP, Rendleman EJ, Marshall SA, Woodfin AR, Chen FX, Shiekhattar R, Shilatifard A	Molecular cell	32155413	Mol Cell	2020 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/32155413
The Integrator complex at the crossroad of coding and noncoding RNA.	Kirstein N, Gomes Dos Santos H, Blumenthal E, Shiekhattar R	Current opinion in cell biology	33340967	Curr Opin Cell Biol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33340967
Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1.	Barra J, Gaidosh GS, Blumenthal E, Beckedorff F, Tayari MM, Kirstein N, Karakach TK, Jensen TH, Impens F, Gevaert K, Leucci E, Shiekhattar R, Marine JC	Science advances	32923585	Sci Adv	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32923585
Detailed longitudinal sampling of glioma stem cells in situ reveals Chr7 gain and Chr10 loss as repeated events in primary tumor formation and recurrence.	Baysan M, Woolard K, Cam MC, Zhang W, Song H, Kotliarova S, Balamatsias D, Linkous A, Ahn S, Walling J, Belova GI, Fine HA	International journal of cancer	28710771	Int J Cancer	2017 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/28710771
Generating Patient-Derived Gliomas within Cerebral Organoids.	Linkous A, Fine HA	STAR protocols	33103125	STAR Protoc	2020 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/33103125
Pluripotent stem cell-derived epithelium misidentified as brain microvascular endothelium requires ETS factors to acquire vascular fate.	Lu TM, Houghton S, Magdeldin T, Durán JGB, Minotti AP, Snead A, Sproul A, Nguyen DT, Xiang J, Fine HA, Rosenwaks Z, Studer L, Rafii S, Agalliu D, Redmond D, Lis R	Proceedings of the National Academy of Sciences of the United States of America	33542154	Proc Natl Acad Sci U S A	2021 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/33542154
Reirradiation for Recurrent Glioblastoma: What We Know and What We Do Not.	Knisely JPS, Fine HA	Journal of clinical oncology : official journal of the American Society of Clinical Oncology	36260825	J Clin Oncol	2023 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/36260825
Tumor Microenvironment Is Critical for the Maintenance of Cellular States Found in Primary Glioblastomas.	Pine AR, Cirigliano SM, Nicholson JG, Hu Y, Linkous A, Miyaguchi K, Edwards L, Singhania R, Schwartz TH, Ramakrishna R, Pisapia DJ, Snuderl M, Elemento O, Fine HA	Cancer discovery	32253265	Cancer Discov	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32253265
Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer.	Sailer V, Eng KW, Zhang T, Bareja R, Pisapia DJ, Sigaras A, Bhinder B, Romanel A, Wilkes D, Sticca E, Cyrta J, Rao R, Sahota S, Pauli C, Beg S, Motanagh S, Kossai M, Fontunge J, Puca L, Rennert H, Zhaoying Xiang J, Greco N, Kim R, MacDonald TY, McNary T, Blattner-Johnson M, Schiffman MH, Faltas BM, Greenfield JP, Rickman D, Andreopoulou E, Holcomb K, Vahdat LT, Scherr DS, van Besien K, Barbieri CE, Robinson BD, Fine HA, Ocean AJ, Molina A, Shah MA, Nanus DM, Pan Q, Demichelis F, Tagawa ST, Song W, Mosquera JM, Sboner A, Rubin MA, Elemento O, Beltran H	JCO precision oncology	31592503	JCO Precis Oncol	2019	https://www.ncbi.nlm.nih.gov/pubmed/31592503
Malignant Gliomas: Simplifying the Complexity.	Fine HA	Cancer discovery	31792122	Cancer Discov	2019 Dec	https://www.ncbi.nlm.nih.gov/pubmed/31792122
Diffuse Glioma Heterogeneity and Its Therapeutic Implications.	Nicholson JG, Fine HA	Cancer discovery	33558264	Cancer Discov	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33558264
Microenvironment-Driven Dynamic Chromatin Changes in Glioblastoma Recapitulate Early Neural Development at Single-Cell Resolution.	Pine AR, Cirigliano SM, Singhania R, Nicholson J, da Silva B, Leslie CS, Fine HA	Cancer research	36877162	Cancer Res	2023 May 15	https://www.ncbi.nlm.nih.gov/pubmed/36877162
Modeling Patient-Derived Glioblastoma with Cerebral Organoids.	Linkous A, Balamatsias D, Snuderl M, Edwards L, Miyaguchi K, Milner T, Reich B, Cohen-Gould L, Storaska A, Nakayama Y, Schenkein E, Singhania R, Cirigliano S, Magdeldin T, Lin Y, Nanjangud G, Chadalavada K, Pisapia D, Liston C, Fine HA	Cell reports	30893594	Cell Rep	2019 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/30893594
Nuclear condensates in YAP1-driven ependymoma.	Dadras MS, Fine HA	Nature cell biology	36732630	Nat Cell Biol	2023 Feb	https://www.ncbi.nlm.nih.gov/pubmed/36732630
Chronic hypoxia remodels the tumor microenvironment to support glioma stem cell growth.	Nicholson JG, Cirigliano S, Singhania R, Haywood C, Shahidi Dadras M, Yoshimura M, Vanderbilt D, Liechty B, Fine HA	Acta neuropathologica communications	38528608	Acta Neuropathol Commun	2024 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/38528608
Epigenetic plasticity and the hallmarks of cancer.	Flavahan WA, Gaskell E, Bernstein BE	Science (New York, N.Y.)	28729483	Science	2017 Jul 21	https://www.ncbi.nlm.nih.gov/pubmed/28729483
An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma.	Neftel C, Laffy J, Filbin MG, Hara T, Shore ME, Rahme GJ, Richman AR, Silverbush D, Shaw ML, Hebert CM, Dewitt J, Gritsch S, Perez EM, Gonzalez Castro LN, Lan X, Druck N, Rodman C, Dionne D, Kaplan A, Bertalan MS, Small J, Pelton K, Becker S, Bonal D, Nguyen QD, Servis RL, Fung JM, Mylvaganam R, Mayr L, Gojo J, Haberler C, Geyeregger R, Czech T, Slavc I, Nahed BV, Curry WT, Carter BS, Wakimoto H, Brastianos PK, Batchelor TT, Stemmer-Rachamimov A, Martinez-Lage M, Frosch MP, Stamenkovic I, Riggi N, Rheinbay E, Monje M, Rozenblatt-Rosen O, Cahill DP, Patel AP, Hunter T, Verma IM, Ligon KL, Louis DN, Regev A, Bernstein BE, Tirosh I, Suvà ML	Cell	31327527	Cell	2019 Aug 8	https://www.ncbi.nlm.nih.gov/pubmed/31327527
Resolving medulloblastoma cellular architecture by single-cell genomics.	Hovestadt V, Smith KS, Bihannic L, Filbin MG, Shaw ML, Baumgartner A, DeWitt JC, Groves A, Mayr L, Weisman HR, Richman AR, Shore ME, Goumnerova L, Rosencrance C, Carter RA, Phoenix TN, Hadley JL, Tong Y, Houston J, Ashmun RA, DeCuypere M, Sharma T, Flasch D, Silkov A, Ligon KL, Pomeroy SL, Rivera MN, Rozenblatt-Rosen O, Rusert JM, Wechsler-Reya RJ, Li XN, Peyrl A, Gojo J, Kirchhofer D, Lötsch D, Czech T, Dorfer C, Haberler C, Geyeregger R, Halfmann A, Gawad C, Easton J, Pfister SM, Regev A, Gajjar A, Orr BA, Slavc I, Robinson GW, Bernstein BE, Suvà ML, Northcott PA	Nature	31341285	Nature	2019 Aug	https://www.ncbi.nlm.nih.gov/pubmed/31341285
Chromatin complex dependencies reveal targeting opportunities in leukemia.	Najm FJ, DeWeirdt P, Moore MM, Bevill SM, El Farran CA, Macias KA, Hegde M, Waterbury AL, Liau BB, van Galen P, Doench JG, Bernstein BE	Nature communications	36707513	Nat Commun	2023 Jan 27	https://www.ncbi.nlm.nih.gov/pubmed/36707513
Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation.	Kim KL, Rahme GJ, Goel VY, El Farran CA, Hansen AS, Bernstein BE	Molecular cell	38452764	Mol Cell	2024 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/38452764
Insulator dysfunction and oncogene activation in IDH mutant gliomas.	Flavahan WA, Drier Y, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, Suvà ML, Bernstein BE	Nature	26700815	Nature	2016 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/26700815
Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.	Kim IS, Wu J, Rahme GJ, Battaglia S, Dixit A, Gaskell E, Chen H, Pinello L, Bernstein BE	Cell reports	33027665	Cell Rep	2020 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/33027665
Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.	Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE	Cell	32841603	Cell	2020 Sep 17	https://www.ncbi.nlm.nih.gov/pubmed/32841603
Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance.	Liau BB, Sievers C, Donohue LK, Gillespie SM, Flavahan WA, Miller TE, Venteicher AS, Hebert CH, Carey CD, Rodig SJ, Shareef SJ, Najm FJ, van Galen P, Wakimoto H, Cahill DP, Rich JN, Aster JC, Suvà ML, Patel AP, Bernstein BE	Cell stem cell	27989769	Cell Stem Cell	2017 Feb 2	https://www.ncbi.nlm.nih.gov/pubmed/27989769
Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs.	Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE	Nature	31666694	Nature	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31666694
Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.	Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS	Cell	33838111	Cell	2021 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/33838111
Impact of supraphysiologic MDM2 expression on chromatin networks and therapeutic responses in sarcoma.	Bevill SM, Casaní-Galdón S, El Farran CA, Cytrynbaum EG, Macias KA, Oldeman SE, Oliveira KJ, Moore MM, Hegazi E, Adriaens C, Najm FJ, Demetri GD, Cohen S, Mullen JT, Riggi N, Johnstone SE, Bernstein BE	Cell genomics	37492096	Cell Genom	2023 Jul 12	https://www.ncbi.nlm.nih.gov/pubmed/37492096
Modeling epigenetic lesions that cause gliomas.	Rahme GJ, Javed NM, Puorro KL, Xin S, Hovestadt V, Johnstone SE, Bernstein BE	Cell	37494934	Cell	2023 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/37494934
Epigenome editing strategies for the functional annotation of CTCF insulators.	Tarjan DR, Flavahan WA, Bernstein BE	Nature communications	31534142	Nat Commun	2019 Sep 18	https://www.ncbi.nlm.nih.gov/pubmed/31534142
Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.	Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG	Nature biotechnology	29251726	Nat Biotechnol	2018 Feb	https://www.ncbi.nlm.nih.gov/pubmed/29251726
Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.	Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, Neftel C, Frank N, Pelton K, Hebert CM, Haberler C, Yizhak K, Gojo J, Egervari K, Mount C, van Galen P, Bonal DM, Nguyen QD, Beck A, Sinai C, Czech T, Dorfer C, Goumnerova L, Lavarino C, Carcaboso AM, Mora J, Mylvaganam R, Luo CC, Peyrl A, Popović M, Azizi A, Batchelor TT, Frosch MP, Martinez-Lage M, Kieran MW, Bandopadhayay P, Beroukhim R, Fritsch G, Getz G, Rozenblatt-Rosen O, Wucherpfennig KW, Louis DN, Monje M, Slavc I, Ligon KL, Golub TR, Regev A, Bernstein BE, Suvà ML	Science (New York, N.Y.)	29674595	Science	2018 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/29674595
Integrative dissection of gene regulatory elements at base resolution.	Chen Z, Javed N, Moore M, Wu J, Sun G, Vinyard M, Collins A, Pinello L, Najm FJ, Bernstein BE	Cell genomics	37388913	Cell Genom	2023 Jun 14	https://www.ncbi.nlm.nih.gov/pubmed/37388913
Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements.	Battaglia S, Dong K, Wu J, Chen Z, Najm FJ, Zhang Y, Moore MM, Hecht V, Shoresh N, Bernstein BE	Nature genetics	36195755	Nat Genet	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36195755
Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer.	Puram SV, Tirosh I, Parikh AS, Patel AP, Yizhak K, Gillespie S, Rodman C, Luo CL, Mroz EA, Emerick KS, Deschler DG, Varvares MA, Mylvaganam R, Rozenblatt-Rosen O, Rocco JW, Faquin WC, Lin DT, Regev A, Bernstein BE	Cell	29198524	Cell	2017 Dec 14	https://www.ncbi.nlm.nih.gov/pubmed/29198524
A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas.	Ryan RJH, Petrovic J, Rausch DM, Zhou Y, Lareau CA, Kluk MJ, Christie AL, Lee WY, Tarjan DR, Guo B, Donohue LKH, Gillespie SM, Nardi V, Hochberg EP, Blacklow SC, Weinstock DM, Faryabi RB, Bernstein BE, Aster JC, Pear WS	Cell reports	29045844	Cell Rep	2017 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/29045844
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.	van Galen P, Hovestadt V, Wadsworth Ii MH, Hughes TK, Griffin GK, Battaglia S, Verga JA, Stephansky J, Pastika TJ, Lombardi Story J, Pinkus GS, Pozdnyakova O, Galinsky I, Stone RM, Graubert TA, Shalek AK, Aster JC, Lane AA, Bernstein BE	Cell	30827681	Cell	2019 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/30827681
Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity.	Griffin GK, Wu J, Iracheta-Vellve A, Patti JC, Hsu J, Davis T, Dele-Oni D, Du PP, Halawi AG, Ishizuka JJ, Kim SY, Klaeger S, Knudsen NH, Miller BC, Nguyen TH, Olander KE, Papanastasiou M, Rachimi S, Robitschek EJ, Schneider EM, Yeary MD, Zimmer MD, Jaffe JD, Carr SA, Doench JG, Haining WN, Yates KB, Manguso RT, Bernstein BE	Nature	33953401	Nature	2021 Jul	https://www.ncbi.nlm.nih.gov/pubmed/33953401
Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.	Shareef SJ, Bevill SM, Raman AT, Aryee MJ, van Galen P, Hovestadt V, Bernstein BE	Nature biotechnology	33958785	Nat Biotechnol	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/33958785
Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance.	Eyler CE, Matsunaga H, Hovestadt V, Vantine SJ, van Galen P, Bernstein BE	Genome biology	32669109	Genome Biol	2020 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/32669109
Q&A: Cellular near death experiences-what is anastasis?	Sun G, Montell DJ	BMC biology	29065871	BMC Biol	2017 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/29065871
Unconventional Ways to Live and Die: Cell Death and Survival in Development, Homeostasis, and Disease.	Gudipaty SA, Conner CM, Rosenblatt J, Montell DJ	Annual review of cell and developmental biology	30089222	Annu Rev Cell Dev Biol	2018 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/30089222
Akt1 and dCIZ1 promote cell survival from apoptotic caspase activation during regeneration and oncogenic overgrowth.	Sun G, Ding XA, Argaw Y, Guo X, Montell DJ	Nature communications	33184261	Nat Commun	2020 Nov 12	https://www.ncbi.nlm.nih.gov/pubmed/33184261
A molecular signature for anastasis, recovery from the brink of apoptotic cell death.	Sun G, Guzman E, Balasanyan V, Conner CM, Wong K, Zhou HR, Kosik KS, Montell DJ	The Journal of cell biology	28768686	J Cell Biol	2017 Oct 2	https://www.ncbi.nlm.nih.gov/pubmed/28768686
Single cell transcriptome amplification with MALBAC.	Chapman AR, He Z, Lu S, Yong J, Tan L, Tang F, Xie XS	PloS one	25822772	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/25822772
Single molecules meet genomics: pinpointing precision medicine.	Xie XS	JAMA	25974149	JAMA	2015 May 26	https://www.ncbi.nlm.nih.gov/pubmed/25974149
A Near-Complete Spatial Map of Olfactory Receptors in the Mouse Main Olfactory Epithelium.	Tan L, Xie XS	Chemical senses	29796642	Chem Senses	2018 Jul 5	https://www.ncbi.nlm.nih.gov/pubmed/29796642
Coordination of two enhancers drives expression of olfactory trace amine-associated receptors.	Fei A, Wu W, Tan L, Tang C, Xu Z, Huo X, Bao H, Kong Y, Johnson M, Hartmann G, Talay M, Yang C, Riegler C, Herrera KJ, Engert F, Xie XS, Barnea G, Liberles SD, Yang H, Li Q	Nature communications	34145235	Nat Commun	2021 Jun 18	https://www.ncbi.nlm.nih.gov/pubmed/34145235
Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications.	Huang L, Ma F, Chapman A, Lu S, Xie XS	Annual review of genomics and human genetics	26077818	Annu Rev Genomics Hum Genet	2015	https://www.ncbi.nlm.nih.gov/pubmed/26077818
Olfactory sensory neurons transiently express multiple olfactory receptors during development.	Tan L, Li Q, Xie XS	Molecular systems biology	26646940	Mol Syst Biol	2015 Dec 8	https://www.ncbi.nlm.nih.gov/pubmed/26646940
Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI).	Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS	Science (New York, N.Y.)	28408603	Science	2017 Apr 14	https://www.ncbi.nlm.nih.gov/pubmed/28408603
Correlated gene modules uncovered by high-precision single-cell transcriptomics.	Chapman AR, Lee DF, Cai W, Ma W, Li X, Sun W, Xie XS	Proceedings of the National Academy of Sciences of the United States of America	36508663	Proc Natl Acad Sci U S A	2022 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/36508663
Single cell genomics to study DNA and chromosome changes in human gametes and embryos.	Blanshard RC, Chen C, Xie XS, Hoffmann ER	Methods in cell biology	29804682	Methods Cell Biol	2018	https://www.ncbi.nlm.nih.gov/pubmed/29804682
Three-dimensional genome structures of single diploid human cells.	Tan L, Xing D, Chang CH, Li H, Xie XS	Science (New York, N.Y.)	30166492	Science	2018 Aug 31	https://www.ncbi.nlm.nih.gov/pubmed/30166492
Discovery of a Potent GLUT Inhibitor from a Library of Rapafucins by Using 3D Microarrays.	Guo Z, Cheng Z, Wang J, Liu W, Peng H, Wang Y, Rao AVS, Li RJ, Ying X, Korangath P, Liberti MV, Li Y, Xie Y, Hong SY, Schiene-Fischer C, Fischer G, Locasale JW, Sukumar S, Zhu H, Liu JO	Angewandte Chemie (International ed. in English)	31591797	Angew Chem Int Ed Engl	2019 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/31591797
Strategies to discover regulatory circuits of the mammalian immune system.	Amit I, Regev A, Hacohen N	Nature reviews. Immunology	22094988	Nat Rev Immunol	2011 Nov 18	https://www.ncbi.nlm.nih.gov/pubmed/22094988
CD39 and CD161 modulate Th17 responses in Crohn's disease.	Bai A, Moss A, Kokkotou E, Usheva A, Sun X, Cheifetz A, Zheng Y, Longhi MS, Gao W, Wu Y, Robson SC	Journal of immunology (Baltimore, Md. : 1950)	25172498	J Immunol	2014 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/25172498
The evolution of drug resistance in clinical isolates of Candida albicans.	Ford CB, Funt JM, Abbey D, Issi L, Guiducci C, Martinez DA, Delorey T, Li BY, White TC, Cuomo C, Rao RP, Berman J, Thompson DA, Regev A	eLife	25646566	Elife	2015 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/25646566
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.	Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek AK, Hacohen N, Amit I, Regev A	Nature biotechnology	23503680	Nat Biotechnol	2013 Apr	https://www.ncbi.nlm.nih.gov/pubmed/23503680
High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.	Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A	Cell	24269006	Cell	2013 Dec 5	https://www.ncbi.nlm.nih.gov/pubmed/24269006
MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis.	Chindelevitch L, Stanley S, Hung D, Regev A, Berger B	Genome biology	22292986	Genome Biol	2012 Jan 31	https://www.ncbi.nlm.nih.gov/pubmed/22292986
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.	Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE	Cell	22196736	Cell	2011 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/22196736
Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes.	Solomon KV, Haitjema CH, Henske JK, Gilmore SP, Borges-Rivera D, Lipzen A, Brewer HM, Purvine SO, Wright AT, Theodorou MK, Grigoriev IV, Regev A, Thompson DA, O'Malley MA	Science (New York, N.Y.)	26912365	Science	2016 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/26912365
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks.	Habib N, Wapinski I, Margalit H, Regev A, Friedman N	Molecular systems biology	23089682	Mol Syst Biol	2012	https://www.ncbi.nlm.nih.gov/pubmed/23089682
Systematic discovery of TLR signaling components delineates viral-sensing circuits.	Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson J, Sutton A, Andersen MS, Root DE, von Andrian U, Jones RB, Park H, Carr SA, Regev A, Amit I, Hacohen N	Cell	22078882	Cell	2011 Nov 11	https://www.ncbi.nlm.nih.gov/pubmed/22078882
Inflammatory signaling in human tuberculosis granulomas is spatially organized.	Marakalala MJ, Raju RM, Sharma K, Zhang YJ, Eugenin EA, Prideaux B, Daudelin IB, Chen PY, Booty MG, Kim JH, Eum SY, Via LE, Behar SM, Barry CE 3rd, Mann M, Dartois V, Rubin EJ	Nature medicine	27043495	Nat Med	2016 May	https://www.ncbi.nlm.nih.gov/pubmed/27043495
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization.	Tsankov A, Yanagisawa Y, Rhind N, Regev A, Rando OJ	Genome research	21914852	Genome Res	2011 Nov	https://www.ncbi.nlm.nih.gov/pubmed/21914852
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.	Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL	Genes & development	21890647	Genes Dev	2011 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/21890647
Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.	Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A	Genome research	23640720	Genome Res	2013 Jun	https://www.ncbi.nlm.nih.gov/pubmed/23640720
Correction: Evolutionary principles of modular gene regulation in yeasts.	Thompson DA, Roy S, Chan M, Styczynski MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A	eLife	23840936	Elife	2013 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/23840936
Reactivation of Latent HIV-1 Expression by Engineered TALE Transcription Factors.	Perdigão P, Gaj T, Santa-Marta M, Barbas CF 3rd, Goncalves J	PloS one	26933881	PLoS One	2016	https://www.ncbi.nlm.nih.gov/pubmed/26933881
ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering.	Gaj T, Gersbach CA, Barbas CF 3rd	Trends in biotechnology	23664777	Trends Biotechnol	2013 Jul	https://www.ncbi.nlm.nih.gov/pubmed/23664777
Genome engineering with custom recombinases.	Gaj T, Barbas CF 3rd	Methods in enzymology	25398336	Methods Enzymol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25398336
Protein Delivery of Cell-Penetrating Zinc-Finger Activators Stimulates Latent HIV-1-Infected Cells.	Perdigão PRL, Cunha-Santos C, Barbas CF 3rd, Santa-Marta M, Goncalves J	Molecular therapy. Methods & clinical development	32637446	Mol Ther Methods Clin Dev	2020 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/32637446
A chemically programmed antibody is a long-lasting and potent inhibitor of influenza neuraminidase.	Hayakawa M, Toda N, Carrillo N, Thornburg NJ, Crowe JE Jr, Barbas CF 3rd	Chembiochem : a European journal of chemical biology	22965667	Chembiochem	2012 Oct 15	https://www.ncbi.nlm.nih.gov/pubmed/22965667
Chimeric TALE recombinases with programmable DNA sequence specificity.	Mercer AC, Gaj T, Fuller RP, Barbas CF 3rd	Nucleic acids research	23019222	Nucleic Acids Res	2012 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23019222
Directed evolution of the TALE N-terminal domain for recognition of all 5' bases.	Lamb BM, Mercer AC, Barbas CF 3rd	Nucleic acids research	23980031	Nucleic Acids Res	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/23980031
Expanding the scope of site-specific recombinases for genetic and metabolic engineering.	Gaj T, Sirk SJ, Barbas CF 3rd	Biotechnology and bioengineering	23982993	Biotechnol Bioeng	2014 Jan	https://www.ncbi.nlm.nih.gov/pubmed/23982993
Facile and stabile linkages through tyrosine: bioconjugation strategies with the tyrosine-click reaction.	Ban H, Nagano M, Gavrilyuk J, Hakamata W, Inokuma T, Barbas CF 3rd	Bioconjugate chemistry	23534985	Bioconjug Chem	2013 Apr 17	https://www.ncbi.nlm.nih.gov/pubmed/23534985
Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants.	Sirk SJ, Gaj T, Jonsson A, Mercer AC, Barbas CF 3rd	Nucleic acids research	24452803	Nucleic Acids Res	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24452803
N-Sulfonyl-β-lactam hapten as an effective labeling reagent for aldolase mAb.	Inokuma T, Fuller RP, Barbas CF 3rd	Bioorganic & medicinal chemistry letters	25791455	Bioorg Med Chem Lett	2015 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/25791455
Redesigning Recombinase Specificity for Safe Harbor Sites in the Human Genome.	Wallen MC, Gaj T, Barbas CF 3rd	PloS one	26414179	PLoS One	2015	https://www.ncbi.nlm.nih.gov/pubmed/26414179
Improving the serum stability of site-specific antibody conjugates with sulfone linkers.	Patterson JT, Asano S, Li X, Rader C, Barbas CF 3rd	Bioconjugate chemistry	25099687	Bioconjug Chem	2014 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/25099687
Enhancing the specificity of recombinase-mediated genome engineering through dimer interface redesign.	Gaj T, Sirk SJ, Tingle RD, Mercer AC, Wallen MC, Barbas CF 3rd	Journal of the American Chemical Society	24611715	J Am Chem Soc	2014 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/24611715
A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells.	Gaj T, Mercer AC, Sirk SJ, Smith HL, Barbas CF 3rd	Nucleic acids research	23393187	Nucleic Acids Res	2013 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/23393187
Rapid, stable, chemoselective labeling of thiols with Julia-Kocieński-like reagents: a serum-stable alternative to maleimide-based protein conjugation.	Toda N, Asano S, Barbas CF 3rd	Angewandte Chemie (International ed. in English)	24123851	Angew Chem Int Ed Engl	2013 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/24123851
Regulation of endogenous human gene expression by ligand-inducible TALE transcription factors.	Mercer AC, Gaj T, Sirk SJ, Lamb BM, Barbas CF 3rd	ACS synthetic biology	24251925	ACS Synth Biol	2014 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/24251925
Cell-penetrating peptide-mediated delivery of TALEN proteins via bioconjugation for genome engineering.	Liu J, Gaj T, Patterson JT, Sirk SJ, Barbas CF 3rd	PloS one	24465685	PLoS One	2014	https://www.ncbi.nlm.nih.gov/pubmed/24465685
In vivo programming of endogenous antibodies via oral administration of adaptor ligands.	Nagano M, Carrillo N, Otsubo N, Hakamata W, Ban H, Fuller RP, Bashiruddin NK, Barbas CF 3rd	Bioorganic & medicinal chemistry	28988625	Bioorg Med Chem	2017 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/28988625
Improved cell-penetrating zinc-finger nuclease proteins for precision genome engineering.	Liu J, Gaj T, Wallen MC, Barbas CF 3rd	Molecular therapy. Nucleic acids	25756962	Mol Ther Nucleic Acids	2015 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/25756962
Human Serum Albumin Domain I Fusion Protein for Antibody Conjugation.	Patterson JT, Wilson HD, Asano S, Nilchan N, Fuller RP, Roush WR, Rader C, Barbas CF 3rd	Bioconjugate chemistry	27666414	Bioconjug Chem	2016 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/27666414
Synthetic zinc finger proteins: the advent of targeted gene regulation and genome modification technologies.	Gersbach CA, Gaj T, Barbas CF 3rd	Accounts of chemical research	24877793	Acc Chem Res	2014 Aug 19	https://www.ncbi.nlm.nih.gov/pubmed/24877793
Direct protein delivery to mammalian cells using cell-permeable Cys2-His2 zinc-finger domains.	Gaj T, Liu J	Journal of visualized experiments : JoVE	25866937	J Vis Exp	2015 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/25866937
Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells.	Liu J, Gaj T, Yang Y, Wang N, Shui S, Kim S, Kanchiswamy CN, Kim JS, Barbas CF 3rd	Nature protocols	26492140	Nat Protoc	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26492140
Protein delivery using Cys2-His2 zinc-finger domains.	Gaj T, Liu J, Anderson KE, Sirk SJ, Barbas CF 3rd	ACS chemical biology	24936957	ACS Chem Biol	2014 Aug 15	https://www.ncbi.nlm.nih.gov/pubmed/24936957
The effect of particle size on the biodistribution of low-modulus hydrogel PRINT particles.	Merkel TJ, Chen K, Jones SW, Pandya AA, Tian S, Napier ME, Zamboni WE, DeSimone JM	Journal of controlled release : official journal of the Controlled Release Society	22705460	J Control Release	2012 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/22705460
Incorporation and controlled release of silyl ether prodrugs from PRINT nanoparticles.	Parrott MC, Finniss M, Luft JC, Pandya A, Gullapalli A, Napier ME, DeSimone JM	Journal of the American Chemical Society	22545784	J Am Chem Soc	2012 May 9	https://www.ncbi.nlm.nih.gov/pubmed/22545784
Particles for Local Delivery of Proteins Using Intra-Articular Route.	Khodabandehlou K, Tian S, Luft JC, Khan SA, DeSimone JM	Advanced healthcare materials	26833828	Adv Healthc Mater	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26833828
Analysis of the murine immune response to pulmonary delivery of precisely fabricated nano- and microscale particles.	Roberts RA, Shen T, Allen IC, Hasan W, DeSimone JM, Ting JP	PloS one	23593509	PLoS One	2013	https://www.ncbi.nlm.nih.gov/pubmed/23593509
Silylated precision particles for controlled release of proteins.	Khodabandehlou K, Kumbhar AS, Habibi S, Pandya AA, Luft JC, Khan SA, DeSimone JM	ACS applied materials & interfaces	25742193	ACS Appl Mater Interfaces	2015 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/25742193
Rapid and Persistent Delivery of Antigen by Lymph Node Targeting PRINT Nanoparticle Vaccine Carrier To Promote Humoral Immunity.	Mueller SN, Tian S, DeSimone JM	Molecular pharmaceutics	25817072	Mol Pharm	2015 May 4	https://www.ncbi.nlm.nih.gov/pubmed/25817072
Analysis of human innate immune responses to PRINT fabricated nanoparticles with cross validation using a humanized mouse model.	Robbins GR, Roberts RA, Guo H, Reuter K, Shen T, Sempowski GD, McKinnon KP, Su L, DeSimone JM, Ting JP	Nanomedicine : nanotechnology, biology, and medicine	25596079	Nanomedicine	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25596079
Towards programming immune tolerance through geometric manipulation of phosphatidylserine.	Roberts RA, Eitas TK, Byrne JD, Johnson BM, Short PJ, McKinnon KP, Reisdorf S, Luft JC, DeSimone JM, Ting JP	Biomaterials	26325217	Biomaterials	2015 Dec	https://www.ncbi.nlm.nih.gov/pubmed/26325217
Reductively Responsive Hydrogel Nanoparticles with Uniform Size, Shape, and Tunable Composition for Systemic siRNA Delivery in Vivo.	Ma D, Tian S, Baryza J, Luft JC, DeSimone JM	Molecular pharmaceutics	26287725	Mol Pharm	2015 Oct 5	https://www.ncbi.nlm.nih.gov/pubmed/26287725
Delivery of multiple siRNAs using lipid-coated PLGA nanoparticles for treatment of prostate cancer.	Hasan W, Chu K, Gullapalli A, Dunn SS, Enlow EM, Luft JC, Tian S, Napier ME, Pohlhaus PD, Rolland JP, DeSimone JM	Nano letters	22165988	Nano Lett	2012 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/22165988
What limits the efficiency of double-strand break-dependent stress-induced mutation in Escherichia coli?	Shee C, Ponder R, Gibson JL, Rosenberg SM	Journal of molecular microbiology and biotechnology	22248539	J Mol Microbiol Biotechnol	2011	https://www.ncbi.nlm.nih.gov/pubmed/22248539
Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli.	Shee C, Gibson JL, Darrow MC, Gonzalez C, Rosenberg SM	Proceedings of the National Academy of Sciences of the United States of America	21808005	Proc Natl Acad Sci U S A	2011 Aug 16	https://www.ncbi.nlm.nih.gov/pubmed/21808005
Gross chromosomal rearrangement mediated by DNA replication in stressed cells: evidence from Escherichia coli.	Moore JM, Wimberly H, Thornton PC, Rosenberg SM, Hastings PJ	Annals of the New York Academy of Sciences	22954223	Ann N Y Acad Sci	2012 Sep	https://www.ncbi.nlm.nih.gov/pubmed/22954223
MioC and GidA proteins promote cell division in E. coli.	Lies M, Visser BJ, Joshi MC, Magnan D, Bates D	Frontiers in microbiology	26074904	Front Microbiol	2015	https://www.ncbi.nlm.nih.gov/pubmed/26074904
Genomic rearrangement in three dimensions.	Hastings PJ, Rosenberg SM	Nature biotechnology	22158363	Nat Biotechnol	2011 Dec 8	https://www.ncbi.nlm.nih.gov/pubmed/22158363
Rare deleterious germline variants and risk of lung cancer.	Liu Y, Xia J, McKay J, Tsavachidis S, Xiao X, Spitz MR, Cheng C, Byun J, Hong W, Li Y, Zhu D, Song Z, Rosenberg SM, Scheurer ME, Kheradmand F, Pikielny CW, Lusk CM, Schwartz AG, Wistuba II, Cho MH, Silverman EK, Bailey-Wilson J, Pinney SM, Anderson M, Kupert E, Gaba C, Mandal D, You M, de Andrade M, Yang P, Liloglou T, Davies MPA, Lissowska J, Swiatkowska B, Zaridze D, Mukeria A, Janout V, Holcatova I, Mates D, Stojsic J, Scelo G, Brennan P, Liu G, Field JK, Hung RJ, Christiani DC, Amos CI	NPJ precision oncology	33594163	NPJ Precis Oncol	2021 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/33594163
Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase.	Xia J, Chen LT, Mei Q, Ma CH, Halliday JA, Lin HY, Magnan D, Pribis JP, Fitzgerald DM, Hamilton HM, Richters M, Nehring RB, Shen X, Li L, Bates D, Hastings PJ, Herman C, Jayaram M, Rosenberg SM	Science advances	28090586	Sci Adv	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/28090586
The transcription fidelity factor GreA impedes DNA break repair.	Sivaramakrishnan P, Sepúlveda LA, Halliday JA, Liu J, Núñez MAB, Golding I, Rosenberg SM, Herman C	Nature	28976965	Nature	2017 Oct 12	https://www.ncbi.nlm.nih.gov/pubmed/28976965
Two mechanisms of chromosome fragility at replication-termination sites in bacteria.	Mei Q, Fitzgerald DM, Liu J, Xia J, Pribis JP, Zhai Y, Nehring RB, Paiano J, Li H, Nussenzweig A, Hastings PJ, Rosenberg SM	Science advances	34144978	Sci Adv	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/34144978
Molecular imaging: exploring the next frontier.	Weissleder R	Radiology	10478223	Radiology	1999 Sep	https://www.ncbi.nlm.nih.gov/pubmed/10478223
R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli.	Wimberly H, Shee C, Thornton PC, Sivaramakrishnan P, Rosenberg SM, Hastings PJ	Nature communications	23828459	Nat Commun	2013	https://www.ncbi.nlm.nih.gov/pubmed/23828459
Engineered proteins detect spontaneous DNA breakage in human and bacterial cells.	Shee C, Cox BD, Gu F, Luengas EM, Joshi MC, Chiu LY, Magnan D, Halliday JA, Frisch RL, Gibson JL, Nehring RB, Do HG, Hernandez M, Li L, Herman C, Hastings PJ, Bates D, Harris RS, Miller KM, Rosenberg SM	eLife	24171103	Elife	2013 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/24171103
Transcriptome-wide association study reveals candidate causal genes for lung cancer.	Bossé Y, Li Z, Xia J, Manem V, Carreras-Torres R, Gabriel A, Gaudreault N, Albanes D, Aldrich MC, Andrew A, Arnold S, Bickeböller H, Bojesen SE, Brennan P, Brunnstrom H, Caporaso N, Chen C, Christiani DC, Field JK, Goodman G, Grankvist K, Houlston R, Johansson M, Johansson M, Kiemeney LA, Lam S, Landi MT, Lazarus P, Le Marchand L, Liu G, Melander O, Rennert G, Risch A, Rosenberg SM, Schabath MB, Shete S, Song Z, Stevens VL, Tardon A, Wichmann HE, Woll P, Zienolddiny S, Obeidat M, Timens W, Hung RJ, Joubert P, Amos CI, McKay JD	International journal of cancer	31696517	Int J Cancer	2020 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/31696517
Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.	Klein HL, Bačinskaja G, Che J, Cheblal A, Elango R, Epshtein A, Fitzgerald DM, Gómez-González B, Khan SR, Kumar S, Leland BA, Marie L, Mei Q, Miné-Hattab J, Piotrowska A, Polleys EJ, Putnam CD, Radchenko EA, Saada AA, Sakofsky CJ, Shim EY, Stracy M, Xia J, Yan Z, Yin Y, Aguilera A, Argueso JL, Freudenreich CH, Gasser SM, Gordenin DA, Haber JE, Ira G, Jinks-Robertson S, King MC, Kolodner RD, Kuzminov A, Lambert SA, Lee SE, Miller KM, Mirkin SM, Petes TD, Rosenberg SM, Rothstein R, Symington LS, Zawadzki P, Kim N, Lisby M, Malkova A	Microbial cell (Graz, Austria)	30652105	Microb Cell	2019 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/30652105
Tools To Live By: Bacterial DNA Structures Illuminate Cancer.	Xia J, Mei Q, Rosenberg SM	Trends in genetics : TIG	30962000	Trends Genet	2019 May	https://www.ncbi.nlm.nih.gov/pubmed/30962000
ppGpp and RNA-polymerase backtracking guide antibiotic-induced mutable gambler cells.	Zhai Y, Minnick PJ, Pribis JP, Garcia-Villada L, Hastings PJ, Herman C, Rosenberg SM	Molecular cell	36965481	Mol Cell	2023 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/36965481
Identity and function of a large gene network underlying mutagenic repair of DNA breaks.	Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM	Science (New York, N.Y.)	23224554	Science	2012 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/23224554
Stress-induced loss of heterozygosity in Candida: a possible missing link in the ability to evolve.	Rosenberg SM	mBio	21933916	mBio	2011	https://www.ncbi.nlm.nih.gov/pubmed/21933916
Medicine. Combating evolution to fight disease.	Rosenberg SM, Queitsch C	Science (New York, N.Y.)	24604189	Science	2014 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/24604189
Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli.	Shee C, Gibson JL, Rosenberg SM	Cell reports	23041320	Cell Rep	2012 Oct 25	https://www.ncbi.nlm.nih.gov/pubmed/23041320
Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage.	Xia J, Chiu LY, Nehring RB, Bravo Núñez MA, Mei Q, Perez M, Zhai Y, Fitzgerald DM, Pribis JP, Wang Y, Hu CW, Powell RT, LaBonte SA, Jalali A, Matadamas Guzmán ML, Lentzsch AM, Szafran AT, Joshi MC, Richters M, Gibson JL, Frisch RL, Hastings PJ, Bates D, Queitsch C, Hilsenbeck SG, Coarfa C, Hu JC, Siegele DA, Scott KL, Liang H, Mancini MA, Herman C, Miller KM, Rosenberg SM	Cell	30633903	Cell	2019 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/30633903
An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli.	Nehring RB, Gu F, Lin HY, Gibson JL, Blythe MJ, Wilson R, Bravo Núñez MA, Hastings PJ, Louis EJ, Frisch RL, Hu JC, Rosenberg SM	Nucleic acids research	26578563	Nucleic Acids Res	2016 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/26578563
DNA Replication Initiation Is Blocked by a Distant Chromosome-Membrane Attachment.	Magnan D, Joshi MC, Barker AK, Visser BJ, Bates D	Current biology : CB	26255849	Curr Biol	2015 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/26255849
Compartmentalized AMPK signaling illuminated by genetically encoded molecular sensors and actuators.	Miyamoto T, Rho E, Sample V, Akano H, Magari M, Ueno T, Gorshkov K, Chen M, Tokumitsu H, Zhang J, Inoue T	Cell reports	25892241	Cell Rep	2015 Apr 28	https://www.ncbi.nlm.nih.gov/pubmed/25892241
Single-cell analysis of G-protein signal transduction.	Clister T, Mehta S, Zhang J	The Journal of biological chemistry	25605723	J Biol Chem	2015 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/25605723
Transcriptional silencing by single-stranded RNAs targeting a noncoding RNA that overlaps a gene promoter.	Matsui M, Prakash TP, Corey DR	ACS chemical biology	23082936	ACS Chem Biol	2013 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/23082936
RefSOFI for Mapping Nanoscale Organization of Protein-Protein Interactions in Living Cells.	Hertel F, Mo GC, Duwé S, Dedecker P, Zhang J	Cell reports	26748717	Cell Rep	2016 Jan 12	https://www.ncbi.nlm.nih.gov/pubmed/26748717
Dynamic visualization of calcium-dependent signaling in cellular microdomains.	Mehta S, Zhang J	Cell calcium	25703691	Cell Calcium	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25703691
Using a kinase-inducible bimolecular switch to control enzyme activity in living cells.	Mehta S, Zhang J	Current protocols in chemical biology	24391085	Curr Protoc Chem Biol	2013	https://www.ncbi.nlm.nih.gov/pubmed/24391085
Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution.	Mo GC, Ross B, Hertel F, Manna P, Yang X, Greenwald E, Booth C, Plummer AM, Tenner B, Chen Z, Wang Y, Kennedy EJ, Cole PA, Fleming KG, Palmer A, Jimenez R, Xiao J, Dedecker P, Zhang J	Nature methods	28288122	Nat Methods	2017 Apr	https://www.ncbi.nlm.nih.gov/pubmed/28288122
Controlling enzymatic action in living cells with a kinase-inducible bimolecular switch.	Sample V, Ni Q, Mehta S, Inoue T, Zhang J	ACS chemical biology	23072367	ACS Chem Biol	2013 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/23072367
Confinement Sensing and Signal Optimization via Piezo1/PKA and Myosin II Pathways.	Hung WC, Yang JR, Yankaskas CL, Wong BS, Wu PH, Pardo-Pastor C, Serra SA, Chiang MJ, Gu Z, Wirtz D, Valverde MA, Yang JT, Zhang J, Konstantopoulos K	Cell reports	27160899	Cell Rep	2016 May 17	https://www.ncbi.nlm.nih.gov/pubmed/27160899
Construction of human activity-based phosphorylation networks.	Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J	Molecular systems biology	23549483	Mol Syst Biol	2013	https://www.ncbi.nlm.nih.gov/pubmed/23549483
Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction.	Hu J, Neiswinger J, Zhang J, Zhu H, Qian J	PLoS computational biology	26393507	PLoS Comput Biol	2015	https://www.ncbi.nlm.nih.gov/pubmed/26393507
Tracking the Activity of mTORC1 in Living Cells Using Genetically Encoded FRET-based Biosensor TORCAR.	Zhou X, Li S, Zhang J	Current protocols in chemical biology	27925667	Curr Protoc Chem Biol	2016 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/27925667
Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems.	Sample V, Mehta S, Zhang J	Journal of cell science	24634506	J Cell Sci	2014 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/24634506
Visualization of Compartmentalized Kinase Activity Dynamics Using Adaptable BimKARs.	Depry C, Mehta S, Li R, Zhang J	Chemistry & biology	26548610	Chem Biol	2015 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/26548610
Monitoring of post-translational modification dynamics with genetically encoded fluorescent reporters.	Hertel F, Zhang J	Biopolymers	23576192	Biopolymers	2014 Feb	https://www.ncbi.nlm.nih.gov/pubmed/23576192
Multiplexed visualization of dynamic signaling networks using genetically encoded fluorescent protein-based biosensors.	Depry C, Mehta S, Zhang J	Pflugers Archiv : European journal of physiology	23138230	Pflugers Arch	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23138230
Ratiometric biosensors based on dimerization-dependent fluorescent protein exchange.	Ding Y, Li J, Enterina JR, Shen Y, Zhang I, Tewson PH, Mo GC, Zhang J, Quinn AM, Hughes TE, Maysinger D, Alford SC, Zhang Y, Campbell RE	Nature methods	25622108	Nat Methods	2015 Mar	https://www.ncbi.nlm.nih.gov/pubmed/25622108
Calmodulin-controlled spatial decoding of oscillatory Ca2+ signals by calcineurin.	Mehta S, Aye-Han NN, Ganesan A, Oldach L, Gorshkov K, Zhang J	eLife	25056880	Elife	2014 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/25056880
Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks.	Greenwald EC, Mehta S, Zhang J	Chemical reviews	30550275	Chem Rev	2018 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/30550275
Dynamic Visualization of mTORC1 Activity in Living Cells.	Zhou X, Clister TL, Lowry PR, Seldin MM, Wong GW, Zhang J	Cell reports	25772363	Cell Rep	2015 Mar 17	https://www.ncbi.nlm.nih.gov/pubmed/25772363
PhosphoNetworks: a database for human phosphorylation networks.	Hu J, Rho HS, Newman RH, Zhang J, Zhu H, Qian J	Bioinformatics (Oxford, England)	24227675	Bioinformatics	2014 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/24227675
Engineering a BCR-ABL-activated caspase for the selective elimination of leukemic cells.	Kurokawa M, Ito T, Yang CS, Zhao C, Macintyre AN, Rizzieri DA, Rathmell JC, Deininger MW, Reya T, Kornbluth S	Proceedings of the National Academy of Sciences of the United States of America	23324740	Proc Natl Acad Sci U S A	2013 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/23324740
CD98-Mediated Adhesive Signaling Enables the Establishment and Propagation of Acute Myelogenous Leukemia.	Bajaj J, Konuma T, Lytle NK, Kwon HY, Ablack JN, Cantor JM, Rizzieri D, Chuah C, Oehler VG, Broome EH, Ball ED, van der Horst EH, Ginsberg MH, Reya T	Cancer cell	27908736	Cancer Cell	2016 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/27908736
An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.	Bajaj J, Hamilton M, Shima Y, Chambers K, Spinler K, Van Nostrand EL, Yee BA, Blue SM, Chen M, Rizzeri D, Chuah C, Oehler VG, Broome HE, Sasik R, Scott-Browne J, Rao A, Yeo GW, Reya T	Nature cancer	34109316	Nat Cancer	2020 Apr	https://www.ncbi.nlm.nih.gov/pubmed/34109316
β-Arrestin2 mediates the initiation and progression of myeloid leukemia.	Fereshteh M, Ito T, Kovacs JJ, Zhao C, Kwon HY, Tornini V, Konuma T, Chen M, Lefkowitz RJ, Reya T	Proceedings of the National Academy of Sciences of the United States of America	22773819	Proc Natl Acad Sci U S A	2012 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/22773819
A stem cell reporter based platform to identify and target drug resistant stem cells in myeloid leukemia.	Spinler K, Bajaj J, Ito T, Zimdahl B, Hamilton M, Ahmadi A, Koechlein CS, Lytle N, Kwon HY, Anower-E-Khuda F, Sun H, Blevins A, Weeks J, Kritzik M, Karlseder J, Ginsberg MH, Park PW, Esko JD, Reya T	Nature communications	33243988	Nat Commun	2020 Nov 26	https://www.ncbi.nlm.nih.gov/pubmed/33243988
Image-based detection and targeting of therapy resistance in pancreatic adenocarcinoma.	Fox RG, Lytle NK, Jaquish DV, Park FD, Ito T, Bajaj J, Koechlein CS, Zimdahl B, Yano M, Kopp J, Kritzik M, Sicklick J, Sander M, Grandgenett PM, Hollingsworth MA, Shibata S, Pizzo D, Valasek M, Sasik R, Scadeng M, Okano H, Kim Y, MacLeod AR, Lowy AM, Reya T	Nature	27281208	Nature	2016 Jun 16	https://www.ncbi.nlm.nih.gov/pubmed/27281208
Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells.	Zheng Q, Cai X, Tan MH, Schaffert S, Arnold CP, Gong X, Chen CZ, Huang S	BioTechniques	25209046	Biotechniques	2014	https://www.ncbi.nlm.nih.gov/pubmed/25209046
Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture.	Li X, Nadauld L, Ootani A, Corney DC, Pai RK, Gevaert O, Cantrell MA, Rack PG, Neal JT, Chan CW, Yeung T, Gong X, Yuan J, Wilhelmy J, Robine S, Attardi LD, Plevritis SK, Hung KE, Chen CZ, Ji HP, Kuo CJ	Nature medicine	24859528	Nat Med	2014 Jul	https://www.ncbi.nlm.nih.gov/pubmed/24859528
Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation.	Wilson BG, Wang X, Shen X, McKenna ES, Lemieux ME, Cho YJ, Koellhoffer EC, Pomeroy SL, Orkin SH, Roberts CW	Cancer cell	20951942	Cancer Cell	2010 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/20951942
Layer-by-layer assembled fluorescent probes in the second near-infrared window for systemic delivery and detection of ovarian cancer.	Dang X, Gu L, Qi J, Correa S, Zhang G, Belcher AM, Hammond PT	Proceedings of the National Academy of Sciences of the United States of America	27114520	Proc Natl Acad Sci U S A	2016 May 10	https://www.ncbi.nlm.nih.gov/pubmed/27114520
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins.	Teytelman L, Thurtle DM, Rine J, van Oudenaarden A	Proceedings of the National Academy of Sciences of the United States of America	24173036	Proc Natl Acad Sci U S A	2013 Nov 12	https://www.ncbi.nlm.nih.gov/pubmed/24173036
Periodic-shRNA molecules are capable of gene silencing, cytotoxicity and innate immune activation in cancer cells.	Shopsowitz KE, Wu C, Liu G, Dreaden EC, Hammond PT	Nucleic acids research	26704983	Nucleic Acids Res	2016 Jan 29	https://www.ncbi.nlm.nih.gov/pubmed/26704983
High Throughput Layer-by-Layer Films for Extracting Film Forming Parameters and Modulating Film Interactions with Cells.	Jaklenec A, Anselmo AC, Hong J, Vegas AJ, Kozminsky M, Langer R, Hammond PT, Anderson DG	ACS applied materials & interfaces	26713554	ACS Appl Mater Interfaces	2016 Jan 27	https://www.ncbi.nlm.nih.gov/pubmed/26713554
High-throughput measurement of single-cell growth rates using serial microfluidic mass sensor arrays.	Cermak N, Olcum S, Delgado FF, Wasserman SC, Payer KR, A Murakami M, Knudsen SM, Kimmerling RJ, Stevens MM, Kikuchi Y, Sandikci A, Ogawa M, Agache V, Baléras F, Weinstock DM, Manalis SR	Nature biotechnology	27598230	Nat Biotechnol	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27598230
Spatial Control of Gene Expression by Nanocarriers Using Heparin Masking and Ultrasound-Targeted Microbubble Destruction.	Chertok B, Langer R, Anderson DG	ACS nano	27472268	ACS Nano	2016 Aug 23	https://www.ncbi.nlm.nih.gov/pubmed/27472268
A Caenorhabditis elegans protein with a PRDM9-like SET domain localizes to chromatin-associated foci and promotes spermatocyte gene expression, sperm production and fertility.	Engert CG, Droste R, van Oudenaarden A, Horvitz HR	PLoS genetics	29702639	PLoS Genet	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29702639
Dampening of expression oscillations by synchronous regulation of a microRNA and its target.	Kim Dh, Grün D, van Oudenaarden A	Nature genetics	24036951	Nat Genet	2013 Nov	https://www.ncbi.nlm.nih.gov/pubmed/24036951
Nanoparticle-based drug delivery systems: a commercial and regulatory outlook as the field matures.	Ragelle H, Danhier F, Préat V, Langer R, Anderson DG	Expert opinion on drug delivery	27730820	Expert Opin Drug Deliv	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/27730820
Materials for non-viral intracellular delivery of messenger RNA therapeutics.	Kauffman KJ, Webber MJ, Anderson DG	Journal of controlled release : official journal of the Controlled Release Society	26718856	J Control Release	2016 Oct 28	https://www.ncbi.nlm.nih.gov/pubmed/26718856
Poly(glycoamidoamine) Brushes Formulated Nanomaterials for Systemic siRNA and mRNA Delivery in Vivo.	Dong Y, Dorkin JR, Wang W, Chang PH, Webber MJ, Tang BC, Yang J, Abutbul-Ionita I, Danino D, DeRosa F, Heartlein M, Langer R, Anderson DG	Nano letters	26727632	Nano Lett	2016 Feb 10	https://www.ncbi.nlm.nih.gov/pubmed/26727632
Cell intrinsic modulation of Wnt signaling controls neuroblast migration in C. elegans.	Mentink RA, Middelkoop TC, Rella L, Ji N, Tang CY, Betist MC, van Oudenaarden A, Korswagen HC	Developmental cell	25373777	Dev Cell	2014 Oct 27	https://www.ncbi.nlm.nih.gov/pubmed/25373777
Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression.	van Zon JS, Kienle S, Huelsz-Prince G, Barkoulas M, van Oudenaarden A	Nature communications	25958991	Nat Commun	2015 May 11	https://www.ncbi.nlm.nih.gov/pubmed/25958991
Allele-specific detection of single mRNA molecules in situ.	Hansen CH, van Oudenaarden A	Nature methods	23934076	Nat Methods	2013 Sep	https://www.ncbi.nlm.nih.gov/pubmed/23934076
Stochastic cytokine expression induces mixed T helper cell States.	Fang M, Xie H, Dougan SK, Ploegh H, van Oudenaarden A	PLoS biology	23935453	PLoS Biol	2013 Jul	https://www.ncbi.nlm.nih.gov/pubmed/23935453
FuseFISH: robust detection of transcribed gene fusions in single cells.	Semrau S, Crosetto N, Bienko M, Boni M, Bernasconi P, Chiarle R, van Oudenaarden A	Cell reports	24373969	Cell Rep	2014 Jan 16	https://www.ncbi.nlm.nih.gov/pubmed/24373969
Transcriptional profiling of cells sorted by RNA abundance.	Klemm S, Semrau S, Wiebrands K, Mooijman D, Faddah DA, Jaenisch R, van Oudenaarden A	Nature methods	24681693	Nat Methods	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24681693
Synchronized cycles of bacterial lysis for in vivo delivery.	Din MO, Danino T, Prindle A, Skalak M, Selimkhanov J, Allen K, Julio E, Atolia E, Tsimring LS, Bhatia SN, Hasty J	Nature	27437587	Nature	2016 Aug 4	https://www.ncbi.nlm.nih.gov/pubmed/27437587
Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors.	Jain PK, Ramanan V, Schepers AG, Dalvie NS, Panda A, Fleming HE, Bhatia SN	Angewandte Chemie (International ed. in English)	27554600	Angew Chem Int Ed Engl	2016 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/27554600
A Facile and Versatile Method to Endow Biomaterial Devices with Zwitterionic Surface Coatings.	Yesilyurt V, Veiseh O, Doloff JC, Li J, Bose S, Xie X, Bader AR, Chen M, Webber MJ, Vegas AJ, Langer R, Anderson DG	Advanced healthcare materials	27976536	Adv Healthc Mater	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/27976536
Drug sensitivity of single cancer cells is predicted by changes in mass accumulation rate.	Stevens MM, Maire CL, Chou N, Murakami MA, Knoff DS, Kikuchi Y, Kimmerling RJ, Liu H, Haidar S, Calistri NL, Cermak N, Olcum S, Cordero NA, Idbaih A, Wen PY, Weinstock DM, Ligon KL, Manalis SR	Nature biotechnology	27723727	Nat Biotechnol	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/27723727
Comparison of Modular PEG Incorporation Strategies for Stabilization of Peptide-siRNA Nanocomplexes.	Lo JH, Kwon EJ, Zhang AQ, Singhal P, Bhatia SN	Bioconjugate chemistry	27583545	Bioconjug Chem	2016 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/27583545
How to regulate a gene: to repress or to activate?	Slavov N, van Oudenaarden A	Molecular cell	22681881	Mol Cell	2012 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/22681881
ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.	Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC	Science (New York, N.Y.)	28751582	Science	2017 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/28751582
Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway.	Ji N, Middelkoop TC, Mentink RA, Betist MC, Tonegawa S, Mooijman D, Korswagen HC, van Oudenaarden A	Cell	24209624	Cell	2013 Nov 7	https://www.ncbi.nlm.nih.gov/pubmed/24209624
Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors.	Davidson SM, Jonas O, Keibler MA, Hou HW, Luengo A, Mayers JR, Wyckoff J, Del Rosario AM, Whitman M, Chin CR, Condon KJ, Lammers A, Kellersberger KA, Stall BK, Stephanopoulos G, Bar-Sagi D, Han J, Rabinowitz JD, Cima MJ, Langer R, Vander Heiden MG	Nature medicine	28024083	Nat Med	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/28024083
Shooting for the Moon: Nanoscale Approaches to Cancer.	Hammond PT	ACS nano	26902596	ACS Nano	2016 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/26902596
Engineering nanolayered particles for modular drug delivery.	Correa S, Dreaden EC, Gu L, Hammond PT	Journal of controlled release : official journal of the Controlled Release Society	26809005	J Control Release	2016 Oct 28	https://www.ncbi.nlm.nih.gov/pubmed/26809005
Integrated genetic and pharmacologic interrogation of rare cancers.	Hong AL, Tseng YY, Cowley GS, Jonas O, Cheah JH, Kynnap BD, Doshi MB, Oh C, Meyer SC, Church AJ, Gill S, Bielski CM, Keskula P, Imamovic A, Howell S, Kryukov GV, Clemons PA, Tsherniak A, Vazquez F, Crompton BD, Shamji AF, Rodriguez-Galindo C, Janeway KA, Roberts CW, Stegmaier K, van Hummelen P, Cima MJ, Langer RS, Garraway LA, Schreiber SL, Root DE, Hahn WC, Boehm JS	Nature communications	27329820	Nat Commun	2016 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/27329820
First In Vivo Testing of Compounds Targeting Group 3 Medulloblastomas Using an Implantable Microdevice as a New Paradigm for Drug Development.	Jonas O, Calligaris D, Methuku KR, Poe MM, Francois JP, Tranghese F, Changelian A, Sieghart W, Ernst M, Krummel DA, Cook JM, Pomeroy SL, Cima M, Agar NY, Langer R, Sengupta S	Journal of biomedical nanotechnology	27319222	J Biomed Nanotechnol	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27319222
Discovery of a potent stapled helix peptide that binds to the 70N domain of replication protein A.	Frank AO, Vangamudi B, Feldkamp MD, Souza-Fagundes EM, Luzwick JW, Cortez D, Olejniczak ET, Waterson AG, Rossanese OW, Chazin WJ, Fesik SW	Journal of medicinal chemistry	24491171	J Med Chem	2014 Mar 27	https://www.ncbi.nlm.nih.gov/pubmed/24491171
Structural arrangement of the intracellular Ca2+ binding domains of the cardiac Na+/Ca2+ exchanger (NCX1.1): effects of Ca2+ binding.	Dixit M, Kim S, Matthews GF, Erreger K, Galli A, Cobb CE, Hustedt EJ, Beth AH	The Journal of biological chemistry	23233681	J Biol Chem	2013 Feb 8	https://www.ncbi.nlm.nih.gov/pubmed/23233681
PIWI proteins are essential for early Drosophila embryogenesis.	Mani SR, Megosh H, Lin H	Developmental biology	24184635	Dev Biol	2014 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/24184635
Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism.	Peng JC, Lin H	Current opinion in cell biology	23465540	Curr Opin Cell Biol	2013 Apr	https://www.ncbi.nlm.nih.gov/pubmed/23465540
Poreless eggshells.	Lin H, Matzuk MM	The Journal of clinical investigation	26485282	J Clin Invest	2015 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/26485282
Chromatin immunoprecipitation assay of Piwi in Drosophila.	Yin H, Lin H	Methods in molecular biology (Clifton, N.J.)	24178552	Methods Mol Biol	2014	https://www.ncbi.nlm.nih.gov/pubmed/24178552
PIWI proteins and PIWI-interacting RNAs in the soma.	Ross RJ, Weiner MM, Lin H	Nature	24429634	Nature	2014 Jan 16	https://www.ncbi.nlm.nih.gov/pubmed/24429634
Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity.	Darricarrère N, Liu N, Watanabe T, Lin H	Proceedings of the National Academy of Sciences of the United States of America	23297219	Proc Natl Acad Sci U S A	2013 Jan 22	https://www.ncbi.nlm.nih.gov/pubmed/23297219
The Role of Maternal HP1a in Early Drosophila Embryogenesis via Regulation of Maternal Transcript Production.	Park AR, Liu N, Neuenkirchen N, Guo Q, Lin H	Genetics	30442760	Genetics	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30442760
Untangling the web: the diverse functions of the PIWI/piRNA pathway.	Mani SR, Juliano CE	Molecular reproduction and development	23712694	Mol Reprod Dev	2013 Aug	https://www.ncbi.nlm.nih.gov/pubmed/23712694
Capturing the cloud: UAP56 in nuage assembly and function.	Lin H	Cell	23141532	Cell	2012 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/23141532
PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression.	Ku HY, Lin H	National science review	25512877	Natl Sci Rev	2014 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25512877
Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins.	Peng JC, Valouev A, Liu N, Lin H	Nature genetics	26780607	Nat Genet	2016 Mar	https://www.ncbi.nlm.nih.gov/pubmed/26780607
Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs.	Watanabe T, Lin H	Molecular cell	25280102	Mol Cell	2014 Oct 2	https://www.ncbi.nlm.nih.gov/pubmed/25280102
Tudor-SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila.	Ku HY, Gangaraju VK, Qi H, Liu N, Lin H	PLoS genetics	26808625	PLoS Genet	2016 Jan	https://www.ncbi.nlm.nih.gov/pubmed/26808625
A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila.	Parikh RY, Lin H, Gangaraju VK	The Journal of biological chemistry	29735528	J Biol Chem	2018 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/29735528
Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries.	Liu N, Neuenkirchen N, Zhong M, Lin H	G3 (Bethesda, Md.)	33609367	G3 (Bethesda)	2021 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/33609367
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush.	Fedosov AE, Zaharias P, Lemarcis T, Modica MV, Holford M, Oliverio M, Kantor YI, Puillandre N	Systematic biology	38456663	Syst Biol	2024 Sep 5	https://www.ncbi.nlm.nih.gov/pubmed/38456663
Targeting Dysregulated Ion Channels in Liver Tumors with Venom Peptides.	Achimba F, Faezov B, Cohen B, Dunbrack R, Holford M	Molecular cancer therapeutics	38015557	Mol Cancer Ther	2024 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/38015557
Changes in Brain Neuroimmunology Following Injury and Disease.	Tabet A, Apra C, Stranahan AM, Anikeeva P	Frontiers in integrative neuroscience	35573444	Front Integr Neurosci	2022	https://www.ncbi.nlm.nih.gov/pubmed/35573444
Multifunctional microelectronic fibers enable wireless modulation of gut and brain neural circuits.	Sahasrabudhe A, Rupprecht LE, Orguc S, Khudiyev T, Tanaka T, Sands J, Zhu W, Tabet A, Manthey M, Allen H, Loke G, Antonini MJ, Rosenfeld D, Park J, Garwood IC, Yan W, Niroui F, Fink Y, Chandrakasan A, Bohórquez DV, Anikeeva P	Nature biotechnology	37349522	Nat Biotechnol	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/37349522
Fiber-based Probes for Electrophysiology, Photometry, Optical and Electrical Stimulation, Drug Delivery, and Fast-Scan Cyclic Voltammetry In Vivo.	Driscoll N, Antonini MJ, Cannon TM, Maretich P, Olaitan G, Phi Van VD, Nagao K, Sahasrabudhe A, Vargas E, Hunt S, Hummel M, Mupparaju S, Jasanoff A, Venton J, Anikeeva P	bioRxiv : the preprint server for biology	38895451	bioRxiv	2024 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/38895451
Multifunctional Neural Probes Enable Bidirectional Electrical, Optical, and Chemical Recording and Stimulation In Vivo.	Driscoll N, Antonini MJ, Cannon TM, Maretich P, Olaitan G, Van VDP, Nagao K, Sahasrabudhe A, Paniagua EV, Frey EJ, Kim YJ, Hunt S, Hummel M, Mupparaju S, Jasanoff A, Venton BJ, Anikeeva P	Advanced materials (Deerfield Beach, Fla.)	39506430	Adv Mater	2024 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/39506430
Magnetoelectric Nanodiscs Enable Wireless Transgene-Free Neuromodulation.	Kim YJ, Driscoll N, Kent N, Paniagua EV, Tabet A, Koehler F, Manthey M, Sahasrabudhe A, Signorelli L, Gregureć D, Anikeeva P	bioRxiv : the preprint server for biology	38234742	bioRxiv	2023 Dec 25	https://www.ncbi.nlm.nih.gov/pubmed/38234742
Modulating cell signalling in vivo with magnetic nanotransducers.	Romero G, Park J, Koehler F, Pralle A, Anikeeva P	Nature reviews. Methods primers	38111858	Nat Rev Methods Primers	2022	https://www.ncbi.nlm.nih.gov/pubmed/38111858
Magnetoelectric nanodiscs enable wireless transgene-free neuromodulation.	Kim YJ, Kent N, Vargas Paniagua E, Driscoll N, Tabet A, Koehler F, Malkin E, Frey E, Manthey M, Sahasrabudhe A, Cannon TM, Nagao K, Mankus D, Bisher M, de Nola G, Lytton-Jean A, Signorelli L, Gregurec D, Anikeeva P	Nature nanotechnology	39394431	Nat Nanotechnol	2025 Jan	https://www.ncbi.nlm.nih.gov/pubmed/39394431
Hypothalamic dopamine neurons motivate mating through persistent cAMP signalling.	Zhang SX, Lutas A, Yang S, Diaz A, Fluhr H, Nagel G, Gao S, Andermann ML	Nature	34433964	Nature	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/34433964
Competition between stochastic neuropeptide signals calibrates the rate of satiation.	Zhang SX, Kim A, Madara JC, Zhu PK, Christenson LF, Lutas A, Kalugin PN, Jin Y, Pal A, Tian L, Lowell BB, Andermann ML	Research square	37546985	Res Sq	2023 Jul 26	https://www.ncbi.nlm.nih.gov/pubmed/37546985
Transient cAMP production drives rapid and sustained spiking in brainstem parabrachial neurons to suppress feeding.	Singh Alvarado J, Lutas A, Madara JC, Isaac J, Lommer C, Massengill C, Andermann ML	Neuron	38417435	Neuron	2024 May 1	https://www.ncbi.nlm.nih.gov/pubmed/38417435
Retinal Inputs to the Thalamus Are Selectively Gated by Arousal.	Liang L, Fratzl A, Reggiani JDS, El Mansour O, Chen C, Andermann ML	Current biology : CB	32795442	Curr Biol	2020 Oct 19	https://www.ncbi.nlm.nih.gov/pubmed/32795442
Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions.	Jeong H, Namboodiri VMK, Jung MW, Andermann ML	bioRxiv : the preprint server for biology	36993665	bioRxiv	2023 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/36993665
Sensitization of meningeal afferents to locomotion-related meningeal deformations in a migraine model.	Blaeser AS, Zhao J, Sugden AU, Carneiro-Nascimento S, Andermann ML, Levy D	bioRxiv : the preprint server for biology	37577675	bioRxiv	2023 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/37577675
A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution.	Nardone S, De Luca R, Zito A, Klymko N, Nicoloutsopoulos D, Amsalem O, Brannigan C, Resch JM, Jacobs CL, Pant D, Veregge M, Srinivasan H, Grippo RM, Yang Z, Zeidel ML, Andermann ML, Harris KD, Tsai LT, Arrigoni E, Verstegen AMJ, Saper CB, Lowell BB	bioRxiv : the preprint server for biology	38014113	bioRxiv	2023 Nov 17	https://www.ncbi.nlm.nih.gov/pubmed/38014113
Sensitization of meningeal afferents to locomotion-related meningeal deformations in a migraine model.	Blaeser AS, Zhao J, Sugden AU, Carneiro-Nascimento S, Andermann ML, Levy D	eLife	38329894	Elife	2024 Feb 8	https://www.ncbi.nlm.nih.gov/pubmed/38329894
Estimation of Current and Future Physiological States in Insular Cortex.	Livneh Y, Sugden AU, Madara JC, Essner RA, Flores VI, Sugden LA, Resch JM, Lowell BB, Andermann ML	Neuron	31955944	Neuron	2020 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/31955944
Tracking Calcium Dynamics and Immune Surveillance at the Choroid Plexus Blood-Cerebrospinal Fluid Interface.	Shipley FB, Dani N, Xu H, Deister C, Cui J, Head JP, Sadegh C, Fame RM, Shannon ML, Flores VI, Kishkovich T, Jang E, Klein EM, Goldey GJ, He K, Zhang Y, Holtzman MJ, Kirchhausen T, Wyart C, Moore CI, Andermann ML, Lehtinen MK	Neuron	32961128	Neuron	2020 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/32961128
Visual association cortex links cues with conjunctions of reward and locomotor contexts.	McGuire KL, Amsalem O, Sugden AU, Ramesh RN, Fernando J, Burgess CR, Andermann ML	Current biology : CB	35245458	Curr Biol	2022 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/35245458
Trigeminal afferents sense locomotion-related meningeal deformations.	Blaeser AS, Sugden AU, Zhao J, Carneiro-Nascimento S, Shipley FB, Carrié H, Andermann ML, Levy D	Cell reports	36384109	Cell Rep	2022 Nov 15	https://www.ncbi.nlm.nih.gov/pubmed/36384109
The choroid plexus synergizes with immune cells during neuroinflammation.	Xu H, Lotfy P, Gelb S, Pragana A, Hehnly C, Byer LIJ, Shipley FB, Zawadzki ME, Cui J, Deng L, Taylor M, Webb M, Lidov HGW, Andermann ML, Chiu IM, Ordovas-Montanes J, Lehtinen MK	Cell	39089253	Cell	2024 Sep 5	https://www.ncbi.nlm.nih.gov/pubmed/39089253
Cellular activity in insular cortex across seconds to hours: Sensations and predictions of bodily states.	Livneh Y, Andermann ML	Neuron	34582784	Neuron	2021 Nov 17	https://www.ncbi.nlm.nih.gov/pubmed/34582784
History-dependent dopamine release increases cAMP levels in most basal amygdala glutamatergic neurons to control learning.	Lutas A, Fernando K, Zhang SX, Sambangi A, Andermann ML	Cell reports	35081349	Cell Rep	2022 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/35081349
Choroid plexus-targeted NKCC1 overexpression to treat post-hemorrhagic hydrocephalus.	Sadegh C, Xu H, Sutin J, Fatou B, Gupta S, Pragana A, Taylor M, Kalugin PN, Zawadzki ME, Alturkistani O, Shipley FB, Dani N, Fame RM, Wurie Z, Talati P, Schleicher RL, Klein EM, Zhang Y, Holtzman MJ, Moore CI, Lin PY, Patel AB, Warf BC, Kimberly WT, Steen H, Andermann ML, Lehtinen MK	Neuron	36893755	Neuron	2023 May 17	https://www.ncbi.nlm.nih.gov/pubmed/36893755
Brainstem serotonin neurons selectively gate retinal information flow to thalamus.	Reggiani JDS, Jiang Q, Barbini M, Lutas A, Liang L, Fernando J, Deng F, Wan J, Li Y, Chen C, Andermann ML	Neuron	36584680	Neuron	2023 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/36584680
Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions.	Jeong H, Namboodiri VMK, Jung MW, Andermann ML	Current biology : CB	37995696	Curr Biol	2023 Dec 4	https://www.ncbi.nlm.nih.gov/pubmed/37995696
Cortical reactivations predict future sensory responses.	Nguyen ND, Lutas A, Amsalem O, Fernando J, Ahn AY, Hakim R, Vergara J, McMahon J, Dimidschstein J, Sabatini BL, Andermann ML	Nature	38093002	Nature	2024 Jan	https://www.ncbi.nlm.nih.gov/pubmed/38093002
Repeated stress triggers seeking of a starvation-like state in anxiety-prone female mice.	Kucukdereli H, Amsalem O, Pottala T, Lim M, Potgieter L, Hasbrouck A, Lutas A, Andermann ML	Neuron	38642553	Neuron	2024 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/38642553
A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution.	Nardone S, De Luca R, Zito A, Klymko N, Nicoloutsopoulos D, Amsalem O, Brannigan C, Resch JM, Jacobs CL, Pant D, Veregge M, Srinivasan H, Grippo RM, Yang Z, Zeidel ML, Andermann ML, Harris KD, Tsai LT, Arrigoni E, Verstegen AMJ, Saper CB, Lowell BB	Nature communications	38438345	Nat Commun	2024 Mar 4	https://www.ncbi.nlm.nih.gov/pubmed/38438345
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.	Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R, Earth Microbiome Project 500 (EMP500) Consortium	Nature microbiology	36443458	Nat Microbiol	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36443458
Robustness of cancer microbiome signals over a broad range of methodological variation.	Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R	Oncogene	38396294	Oncogene	2024 Apr	https://www.ncbi.nlm.nih.gov/pubmed/38396294
The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases.	Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R	Gastroenterology	36841488	Gastroenterology	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/36841488
TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies.	Shi P, Martino C, Han R, Janssen S, Buck G, Serrano M, Owzar K, Knight R, Shenhav L, Zhang AR	Genome biology	39696594	Genome Biol	2024 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/39696594
Global chemical effects of the microbiome include new bile-acid conjugations.	Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC	Nature	32103176	Nature	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/32103176
Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.	Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM	medRxiv : the preprint server for health sciences	33236030	medRxiv	2020 Nov 22	https://www.ncbi.nlm.nih.gov/pubmed/33236030
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.	Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R	BioTechniques	33512248	Biotechniques	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33512248
Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution.	Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R	BioEssays : news and reviews in molecular, cellular and developmental biology	35253252	Bioessays	2022 May	https://www.ncbi.nlm.nih.gov/pubmed/35253252
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.	Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R	Nature	35798029	Nature	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35798029
Enhancing untargeted metabolomics using metadata-based source annotation.	Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP Jr, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC	Nature biotechnology	35798960	Nat Biotechnol	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/35798960
Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions.	Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadiani M, Gal-Yam EN, Patel SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R	Cell	36179670	Cell	2022 Sep 29	https://www.ncbi.nlm.nih.gov/pubmed/36179670
Greengenes2 unifies microbial data in a single reference tree.	McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R	Nature biotechnology	37500913	Nat Biotechnol	2024 May	https://www.ncbi.nlm.nih.gov/pubmed/37500913
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.	Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC	Research square	37577622	Res Sq	2023 Aug 3	https://www.ncbi.nlm.nih.gov/pubmed/37577622
Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase.	Sfiligoi I, Armstrong G, Gonzalez A, McDonald D, Knight R	mSystems	35638356	mSystems	2022 Jun 28	https://www.ncbi.nlm.nih.gov/pubmed/35638356
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.	Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC	Nature microbiology	38316926	Nat Microbiol	2024 Feb	https://www.ncbi.nlm.nih.gov/pubmed/38316926
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.	Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM	Microbiome	34103074	Microbiome	2021 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/34103074
Host variables confound gut microbiota studies of human disease.	Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y	Nature	33149306	Nature	2020 Nov	https://www.ncbi.nlm.nih.gov/pubmed/33149306
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics.	Martino C, Shenhav L, Marotz CA, Armstrong G, McDonald D, Vázquez-Baeza Y, Morton JT, Jiang L, Dominguez-Bello MG, Swafford AD, Halperin E, Knight R	Nature biotechnology	32868914	Nat Biotechnol	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/32868914
Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression.	Fu T, Huan T, Rahman G, Zhi H, Xu Z, Oh TG, Guo J, Coulter S, Tripathi A, Martino C, McCarville JL, Zhu Q, Cayabyab F, Low B, He M, Xing S, Vargas F, Yu RT, Atkins A, Liddle C, Ayres J, Raffatellu M, Dorrestein PC, Downes M, Knight R, Evans RM	Cell reports	37611587	Cell Rep	2023 Aug 29	https://www.ncbi.nlm.nih.gov/pubmed/37611587
Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution.	Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, González A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R	mSystems	37350611	mSystems	2023 Aug 31	https://www.ncbi.nlm.nih.gov/pubmed/37350611
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.	Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC	Nature chemical biology	33199911	Nat Chem Biol	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33199911
A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2.	Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS	medRxiv : the preprint server for health sciences	33106816	medRxiv	2020 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/33106816
A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities.	Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R	BioTechniques	35713407	Biotechniques	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35713407
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.	Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R	mSystems	35369727	mSystems	2022 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/35369727
Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding.	Song SJ, Wang J, Martino C, Jiang L, Thompson WK, Shenhav L, McDonald D, Marotz C, Harris PR, Hernandez CD, Henderson N, Ackley E, Nardella D, Gillihan C, Montacuti V, Schweizer W, Jay M, Combellick J, Sun H, Garcia-Mantrana I, Gil Raga F, Collado MC, Rivera-Viñas JI, Campos-Rivera M, Ruiz-Calderon JF, Knight R, Dominguez-Bello MG	Med (New York, N.Y.)	35590169	Med	2021 Aug 13	https://www.ncbi.nlm.nih.gov/pubmed/35590169
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome.	Huang S, Jiang S, Huo D, Allaband C, Estaki M, Cantu V, Belda-Ferre P, Vázquez-Baeza Y, Zhu Q, Ma C, Li C, Zarrinpar A, Liu YY, Knight R, Zhang J	Microbiome	34193290	Microbiome	2021 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/34193290
Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2.	Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS	ACS sensors	34714054	ACS Sens	2021 Nov 26	https://www.ncbi.nlm.nih.gov/pubmed/34714054
Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References.	Hakim D, Wandro S, Zengler K, Zaramela LS, Nowinski B, Swafford A, Zhu Q, Song SJ, Gonzalez A, McDonald D, Knight R	mSystems	36073806	mSystems	2022 Oct 26	https://www.ncbi.nlm.nih.gov/pubmed/36073806
Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype.	Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, Knight R	mSystems	35477286	mSystems	2022 Jun 28	https://www.ncbi.nlm.nih.gov/pubmed/35477286
SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp.	Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Casas Maya M, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Ostrander RT, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R	mSystems	35575492	mSystems	2022 Jun 28	https://www.ncbi.nlm.nih.gov/pubmed/35575492
Improving microbial phylogeny with citizen science within a mass-market video game.	Sarrazin-Gendron R, Ghasemloo Gheidari P, Butyaev A, Keding T, Cai E, Zheng J, Mutalova R, Mounthanyvong J, Zhu Y, Nazarova E, Drogaris C, Erhart K, Borderlands Science Development Team, Borderlands Science players, Brouillette A, Richard G, Pitchford R, Caisse S, Blanchette M, McDonald D, Knight R, Szantner A, Waldispühl J	Nature biotechnology	38622344	Nat Biotechnol	2025 Jan	https://www.ncbi.nlm.nih.gov/pubmed/38622344
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.	Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R	Research square	39502785	Res Sq	2024 Oct 23	https://www.ncbi.nlm.nih.gov/pubmed/39502785
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.	Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Hightower G, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R	Nature communications	39827261	Nat Commun	2025 Jan 18	https://www.ncbi.nlm.nih.gov/pubmed/39827261
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity.	Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido Benítez RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Havulinna AS, Jousilahti P, Huang S, Haiminen N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R	bioRxiv : the preprint server for biology	32839779	bioRxiv	2020 Aug 18	https://www.ncbi.nlm.nih.gov/pubmed/32839779
Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma.	Guccione C, Yadlapati R, Shah S, Knight R, Curtius K	Microorganisms	34683324	Microorganisms	2021 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/34683324
Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases.	Rahman G, McDonald D, Gonzalez A, Vázquez-Baeza Y, Jiang L, Casals-Pascual C, Hakim D, Dilmore AH, Nowinski B, Peddada S, Knight R	Genes	37372419	Genes (Basel)	2023 Jun 9	https://www.ncbi.nlm.nih.gov/pubmed/37372419
Generation of accurate, expandable phylogenomic trees with uDance.	Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S	Nature biotechnology	37500914	Nat Biotechnol	2024 May	https://www.ncbi.nlm.nih.gov/pubmed/37500914
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data.	Armstrong G, Rahman G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R	Frontiers in bioinformatics	36304280	Front Bioinform	2022	https://www.ncbi.nlm.nih.gov/pubmed/36304280
Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings.	Cantú VJ, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Sanders K, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, Crescini ES, De Hoff P, Eisner E, Hakim A, Kapadia B, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Sathe S, Seaver P, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R	mSystems	35703437	mSystems	2022 Aug 30	https://www.ncbi.nlm.nih.gov/pubmed/35703437
Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic.	Vrbanac A, Patras KA, Jarmusch AK, Mills RH, Shing SR, Quinn RA, Vargas F, Gonzalez DJ, Dorrestein PC, Knight R, Nizet V	mSystems	33024048	mSystems	2020 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/33024048
Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.	Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R	medRxiv : the preprint server for health sciences	35411350	medRxiv	2022 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/35411350
Force-induced conformational changes in PIEZO1.	Lin YC, Guo YR, Miyagi A, Levring J, MacKinnon R, Scheuring S	Nature	31435018	Nature	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31435018
Chemically induced protein cage assembly with programmable opening and cargo release.	Stupka I, Azuma Y, Biela AP, Imamura M, Scheuring S, Pyza E, Woźnicka O, Maskell DP, Heddle JG	Science advances	34985943	Sci Adv	2022 Jan 7	https://www.ncbi.nlm.nih.gov/pubmed/34985943
Localization atomic force microscopy.	Heath GR, Kots E, Robertson JL, Lansky S, Khelashvili G, Weinstein H, Scheuring S	Nature	34135520	Nature	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/34135520
Nanoreporter of an Enzymatic Suicide Inactivation Pathway.	Yaari Z, Cheung JM, Baker HA, Frederiksen RS, Jena PV, Horoszko CP, Jiao F, Scheuring S, Luo M, Heller DA	Nano letters	33119310	Nano Lett	2020 Nov 11	https://www.ncbi.nlm.nih.gov/pubmed/33119310
HS-AFM single-molecule structural biology uncovers basis of transporter wanderlust kinetics.	Jiang Y, Miyagi A, Wang X, Qiu B, Boudker O, Scheuring S	Nature structural & molecular biology	38632360	Nat Struct Mol Biol	2024 Aug	https://www.ncbi.nlm.nih.gov/pubmed/38632360
Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel.	Pan Y, Pohjolainen E, Schmidpeter PAM, Vaiana AC, Nimigean CM, Grubmüller H, Scheuring S	Nature structural & molecular biology	36973509	Nat Struct Mol Biol	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/36973509
The cyanobacterial protein VIPP1 forms ESCRT-III-like structures on lipid bilayers.	Pan S, Gries K, Engel BD, Schroda M, Haselwandter CA, Scheuring S	Nature structural & molecular biology	39060677	Nat Struct Mol Biol	2025 Mar	https://www.ncbi.nlm.nih.gov/pubmed/39060677
Real time dynamics of Gating-Related conformational changes in CorA.	Rangl M, Schmandt N, Perozo E, Scheuring S	eLife	31774394	Elife	2019 Nov 27	https://www.ncbi.nlm.nih.gov/pubmed/31774394
High-speed atomic force microscopy to study pore-forming proteins.	Jiao F, Ruan Y, Scheuring S	Methods in enzymology	33712187	Methods Enzymol	2021	https://www.ncbi.nlm.nih.gov/pubmed/33712187
Structural dynamics of channels and transporters by high-speed atomic force microscopy.	Heath GR, Lin YC, Matin TR, Scheuring S	Methods in enzymology	34059280	Methods Enzymol	2021	https://www.ncbi.nlm.nih.gov/pubmed/34059280
Nanodissected elastically loaded clathrin lattices relax to increased curvature.	Tagiltsev G, Haselwandter CA, Scheuring S	Science advances	34389539	Sci Adv	2021 Aug	https://www.ncbi.nlm.nih.gov/pubmed/34389539
Snf7 spirals sense and alter membrane curvature.	Jukic N, Perrino AP, Humbert F, Roux A, Scheuring S	Nature communications	35449207	Nat Commun	2022 Apr 21	https://www.ncbi.nlm.nih.gov/pubmed/35449207
Forces and energetics of the canonical tetrameric cation channel gating.	Scheuring S	Proceedings of the National Academy of Sciences of the United States of America	37399394	Proc Natl Acad Sci U S A	2023 Jul 11	https://www.ncbi.nlm.nih.gov/pubmed/37399394
Membrane-mediated protein interactions drive membrane protein organization.	Jiang Y, Thienpont B, Sapuru V, Hite RK, Dittman JS, Sturgis JN, Scheuring S	Nature communications	36450733	Nat Commun	2022 Nov 30	https://www.ncbi.nlm.nih.gov/pubmed/36450733
A structural biology compatible file format for atomic force microscopy.	Jiang Y, Wang Z, Scheuring S	Nature communications	39955301	Nat Commun	2025 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/39955301
Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters.	Heath GR, Scheuring S	Current opinion in structural biology	30878714	Curr Opin Struct Biol	2019 Aug	https://www.ncbi.nlm.nih.gov/pubmed/30878714
A concerted ATPase cycle of the protein transporter AAA-ATPase Bcs1.	Pan Y, Zhan J, Jiang Y, Xia D, Scheuring S	Nature communications	37821516	Nat Commun	2023 Oct 11	https://www.ncbi.nlm.nih.gov/pubmed/37821516
Perforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism.	Jiao F, Dehez F, Ni T, Yu X, Dittman JS, Gilbert R, Chipot C, Scheuring S	Nature communications	36028507	Nat Commun	2022 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/36028507
Single molecule kinetics of bacteriorhodopsin by HS-AFM.	Perrino AP, Miyagi A, Scheuring S	Nature communications	34893646	Nat Commun	2021 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/34893646
Annexin-V stabilizes membrane defects by inducing lipid phase transition.	Lin YC, Chipot C, Scheuring S	Nature communications	31932647	Nat Commun	2020 Jan 13	https://www.ncbi.nlm.nih.gov/pubmed/31932647
Intrinsically disordered regions in TRPV2 mediate protein-protein interactions.	Sanganna Gari RR, Tagiltsev G, Pumroy RA, Jiang Y, Blackledge M, Moiseenkova-Bell VY, Scheuring S	Communications biology	37736816	Commun Biol	2023 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/37736816
A pentameric TRPV3 channel with a dilated pore.	Lansky S, Betancourt JM, Zhang J, Jiang Y, Kim ED, Paknejad N, Nimigean CM, Yuan P, Scheuring S	Nature	37648856	Nature	2023 Sep	https://www.ncbi.nlm.nih.gov/pubmed/37648856
High-speed atomic force microscopy tracks the dynamic parts of the ribosome.	Scheuring S	Proceedings of the National Academy of Sciences of the United States of America	33431655	Proc Natl Acad Sci U S A	2021 Jan 26	https://www.ncbi.nlm.nih.gov/pubmed/33431655
Neuronal dynamics direct cerebrospinal fluid perfusion and brain clearance.	Jiang-Xie LF, Drieu A, Bhasiin K, Quintero D, Smirnov I, Kipnis J	Nature	38418877	Nature	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38418877
Age-associated suppression of exploratory activity during sickness is linked to meningeal lymphatic dysfunction and microglia activation.	Goldman DH, Dykstra T, Smirnov I, Blackburn SM, Da Mesquita S, Kipnis J, Herz J	Nature aging	37065770	Nat Aging	2022 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37065770
Meningeal γδ T cells regulate anxiety-like behavior via IL-17a signaling in neurons.	Alves de Lima K, Rustenhoven J, Da Mesquita S, Wall M, Salvador AF, Smirnov I, Martelossi Cebinelli G, Mamuladze T, Baker W, Papadopoulos Z, Lopes MB, Cao WS, Xie XS, Herz J, Kipnis J	Nature immunology	32929273	Nat Immunol	2020 Nov	https://www.ncbi.nlm.nih.gov/pubmed/32929273
Skull and vertebral bone marrow are myeloid cell reservoirs for the meninges and CNS parenchyma.	Cugurra A, Mamuladze T, Rustenhoven J, Dykstra T, Beroshvili G, Greenberg ZJ, Baker W, Papadopoulos Z, Drieu A, Blackburn S, Kanamori M, Brioschi S, Herz J, Schuettpelz LG, Colonna M, Smirnov I, Kipnis J	Science (New York, N.Y.)	34083447	Science	2021 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/34083447
Bypassing the blood-brain barrier.	Rustenhoven J, Kipnis J	Science (New York, N.Y.)	31857468	Science	2019 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/31857468
Skull bone marrow channels as immune gateways to the central nervous system.	Mazzitelli JA, Pulous FE, Smyth LCD, Kaya Z, Rustenhoven J, Moskowitz MA, Kipnis J, Nahrendorf M	Nature neuroscience	37996526	Nat Neurosci	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37996526
Age-dependent immune and lymphatic responses after spinal cord injury.	Salvador AFM, Dykstra T, Rustenhoven J, Gao W, Blackburn SM, Bhasiin K, Dong MQ, Guimarães RM, Gonuguntla S, Smirnov I, Kipnis J, Herz J	Neuron	37148871	Neuron	2023 Jul 19	https://www.ncbi.nlm.nih.gov/pubmed/37148871
Endogenous self-peptides guard immune privilege of the central nervous system.	Kim MW, Gao W, Lichti CF, Gu X, Dykstra T, Cao J, Smirnov I, Boskovic P, Kleverov D, Salvador AFM, Drieu A, Kim K, Blackburn S, Crewe C, Artyomov MN, Unanue ER, Kipnis J	Nature	39476864	Nature	2025 Jan	https://www.ncbi.nlm.nih.gov/pubmed/39476864
Brain borders at the central stage of neuroimmunology.	Rustenhoven J, Kipnis J	Nature	36517712	Nature	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36517712
GABAergic neuronal IL-4R mediates T cell effect on memory.	Herz J, Fu Z, Kim K, Dykstra T, Wall M, Li H, Salvador AF, Zou B, Yan N, Blackburn SM, Andrews PH, Goldman DH, Papadopoulos Z, Smirnov I, Xie XS, Kipnis J	Neuron	34793707	Neuron	2021 Nov 17	https://www.ncbi.nlm.nih.gov/pubmed/34793707
A novel immune modulator IM33 mediates a glia-gut-neuronal axis that controls lifespan.	Xu W, Rustenhoven J, Nelson CA, Dykstra T, Ferreiro A, Papadopoulos Z, Burnham CD, Dantas G, Fremont DH, Kipnis J	Neuron	37582366	Neuron	2023 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/37582366
Cerebrospinal fluid regulates skull bone marrow niches via direct access through dural channels.	Mazzitelli JA, Smyth LCD, Cross KA, Dykstra T, Sun J, Du S, Mamuladze T, Smirnov I, Rustenhoven J, Kipnis J	Nature neuroscience	35301477	Nat Neurosci	2022 May	https://www.ncbi.nlm.nih.gov/pubmed/35301477
Functional characterization of the dural sinuses as a neuroimmune interface.	Rustenhoven J, Drieu A, Mamuladze T, de Lima KA, Dykstra T, Wall M, Papadopoulos Z, Kanamori M, Salvador AF, Baker W, Lemieux M, Da Mesquita S, Cugurra A, Fitzpatrick J, Sviben S, Kossina R, Bayguinov P, Townsend RR, Zhang Q, Erdmann-Gilmore P, Smirnov I, Lopes MB, Herz J, Kipnis J	Cell	33508229	Cell	2021 Feb 18	https://www.ncbi.nlm.nih.gov/pubmed/33508229
Cortical ensembles orchestrate social competition through hypothalamic outputs.	Padilla-Coreano N, Batra K, Patarino M, Chen Z, Rock RR, Zhang R, Hausmann SB, Weddington JC, Patel R, Zhang YE, Fang HS, Mishra S, LeDuke DO, Revanna J, Li H, Borio M, Pamintuan R, Bal A, Keyes LR, Libster A, Wichmann R, Mills F, Taschbach FH, Matthews GA, Curley JP, Fiete IR, Lu C, Tye KM	Nature	35296862	Nature	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/35296862
Dynamic influences on the neural encoding of social valence.	Padilla-Coreano N, Tye KM, Zelikowsky M	Nature reviews. Neuroscience	35831442	Nat Rev Neurosci	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35831442
Neurotensin orchestrates valence assignment in the amygdala.	Li H, Namburi P, Olson JM, Borio M, Lemieux ME, Beyeler A, Calhoon GG, Hitora-Imamura N, Coley AA, Libster A, Bal A, Jin X, Wang H, Jia C, Choudhury SR, Shi X, Felix-Ortiz AC, de la Fuente V, Barth VP, King HO, Izadmehr EM, Revanna JS, Batra K, Fischer KB, Keyes LR, Padilla-Coreano N, Siciliano CA, McCullough KM, Wichmann R, Ressler KJ, Fiete IR, Zhang F, Li Y, Tye KM	Nature	35859170	Nature	2022 Aug	https://www.ncbi.nlm.nih.gov/pubmed/35859170
Valence processing in the PFC: Reconciling circuit-level and systems-level views.	Coley AA, Padilla-Coreano N, Patel R, Tye KM	International review of neurobiology	33785145	Int Rev Neurobiol	2021	https://www.ncbi.nlm.nih.gov/pubmed/33785145
Social isolation recruits amygdala-cortical circuitry to escalate alcohol drinking.	Patel RR, Patarino M, Kim K, Pamintuan R, Taschbach FH, Li H, Lee CR, van Hoek A, Castro R, Cazares C, Miranda RL, Jia C, Delahanty J, Batra K, Keyes LR, Libster A, Wichmann R, Pereira TD, Benna MK, Tye KM	Research square	38562728	Res Sq	2024 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/38562728
Anxiety and depression: A top-down, bottom-up model of circuit function.	LeDuke DO, Borio M, Miranda R, Tye KM	Annals of the New York Academy of Sciences	37129246	Ann N Y Acad Sci	2023 Jul	https://www.ncbi.nlm.nih.gov/pubmed/37129246
Reward contingency gates selective cholinergic suppression of amygdala neurons.	Kimchi EY, Burgos-Robles A, Matthews GA, Chakoma T, Patarino M, Weddington JC, Siciliano C, Yang W, Foutch S, Simons R, Fong MF, Jing M, Li Y, Polley DB, Tye KM	eLife	38376907	Elife	2024 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/38376907
Dopamine enhances signal-to-noise ratio in cortical-brainstem encoding of aversive stimuli.	Vander Weele CM, Siciliano CA, Matthews GA, Namburi P, Izadmehr EM, Espinel IC, Nieh EH, Schut EHS, Padilla-Coreano N, Burgos-Robles A, Chang CJ, Kimchi EY, Beyeler A, Wichmann R, Wildes CP, Tye KM	Nature	30405240	Nature	2018 Nov	https://www.ncbi.nlm.nih.gov/pubmed/30405240
The neural circuitry of social homeostasis: Consequences of acute versus chronic social isolation.	Lee CR, Chen A, Tye KM	Cell	33691140	Cell	2021 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/33691140
Predicting Future Development of Stress-Induced Anhedonia From Cortical Dynamics and Facial Expression.	Coley AA, Batra K, Delahanty JM, Keyes LR, Pamintuan R, Ramot A, Hagemann J, Lee CR, Liu V, Adivikolanu H, Cressy J, Jia C, Massa F, LeDuke D, Gabir M, Durubeh B, Linderhof L, Patel R, Wichmann R, Li H, Fischer KB, Pereira T, Tye KM	bioRxiv : the preprint server for biology	39764017	bioRxiv	2024 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/39764017
Neural Circuit Motifs in Valence Processing.	Tye KM	Neuron	30359607	Neuron	2018 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/30359607
Neural mechanisms of social homeostasis.	Matthews GA, Tye KM	Annals of the New York Academy of Sciences	30875095	Ann N Y Acad Sci	2019 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30875095
Acute social isolation evokes midbrain craving responses similar to hunger.	Tomova L, Wang KL, Thompson T, Matthews GA, Takahashi A, Tye KM, Saxe R	Nature neuroscience	33230328	Nat Neurosci	2020 Dec	https://www.ncbi.nlm.nih.gov/pubmed/33230328
Neural systems that facilitate the representation of social rank.	Dwortz MF, Curley JP, Tye KM, Padilla-Coreano N	Philosophical transactions of the Royal Society of London. Series B, Biological sciences	35000438	Philos Trans R Soc Lond B Biol Sci	2022 Feb 28	https://www.ncbi.nlm.nih.gov/pubmed/35000438
Double threat in striatal dopamine signaling.	Siciliano CA, Mills F, Tye KM	Nature neuroscience	30258236	Nat Neurosci	2018 Oct	https://www.ncbi.nlm.nih.gov/pubmed/30258236
A cortical-brainstem circuit predicts and governs compulsive alcohol drinking.	Siciliano CA, Noamany H, Chang CJ, Brown AR, Chen X, Leible D, Lee JJ, Wang J, Vernon AN, Vander Weele CM, Kimchi EY, Heiman M, Tye KM	Science (New York, N.Y.)	31754002	Science	2019 Nov 22	https://www.ncbi.nlm.nih.gov/pubmed/31754002
Dopamine tunes prefrontal outputs to orchestrate aversive processing.	Weele CMV, Siciliano CA, Tye KM	Brain research	30513287	Brain Res	2019 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/30513287
Thalamus sends information about arousal but not valence to the amygdala.	Leppla CA, Keyes LR, Glober G, Matthews GA, Batra K, Jay M, Feng Y, Chen HS, Mills F, Delahanty J, Olson JM, Nieh EH, Namburi P, Wildes C, Wichmann R, Beyeler A, Kimchi EY, Tye KM	Psychopharmacology	36522481	Psychopharmacology (Berl)	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36522481
Mixed selectivity: Cellular computations for complexity.	Tye KM, Miller EK, Taschbach FH, Benna MK, Rigotti M, Fusi S	Neuron	38729151	Neuron	2024 Jul 17	https://www.ncbi.nlm.nih.gov/pubmed/38729151
Control of innate olfactory valence by segregated cortical amygdala circuits.	Howe JR, Chan CL, Lee D, Blanquart M, Lee JH, Romero HK, Zadina AN, Lemieux ME, Mills F, Desplats PA, Tye KM, Root CM	bioRxiv : the preprint server for biology	38979308	bioRxiv	2024 Oct 22	https://www.ncbi.nlm.nih.gov/pubmed/38979308
Links between environment, diet, and the hunter-gatherer microbiome.	Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL	Gut microbes	30118385	Gut Microbes	2019	https://www.ncbi.nlm.nih.gov/pubmed/30118385
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.	Olm MR, Spencer SP, Takeuchi T, Silva EL, Sonnenburg JL	Nature microbiology	39747692	Nat Microbiol	2025 Jan	https://www.ncbi.nlm.nih.gov/pubmed/39747692
Pursuing Human-Relevant Gut Microbiota-Immune Interactions.	Spencer SP, Fragiadakis GK, Sonnenburg JL	Immunity	31433970	Immunity	2019 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/31433970
Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions.	Hryckowian AJ, Merrill BD, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, Sonnenburg JL	Cell host & microbe	32652063	Cell Host Microbe	2020 Sep 9	https://www.ncbi.nlm.nih.gov/pubmed/32652063
The ancestral and industrialized gut microbiota and implications for human health.	Sonnenburg ED, Sonnenburg JL	Nature reviews. Microbiology	31089293	Nat Rev Microbiol	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31089293
Robust variation in infant gut microbiome assembly across a spectrum of lifestyles.	Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng X, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL	Science (New York, N.Y.)	35679413	Science	2022 Jun 10	https://www.ncbi.nlm.nih.gov/pubmed/35679413
Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.	Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL	Cell	37348505	Cell	2023 Jul 6	https://www.ncbi.nlm.nih.gov/pubmed/37348505
Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice.	Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED	Cell reports	38510311	Cell Rep	2023 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/38510311
Vulnerability of the industrialized microbiota.	Sonnenburg JL, Sonnenburg ED	Science (New York, N.Y.)	31649168	Science	2019 Oct 25	https://www.ncbi.nlm.nih.gov/pubmed/31649168
Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes.	Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL	bioRxiv : the preprint server for biology	36238714	bioRxiv	2022 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/36238714
Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice.	Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED	bioRxiv : the preprint server for biology	36945614	bioRxiv	2023 Mar 9	https://www.ncbi.nlm.nih.gov/pubmed/36945614
Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome.	Olm MR, Spencer SP, Silva EL, Sonnenburg JL	bioRxiv : the preprint server for biology	38045399	bioRxiv	2023 Nov 21	https://www.ncbi.nlm.nih.gov/pubmed/38045399
A brainstem circuit for nausea suppression.	Zhang C, Vincelette LK, Reimann F, Liberles SD	Cell reports	35705049	Cell Rep	2022 Jun 14	https://www.ncbi.nlm.nih.gov/pubmed/35705049
PIEZOs mediate neuronal sensing of blood pressure and the baroreceptor reflex.	Zeng WZ, Marshall KL, Min S, Daou I, Chapleau MW, Abboud FM, Liberles SD, Patapoutian A	Science (New York, N.Y.)	30361375	Science	2018 Oct 26	https://www.ncbi.nlm.nih.gov/pubmed/30361375
Arterial Baroreceptors Sense Blood Pressure through Decorated Aortic Claws.	Min S, Chang RB, Prescott SL, Beeler B, Joshi NR, Strochlic DE, Liberles SD	Cell reports	31747594	Cell Rep	2019 Nov 19	https://www.ncbi.nlm.nih.gov/pubmed/31747594
A vagal reflex evoked by airway closure.	Schappe MS, Brinn PA, Joshi NR, Greenberg RS, Min S, Alabi AA, Zhang C, Liberles SD	Nature	38448588	Nature	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38448588
Area Postrema Cell Types that Mediate Nausea-Associated Behaviors.	Zhang C, Kaye JA, Cai Z, Wang Y, Prescott SL, Liberles SD	Neuron	33278342	Neuron	2021 Feb 3	https://www.ncbi.nlm.nih.gov/pubmed/33278342
An Airway Protection Program Revealed by Sweeping Genetic Control of Vagal Afferents.	Prescott SL, Umans BD, Williams EK, Brust RD, Liberles SD	Cell	32259485	Cell	2020 Apr 30	https://www.ncbi.nlm.nih.gov/pubmed/32259485
Cellular and Neural Responses to Sour Stimuli Require the Proton Channel Otop1.	Teng B, Wilson CE, Tu YH, Joshi NR, Kinnamon SC, Liman ER	Current biology : CB	31543453	Curr Biol	2019 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/31543453
Piezo2 senses airway stretch and mediates lung inflation-induced apnoea.	Nonomura K, Woo SH, Chang RB, Gillich A, Qiu Z, Francisco AG, Ranade SS, Liberles SD, Patapoutian A	Nature	28002412	Nature	2017 Jan 12	https://www.ncbi.nlm.nih.gov/pubmed/28002412
Internal senses of the vagus nerve.	Prescott SL, Liberles SD	Neuron	35051375	Neuron	2022 Feb 16	https://www.ncbi.nlm.nih.gov/pubmed/35051375
Enteroendocrine cell lineages that differentially control feeding and gut motility.	Hayashi M, Kaye JA, Douglas ER, Joshi NR, Gribble FM, Reimann F, Liberles SD	eLife	36810133	Elife	2023 Feb 22	https://www.ncbi.nlm.nih.gov/pubmed/36810133
Neural Sensing of Organ Volume.	Umans BD, Liberles SD	Trends in neurosciences	30143276	Trends Neurosci	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30143276
A brainstem map for visceral sensations.	Ran C, Boettcher JC, Kaye JA, Gallori CE, Liberles SD	Nature	36045291	Nature	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/36045291
An airway-to-brain sensory pathway mediates influenza-induced sickness.	Bin NR, Prescott SL, Horio N, Wang Y, Chiu IM, Liberles SD	Nature	36890237	Nature	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36890237
Molecular tools for chemical biotechnology.	Galanie S, Siddiqui MS, Smolke CD	Current opinion in biotechnology	23528237	Curr Opin Biotechnol	2013 Dec	https://www.ncbi.nlm.nih.gov/pubmed/23528237
Complete biosynthesis of noscapine and halogenated alkaloids in yeast.	Li Y, Li S, Thodey K, Trenchard I, Cravens A, Smolke CD	Proceedings of the National Academy of Sciences of the United States of America	29610307	Proc Natl Acad Sci U S A	2018 Apr 24	https://www.ncbi.nlm.nih.gov/pubmed/29610307
High-throughput cellular RNA device engineering.	Townshend B, Kennedy AB, Xiang JS, Smolke CD	Nature methods	26258292	Nat Methods	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26258292
Realizing the potential of synthetic biology.	Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R	Nature reviews. Molecular cell biology	24622617	Nat Rev Mol Cell Biol	2014 Apr	https://www.ncbi.nlm.nih.gov/pubmed/24622617
Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases.	Michener JK, Nielsen J, Smolke CD	Proceedings of the National Academy of Sciences of the United States of America	23129650	Proc Natl Acad Sci U S A	2012 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/23129650
Kinetic and equilibrium binding characterization of aptamers to small molecules using a label-free, sensitive, and scalable platform.	Chang AL, McKeague M, Liang JC, Smolke CD	Analytical chemistry	24548121	Anal Chem	2014 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/24548121
A system for multilocus chromosomal integration and transformation-free selection marker rescue.	Siddiqui MS, Choksi A, Smolke CD	FEMS yeast research	25226817	FEMS Yeast Res	2014 Dec	https://www.ncbi.nlm.nih.gov/pubmed/25226817
Engineering biosynthesis of the anticancer alkaloid noscapine in yeast.	Li Y, Smolke CD	Nature communications	27378283	Nat Commun	2016 Jul 5	https://www.ncbi.nlm.nih.gov/pubmed/27378283
Optimization of yeast-based production of medicinal protoberberine alkaloids.	Galanie S, Smolke CD	Microbial cell factories	26376732	Microb Cell Fact	2015 Sep 16	https://www.ncbi.nlm.nih.gov/pubmed/26376732
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives.	Hafner J, Payne J, MohammadiPeyhani H, Hatzimanikatis V, Smolke C	Nature communications	33741955	Nat Commun	2021 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/33741955
Design and Construction of Generalizable RNA-Protein Hybrid Controllers by Level-Matched Genetic Signal Amplification.	Wang YH, McKeague M, Hsu TM, Smolke CD	Cell systems	27840078	Cell Syst	2016 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/27840078
Synthetic biology strategies for microbial biosynthesis of plant natural products.	Cravens A, Payne J, Smolke CD	Nature communications	31086174	Nat Commun	2019 May 13	https://www.ncbi.nlm.nih.gov/pubmed/31086174
Engineering cellular metabolite transport for biosynthesis of computationally predicted tropane alkaloid derivatives in yeast.	Srinivasan P, Smolke CD	Proceedings of the National Academy of Sciences of the United States of America	34140414	Proc Natl Acad Sci U S A	2021 Jun 22	https://www.ncbi.nlm.nih.gov/pubmed/34140414
De novo production of the key branch point benzylisoquinoline alkaloid reticuline in yeast.	Trenchard IJ, Siddiqui MS, Thodey K, Smolke CD	Metabolic engineering	26166409	Metab Eng	2015 Sep	https://www.ncbi.nlm.nih.gov/pubmed/26166409
Complete biosynthesis of opioids in yeast.	Galanie S, Thodey K, Trenchard IJ, Filsinger Interrante M, Smolke CD	Science (New York, N.Y.)	26272907	Science	2015 Sep 4	https://www.ncbi.nlm.nih.gov/pubmed/26272907
Biosynthesis of medicinal tropane alkaloids in yeast.	Srinivasan P, Smolke CD	Nature	32879484	Nature	2020 Sep	https://www.ncbi.nlm.nih.gov/pubmed/32879484
Engineering strategies for the fermentative production of plant alkaloids in yeast.	Trenchard IJ, Smolke CD	Metabolic engineering	25981946	Metab Eng	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/25981946
A microbial biomanufacturing platform for natural and semisynthetic opioids.	Thodey K, Galanie S, Smolke CD	Nature chemical biology	25151135	Nat Chem Biol	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25151135
Synthetic biology: advancing the design of diverse genetic systems.	Wang YH, Wei KY, Smolke CD	Annual review of chemical and biomolecular engineering	23413816	Annu Rev Chem Biomol Eng	2013	https://www.ncbi.nlm.nih.gov/pubmed/23413816
Engineering a microbial platform for de novo biosynthesis of diverse methylxanthines.	McKeague M, Wang YH, Cravens A, Win MN, Smolke CD	Metabolic engineering	27519552	Metab Eng	2016 Nov	https://www.ncbi.nlm.nih.gov/pubmed/27519552
Complete biosynthesis of the bisbenzylisoquinoline alkaloids guattegaumerine and berbamunine in yeast.	Payne JT, Valentic TR, Smolke CD	Proceedings of the National Academy of Sciences of the United States of America	34903659	Proc Natl Acad Sci U S A	2021 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/34903659
Facile characterization of aptamer kinetic and equilibrium binding properties using surface plasmon resonance.	Chang AL, McKeague M, Smolke CD	Methods in enzymology	25432760	Methods Enzymol	2014	https://www.ncbi.nlm.nih.gov/pubmed/25432760
Synthetic RNA switches for yeast metabolic engineering: screening recombinant enzyme libraries.	Michener JK, Smolke CD	Methods in molecular biology (Clifton, N.J.)	24744030	Methods Mol Biol	2014	https://www.ncbi.nlm.nih.gov/pubmed/24744030
Protein-responsive ribozyme switches in eukaryotic cells.	Kennedy AB, Vowles JV, d'Espaux L, Smolke CD	Nucleic acids research	25274734	Nucleic Acids Res	2014 Oct 29	https://www.ncbi.nlm.nih.gov/pubmed/25274734
In Vitro Screening and in Silico Modeling of RNA-Based Gene Expression Control.	McKeague M, Wang YH, Smolke CD	ACS chemical biology	26359915	ACS Chem Biol	2015 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/26359915
Opportunities in the design and application of RNA for gene expression control.	McKeague M, Wong RS, Smolke CD	Nucleic acids research	26969733	Nucleic Acids Res	2016 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/26969733
Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering.	Cravens A, Jamil OK, Kong D, Sockolosky JT, Smolke CD	Nature communications	33707425	Nat Commun	2021 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/33707425
Elucidation of tropane alkaloid biosynthesis in Erythroxylum coca using a microbial pathway discovery platform.	Chavez BG, Srinivasan P, Glockzin K, Kim N, Montero Estrada O, Jirschitzka J, Rowden G, Shao J, Meinhardt L, Smolke CD, D'Auria JC	Proceedings of the National Academy of Sciences of the United States of America	36442128	Proc Natl Acad Sci U S A	2022 Dec 6	https://www.ncbi.nlm.nih.gov/pubmed/36442128
Listeria monocytogenes infection causes metabolic shifts in Drosophila melanogaster.	Chambers MC, Song KH, Schneider DS	PloS one	23272066	PLoS One	2012	https://www.ncbi.nlm.nih.gov/pubmed/23272066
Defining Resistance and Tolerance to Cancer.	Dillman AR, Schneider DS	Cell reports	26565901	Cell Rep	2015 Nov 3	https://www.ncbi.nlm.nih.gov/pubmed/26565901
Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury.	Lissner MM, Cumnock K, Davis NM, Vilches-Moure JG, Basak P, Navarrete DJ, Allen JA, Schneider D	eLife	33021470	Elife	2020 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/33021470
Tracking Resilience to Infections by Mapping Disease Space.	Torres BY, Oliveira JH, Thomas Tate A, Rath P, Cumnock K, Schneider DS	PLoS biology	27088359	PLoS Biol	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/27088359
Predicting position along a looping immune response trajectory.	Rath P, Allen JA, Schneider DS	PloS one	30296270	PLoS One	2018	https://www.ncbi.nlm.nih.gov/pubmed/30296270
Host Energy Source Is Important for Disease Tolerance to Malaria.	Cumnock K, Gupta AS, Lissner M, Chevee V, Davis NM, Schneider DS	Current biology : CB	29754902	Curr Biol	2018 May 21	https://www.ncbi.nlm.nih.gov/pubmed/29754902
Drosophila melanogaster Natural Variation Affects Growth Dynamics of Infecting Listeria monocytogenes.	Hotson AG, Schneider DS	G3 (Bethesda, Md.)	26438294	G3 (Bethesda)	2015 Oct 4	https://www.ncbi.nlm.nih.gov/pubmed/26438294
How Many Parameters Does It Take to Describe Disease Tolerance?	Louie A, Song KH, Hotson A, Thomas Tate A, Schneider DS	PLoS biology	27088212	PLoS Biol	2016 Apr	https://www.ncbi.nlm.nih.gov/pubmed/27088212
The Immune System and Its Contribution to Variability in Regenerative Medicine.	Moore EM, Maestas DR Jr, Comeau HY, Elisseeff JH	Tissue engineering. Part B, Reviews	32635878	Tissue Eng Part B Rev	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/32635878
Biomaterials direct functional B cell response in a material-specific manner.	Moore EM, Maestas DR Jr, Cherry CC, Garcia JA, Comeau HY, Davenport Huyer L, Kelly SH, Peña AN, Blosser RL, Rosson GD, Elisseeff JH	Science advances	34851674	Sci Adv	2021 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/34851674
IL-17 and immunologically induced senescence regulate response to injury in osteoarthritis.	Faust HJ, Zhang H, Han J, Wolf MT, Jeon OH, Sadtler K, Peña AN, Chung L, Maestas DR Jr, Tam AJ, Pardoll DM, Campisi J, Housseau F, Zhou D, Bingham CO 3rd, Elisseeff JH	The Journal of clinical investigation	32955487	J Clin Invest	2020 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/32955487
Helminth egg derivatives as proregenerative immunotherapies.	Maestas DR Jr, Chung L, Han J, Wang X, Sommerfeld SD, Kelly SH, Moore E, Nguyen HH, Mejías JC, Peña AN, Zhang H, Hooks JST, Chin AF, Andorko JI, Berlinicke CA, Krishnan K, Choi Y, Anderson AE, Mahatme R, Mejia C, Eric M, Woo J, Ganguly S, Zack DJ, Zhao L, Pearce EJ, Housseau F, Pardoll DM, Elisseeff JH	Proceedings of the National Academy of Sciences of the United States of America	36780522	Proc Natl Acad Sci U S A	2023 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/36780522
Biomaterials-based immunomodulation enhances survival of murine vascularized composite allografts.	Sommerfeld SD, Zhou X, Mejías JC, Oh BC, Maestas DR Jr, Furtmüller GJ, Laffont PA, Elisseeff JH, Brandacher G	Biomaterials science	37129566	Biomater Sci	2023 May 30	https://www.ncbi.nlm.nih.gov/pubmed/37129566
Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies.	Cherry C, Andorko JI, Krishnan K, Mejías JC, Nguyen HH, Stivers KB, Gray-Gaillard EF, Ruta A, Han J, Hamada N, Hamada M, Sturmlechner I, Trewartha S, Michel JH, Davenport Huyer L, Wolf MT, Tam AJ, Peña AN, Keerthivasan S, Le Saux CJ, Fertig EJ, Baker DJ, Housseau F, van Deursen JM, Pardoll DM, Elisseeff JH	GeroScience	37079217	Geroscience	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37079217
Immunoengineering Biomaterials for Musculoskeletal Tissue Repair across Lifespan.	Han J, Rindone AN, Elisseeff JH	Advanced materials (Deerfield Beach, Fla.)	38416061	Adv Mater	2024 Jul	https://www.ncbi.nlm.nih.gov/pubmed/38416061
Interleukin-36γ-producing macrophages drive IL-17-mediated fibrosis.	Sommerfeld SD, Cherry C, Schwab RM, Chung L, Maestas DR Jr, Laffont P, Stein JE, Tam A, Ganguly S, Housseau F, Taube JM, Pardoll DM, Cahan P, Elisseeff JH	Science immunology	31604843	Sci Immunol	2019 Oct 11	https://www.ncbi.nlm.nih.gov/pubmed/31604843
Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds.	Yang H, Ulge UY, Quijano-Rubio A, Bernstein ZJ, Maestas DR, Chun JH, Wang W, Lin JX, Jude KM, Singh S, Orcutt-Jahns BT, Li P, Mou J, Chung L, Kuo YH, Ali YH, Meyer AS, Grayson WL, Heller NM, Garcia KC, Leonard WJ, Silva DA, Elisseeff JH, Baker D, Spangler JB	Nature chemical biology	37024727	Nat Chem Biol	2023 Sep	https://www.ncbi.nlm.nih.gov/pubmed/37024727
Autologous Protein Solution processing alters lymphoid and myeloid cell populations and modulates gene expression dependent on cell type.	Peña AN, Sommerfeld SD, Anderson AE, Han J, Maestas DR Jr, Mejias JC, Woodell-May J, King W, Ganguly S, Elisseeff JH	Arthritis research & therapy	36096945	Arthritis Res Ther	2022 Sep 12	https://www.ncbi.nlm.nih.gov/pubmed/36096945
Single-cell transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states associated with senescence.	Walter LD, Orton JL, Hannah Fong EH, Maymi VI, Rudd BD, Elisseeff JH, Cosgrove BD	bioRxiv : the preprint server for biology	37292698	bioRxiv	2023 May 26	https://www.ncbi.nlm.nih.gov/pubmed/37292698
Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics.	Cherry C, Maestas DR, Han J, Andorko JI, Cahan P, Fertig EJ, Garmire LX, Elisseeff JH	Nature biomedical engineering	34341534	Nat Biomed Eng	2021 Oct	https://www.ncbi.nlm.nih.gov/pubmed/34341534
Interleukin 17 and senescent cells regulate the foreign body response to synthetic material implants in mice and humans.	Chung L, Maestas DR Jr, Lebid A, Mageau A, Rosson GD, Wu X, Wolf MT, Tam AJ, Vanderzee I, Wang X, Andorko JI, Zhang H, Narain R, Sadtler K, Fan H, Čiháková D, Le Saux CJ, Housseau F, Pardoll DM, Elisseeff JH	Science translational medicine	32295900	Sci Transl Med	2020 Apr 15	https://www.ncbi.nlm.nih.gov/pubmed/32295900
Sirolimus-eluting airway stent reduces profibrotic Th17 cells and inhibits laryngotracheal stenosis.	Motz KM, Lina IA, Samad I, Murphy MK, Duvvuri M, Davis RJ, Gelbard A, Chung L, Chan-Li Y, Collins S, Powell JD, Elisseeff JH, Horton MR, Hillel AT	JCI insight	37159282	JCI Insight	2023 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/37159282
Immune and Genome Engineering as the Future of Transplantable Tissue.	Elisseeff J, Badylak SF, Boeke JD	The New England journal of medicine	34936741	N Engl J Med	2021 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/34936741
Senescent cells in tissue engineering.	Chin AF, Elisseeff JH	Current opinion in biotechnology	35660479	Curr Opin Biotechnol	2022 Aug	https://www.ncbi.nlm.nih.gov/pubmed/35660479
Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states.	Walter LD, Orton JL, Ntekas I, Fong EHH, Maymi VI, Rudd BD, De Vlaminck I, Elisseeff JH, Cosgrove BD	Nature aging	39578558	Nat Aging	2024 Dec	https://www.ncbi.nlm.nih.gov/pubmed/39578558
Engineered stem cell niche matrices for rotator cuff tendon regenerative engineering.	Peach MS, Ramos DM, James R, Morozowich NL, Mazzocca AD, Doty SB, Allcock HR, Kumbar SG, Laurencin CT	PloS one	28369135	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28369135
Synthesis, Physicochemical Analysis, and Side Group Optimization of Degradable Dipeptide-Based Polyphosphazenes as Potential Regenerative Biomaterials.	Ogueri KS, Escobar Ivirico JL, Li Z, Blumenfield RH, Allcock HR, Laurencin CT	ACS applied polymer materials	32699835	ACS Appl Polym Mater	2019 Jun 14	https://www.ncbi.nlm.nih.gov/pubmed/32699835
Robust phenotypic maintenance of limb cells during heterogeneous culture in a physiologically relevant polymeric-based constructed graft system.	Barajaa MA, Nair LS, Laurencin CT	Scientific reports	32678185	Sci Rep	2020 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/32678185
Evaluation of a bioengineered ACL matrix's osteointegration with BMP-2 supplementation.	Mengsteab PY, Conroy P, Badon M, Otsuka T, Kan HM, Vella AT, Nair LS, Laurencin CT	PloS one	31910231	PLoS One	2020	https://www.ncbi.nlm.nih.gov/pubmed/31910231
Development of Tripolymeric Triaxial Electrospun Fibrous Matrices for Dual Drug Delivery Applications.	Nagiah N, Murdock CJ, Bhattacharjee M, Nair L, Laurencin CT	Scientific reports	31953439	Sci Rep	2020 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/31953439
The synthetic artificial stem cell (SASC): Shifting the paradigm of cell therapy in regenerative engineering.	Shah S, Esdaille CJ, Bhattacharjee M, Kan HM, Laurencin CT	Proceedings of the National Academy of Sciences of the United States of America	34987101	Proc Natl Acad Sci U S A	2022 Jan 11	https://www.ncbi.nlm.nih.gov/pubmed/34987101
Regenerative Engineering of Cartilage Using Adipose-Derived Stem Cells.	Kasir R, Vernekar VN, Laurencin CT	Regenerative engineering and translational medicine	26998511	Regen Eng Transl Med	2015 Dec 1	https://www.ncbi.nlm.nih.gov/pubmed/26998511
Poly (lactic acid)-based biomaterials for orthopaedic regenerative engineering.	Narayanan G, Vernekar VN, Kuyinu EL, Laurencin CT	Advanced drug delivery reviews	27125191	Adv Drug Deliv Rev	2016 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/27125191
The Mechanism of Metallosis After Total Hip Arthroplasty.	Ude CC, Esdaille CJ, Ogueri KS, Ho-Man K, Laurencin SJ, Nair LS, Laurencin CT	Regenerative engineering and translational medicine	35530571	Regen Eng Transl Med	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35530571
Regulation of regeneration by Heparan Sulfate Proteoglycans in the Extracellular Matrix.	Gardiner DM	Regenerative engineering and translational medicine	29242821	Regen Eng Transl Med	2017 Sep	https://www.ncbi.nlm.nih.gov/pubmed/29242821
Nail matrix regenerative engineering: in vitro evaluation of poly(lactide-co-glycolide)/gelatin fibrous substrates.	Montgomery AB, McClinton A, Nair L, Laurencin CT	Journal of biomedical materials research. Part A	31981298	J Biomed Mater Res A	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/31981298
Muscle degeneration in chronic massive rotator cuff tears of the shoulder: Addressing the real problem using a graphene matrix.	Saveh Shemshaki N, Kan HM, Barajaa M, Otsuka T, Lebaschi A, Mishra N, Nair LS, Laurencin CT	Proceedings of the National Academy of Sciences of the United States of America	35939692	Proc Natl Acad Sci U S A	2022 Aug 16	https://www.ncbi.nlm.nih.gov/pubmed/35939692
Stromal Vascular Fraction for Osteoarthritis of the Knee Regenerative Engineering.	Ude CC, Shah S, Ogueri KS, Nair LS, Laurencin CT	Regenerative engineering and translational medicine	35958164	Regen Eng Transl Med	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35958164
Corrosion of Metals During Use in Arthroplasty.	Ude CC, Dzidotor GK, Iloeje K, Nair LS, Laurencin CT	ACS applied bio materials	37261398	ACS Appl Bio Mater	2023 Jun 19	https://www.ncbi.nlm.nih.gov/pubmed/37261398
Hyaluronic acid-British anti-Lewisite as a safer chelation therapy for the treatment of arthroplasty-related metallosis.	Ude CC, Schmidt SJ, Laurencin S, Shah S, Esdaille J, Kan HM, Holt BD, Arnold AM, Wolf ME, Nair LS, Sydlik SA, Laurencin CT	Proceedings of the National Academy of Sciences of the United States of America	37903261	Proc Natl Acad Sci U S A	2023 Nov 7	https://www.ncbi.nlm.nih.gov/pubmed/37903261
Efficacy of a Novel Electroconductive Matrix To Treat Muscle Atrophy and Fat Accumulation in Chronic Massive Rotator Cuff Tears of the Shoulder.	Shemshaki NS, Kan HM, Barajaa MA, Lebaschi A, Otsuka T, Mishra N, Nair LS, Laurencin CT	ACS biomaterials science & engineering	37769114	ACS Biomater Sci Eng	2023 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/37769114
POLYMERIC BIOMATERIALS FOR SCAFFOLD-BASED BONE REGENERATIVE ENGINEERING.	Ogueri KS, Jafari T, Escobar Ivirico JL, Laurencin CT	Regenerative engineering and translational medicine	31423461	Regen Eng Transl Med	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31423461
Nanofiber technology: its transformative role in nanomedicine.	James R, Laurencin CT	Nanomedicine (London, England)	27246812	Nanomedicine (Lond)	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27246812
REGENERATIVE ENGINEERING: APPROACHES TO LIMB REGENERATION AND OTHER GRAND CHALLENGES.	Laurencin CT, Nair LS	Regenerative engineering and translational medicine	26985451	Regen Eng Transl Med	2015 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/26985451
Regenerative Cell-Based Therapies: Cutting Edge, Bleeding Edge, and Off the Edge.	Laurencin CT, McClinton A	Regenerative engineering and translational medicine	33344756	Regen Eng Transl Med	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33344756
Bioinspired Scaffold Designs for Regenerating Musculoskeletal Tissue Interfaces.	Barajaa MA, Nair LS, Laurencin CT	Regenerative engineering and translational medicine	33344758	Regen Eng Transl Med	2020 Dec	https://www.ncbi.nlm.nih.gov/pubmed/33344758
Mechanically superior matrices promote osteointegration and regeneration of anterior cruciate ligament tissue in rabbits.	Mengsteab PY, Otsuka T, McClinton A, Shemshaki NS, Shah S, Kan HM, Obopilwe E, Vella AT, Nair LS, Laurencin CT	Proceedings of the National Academy of Sciences of the United States of America	33144508	Proc Natl Acad Sci U S A	2020 Nov 17	https://www.ncbi.nlm.nih.gov/pubmed/33144508
Nanofiber Technology for Regenerative Engineering.	Ogueri KS, Laurencin CT	ACS nano	32678581	ACS Nano	2020 Aug 25	https://www.ncbi.nlm.nih.gov/pubmed/32678581
Spatial alignment of 3D printed scaffolds modulates genotypic expression in pre-osteoblasts.	Nagiah N, Bhattacharjee M, Murdock CJ, Kan HM, Barajaa M, Laurencin CT	Materials letters	32773913	Mater Lett	2020 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/32773913
Animal models of osteoarthritis: classification, update, and measurement of outcomes.	Kuyinu EL, Narayanan G, Nair LS, Laurencin CT	Journal of orthopaedic surgery and research	26837951	J Orthop Surg Res	2016 Feb 2	https://www.ncbi.nlm.nih.gov/pubmed/26837951
Polyphosphazene polymers: The next generation of biomaterials for regenerative engineering and therapeutic drug delivery.	Ogueri KS, Ogueri KS, Allcock HR, Laurencin CT	Journal of vacuum science and technology. B, Nanotechnology & microelectronics : materials, processing, measurement, & phenomena : JVST B	32309041	J Vac Sci Technol B Nanotechnol Microelectron	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/32309041
Skeletal Muscle Regenerative Engineering.	Tang X, Daneshmandi L, Awale G, Nair LS, Laurencin CT	Regenerative engineering and translational medicine	33778155	Regen Eng Transl Med	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/33778155
A Regenerative Polymer Blend Composed of Glycylglycine ethyl ester-substituted Polyphosphazene and Poly (lactic-co-glycolic acid).	Ogueri KS, Ogueri KS, Allcock HR, Laurencin CT	ACS applied polymer materials	32699836	ACS Appl Polym Mater	2020 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/32699836
A Pandemic on a Pandemic: Racism and COVID-19 in Blacks.	Laurencin CT, Walker JM	Cell systems	32702320	Cell Syst	2020 Jul 22	https://www.ncbi.nlm.nih.gov/pubmed/32702320
The Role of Nanomaterials and Biological Agents on Rotator Cuff Regeneration.	Washington KS, Shemshaki NS, Laurencin CT	Regenerative engineering and translational medicine	35005215	Regen Eng Transl Med	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/35005215
Injectable amnion hydrogel-mediated delivery of adipose-derived stem cells for osteoarthritis treatment.	Bhattacharjee M, Escobar Ivirico JL, Kan HM, Shah S, Otsuka T, Bordett R, Barajaa M, Nagiah N, Pandey R, Nair LS, Laurencin CT	Proceedings of the National Academy of Sciences of the United States of America	35046053	Proc Natl Acad Sci U S A	2022 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/35046053
Ligament Regenerative Engineering: Braiding Scalable and Tunable Bioengineered Ligaments Using a Bench-Top Braiding Machine.	Mengsteab PY, Freeman J, Barajaa MA, Nair LS, Laurencin CT	Regenerative engineering and translational medicine	35005216	Regen Eng Transl Med	2021 Dec	https://www.ncbi.nlm.nih.gov/pubmed/35005216
Ultra-low binder content 3D printed calcium phosphate graphene scaffolds as resorbable, osteoinductive matrices that support bone formation in vivo.	Daneshmandi L, Holt BD, Arnold AM, Laurencin CT, Sydlik SA	Scientific reports	35484292	Sci Rep	2022 Apr 28	https://www.ncbi.nlm.nih.gov/pubmed/35484292
Biomedical applications of polyphosphazenes.	Ogueri KS, Ogueri KS, Ude CC, Allcock HR, Laurencin CT	Medical devices & sensors	33889811	Med Devices Sens	2020 Dec	https://www.ncbi.nlm.nih.gov/pubmed/33889811
Overexpression of NDST1 Attenuates Fibrotic Response in Murine Adipose-Derived Stem Cells.	Otsuka T, Kan HM, Mason TD, Nair LS, Laurencin CT	Stem cells and development	35920108	Stem Cells Dev	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/35920108
Regenerative Engineering Animal Models for Knee Osteoarthritis.	Esdaille CJ, Ude CC, Laurencin CT	Regenerative engineering and translational medicine	35958163	Regen Eng Transl Med	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35958163
Phosphate graphene as an intrinsically osteoinductive scaffold for stem cell-driven bone regeneration.	Arnold AM, Holt BD, Daneshmandi L, Laurencin CT, Sydlik SA	Proceedings of the National Academy of Sciences of the United States of America	30796184	Proc Natl Acad Sci U S A	2019 Mar 12	https://www.ncbi.nlm.nih.gov/pubmed/30796184
Biomimetic electroconductive nanofibrous matrices for skeletal muscle regenerative engineering.	Tang X, Saveh-Shemshaki N, Kan HM, Khan Y, Laurencin CT	Regenerative engineering and translational medicine	33426269	Regen Eng Transl Med	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33426269
Regenerative Engineering of the Rotator Cuff of the Shoulder.	Narayanan G, Nair LS, Laurencin CT	ACS biomaterials science & engineering	33418763	ACS Biomater Sci Eng	2018 Mar 12	https://www.ncbi.nlm.nih.gov/pubmed/33418763
Inductive Materials for Regenerative Engineering.	Hosseini FS, Nair LS, Laurencin CT	Journal of dental research	33906507	J Dent Res	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/33906507
Regenerative engineering: a review of recent advances and future directions.	Esdaille CJ, Washington KS, Laurencin CT	Regenerative medicine	34030463	Regen Med	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/34030463
Identification of Heparan-Sulfate Rich Cells in the Loose Connective Tissues of the Axolotl (Ambystoma mexicanum) with the Potential to Mediate Growth Factor Signaling during Regeneration.	Otsuka T, Phan AQ, Laurencin CT, Esko JD, Bryant SV, Gardiner DM	Regenerative engineering and translational medicine	33748405	Regen Eng Transl Med	2020 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33748405
Regenerative Engineering and Bionic Limbs.	James R, Laurencin CT	Rare metals	25983525	Rare Metals	2015 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/25983525
Biodegradable Polyphosphazene-Based Blends for Regenerative Engineering.	Ogueri KS, Escobar Ivirico JL, Nair LS, Allcock HR, Laurencin CT	Regenerative engineering and translational medicine	28596987	Regen Eng Transl Med	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28596987
Fabrication and characterization of mechanically competent 3D printed polycaprolactone-reduced graphene oxide scaffolds.	Seyedsalehi A, Daneshmandi L, Barajaa M, Riordan J, Laurencin CT	Scientific reports	33335152	Sci Rep	2020 Dec 17	https://www.ncbi.nlm.nih.gov/pubmed/33335152
The past, present and future of ligament regenerative engineering.	Mengsteab PY, Nair LS, Laurencin CT	Regenerative medicine	27879170	Regen Med	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27879170
Harnessing cAMP signaling in musculoskeletal regenerative engineering.	Ifegwu OC, Awale G, Rajpura K, Lo KW, Laurencin CT	Drug discovery today	28359841	Drug Discov Today	2017 Jul	https://www.ncbi.nlm.nih.gov/pubmed/28359841
Emergence of the Stem Cell Secretome in Regenerative Engineering.	Daneshmandi L, Shah S, Jafari T, Bhattacharjee M, Momah D, Saveh-Shemshaki N, Lo KW, Laurencin CT	Trends in biotechnology	32622558	Trends Biotechnol	2020 Dec	https://www.ncbi.nlm.nih.gov/pubmed/32622558
Regenerative engineering of long bones using the small molecule forskolin.	Awale GM, Barajaa MA, Kan HM, Seyedsalehi A, Nam GH, Hosseini FS, Ude CC, Schmidt TA, Lo KW, Laurencin CT	Proceedings of the National Academy of Sciences of the United States of America	37216527	Proc Natl Acad Sci U S A	2023 May 30	https://www.ncbi.nlm.nih.gov/pubmed/37216527
Graphene-Based Biomaterials for Bone Regenerative Engineering: A Comprehensive Review of the Field and Considerations Regarding Biocompatibility and Biodegradation.	Daneshmandi L, Barajaa M, Tahmasbi Rad A, Sydlik SA, Laurencin CT	Advanced healthcare materials	33103370	Adv Healthc Mater	2021 Jan	https://www.ncbi.nlm.nih.gov/pubmed/33103370
Fibroblast growth factor 8b (FGF-8b) enhances myogenesis and inhibits adipogenesis in rotator cuff muscle cell populations in vitro.	Otsuka T, Kan HM, Mengsteab PY, Tyson B, Laurencin CT	Proceedings of the National Academy of Sciences of the United States of America	38147545	Proc Natl Acad Sci U S A	2024 Jan 2	https://www.ncbi.nlm.nih.gov/pubmed/38147545
Regenerative Engineering for Knee Osteoarthritis Treatment: Biomaterials and Cell-Based Technologies.	Escobar Ivirico JL, Bhattacharjee M, Kuyinu E, Nair LS, Laurencin CT	Engineering (Beijing, China)	35392109	Engineering (Beijing)	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/35392109
The Quest toward limb regeneration: a regenerative engineering approach.	Laurencin CT, Nair LS	Regenerative biomaterials	27047679	Regen Biomater	2016 Jun	https://www.ncbi.nlm.nih.gov/pubmed/27047679
Preparation and characterization of amnion hydrogel and its synergistic effect with adipose derived stem cells towards IL1β activated chondrocytes.	Bhattacharjee M, Ivirico JLE, Kan HM, Bordett R, Pandey R, Otsuka T, Nair LS, Laurencin CT	Scientific reports	33127964	Sci Rep	2020 Oct 30	https://www.ncbi.nlm.nih.gov/pubmed/33127964
Kinetic degradation and biocompatibility evaluation of polycaprolactone-based biologics delivery matrices for regenerative engineering of the rotator cuff.	Prabhath A, Vernekar VN, Vasu V, Badon M, Avochinou JE, Asandei AD, Kumbar SG, Weber E, Laurencin CT	Journal of biomedical materials research. Part A	33974735	J Biomed Mater Res A	2021 Nov	https://www.ncbi.nlm.nih.gov/pubmed/33974735
Enhancing the Surface Properties of a Bioengineered Anterior Cruciate Ligament Matrix for Use with Point-of-Care Stem Cell Therapy.	Yu X, Mengsteab PY, Narayanan G, Nair LS, Laurencin CT	Engineering (Beijing, China)	34136308	Engineering (Beijing)	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/34136308
Regenerative engineered vascularized bone mediated by calcium peroxide.	Daneshmandi L, Laurencin CT	Journal of biomedical materials research. Part A	31925886	J Biomed Mater Res A	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/31925886
Nanofiber/Microsphere Hybrid Matrices In Vivo for Bone Regenerative Engineering: A Preliminary Report.	Nelson C, Khan Y, Laurencin CT	Regenerative engineering and translational medicine	30687776	Regen Eng Transl Med	2018 Sep	https://www.ncbi.nlm.nih.gov/pubmed/30687776
Generational Biodegradable and Regenerative Polyphosphazene Polymers and their Blends with Poly (lactic-co-glycolic acid).	Ogueri KS, Allcock HR, Laurencin CT	Progress in polymer science	31551636	Prog Polym Sci	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31551636
The Axolotl Limb Regeneration Model as a Discovery Tool for Engineering the Stem Cell Niche.	Seyedhassantehrani N, Otsuka T, Singh S, Gardiner DM	Current stem cell reports	29230380	Curr Stem Cell Rep	2017 Sep	https://www.ncbi.nlm.nih.gov/pubmed/29230380
Growth factor delivery strategies for rotator cuff repair and regeneration.	Prabhath A, Vernekar VN, Sanchez E, Laurencin CT	International journal of pharmaceutics	29317260	Int J Pharm	2018 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/29317260
Addressing Justified Vaccine Hesitancy in the Black Community.	Laurencin CT	Journal of racial and ethnic health disparities	33783755	J Racial Ethn Health Disparities	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33783755
In Vivo Evaluation of the Regenerative Capability of Glycylglycine Ethyl Ester-Substituted Polyphosphazene and Poly(lactic-co-glycolic acid) Blends: A Rabbit Critical-Sized Bone Defect Model.	Ogueri KS, Ogueri KS, McClinton A, Kan HM, Ude CC, Barajaa MA, Allcock HR, Laurencin CT	ACS biomaterials science & engineering	33792283	ACS Biomater Sci Eng	2021 Apr 12	https://www.ncbi.nlm.nih.gov/pubmed/33792283
The Treatment of Muscle Atrophy after Rotator Cuff Tears Using Electroconductive Nanofibrous Matrices.	Tang X, Shemshaki NS, Vernekar VN, Prabhath A, Kuyinu E, Kan HM, Barajaa M, Khan Y, Laurencin CT	Regenerative engineering and translational medicine	33816776	Regen Eng Transl Med	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33816776
Control of mesenchymal cell fate via application of FGF-8b in vitro.	Otsuka T, Mengsteab PY, Laurencin CT	Stem cell research	33445073	Stem Cell Res	2021 Mar	https://www.ncbi.nlm.nih.gov/pubmed/33445073
Racial Profiling Is a Public Health and Health Disparities Issue.	Laurencin CT, Walker JM	Journal of racial and ethnic health disparities	32253746	J Racial Ethn Health Disparities	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/32253746
Microsphere-Based Scaffolds in Regenerative Engineering.	Gupta V, Khan Y, Berkland CJ, Laurencin CT, Detamore MS	Annual review of biomedical engineering	28633566	Annu Rev Biomed Eng	2017 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/28633566
An American Crisis: the Lack of Black Men in Medicine.	Laurencin CT, Murray M	Journal of racial and ethnic health disparities	28534304	J Racial Ethn Health Disparities	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28534304
Perinatal Licensing of Thermogenesis by IL-33 and ST2.	Odegaard JI, Lee MW, Sogawa Y, Bertholet AM, Locksley RM, Weinberg DE, Kirichok Y, Deo RC, Chawla A	Cell	27453471	Cell	2016 Aug 11	https://www.ncbi.nlm.nih.gov/pubmed/27453471
Type 2 responses at the interface between immunity and fat metabolism.	Odegaard JI, Chawla A	Current opinion in immunology	26204571	Curr Opin Immunol	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26204571
Thermoneutral Housing Accelerates Metabolic Inflammation to Potentiate Atherosclerosis but Not Insulin Resistance.	Tian XY, Ganeshan K, Hong C, Nguyen KD, Qiu Y, Kim J, Tangirala RK, Tontonoz P, Chawla A	Cell metabolism	26549485	Cell Metab	2016 Jan 12	https://www.ncbi.nlm.nih.gov/pubmed/26549485
Circadian gene Bmal1 regulates diurnal oscillations of Ly6C(hi) inflammatory monocytes.	Nguyen KD, Fentress SJ, Qiu Y, Yun K, Cox JS, Chawla A	Science (New York, N.Y.)	23970558	Science	2013 Sep 27	https://www.ncbi.nlm.nih.gov/pubmed/23970558
Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long-term persistence.	Eisele NA, Ruby T, Jacobson A, Manzanillo PS, Cox JS, Lam L, Mukundan L, Chawla A, Monack DM	Cell host & microbe	23954156	Cell Host Microbe	2013 Aug 14	https://www.ncbi.nlm.nih.gov/pubmed/23954156
Human CD68 promoter GFP transgenic mice allow analysis of monocyte to macrophage differentiation in vivo.	Iqbal AJ, McNeill E, Kapellos TS, Regan-Komito D, Norman S, Burd S, Smart N, Machemer DE, Stylianou E, McShane H, Channon KM, Chawla A, Greaves DR	Blood	25030063	Blood	2014 Oct 9	https://www.ncbi.nlm.nih.gov/pubmed/25030063
Activated type 2 innate lymphoid cells regulate beige fat biogenesis.	Lee MW, Odegaard JI, Mukundan L, Qiu Y, Molofsky AB, Nussbaum JC, Yun K, Locksley RM, Chawla A	Cell	25543153	Cell	2015 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/25543153
Tissue Immunometabolism: Development, Physiology, and Pathobiology.	Man K, Kutyavin VI, Chawla A	Cell metabolism	27693378	Cell Metab	2017 Jan 10	https://www.ncbi.nlm.nih.gov/pubmed/27693378
Blood spotlight on leukocytes and obesity.	Carvalheira JB, Qiu Y, Chawla A	Blood	24065242	Blood	2013 Nov 7	https://www.ncbi.nlm.nih.gov/pubmed/24065242
Immunity around the clock.	Man K, Loudon A, Chawla A	Science (New York, N.Y.)	27885005	Science	2016 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/27885005
Adipose tissue macrophages: Amicus adipem?	Odegaard JI, Ganeshan K, Chawla A	Cell metabolism	24315364	Cell Metab	2013 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/24315364
Signaling by IL-6 promotes alternative activation of macrophages to limit endotoxemia and obesity-associated resistance to insulin.	Mauer J, Chaurasia B, Goldau J, Vogt MC, Ruud J, Nguyen KD, Theurich S, Hausen AC, Schmitz J, Brönneke HS, Estevez E, Allen TL, Mesaros A, Partridge L, Febbraio MA, Chawla A, Wunderlich FT, Brüning JC	Nature immunology	24681566	Nat Immunol	2014 May	https://www.ncbi.nlm.nih.gov/pubmed/24681566
Eosinophils secrete IL-4 to facilitate liver regeneration.	Goh YP, Henderson NC, Heredia JE, Red Eagle A, Odegaard JI, Lehwald N, Nguyen KD, Sheppard D, Mukundan L, Locksley RM, Chawla A	Proceedings of the National Academy of Sciences of the United States of America	23716700	Proc Natl Acad Sci U S A	2013 Jun 11	https://www.ncbi.nlm.nih.gov/pubmed/23716700
Type 2 innate lymphoid cells control eosinophil homeostasis.	Nussbaum JC, Van Dyken SJ, von Moltke J, Cheng LE, Mohapatra A, Molofsky AB, Thornton EE, Krummel MF, Chawla A, Liang HE, Locksley RM	Nature	24037376	Nature	2013 Oct 10	https://www.ncbi.nlm.nih.gov/pubmed/24037376
RNase L activation in the cytoplasm induces aberrant processing of mRNAs in the nucleus.	Burke JM, Ripin N, Ferretti MB, St Clair LA, Worden-Sapper ER, Salgado F, Sawyer SL, Perera R, Lynch KW, Parker R	PLoS pathogens	36318584	PLoS Pathog	2022 Nov	https://www.ncbi.nlm.nih.gov/pubmed/36318584
Quantification of virus-infected cells using RNA FISH-Flow.	Warren CJ, Barbachano-Guerrero A, Huey D, Yang Q, Worden-Sapper ER, Kuhn JH, Sawyer SL	STAR protocols	37209094	STAR Protoc	2023 May 18	https://www.ncbi.nlm.nih.gov/pubmed/37209094
Regulation of human interferon signaling by transposon exonization.	Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen LL, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB	Cell	39672162	Cell	2024 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/39672162
How avian influenza viruses spill over to mammals.	Barbachano-Guerrero A, Perez DR, Sawyer SL	eLife	37039775	Elife	2023 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/37039775
Identifying animal viruses in humans.	Warren CJ, Sawyer SL	Science (New York, N.Y.)	36893227	Science	2023 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/36893227
Human ACE2 Polymorphisms from Different Human Populations Modulate SARS-CoV-2 Infection.	Hu P, Bauer VL, Sawyer SL, Diaz-Griffero F	Viruses	35891433	Viruses	2022 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/35891433
On the lookout for viruses that could leap from animals into humans.	Makin S	Nature	36289378	Nature	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36289378
Monkeypox emergency: Urgent questions and perspectives.	Rothenburg S, Yang Z, Beard P, Sawyer SL, Titanji B, Gonsalves G, Kindrachuk J	Cell	35998628	Cell	2022 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/35998628
Structurally divergent and recurrently mutated regions of primate genomes.	Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE	Cell	38428424	Cell	2024 Mar 14	https://www.ncbi.nlm.nih.gov/pubmed/38428424
Human mRNA in saliva can correctly identify individuals harboring acute infection.	Yang Q, Meyerson NR, Paige CL, Morrison JH, Clark SK, Fattor WT, Decker CJ, Steiner HR, Lian E, Larremore DB, Perera R, Poeschla EM, Parker R, Dowell RD, Sawyer SL	mBio	37943059	mBio	2023 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/37943059
High rates of observed face mask use at Colorado universities align with students' opinions about masking and support the safety and viability of in-person higher education during the COVID-19 pandemic.	Clark KC, Bailey MJ, Wasshuber S, Huntley R, Bjorkman KK, Bauer LC, Paige CL, Sawyer SL, Czarnik M, Riggs MA, Gutilla MJ, Alderete TL	BMC public health	36759815	BMC Public Health	2023 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/36759815
Macrophages derived from human induced pluripotent stem cells (iPSCs) serve as a high-fidelity cellular model for investigating HIV-1, dengue, and influenza viruses.	Yang Q, Barbachano-Guerrero A, Fairchild LM, Rowland TJ, Dowell RD, Allen MA, Warren CJ, Sawyer SL	Journal of virology	38323811	J Virol	2024 Mar 19	https://www.ncbi.nlm.nih.gov/pubmed/38323811
Estimating the effect of non-pharmaceutical interventions on US SARS-CoV-2 infections in the first year of the pandemic.	Duncan NA, L'Her GF, Osborne AG, Sawyer SL, Deinert MR	Royal Society open science	35774134	R Soc Open Sci	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35774134
Primate hemorrhagic fever-causing arteriviruses are poised for spillover to humans.	Warren CJ, Yu S, Peters DK, Barbachano-Guerrero A, Yang Q, Burris BL, Worwa G, Huang IC, Wilkerson GK, Goldberg TL, Kuhn JH, Sawyer SL	Cell	36182704	Cell	2022 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/36182704
Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses.	Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell AC, Dirasantha O, Yang Q, Sawyer SL	bioRxiv : the preprint server for biology	38014262	bioRxiv	2024 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/38014262
Atypical activation of the RNA sensor MDA5 by hepatitis C virus.	Chakraborty S, Zhu J, Gack MU	The FEBS journal	38102741	FEBS J	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38102741
Viral evasion of the interferon response at a glance.	Zhu J, Chiang C, Gack MU	Journal of cell science	37341132	J Cell Sci	2023 Jun 15	https://www.ncbi.nlm.nih.gov/pubmed/37341132
Insights into pandemic respiratory viruses: manipulation of the antiviral interferon response by SARS-CoV-2 and influenza A virus.	Liu G, Gack MU	Current opinion in immunology	36215931	Curr Opin Immunol	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36215931
ISGylation of the SARS-CoV-2 N protein by HERC5 impedes N oligomerization and thereby viral RNA synthesis.	Zhu J, Liu G, Sayyad Z, Goins CM, Stauffer SR, Gack MU	Journal of virology	39194248	J Virol	2024 Sep 17	https://www.ncbi.nlm.nih.gov/pubmed/39194248
Acetylation of the NS3 helicase by KAT5γ is essential for flavivirus replication.	Serman T, Chiang C, Liu G, Sayyad Z, Pandey S, Volcic M, Lee H, Muppala S, Acharya D, Goins C, Stauffer SR, Sparrer KMJ, Gack MU	Cell host & microbe	37478852	Cell Host Microbe	2023 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/37478852
The RNA polymerase III-RIG-I axis in antiviral immunity and inflammation.	Naesens L, Haerynck F, Gack MU	Trends in immunology	37149405	Trends Immunol	2023 Jun	https://www.ncbi.nlm.nih.gov/pubmed/37149405
ISG15: its roles in SARS-CoV-2 and other viral infections.	Sarkar L, Liu G, Gack MU	Trends in microbiology	37573184	Trends Microbiol	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/37573184
ISGylation of the SARS-CoV-2 N protein by HERC5 impedes N oligomerization and thereby viral RNA synthesis.	Zhu J, Liu G, Goins CM, Stauffer SR, Gack MU	bioRxiv : the preprint server for biology	39149229	bioRxiv	2024 May 20	https://www.ncbi.nlm.nih.gov/pubmed/39149229
TRIM Proteins: Key Regulators of Immunity to Herpesvirus Infection.	Sayyad Z, Acharya D, Gack MU	Viruses	39599852	Viruses	2024 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/39599852
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.	Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González-Candelas F, SeqCOVID-SPAIN consortium, Stadler T, Neher RA	Nature	34098568	Nature	2021 Jul	https://www.ncbi.nlm.nih.gov/pubmed/34098568
ACE2 binding is an ancestral and evolvable trait of sarbecoviruses.	Starr TN, Zepeda SK, Walls AC, Greaney AJ, Alkhovsky S, Veesler D, Bloom JD	Nature	35114688	Nature	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/35114688
Antigen- and scaffold-specific antibody responses to protein nanoparticle immunogens.	Kraft JC, Pham MN, Shehata L, Brinkkemper M, Boyoglu-Barnum S, Sprouse KR, Walls AC, Cheng S, Murphy M, Pettie D, Ahlrichs M, Sydeman C, Johnson M, Blackstone A, Ellis D, Ravichandran R, Fiala B, Wrenn S, Miranda M, Sliepen K, Brouwer PJM, Antanasijevic A, Veesler D, Ward AB, Kanekiyo M, Pepper M, Sanders RW, King NP	Cell reports. Medicine	36206752	Cell Rep Med	2022 Oct 18	https://www.ncbi.nlm.nih.gov/pubmed/36206752
Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.	Park YJ, Pinto D, Walls AC, Liu Z, De Marco A, Benigni F, Zatta F, Silacci-Fregni C, Bassi J, Sprouse KR, Addetia A, Bowen JE, Stewart C, Giurdanella M, Saliba C, Guarino B, Schmid MA, Franko NM, Logue JK, Dang HV, Hauser K, di Iulio J, Rivera W, Schnell G, Rajesh A, Zhou J, Farhat N, Kaiser H, Montiel-Ruiz M, Noack J, Lempp FA, Janer J, Abdelnabi R, Maes P, Ferrari P, Ceschi A, Giannini O, de Melo GD, Kergoat L, Bourhy H, Neyts J, Soriaga L, Purcell LA, Snell G, Whelan SPJ, Lanzavecchia A, Virgin HW, Piccoli L, Chu HY, Pizzuto MS, Corti D, Veesler D	Science (New York, N.Y.)	36264829	Science	2022 Nov 11	https://www.ncbi.nlm.nih.gov/pubmed/36264829
SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines.	Bowen JE, Park YJ, Stewart C, Brown JT, Sharkey WK, Walls AC, Joshi A, Sprouse KR, McCallum M, Tortorici MA, Franko NM, Logue JK, Mazzitelli IG, Nguyen AW, Silva RP, Huang Y, Low JS, Jerak J, Tiles SW, Ahmed K, Shariq A, Dan JM, Zhang Z, Weiskopf D, Sette A, Snell G, Posavad CM, Iqbal NT, Geffner J, Bandera A, Gori A, Sallusto F, Maynard JA, Crotty S, Van Voorhis WC, Simmerling C, Grifantini R, Chu HY, Corti D, Veesler D	Science immunology	36356052	Sci Immunol	2022 Dec 23	https://www.ncbi.nlm.nih.gov/pubmed/36356052
Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice.	Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken SE, Ljubetič A, Edman N, Ueda G, Chow CM, Johnson M, Addetia A, Navarro MJ, Panpradist N, Gale M Jr, Freedman BS, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D	Science translational medicine	35412328	Sci Transl Med	2022 May 25	https://www.ncbi.nlm.nih.gov/pubmed/35412328
Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.	Park YJ, De Marco A, Starr TN, Liu Z, Pinto D, Walls AC, Zatta F, Zepeda SK, Bowen J, Sprouse KS, Joshi A, Giurdanella M, Guarino B, Noack J, Abdelnabi R, Foo SC, Lempp FA, Benigni F, Snell G, Neyts J, Whelan SP, Virgin HW, Bloom JD, Corti D, Pizzuto MS, Veesler D	bioRxiv : the preprint server for biology	34671770	bioRxiv	2021 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/34671770
N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.	McCallum M, De Marco A, Lempp FA, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Foo SC, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D	Cell	33761326	Cell	2021 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/33761326
Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.	Park YJ, Pinto D, Walls AC, Liu Z, Marco A, Benigni F, Zatta F, Silacci-Fregni C, Bassi J, Sprouse KR, Addetia A, Bowen JE, Stewart C, Giurdanella M, Saliba C, Guarino B, Schmid MA, Franko N, Logue J, Dang HV, Hauser K, Iulio JD, Rivera W, Schnell G, Rajesh A, Zhou J, Farhat N, Kaiser H, Montiel-Ruiz M, Noack J, Lempp FA, Janer J, Abdelnabi R, Maes P, Ferrari P, Ceschi A, Giannini O, de Melo GD, Kergoat L, Bourhy H, Neyts J, Soriaga L, Purcell LA, Snell G, Whelan SPJ, Lanzavecchia A, Virgin HW, Piccoli L, Chu H, Pizzuto MS, Corti D, Veesler D	bioRxiv : the preprint server for biology	35677069	bioRxiv	2022 Aug 22	https://www.ncbi.nlm.nih.gov/pubmed/35677069
Close relatives of MERS-CoV in bats use ACE2 as their functional receptors.	Xiong Q, Cao L, Ma C, Tortorici MA, Liu C, Si J, Liu P, Gu M, Walls AC, Wang C, Shi L, Tong F, Huang M, Li J, Zhao C, Shen C, Chen Y, Zhao H, Lan K, Corti D, Veesler D, Wang X, Yan H	Nature	36477529	Nature	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36477529
Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail.	Addetia A, Park YJ, Starr T, Greaney AJ, Sprouse KR, Bowen JE, Tiles SW, Van Voorhis WC, Bloom JD, Corti D, Walls AC, Veesler D	Cell reports	37300832	Cell Rep	2023 Jun 27	https://www.ncbi.nlm.nih.gov/pubmed/37300832
Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features.	Magaret CA, Li L, deCamp AC, Rolland M, Juraska M, Williamson BD, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Heng F, Sun Y, Carpp LN, Bai H, Dearlove BL, Giorgi EE, Jongeneelen M, Brandenburg B, McCallum M, Bowen JE, Veesler D, Sadoff J, Gray GE, Roels S, Vandebosch A, Stieh DJ, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert PA, de Sousa LP, Silva MST, Casapia M, Losso MH, Little SJ, Gaur A, Bekker LG, Garrett N, Truyers C, Van Dromme I, Swann E, Marovich MA, Follmann D, Neuzil KM, Corey L, Greninger AL, Roychoudhury P, Hyrien O, Gilbert PB	Nature communications	38467646	Nat Commun	2024 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/38467646
Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans.	Addetia A, Stewart C, Seo AJ, Sprouse KR, Asiri AY, Al-Mozaini M, Memish ZA, Alshukairi A, Veesler D	bioRxiv : the preprint server for biology	38617298	bioRxiv	2024 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/38617298
Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.	Feng Y, Yuan M, Powers JM, Hu M, Munt JE, Arunachalam PS, Leist SR, Bellusci L, Kim J, Sprouse KR, Adams LE, Sundaramurthy S, Zhu X, Shirreff LM, Mallory ML, Scobey TD, Moreno A, O'Hagan DT, Kleanthous H, Villinger FJ, Veesler D, King NP, Suthar MS, Khurana S, Baric RS, Wilson IA, Pulendran B	Science translational medicine	37163615	Sci Transl Med	2023 May 10	https://www.ncbi.nlm.nih.gov/pubmed/37163615
Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades.	Dadonaite B, Brown J, McMahon TE, Farrell AG, Asarnow D, Stewart C, Logue J, Murrell B, Chu HY, Veesler D, Bloom JD	bioRxiv : the preprint server for biology	38014024	bioRxiv	2023 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/38014024
Neutralization, effector function and immune imprinting of Omicron variants.	Addetia A, Piccoli L, Case JB, Park YJ, Beltramello M, Guarino B, Dang H, de Melo GD, Pinto D, Sprouse K, Scheaffer SM, Bassi J, Silacci-Fregni C, Muoio F, Dini M, Vincenzetti L, Acosta R, Johnson D, Subramanian S, Saliba C, Giurdanella M, Lombardo G, Leoni G, Culap K, McAlister C, Rajesh A, Dellota E Jr, Zhou J, Farhat N, Bohan D, Noack J, Chen A, Lempp FA, Quispe J, Kergoat L, Larrous F, Cameroni E, Whitener B, Giannini O, Cippà P, Ceschi A, Ferrari P, Franzetti-Pellanda A, Biggiogero M, Garzoni C, Zappi S, Bernasconi L, Kim MJ, Rosen LE, Schnell G, Czudnochowski N, Benigni F, Franko N, Logue JK, Yoshiyama C, Stewart C, Chu H, Bourhy H, Schmid MA, Purcell LA, Snell G, Lanzavecchia A, Diamond MS, Corti D, Veesler D	Nature	37648855	Nature	2023 Sep	https://www.ncbi.nlm.nih.gov/pubmed/37648855
Functional and antigenic landscape of the Nipah virus receptor binding protein.	Larsen BB, McMahon T, Brown JT, Wang Z, Radford CE, Crowe JE Jr, Veesler D, Bloom JD	bioRxiv : the preprint server for biology	38659959	bioRxiv	2024 Apr 19	https://www.ncbi.nlm.nih.gov/pubmed/38659959
Computationally designed mRNA-launched protein nanoparticle vaccines.	Hendricks GG, Grigoryan L, Navarro MJ, Catanzaro NJ, Hubbard ML, Powers JM, Mattocks M, Treichel C, Walls AC, Lee J, Ellis D, Wang JYJ, Cheng S, Miranda MC, Valdez A, Chao CW, Chan S, Men C, Johnson MR, Hui H, Wu SY, Lujan V, Muramatsu H, Lin PJC, Sung MMH, Tam YK, Leaf EM, Pardi N, Baric RS, Pulendran B, Veesler D, Schäfer A, King NP	bioRxiv : the preprint server for biology	39091730	bioRxiv	2024 Jul 23	https://www.ncbi.nlm.nih.gov/pubmed/39091730
Hierarchical design of pseudosymmetric protein nanocages.	Dowling QM, Park YJ, Fries CN, Gerstenmaier NC, Ols S, Yang EC, Wargacki AJ, Dosey A, Hsia Y, Ravichandran R, Walkey CD, Burrell AL, Veesler D, Baker D, King NP	Nature	39695230	Nature	2025 Feb	https://www.ncbi.nlm.nih.gov/pubmed/39695230
A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.	Rosen LE, Tortorici MA, De Marco A, Pinto D, Foreman WB, Taylor AL, Park YJ, Bohan D, Rietz T, Errico JM, Hauser K, Dang HV, Chartron JW, Giurdanella M, Cusumano G, Saliba C, Zatta F, Sprouse KR, Addetia A, Zepeda SK, Brown J, Lee J, Dellota E Jr, Rajesh A, Noack J, Tao Q, DaCosta Y, Tsu B, Acosta R, Subramanian S, de Melo GD, Kergoat L, Zhang I, Liu Z, Guarino B, Schmid MA, Schnell G, Miller JL, Lempp FA, Czudnochowski N, Cameroni E, Whelan SPJ, Bourhy H, Purcell LA, Benigni F, di Iulio J, Pizzuto MS, Lanzavecchia A, Telenti A, Snell G, Corti D, Veesler D, Starr TN	Cell	39383863	Cell	2024 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/39383863
Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.	Piccoli L, Park YJ, Tortorici MA, Czudnochowski N, Walls AC, Beltramello M, Silacci-Fregni C, Pinto D, Rosen LE, Bowen JE, Acton OJ, Jaconi S, Guarino B, Minola A, Zatta F, Sprugasci N, Bassi J, Peter A, De Marco A, Nix JC, Mele F, Jovic S, Rodriguez BF, Gupta SV, Jin F, Piumatti G, Lo Presti G, Pellanda AF, Biggiogero M, Tarkowski M, Pizzuto MS, Cameroni E, Havenar-Daughton C, Smithey M, Hong D, Lepori V, Albanese E, Ceschi A, Bernasconi E, Elzi L, Ferrari P, Garzoni C, Riva A, Snell G, Sallusto F, Fink K, Virgin HW, Lanzavecchia A, Corti D, Veesler D	Cell	32991844	Cell	2020 Nov 12	https://www.ncbi.nlm.nih.gov/pubmed/32991844
SARS-CoV-2 Omicron spike mediated immune escape and tropism shift.	Gupta R	Research square	35075452	Res Sq	2022 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/35075452
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy.	Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD	PLoS pathogens	35134084	PLoS Pathog	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/35134084
Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein.	Tortorici MA, Walls AC, Joshi A, Park YJ, Eguia RT, Miranda MC, Kepl E, Dosey A, Stevens-Ayers T, Boeckh MJ, Telenti A, Lanzavecchia A, King NP, Corti D, Bloom JD, Veesler D	Cell	35700730	Cell	2022 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/35700730
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy.	Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD	bioRxiv : the preprint server for biology	34671768	bioRxiv	2021 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/34671768
Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift.	Cameroni E, Bowen JE, Rosen LE, Saliba C, Zepeda SK, Culap K, Pinto D, VanBlargan LA, De Marco A, di Iulio J, Zatta F, Kaiser H, Noack J, Farhat N, Czudnochowski N, Havenar-Daughton C, Sprouse KR, Dillen JR, Powell AE, Chen A, Maher C, Yin L, Sun D, Soriaga L, Bassi J, Silacci-Fregni C, Gustafsson C, Franko NM, Logue J, Iqbal NT, Mazzitelli I, Geffner J, Grifantini R, Chu H, Gori A, Riva A, Giannini O, Ceschi A, Ferrari P, Cippà PE, Franzetti-Pellanda A, Garzoni C, Halfmann PJ, Kawaoka Y, Hebner C, Purcell LA, Piccoli L, Pizzuto MS, Walls AC, Diamond MS, Telenti A, Virgin HW, Lanzavecchia A, Snell G, Veesler D, Corti D	Nature	35016195	Nature	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/35016195
SARS-CoV-2 breakthrough infections elicit potent, broad, and durable neutralizing antibody responses.	Walls AC, Sprouse KR, Bowen JE, Joshi A, Franko N, Navarro MJ, Stewart C, Cameroni E, McCallum M, Goecker EA, Degli-Angeli EJ, Logue J, Greninger A, Corti D, Chu HY, Veesler D	Cell	35123650	Cell	2022 Mar 3	https://www.ncbi.nlm.nih.gov/pubmed/35123650
Delta breakthrough infections elicit potent, broad and durable neutralizing antibody responses.	Walls AC, Sprouse KR, Joshi A, Bowen JE, Franko N, Navarro MJ, Stewart C, McCallum M, Goecker EA, Degli-Angeli EJ, Logue J, Greninger A, Chu H, Veesler D	bioRxiv : the preprint server for biology	34931192	bioRxiv	2021 Dec 13	https://www.ncbi.nlm.nih.gov/pubmed/34931192
Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.	Park YJ, De Marco A, Starr TN, Liu Z, Pinto D, Walls AC, Zatta F, Zepeda SK, Bowen JE, Sprouse KR, Joshi A, Giurdanella M, Guarino B, Noack J, Abdelnabi R, Foo SC, Rosen LE, Lempp FA, Benigni F, Snell G, Neyts J, Whelan SPJ, Virgin HW, Bloom JD, Corti D, Pizzuto MS, Veesler D	Science (New York, N.Y.)	34990214	Science	2022 Jan 28	https://www.ncbi.nlm.nih.gov/pubmed/34990214
Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design.	Ellis D, Brunette N, Crawford KHD, Walls AC, Pham MN, Chen C, Herpoldt KL, Fiala B, Murphy M, Pettie D, Kraft JC, Malone KD, Navarro MJ, Ogohara C, Kepl E, Ravichandran R, Sydeman C, Ahlrichs M, Johnson M, Blackstone A, Carter L, Starr TN, Greaney AJ, Lee KK, Veesler D, Bloom JD, King NP	Frontiers in immunology	34267764	Front Immunol	2021	https://www.ncbi.nlm.nih.gov/pubmed/34267764
Structure-based design of stabilized recombinant influenza neuraminidase tetramers.	Ellis D, Lederhofer J, Acton OJ, Tsybovsky Y, Kephart S, Yap C, Gillespie RA, Creanga A, Olshefsky A, Stephens T, Pettie D, Murphy M, Sydeman C, Ahlrichs M, Chan S, Borst AJ, Park YJ, Lee KK, Graham BS, Veesler D, King NP, Kanekiyo M	Nature communications	35383176	Nat Commun	2022 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/35383176
Omicron BA.1 and BA.2 neutralizing activity elicited by a comprehensive panel of human vaccines.	Bowen JE, Sprouse KR, Walls AC, Mazzitelli IG, Logue JK, Franko NM, Ahmed K, Shariq A, Cameroni E, Gori A, Bandera A, Posavad CM, Dan JM, Zhang Z, Weiskopf D, Sette A, Crotty S, Iqbal NT, Corti D, Geffner J, Grifantini R, Chu HY, Veesler D	bioRxiv : the preprint server for biology	35313570	bioRxiv	2022 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/35313570
Adjuvanting a subunit COVID-19 vaccine to induce protective immunity.	Arunachalam PS, Walls AC, Golden N, Atyeo C, Fischinger S, Li C, Aye P, Navarro MJ, Lai L, Edara VV, Röltgen K, Rogers K, Shirreff L, Ferrell DE, Wrenn S, Pettie D, Kraft JC, Miranda MC, Kepl E, Sydeman C, Brunette N, Murphy M, Fiala B, Carter L, White AG, Trisal M, Hsieh CL, Russell-Lodrigue K, Monjure C, Dufour J, Spencer S, Doyle-Meyers L, Bohm RP, Maness NJ, Roy C, Plante JA, Plante KS, Zhu A, Gorman MJ, Shin S, Shen X, Fontenot J, Gupta S, O'Hagan DT, Van Der Most R, Rappuoli R, Coffman RL, Novack D, McLellan JS, Subramaniam S, Montefiori D, Boyd SD, Flynn JL, Alter G, Villinger F, Kleanthous H, Rappaport J, Suthar MS, King NP, Veesler D, Pulendran B	Nature	33873199	Nature	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33873199
Quadrivalent influenza nanoparticle vaccines induce broad protection.	Boyoglu-Barnum S, Ellis D, Gillespie RA, Hutchinson GB, Park YJ, Moin SM, Acton OJ, Ravichandran R, Murphy M, Pettie D, Matheson N, Carter L, Creanga A, Watson MJ, Kephart S, Ataca S, Vaile JR, Ueda G, Crank MC, Stewart L, Lee KK, Guttman M, Baker D, Mascola JR, Veesler D, Graham BS, King NP, Kanekiyo M	Nature	33762730	Nature	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/33762730
Designed proteins assemble antibodies into modular nanocages.	Divine R, Dang HV, Ueda G, Fallas JA, Vulovic I, Sheffler W, Saini S, Zhao YT, Raj IX, Morawski PA, Jennewein MF, Homad LJ, Wan YH, Tooley MR, Seeger F, Etemadi A, Fahning ML, Lazarovits J, Roederer A, Walls AC, Stewart L, Mazloomi M, King NP, Campbell DJ, McGuire AT, Stamatatos L, Ruohola-Baker H, Mathieu J, Veesler D, Baker D	Science (New York, N.Y.)	33795432	Science	2021 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/33795432
Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution.	Starr TN, Greaney AJ, Hannon WW, Loes AN, Hauser K, Dillen JR, Ferri E, Farrell AG, Dadonaite B, McCallum M, Matreyek KA, Corti D, Veesler D, Snell G, Bloom JD	Science (New York, N.Y.)	35762884	Science	2022 Jul 22	https://www.ncbi.nlm.nih.gov/pubmed/35762884
ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.	Low JS, Jerak J, Tortorici MA, McCallum M, Pinto D, Cassotta A, Foglierini M, Mele F, Abdelnabi R, Weynand B, Noack J, Montiel-Ruiz M, Bianchi S, Benigni F, Sprugasci N, Joshi A, Bowen JE, Stewart C, Rexhepaj M, Walls AC, Jarrossay D, Morone D, Paparoditis P, Garzoni C, Ferrari P, Ceschi A, Neyts J, Purcell LA, Snell G, Corti D, Lanzavecchia A, Veesler D, Sallusto F	Science (New York, N.Y.)	35857703	Science	2022 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/35857703
Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape.	Marzi R, Bassi J, Silacci-Fregni C, Bartha I, Muoio F, Culap K, Sprugasci N, Lombardo G, Saliba C, Cameroni E, Cassotta A, Low JS, Walls AC, McCallum M, Tortorici MA, Bowen JE, Dellota EA Jr, Dillen JR, Czudnochowski N, Pertusini L, Terrot T, Lepori V, Tarkowski M, Riva A, Biggiogero M, Pellanda AF, Garzoni C, Ferrari P, Ceschi A, Giannini O, Havenar-Daughton C, Telenti A, Arvin A, Virgin HW, Sallusto F, Veesler D, Lanzavecchia A, Corti D, Piccoli L	bioRxiv : the preprint server for biology	36203553	bioRxiv	2022 Sep 30	https://www.ncbi.nlm.nih.gov/pubmed/36203553
Hierarchical design of pseudosymmetric protein nanoparticles.	Dowling QM, Park YJ, Gerstenmaier N, Yang EC, Wargacki A, Hsia Y, Fries CN, Ravichandran R, Walkey C, Burrell A, Veesler D, Baker D, King NP	Research square	37503272	Res Sq	2023 Jul 10	https://www.ncbi.nlm.nih.gov/pubmed/37503272
Potent monoclonal antibody-mediated neutralization of a divergent Hendra virus variant.	Wang Z, Dang HV, Amaya M, Xu Y, Yin R, Yan L, Hickey AC, Annand EJ, Horsburgh BA, Reid PA, Smith I, Eden JS, Xu K, Broder CC, Veesler D	Proceedings of the National Academy of Sciences of the United States of America	35617431	Proc Natl Acad Sci U S A	2022 May 31	https://www.ncbi.nlm.nih.gov/pubmed/35617431
A pan-variant miniprotein inhibitor protects against SARS-CoV-2 variants.	Lee J, Case JB, Park YJ, Ravichandran R, Asarnow D, Tortorici MA, Brown JT, Sanapala S, Carter L, Baker D, Diamond MS, Veesler D	bioRxiv : the preprint server for biology	39149384	bioRxiv	2024 Aug 10	https://www.ncbi.nlm.nih.gov/pubmed/39149384
Structure and design of Langya virus glycoprotein antigens.	Wang Z, McCallum M, Yan L, Gibson CA, Sharkey W, Park YJ, Dang HV, Amaya M, Person A, Broder CC, Veesler D	Proceedings of the National Academy of Sciences of the United States of America	38593070	Proc Natl Acad Sci U S A	2024 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/38593070
Broadly neutralizing antibodies against emerging delta-coronaviruses.	Rexhepaj M, Park YJ, Perruzza L, Asarnow D, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Starr TN, Corti D, Benigni F, Veesler D	bioRxiv : the preprint server for biology	38617231	bioRxiv	2024 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/38617231
Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape.	Marzi R, Bassi J, Silacci-Fregni C, Bartha I, Muoio F, Culap K, Sprugasci N, Lombardo G, Saliba C, Cameroni E, Cassotta A, Low JS, Walls AC, McCallum M, Tortorici MA, Bowen JE, Dellota EA Jr, Dillen JR, Czudnochowski N, Pertusini L, Terrot T, Lepori V, Tarkowski M, Riva A, Biggiogero M, Franzetti-Pellanda A, Garzoni C, Ferrari P, Ceschi A, Giannini O, Havenar-Daughton C, Telenti A, Arvin A, Virgin HW, Sallusto F, Veesler D, Lanzavecchia A, Corti D, Piccoli L	iScience	36507220	iScience	2023 Jan 20	https://www.ncbi.nlm.nih.gov/pubmed/36507220
Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus.	Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D	Cell host & microbe	37989312	Cell Host Microbe	2023 Dec 13	https://www.ncbi.nlm.nih.gov/pubmed/37989312
Computational design of prefusion-stabilized Herpesvirus gB trimers.	McCallum M, Veesler D	bioRxiv : the preprint server for biology	39484573	bioRxiv	2024 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/39484573
Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses.	Rexhepaj M, Asarnow D, Perruzza L, Park YJ, Guarino B, Mccallum M, Culap K, Saliba C, Leoni G, Balmelli A, Yoshiyama CN, Dickinson MS, Quispe J, Brown JT, Tortorici MA, Sprouse KR, Taylor AL, Corti D, Starr TN, Benigni F, Veesler D	Immunity	39488210	Immunity	2024 Dec 10	https://www.ncbi.nlm.nih.gov/pubmed/39488210
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.	Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, CITIID-NIHR BioResource COVID-19 Collaboration, Elmer A, Kingston N, Graves B, McCoy LE, Smith KGC, Bradley JR, Temperton N, Ceron-Gutierrez L, Barcenas-Morales G, COVID-19 Genomics UK (COG-UK) Consortium, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK	Nature	33706364	Nature	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/33706364
Discovery and Characterization of Spike N-Terminal Domain-Binding Aptamers for Rapid SARS-CoV-2 Detection.	Kacherovsky N, Yang LF, Dang HV, Cheng EL, Cardle II, Walls AC, McCallum M, Sellers DL, DiMaio F, Salipante SJ, Corti D, Veesler D, Pun SH	Angewandte Chemie (International ed. in English)	34328683	Angew Chem Int Ed Engl	2021 Sep 20	https://www.ncbi.nlm.nih.gov/pubmed/34328683
Multivalent designed proteins protect against SARS-CoV-2 variants of concern.	Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M Jr, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D	bioRxiv : the preprint server for biology	34268509	bioRxiv	2021 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/34268509
Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines.	Walls AC, Miranda MC, Pham MN, Schäfer A, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shireff L, Ferrell DE, Brunette N, Kepl E, Bowen J, Zepeda SK, Starr T, Hsieh CL, Fiala B, Wrenn S, Pettie D, Sydeman C, Johnson M, Blackstone A, Ravichandran R, Ogohara C, Carter L, Tilles SW, Rappuoli R, O'Hagan DT, Van Der Most R, Van Voorhis WC, McLellan JS, Kleanthous H, Sheahan TP, Fuller DH, Villinger F, Bloom J, Pulendran B, Baric R, King N, Veesler D	bioRxiv : the preprint server for biology	33758839	bioRxiv	2021 Mar 16	https://www.ncbi.nlm.nih.gov/pubmed/33758839
Structural basis for broad coronavirus neutralization.	Sauer MM, Tortorici MA, Park YJ, Walls AC, Homad L, Acton OJ, Bowen JE, Wang C, Xiong X, de van der Schueren W, Quispe J, Hoffstrom BG, Bosch BJ, McGuire AT, Veesler D	Nature structural & molecular biology	33981021	Nat Struct Mol Biol	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33981021
Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins.	Dang HV, Cross RW, Borisevich V, Bornholdt ZA, West BR, Chan YP, Mire CE, Da Silva SC, Dimitrov AS, Yan L, Amaya M, Navaratnarajah CK, Zeitlin L, Geisbert TW, Broder CC, Veesler D	Nature structural & molecular biology	33927387	Nat Struct Mol Biol	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/33927387
Functional Analysis of the Fusion and Attachment Glycoproteins of Mojiang Henipavirus.	Cheliout Da Silva S, Yan L, Dang HV, Xu K, Epstein JH, Veesler D, Broder CC	Viruses	33809833	Viruses	2021 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/33809833
Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape.	Starr TN, Czudnochowski N, Zatta F, Park YJ, Liu Z, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Tucker H, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E, Cameroni E, Croll TI, Nix JC, Havenar-Daughton C, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Whelan SPJ, Virgin HW, Veesler D, Corti D, Bloom JD, Snell G	bioRxiv : the preprint server for biology	33851154	bioRxiv	2021 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/33851154
Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody.	Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, di Iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E Jr, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Silacci Fregni C, Abdelnabi R, Caroline Foo SY, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Snell G, Virgin HW, Whelan SPJ, Bloom JD, Corti D, Veesler D, Pizzuto MS	bioRxiv : the preprint server for biology	33851169	bioRxiv	2021 Apr 8	https://www.ncbi.nlm.nih.gov/pubmed/33851169
Generation of ordered protein assemblies using rigid three-body fusion.	Vulovic I, Yao Q, Park YJ, Courbet A, Norris A, Busch F, Sahasrabuddhe A, Merten H, Sahtoe DD, Ueda G, Fallas JA, Weaver SJ, Hsia Y, Langan RA, Plückthun A, Wysocki VH, Veesler D, Jensen GJ, Baker D	Proceedings of the National Academy of Sciences of the United States of America	34074752	Proc Natl Acad Sci U S A	2021 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/34074752
Tackling COVID-19 with neutralizing monoclonal antibodies.	Corti D, Purcell LA, Snell G, Veesler D	Cell	34416148	Cell	2021 Aug 19	https://www.ncbi.nlm.nih.gov/pubmed/34416148
Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020.	Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González Candelas F, SeqCOVID-SPAIN consortium, Stadler T, Neher RA	medRxiv : the preprint server for health sciences	33269368	medRxiv	2021 Mar 24	https://www.ncbi.nlm.nih.gov/pubmed/33269368
Human coronavirus HKU1 recognition of the TMPRSS2 host receptor.	McCallum M, Park YJ, Stewart C, Sprouse KR, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D	bioRxiv : the preprint server for biology	38260518	bioRxiv	2024 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/38260518
Hierarchical design of pseudosymmetric protein nanoparticles.	Dowling QM, Park YJ, Gerstenmaier N, Yang EC, Wargacki A, Hsia Y, Fries CN, Ravichandran R, Walkey C, Burrell A, Veesler D, Baker D, King NP	bioRxiv : the preprint server for biology	37398374	bioRxiv	2023 Jun 17	https://www.ncbi.nlm.nih.gov/pubmed/37398374
A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines.	Lee J, Stewart C, Schaefer A, Leaf EM, Park YJ, Asarnow D, Powers JM, Treichel C, Corti D, Baric R, King NP, Veesler D	bioRxiv : the preprint server for biology	38168207	bioRxiv	2023 Dec 20	https://www.ncbi.nlm.nih.gov/pubmed/38168207
Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2.	Walls AC, Fiala B, Schäfer A, Wrenn S, Pham MN, Murphy M, Tse LV, Shehata L, O'Connor MA, Chen C, Navarro MJ, Miranda MC, Pettie D, Ravichandran R, Kraft JC, Ogohara C, Palser A, Chalk S, Lee EC, Guerriero K, Kepl E, Chow CM, Sydeman C, Hodge EA, Brown B, Fuller JT, Dinnon KH 3rd, Gralinski LE, Leist SR, Gully KL, Lewis TB, Guttman M, Chu HY, Lee KK, Fuller DH, Baric RS, Kellam P, Carter L, Pepper M, Sheahan TP, Veesler D, King NP	Cell	33160446	Cell	2020 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/33160446
SARS-CoV-2 spike conformation determines plasma neutralizing activity.	Bowen JE, Walls AC, Joshi A, Sprouse KR, Stewart C, Tortorici MA, Franko NM, Logue JK, Mazzitelli IG, Tiles SW, Ahmed K, Shariq A, Snell G, Iqbal NT, Geffner J, Bandera A, Gori A, Grifantini R, Chu HY, Van Voorhis WC, Corti D, Veesler D	bioRxiv : the preprint server for biology	34981060	bioRxiv	2021 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/34981060
Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.	Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK	Nature	35104837	Nature	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/35104837
Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail.	Addetia A, Park YJ, Starr T, Greaney AJ, Sprouse KR, Bowen JE, Tiles SW, Van Voorhis WC, Bloom JD, Corti D, Walls AC, Veesler D	bioRxiv : the preprint server for biology	35118471	bioRxiv	2022 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/35118471
Omicron spike function and neutralizing activity elicited by a comprehensive panel of vaccines.	Bowen JE, Addetia A, Dang HV, Stewart C, Brown JT, Sharkey WK, Sprouse KR, Walls AC, Mazzitelli IG, Logue JK, Franko NM, Czudnochowski N, Powell AE, Dellota E Jr, Ahmed K, Ansari AS, Cameroni E, Gori A, Bandera A, Posavad CM, Dan JM, Zhang Z, Weiskopf D, Sette A, Crotty S, Iqbal NT, Corti D, Geffner J, Snell G, Grifantini R, Chu HY, Veesler D	Science (New York, N.Y.)	35857529	Science	2022 Aug 19	https://www.ncbi.nlm.nih.gov/pubmed/35857529
Durable protection against the SARS-CoV-2 Omicron variant is induced by an adjuvanted subunit vaccine.	Arunachalam PS, Feng Y, Ashraf U, Hu M, Walls AC, Edara VV, Zarnitsyna VI, Aye PP, Golden N, Miranda MC, Green KWM, Threeton BM, Maness NJ, Beddingfield BJ, Bohm RP, Scheuermann SE, Goff K, Dufour J, Russell-Lodrigue K, Kepl E, Fiala B, Wrenn S, Ravichandran R, Ellis D, Carter L, Rogers K, Shirreff LM, Ferrell DE, Deb Adhikary NR, Fontenot J, Hammond HL, Frieman M, Grifoni A, Sette A, O'Hagan DT, Van Der Most R, Rappuoli R, Villinger F, Kleanthous H, Rappaport J, Suthar MS, Veesler D, Wang TT, King NP, Pulendran B	Science translational medicine	35976993	Sci Transl Med	2022 Aug 17	https://www.ncbi.nlm.nih.gov/pubmed/35976993
Computational design of mechanically coupled axle-rotor protein assemblies.	Courbet A, Hansen J, Hsia Y, Bethel N, Park YJ, Xu C, Moyer A, Boyken SE, Ueda G, Nattermann U, Nagarajan D, Silva DA, Sheffler W, Quispe J, Nord A, King N, Bradley P, Veesler D, Kollman J, Baker D	Science (New York, N.Y.)	35446645	Science	2022 Apr 22	https://www.ncbi.nlm.nih.gov/pubmed/35446645
Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps.	Muenks A, Zepeda S, Zhou G, Veesler D, DiMaio F	Nature communications	36859493	Nat Commun	2023 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/36859493
Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies.	Lempp FA, Soriaga LB, Montiel-Ruiz M, Benigni F, Noack J, Park YJ, Bianchi S, Walls AC, Bowen JE, Zhou J, Kaiser H, Joshi A, Agostini M, Meury M, Dellota E Jr, Jaconi S, Cameroni E, Martinez-Picado J, Vergara-Alert J, Izquierdo-Useros N, Virgin HW, Lanzavecchia A, Veesler D, Purcell LA, Telenti A, Corti D	Nature	34464958	Nature	2021 Oct	https://www.ncbi.nlm.nih.gov/pubmed/34464958
Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains.	Starr TN, Greaney AJ, Stewart CM, Walls AC, Hannon WW, Veesler D, Bloom JD	PLoS pathogens	36399443	PLoS Pathog	2022 Nov	https://www.ncbi.nlm.nih.gov/pubmed/36399443
Distinct sensitivities to SARS-CoV-2 variants in vaccinated humans and mice.	Walls AC, VanBlargan LA, Wu K, Choi A, Navarro MJ, Lee D, Avena L, Berrueta DM, Pham MN, Elbashir S, Kraft JC, Miranda MC, Kepl E, Johnson M, Blackstone A, Sprouse K, Fiala B, O'Connor MA, Brunette N, Arunachalam PS, Shirreff L, Rogers K, Carter L, Fuller DH, Villinger F, Pulendran B, Diamond MS, Edwards DK, King NP, Veesler D	Cell reports	35988541	Cell Rep	2022 Aug 30	https://www.ncbi.nlm.nih.gov/pubmed/35988541
Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines.	Walls AC, Miranda MC, Schäfer A, Pham MN, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shirreff L, Ferrell DE, Bowen J, Brunette N, Kepl E, Zepeda SK, Starr T, Hsieh CL, Fiala B, Wrenn S, Pettie D, Sydeman C, Sprouse KR, Johnson M, Blackstone A, Ravichandran R, Ogohara C, Carter L, Tilles SW, Rappuoli R, Leist SR, Martinez DR, Clark M, Tisch R, O'Hagan DT, Van Der Most R, Van Voorhis WC, Corti D, McLellan JS, Kleanthous H, Sheahan TP, Smith KD, Fuller DH, Villinger F, Bloom J, Pulendran B, Baric RS, King NP, Veesler D	Cell	34619077	Cell	2021 Oct 14	https://www.ncbi.nlm.nih.gov/pubmed/34619077
Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.	McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D	Science (New York, N.Y.)	34751595	Science	2021 Dec 24	https://www.ncbi.nlm.nih.gov/pubmed/34751595
Designed miniproteins potently inhibit and protect against MERS-CoV.	Ragotte RJ, Tortorici MA, Catanzaro NJ, Addetia A, Coventry B, Froggatt HM, Lee J, Stewart C, Brown JT, Goreshnik I, Sims JN, Milles LF, Wicky BIM, Glögl M, Gerben S, Kang A, Bera AK, Sharkey W, Schäfer A, Baric RS, Baker D, Veesler D	bioRxiv : the preprint server for biology	39574666	bioRxiv	2024 Nov 4	https://www.ncbi.nlm.nih.gov/pubmed/39574666
Potent neutralization of SARS-CoV-2 variants by RBD nanoparticle and prefusion-stabilized spike immunogens.	Miranda MC, Kepl E, Navarro MJ, Chen C, Johnson M, Sprouse KR, Stewart C, Palser A, Valdez A, Pettie D, Sydeman C, Ogohara C, Kraft JC, Pham M, Murphy M, Wrenn S, Fiala B, Ravichandran R, Ellis D, Carter L, Corti D, Kellam P, Lee K, Walls AC, Veesler D, King NP	NPJ vaccines	39379400	NPJ Vaccines	2024 Oct 8	https://www.ncbi.nlm.nih.gov/pubmed/39379400
ACE2 utilization of HKU25 clade MERS-related coronaviruses with broad geographic distribution.	Liu C, Park YJ, Ma CB, Stuart C, Gen R, Sun YC, Yang X, Lin MY, Xiong Q, Si JY, Liu P, Veesler D, Yan H	bioRxiv : the preprint server for biology	40027745	bioRxiv	2025 Feb 19	https://www.ncbi.nlm.nih.gov/pubmed/40027745
SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.	Gen R, Addetia A, Asarnow D, Park YJ, Quispe J, Chan MC, Brown JT, Lee J, Campbell MG, Lapointe CP, Veesler D	bioRxiv : the preprint server for biology	39868184	bioRxiv	2025 Jan 15	https://www.ncbi.nlm.nih.gov/pubmed/39868184
SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.	Starr TN, Czudnochowski N, Liu Z, Zatta F, Park YJ, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Tortorici MA, Walls AC, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Dillen JR, Tucker H, Bassi J, Silacci-Fregni C, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E Jr, Abdelnabi R, Foo SC, Cameroni E, Stumpf S, Croll TI, Nix JC, Havenar-Daughton C, Piccoli L, Benigni F, Neyts J, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Virgin HW, Whelan SPJ, Veesler D, Corti D, Bloom JD, Snell G	Nature	34261126	Nature	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/34261126
Broad sarbecovirus neutralization by a human monoclonal antibody.	Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, Di Iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E Jr, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Fregni CS, Abdelnabi R, Foo SC, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Virgin HW, Whelan SPJ, Snell G, Bloom JD, Corti D, Veesler D, Pizzuto MS	Nature	34280951	Nature	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/34280951
Regulatory T cell-like response to SARS-CoV-2 in Jamaican fruit bats (Artibeus jamaicensis) transduced with human ACE2.	Burke B, Rocha SM, Zhan S, Eckley M, Reasoner C, Addetia A, Lewis J, Fagre A, Charley PA, Richt JA, Weiss SR, Tjalkens RB, Veesler D, Aboellail T, Schountz T	PLoS pathogens	37856551	PLoS Pathog	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37856551
Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus.	Lee J, Zepeda SK, Park YJ, Taylor AL, Quispe J, Stewart C, Leaf EM, Treichel C, Corti D, King NP, Starr TN, Veesler D	bioRxiv : the preprint server for biology	37745523	bioRxiv	2023 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/37745523
Structure and design of Langya virus glycoprotein antigens.	Wang Z, McCallum M, Yan L, Sharkey W, Park YJ, Dang HV, Amaya M, Person A, Broder CC, Veesler D	bioRxiv : the preprint server for biology	37645760	bioRxiv	2023 Aug 26	https://www.ncbi.nlm.nih.gov/pubmed/37645760
Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement.	McCallum M, Czudnochowski N, Rosen LE, Zepeda SK, Bowen JE, Walls AC, Hauser K, Joshi A, Stewart C, Dillen JR, Powell AE, Croll TI, Nix J, Virgin HW, Corti D, Snell G, Veesler D	Science (New York, N.Y.)	35076256	Science	2022 Feb 25	https://www.ncbi.nlm.nih.gov/pubmed/35076256
Immunization with a self-assembling nanoparticle vaccine displaying EBV gH/gL protects humanized mice against lethal viral challenge.	Malhi H, Homad LJ, Wan YH, Poudel B, Fiala B, Borst AJ, Wang JY, Walkey C, Price J, Wall A, Singh S, Moodie Z, Carter L, Handa S, Correnti CE, Stoddard BL, Veesler D, Pancera M, Olson J, King NP, McGuire AT	Cell reports. Medicine	35705092	Cell Rep Med	2022 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/35705092
Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants.	Zhang JZ, Yeh HW, Walls AC, Wicky BIM, Sprouse KR, VanBlargan LA, Treger R, Quijano-Rubio A, Pham MN, Kraft JC, Haydon IC, Yang W, DeWitt M, Bowen JE, Chow CM, Carter L, Ravichandran R, Wener MH, Stewart L, Veesler D, Diamond MS, Greninger AL, Koelle DM, Baker D	Nature biotechnology	35484405	Nat Biotechnol	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35484405
Architecture and antigenicity of the Nipah virus attachment glycoprotein.	Wang Z, Amaya M, Addetia A, Dang HV, Reggiano G, Yan L, Hickey AC, DiMaio F, Broder CC, Veesler D	Science (New York, N.Y.)	35239409	Science	2022 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/35239409
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies.	Collier DA, De Marco A, Ferreira IATM, Meng B, Datir R, Walls AC, Kemp S SA, Bassi J, Pinto D, Fregni CS, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, CITIID-NIHR BioResource COVID-19 Collaboration, Elmer A, Kingston N, Graves B, McCoy LE, Smith KG, Bradley JR, Temperton N, Ceron-Gutierrez L L, Barcenas-Morales G, COVID-19 Genomics UK (COG-UK) consortium, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK	medRxiv : the preprint server for health sciences	33619509	medRxiv	2021 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/33619509
Structural basis for broad coronavirus neutralization.	Sauer MM, Tortorici MA, Park YJ, Walls AC, Homad L, Acton O, Bowen J, Wang C, Xiong X, de van der Schueren W, Quispe J, Hoffstrom BG, Bosch BJ, McGuire AT, Veesler D	bioRxiv : the preprint server for biology	33398277	bioRxiv	2021 Jan 4	https://www.ncbi.nlm.nih.gov/pubmed/33398277
Persistent immune imprinting after XBB.1.5 COVID vaccination in humans.	Tortorici MA, Addetia A, Seo AJ, Brown J, Sprouse KR, Logue J, Clark E, Franko N, Chu H, Veesler D	bioRxiv : the preprint server for biology	38076876	bioRxiv	2023 Nov 30	https://www.ncbi.nlm.nih.gov/pubmed/38076876
Spike deep mutational scanning helps predict success of SARS-CoV-2 clades.	Dadonaite B, Brown J, McMahon TE, Farrell AG, Figgins MD, Asarnow D, Stewart C, Lee J, Logue J, Bedford T, Murrell B, Chu HY, Veesler D, Bloom JD	Nature	38961298	Nature	2024 Jul	https://www.ncbi.nlm.nih.gov/pubmed/38961298
A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines.	Lee J, Stewart C, Schäfer A, Leaf EM, Park YJ, Asarnow D, Powers JM, Treichel C, Sprouse KR, Corti D, Baric R, King NP, Veesler D	Nature communications	38944664	Nat Commun	2024 Jun 28	https://www.ncbi.nlm.nih.gov/pubmed/38944664
Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses.	Park YJ, Liu C, Lee J, Brown JT, Ma CB, Liu P, Xiong Q, Stewart C, Addetia A, Craig CJ, Tortorici MA, Alshukari A, Starr T, Yan H, Veesler D	bioRxiv : the preprint server for biology	39253417	bioRxiv	2024 Aug 28	https://www.ncbi.nlm.nih.gov/pubmed/39253417
A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates.	Weidenbacher PA, Sanyal M, Friedland N, Tang S, Arunachalam PS, Hu M, Kumru OS, Morris MK, Fontenot J, Shirreff L, Do J, Cheng YC, Vasudevan G, Feinberg MB, Villinger FJ, Hanson C, Joshi SB, Volkin DB, Pulendran B, Kim PS	bioRxiv : the preprint server for biology	36597527	bioRxiv	2022 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/36597527
HIV-1 prehairpin intermediate inhibitors show efficacy independent of neutralization tier.	Bell BN, Bruun TUJ, Friedland N, Kim PS	Proceedings of the National Academy of Sciences of the United States of America	36795752	Proc Natl Acad Sci U S A	2023 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/36795752
Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies.	Bruun TUJ, Tang S, Erwin G, Deis L, Fernandez D, Kim PS	The Journal of biological chemistry	36841484	J Biol Chem	2023 Apr	https://www.ncbi.nlm.nih.gov/pubmed/36841484
Decreased efficacy of a COVID-19 vaccine due to mutations present in early SARS-CoV-2 variants of concern.	Weidenbacher PA, Friedland N, Sanyal M, Morris MK, Do J, Hanson C, Kim PS	bioRxiv : the preprint server for biology	37425802	bioRxiv	2023 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/37425802
Vaccine design via antigen reorientation.	Xu D, Carter JJ, Li C, Utz A, Weidenbacher PAB, Tang S, Sanyal M, Pulendran B, Barnes CO, Kim PS	Nature chemical biology	38225471	Nat Chem Biol	2024 Aug	https://www.ncbi.nlm.nih.gov/pubmed/38225471
A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates.	Weidenbacher PA, Sanyal M, Friedland N, Tang S, Arunachalam PS, Hu M, Kumru OS, Morris MK, Fontenot J, Shirreff L, Do J, Cheng YC, Vasudevan G, Feinberg MB, Villinger FJ, Hanson C, Joshi SB, Volkin DB, Pulendran B, Kim PS	Nature communications	37069151	Nat Commun	2023 Apr 17	https://www.ncbi.nlm.nih.gov/pubmed/37069151
Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 Spike ferritin nanoparticle vaccine antigen produced from two different cell lines.	Kumru OS, Sanyal M, Friedland N, Hickey J, Joshi R, Weidenbacher P, Do J, Cheng YC, Kim PS, Joshi SB, Volkin DB	bioRxiv : the preprint server for biology	37066156	bioRxiv	2023 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/37066156
Design of universal Ebola virus vaccine candidates via immunofocusing.	Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten JJ, Moliva JI, Sullivan NJ, Davey RA, Kim PS	Proceedings of the National Academy of Sciences of the United States of America	38319964	Proc Natl Acad Sci U S A	2024 Feb 13	https://www.ncbi.nlm.nih.gov/pubmed/38319964
Enhancing HIV-1 Neutralization by Increasing the Local Concentration of Membrane-Proximal External Region-Directed Broadly Neutralizing Antibodies.	Kim S, Filsinger Interrante MV, Kim PS	Journal of virology	36541800	J Virol	2023 Jan 31	https://www.ncbi.nlm.nih.gov/pubmed/36541800
Engineering a SARS-CoV-2 Vaccine Targeting the Receptor-Binding Domain Cryptic-Face via Immunofocusing.	Bruun TUJ, Do J, Weidenbacher PA, Utz A, Kim PS	ACS central science	39463836	ACS Cent Sci	2024 Oct 23	https://www.ncbi.nlm.nih.gov/pubmed/39463836
Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 spike ferritin nanoparticle vaccine antigen produced from two different cell lines.	Kumru OS, Sanyal M, Friedland N, Hickey JM, Joshi R, Weidenbacher P, Do J, Cheng YC, Kim PS, Joshi SB, Volkin DB	Vaccine	37620203	Vaccine	2023 Oct 20	https://www.ncbi.nlm.nih.gov/pubmed/37620203
Design of universal Ebola virus vaccine candidates via immunofocusing.	Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten JJ, Moliva JI, Sullivan NJ, Davey RA, Kim PS	bioRxiv : the preprint server for biology	37904982	bioRxiv	2023 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/37904982
Bringing immunofocusing into focus.	Musunuri S, Weidenbacher PAB, Kim PS	NPJ vaccines	38195562	NPJ Vaccines	2024 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/38195562
Simplified Purification of Glycoprotein-Modified Ferritin Nanoparticles for Vaccine Development.	Weidenbacher P, Musunuri S, Powell AE, Tang S, Do J, Sanyal M, Kim PS	Biochemistry	35960597	Biochemistry	2023 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/35960597
Designing epitope-focused vaccines via antigen reorientation.	Xu D, Li C, Utz A, Weidenbacher PAB, Tang S, Sanyal M, Pulendran B, Kim PS	bioRxiv : the preprint server for biology	36597536	bioRxiv	2022 Dec 21	https://www.ncbi.nlm.nih.gov/pubmed/36597536
Converting non-neutralizing SARS-CoV-2 antibodies into broad-spectrum inhibitors.	Weidenbacher PA, Waltari E, de Los Rios Kobara I, Bell BN, Morris MK, Cheng YC, Hanson C, Pak JE, Kim PS	Nature chemical biology	36076082	Nat Chem Biol	2022 Nov	https://www.ncbi.nlm.nih.gov/pubmed/36076082
Engineering a SARS-CoV-2 vaccine targeting the RBD cryptic-face via immunofocusing.	Bruun TUJ, Do J, Weidenbacher PA, Kim PS	bioRxiv : the preprint server for biology	38895327	bioRxiv	2024 Jun 5	https://www.ncbi.nlm.nih.gov/pubmed/38895327
Efficient evolution of human antibodies from general protein language models.	Hie BL, Shanker VR, Xu D, Bruun TUJ, Weidenbacher PA, Tang S, Wu W, Pak JE, Kim PS	Nature biotechnology	37095349	Nat Biotechnol	2024 Feb	https://www.ncbi.nlm.nih.gov/pubmed/37095349
Multimerization of Ebola GPΔmucin on protein nanoparticle vaccines has minimal effect on elicitation of neutralizing antibodies.	Powell AE, Xu D, Roth GA, Zhang K, Chiu W, Appel EA, Kim PS	Frontiers in immunology	36091016	Front Immunol	2022	https://www.ncbi.nlm.nih.gov/pubmed/36091016
Genome-Scale CRISPR Screening Reveals Host Factors Required for Ribosome Formation and Viral Replication.	Ohlson MB, Eitson JL, Wells AI, Kumar A, Jang S, Ni C, Xing C, Buszczak M, Schoggins JW	mBio	36809113	mBio	2023 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/36809113
Shiftless inhibits flavivirus replication in vitro and is neuroprotective in a mouse model of Zika virus pathogenesis.	Hanners NW, Mar KB, Boys IN, Eitson JL, De La Cruz-Rivera PC, Richardson RB, Fan W, Wight-Carter M, Schoggins JW	Proceedings of the National Academy of Sciences of the United States of America	34873063	Proc Natl Acad Sci U S A	2021 Dec 7	https://www.ncbi.nlm.nih.gov/pubmed/34873063
Overexpression screen of interferon-stimulated genes identifies RARRES3 as a restrictor of Toxoplasma gondii infection.	Rinkenberger N, Abrams ME, Matta SK, Schoggins JW, Alto NM, Sibley LD	eLife	34871166	Elife	2021 Dec 6	https://www.ncbi.nlm.nih.gov/pubmed/34871166
A concerted mechanism involving ACAT and SREBPs by which oxysterols deplete accessible cholesterol to restrict microbial infection.	Heisler DB, Johnson KA, Ma DH, Ohlson MB, Zhang L, Tran M, Corley CD, Abrams ME, McDonald JG, Schoggins JW, Alto NM, Radhakrishnan A	eLife	36695568	Elife	2023 Jan 25	https://www.ncbi.nlm.nih.gov/pubmed/36695568
TRIM7 inhibits enterovirus replication and promotes emergence of a viral variant with increased pathogenicity.	Fan W, Mar KB, Sari L, Gaszek IK, Cheng Q, Evers BM, Shelton JM, Wight-Carter M, Siegwart DJ, Lin MM, Schoggins JW	Cell	34062120	Cell	2021 Jun 24	https://www.ncbi.nlm.nih.gov/pubmed/34062120
The mechanism of RNA capping by SARS-CoV-2.	Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS	Research square	35194601	Res Sq	2022 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/35194601
Laboratory Action Plan for Emerging SARS-CoV-2 Variants.	Filkins L, SoRelle JA, Schoggins J, Park JY	Clinical chemistry	33515256	Clin Chem	2021 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/33515256
LY6E is a pan-coronavirus restriction factor in the respiratory tract.	Mar KB, Wells AI, Caballero Van Dyke MC, Lopez AH, Eitson JL, Fan W, Hanners NW, Evers BM, Shelton JM, Schoggins JW	Nature microbiology	37443277	Nat Microbiol	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37443277
Enterovirus 3C Protease Cleaves TRIM7 To Dampen Its Antiviral Activity.	Fan W, McDougal MB, Schoggins JW	Journal of virology	36106874	J Virol	2022 Oct 12	https://www.ncbi.nlm.nih.gov/pubmed/36106874
SARS-CoV-2 spike protein induces inflammation via TLR2-dependent activation of the NF-κB pathway.	Khan S, Shafiei MS, Longoria C, Schoggins JW, Savani RC, Zaki H	eLife	34866574	Elife	2021 Dec 6	https://www.ncbi.nlm.nih.gov/pubmed/34866574
TRIM32 inhibits Venezuelan Equine Encephalitis Virus Infection by targeting a late step in viral entry.	Xie Y, Cao J, Gan S, Xu L, Zhang D, Qian S, Xu F, Ding Q, Schoggins JW, Fan W	bioRxiv : the preprint server for biology	38895352	bioRxiv	2024 Jun 4	https://www.ncbi.nlm.nih.gov/pubmed/38895352
Interferon inhibits a model RNA virus via a limited set of inducible effector genes.	McDougal MB, De Maria AM, Ohlson MB, Kumar A, Xing C, Schoggins JW	EMBO reports	37497756	EMBO Rep	2023 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/37497756
The mechanism of RNA capping by SARS-CoV-2.	Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS	Nature	35944563	Nature	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35944563
Functional-genomic analysis reveals intraspecies diversification of antiviral receptor transporter proteins in Xenopus laevis.	Boys IN, Mar KB, Schoggins JW	PLoS genetics	34014925	PLoS Genet	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/34014925
TRIM32 inhibits Venezuelan equine encephalitis virus infection by targeting a late step in viral entry.	Xie Y, Cao J, Gan S, Xu L, Zhang D, Qian S, Xu F, Ding Q, Schoggins JW, Fan W	PLoS pathogens	39527628	PLoS Pathog	2024 Nov	https://www.ncbi.nlm.nih.gov/pubmed/39527628
CRISPR screening reveals a dependency on ribosome recycling for efficient SARS-CoV-2 programmed ribosomal frameshifting and viral replication.	Rehfeld F, Eitson JL, Ohlson MB, Chang TC, Schoggins JW, Mendell JT	Cell reports	36753415	Cell Rep	2023 Feb 28	https://www.ncbi.nlm.nih.gov/pubmed/36753415
Cellular origins of dsRNA, their recognition and consequences.	Chen YG, Hur S	Nature reviews. Molecular cell biology	34815573	Nat Rev Mol Cell Biol	2022 Apr	https://www.ncbi.nlm.nih.gov/pubmed/34815573
Immunogenicity of In Vitro-Transcribed RNA.	Mu X, Hur S	Accounts of chemical research	34677064	Acc Chem Res	2021 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/34677064
Clinical outcomes and inflammatory marker levels in patients with Covid-19 and obesity at an inner-city safety net hospital.	Mostaghim A, Sinha P, Bielick C, Knudsen S, Beeram I, White LF, Apovian C, Sagar M, Hochberg NS	PloS one	33326480	PLoS One	2020	https://www.ncbi.nlm.nih.gov/pubmed/33326480
Filament-like Assemblies of Intracellular Nucleic Acid Sensors: Commonalities and Differences.	Cadena C, Hur S	Molecular cell	31626748	Mol Cell	2019 Oct 17	https://www.ncbi.nlm.nih.gov/pubmed/31626748
Death domain fold proteins in immune signaling and transcriptional regulation.	Huoh YS, Hur S	The FEBS journal	33905163	FEBS J	2022 Jul	https://www.ncbi.nlm.nih.gov/pubmed/33905163
Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases.	Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S	Molecular cell	33373584	Mol Cell	2021 Feb 4	https://www.ncbi.nlm.nih.gov/pubmed/33373584
The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis.	Leng F, Zhang W, Ramirez RN, Leon J, Zhong Y, Hou L, Yuki K, van der Veeken J, Rudensky AY, Benoist C, Hur S	Immunity	35926508	Immunity	2022 Aug 9	https://www.ncbi.nlm.nih.gov/pubmed/35926508
Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA.	Paget M, Cadena C, Ahmad S, Wang HT, Jordan TX, Kim E, Koo B, Lyons SM, Ivanov P, tenOever B, Mu X, Hur S	Molecular cell	37028415	Mol Cell	2023 Apr 6	https://www.ncbi.nlm.nih.gov/pubmed/37028415
Pathogenesis of COVID-19 from the Perspective of the Damage-Response Framework.	Pirofski LA, Casadevall A	mBio	32616514	mBio	2020 Jul 2	https://www.ncbi.nlm.nih.gov/pubmed/32616514
Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli.	Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O	Nature communications	35680894	Nat Commun	2022 Jun 9	https://www.ncbi.nlm.nih.gov/pubmed/35680894
Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex.	Cooke MB, Herman C	Journal of bacteriology	36847532	J Bacteriol	2023 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/36847532
RNA polymerase inaccuracy underlies SARS-CoV-2 variants and vaccine heterogeneity.	Bradley CC, Gordon AJE, Wang C, Cooke MB, Kohrn BF, Kennedy SR, Lichtarge O, Ronca SE, Herman C	Research square	35677076	Res Sq	2022 Jun 2	https://www.ncbi.nlm.nih.gov/pubmed/35677076
Convalescent plasma for COVID-19 - encouraging signals of efficacy.	Casadevall A, Tobian AAR	British journal of haematology	33524158	Br J Haematol	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33524158
Markers of Polyfunctional SARS-CoV-2 Antibodies in Convalescent Plasma.	Natarajan H, Crowley AR, Butler SE, Xu S, Weiner JA, Bloch EM, Littlefield K, Wieland-Alter W, Connor RI, Wright PF, Benner SE, Bonny TS, Laeyendecker O, Sullivan D, Shoham S, Quinn TC, Larman HB, Casadevall A, Pekosz A, Redd AD, Tobian AAR, Ackerman ME	mBio	33879585	mBio	2021 Apr 20	https://www.ncbi.nlm.nih.gov/pubmed/33879585
The Principles of Antibody Therapy for Infectious Diseases with Relevance for COVID-19.	Casadevall A, Pirofski LA, Joyner MJ	mBio	33653885	mBio	2021 Mar 2	https://www.ncbi.nlm.nih.gov/pubmed/33653885
Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells.	Wen AX, Herman C	Current opinion in microbiology	39190937	Curr Opin Microbiol	2024 Oct	https://www.ncbi.nlm.nih.gov/pubmed/39190937
Antigen discovery tools for adaptive immune receptor repertoire research.	Bousbaine D, Ploegh HL	Current opinion in systems biology	33195881	Curr Opin Syst Biol	2020 Dec	https://www.ncbi.nlm.nih.gov/pubmed/33195881
Nanobodies as non-invasive imaging tools.	Rashidian M, Ploegh H	Immuno-oncology technology	35754459	Immunooncol Technol	2020 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35754459
USP16 is an ISG15 cross-reactive deubiquitinase that targets pro-ISG15 and ISGylated proteins involved in metabolism.	Gan J, Pinto-Fernández A, Flierman D, Akkermans JJLL, O'Brien DP, Greenwood H, Scott HC, Fritz G, Knobeloch KP, Neefjes J, van Dam H, Ovaa H, Ploegh HL, Kessler BM, Geurink PP, Sapmaz A	Proceedings of the National Academy of Sciences of the United States of America	38055744	Proc Natl Acad Sci U S A	2023 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/38055744
Nanobodies in cancer.	Verhaar ER, Woodham AW, Ploegh HL	Seminars in immunology	33272897	Semin Immunol	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33272897
Exploring cellular biochemistry with nanobodies.	Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL	The Journal of biological chemistry	32868455	J Biol Chem	2020 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/32868455
Induction of antigen-specific tolerance by nanobody-antigen adducts that target class-II major histocompatibility complexes.	Pishesha N, Harmand T, Smeding LY, Ma W, Ludwig LS, Janssen R, Islam A, Xie YJ, Fang T, McCaul N, Pinney W 3rd, Sugito HR, Rossotti MA, Gonzalez-Sapienza G, Ploegh HL	Nature biomedical engineering	34127819	Nat Biomed Eng	2021 Nov	https://www.ncbi.nlm.nih.gov/pubmed/34127819
A class II MHC-targeted vaccine elicits immunity against SARS-CoV-2 and its variants.	Pishesha N, Harmand TJ, Rothlauf PW, Praest P, Alexander RK, van den Doel R, Liebeskind MJ, Vakaki MA, McCaul N, Wijne C, Verhaar E, Pinney W 3rd, Heston H, Bloyet LM, Pontelli MC, Ilagan MXG, Jan Lebbink R, Buchser WJ, Wiertz EJHJ, Whelan SPJ, Ploegh HL	Proceedings of the National Academy of Sciences of the United States of America	34654739	Proc Natl Acad Sci U S A	2021 Nov 2	https://www.ncbi.nlm.nih.gov/pubmed/34654739
A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes.	Bousbaine D, Fisch LI, London M, Bhagchandani P, Rezende de Castro TB, Mimee M, Olesen S, Reis BS, VanInsberghe D, Bortolatto J, Poyet M, Cheloha RW, Sidney J, Ling J, Gupta A, Lu TK, Sette A, Alm EJ, Moon JJ, Victora GD, Mucida D, Ploegh HL, Bilate AM	Science (New York, N.Y.)	35926021	Science	2022 Aug 5	https://www.ncbi.nlm.nih.gov/pubmed/35926021
Improved GPCR ligands from nanobody tethering.	Cheloha RW, Fischer FA, Woodham AW, Daley E, Suminski N, Gardella TJ, Ploegh HL	Nature communications	32350260	Nat Commun	2020 Apr 29	https://www.ncbi.nlm.nih.gov/pubmed/32350260
Nanobody-based CAR NK cells for possible immunotherapy of MICA(+) tumors.	Verhaar ER, van Keizerswaard WJC, Knoflook A, Balligand T, Ploegh HL	PNAS nexus	38756234	PNAS Nexus	2024 May	https://www.ncbi.nlm.nih.gov/pubmed/38756234
MICA-specific nanobodies for diagnosis and immunotherapy of MICA(+) tumors.	Verhaar ER, Knoflook A, Pishesha N, Liu X, van Keizerswaard WJC, Wucherpfennig KW, Ploegh HL	Frontiers in immunology	38550583	Front Immunol	2024	https://www.ncbi.nlm.nih.gov/pubmed/38550583
Bi-specific antibody engagers for cancer immunotherapy.	Ploegh H, Liu X, Le Gall C, Alexander R, Borgman E, Balligand T	Research square	39149504	Res Sq	2024 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/39149504
Asparaginyl Ligase-Catalyzed One-Step Cell Surface Modification of Red Blood Cells.	Harmand TJ, Pishesha N, Rehm FBH, Ma W, Pinney WB, Xie YJ, Ploegh HL	ACS chemical biology	34129316	ACS Chem Biol	2021 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/34129316
An armed anti-immunoglobulin light chain nanobody protects mice against influenza A and B infections.	Liu X, Balligand T, Carpenet C, Ploegh HL	Science immunology	37352373	Sci Immunol	2023 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/37352373
A monoclonal antibody that recognizes a unique 13-residue epitope in the cytoplasmic tail of HLA-E.	Verhaar ER, Gan J, Buhl S, Li Z, Horowitz A, Ploegh HL	Molecular immunology	38901180	Mol Immunol	2024 Aug	https://www.ncbi.nlm.nih.gov/pubmed/38901180
Surviving COVID-19: A disease tolerance perspective.	Ayres JS	Science advances	32494691	Sci Adv	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/32494691
Microbiota Metabolites in Health and Disease.	McCarville JL, Chen GY, Cuevas VD, Troha K, Ayres JS	Annual review of immunology	32340573	Annu Rev Immunol	2020 Apr 26	https://www.ncbi.nlm.nih.gov/pubmed/32340573
Beyond tug-of-war: Iron metabolism in cooperative host-microbe interactions.	Chen GY, Ayres JS	PLoS pathogens	32785251	PLoS Pathog	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32785251
Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen.	Chen GY, Thorup NR, Miller AJ, Li YC, Ayres JS	Science advances	37352357	Sci Adv	2023 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/37352357
Immunometabolism of infections.	Ayres JS	Nature reviews. Immunology	31892735	Nat Rev Immunol	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/31892735
Metabolic Adaptations to Infections at the Organismal Level.	Troha K, Ayres JS	Trends in immunology	31959515	Trends Immunol	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/31959515
CD4+ T cells regulate sickness-induced anorexia and fat wasting during a chronic parasitic infection.	Redford SE, Varanasi SK, Sanchez KK, Thorup NR, Ayres JS	Cell reports	37490905	Cell Rep	2023 Aug 29	https://www.ncbi.nlm.nih.gov/pubmed/37490905
Fluoxetine promotes immunometabolic defenses to mediate host-pathogen cooperation during sepsis.	Gallant RM, Snyder JM, Ayres JS	bioRxiv : the preprint server for biology	38013994	bioRxiv	2023 Nov 18	https://www.ncbi.nlm.nih.gov/pubmed/38013994
Age-dependent roles of cardiac remodeling in sepsis defense and pathogenesis.	Sanchez KK, McCarville JL, Stengel SJ, Snyder JM, Williams AE, Ayres JS	bioRxiv : the preprint server for biology	36993409	bioRxiv	2023 Mar 15	https://www.ncbi.nlm.nih.gov/pubmed/36993409
Adipose triglyceride lipase mediates lipolysis and lipid mobilization in response to iron-mediated negative energy balance.	Romero AR, Mu A, Ayres JS	iScience	35265813	iScience	2022 Mar 18	https://www.ncbi.nlm.nih.gov/pubmed/35265813
Chronic Leptin Deficiency Improves Tolerance of Physiological Damage and Host-Pathogen Cooperation during Yersinia pseudotuberculosis Infection.	Sanchez KK, Troha K, Mu A, Redford SE, McCarville JL, Insenga A, Stengel S, Lee YM, Ayres JS	Infection and immunity	35924898	Infect Immun	2022 Sep 15	https://www.ncbi.nlm.nih.gov/pubmed/35924898
The Biology of Physiological Health.	Ayres JS	Cell	32302569	Cell	2020 Apr 16	https://www.ncbi.nlm.nih.gov/pubmed/32302569
Cooperative defenses during enteropathogenic infection.	Troha K, Ayres JS	Current opinion in microbiology	34847524	Curr Opin Microbiol	2022 Feb	https://www.ncbi.nlm.nih.gov/pubmed/34847524
Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen.	Chen GY, Thorup NR, Miller AJ, Li YC, Ayres JS	bioRxiv : the preprint server for biology	36711884	bioRxiv	2023 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/36711884
Fluoxetine promotes IL-10-dependent metabolic defenses to protect from sepsis-induced lethality.	Gallant RM, Sanchez KK, Joulia E, Snyder JM, Metallo CM, Ayres JS	Science advances	39951524	Sci Adv	2025 Feb 14	https://www.ncbi.nlm.nih.gov/pubmed/39951524
Universal recording of immune cell interactions in vivo.	Nakandakari-Higa S, Walker S, Canesso MCC, van der Heide V, Chudnovskiy A, Kim DY, Jacobsen JT, Parsa R, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Kamphorst AO, Pritykin Y, Victora GD	Nature	38448581	Nature	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38448581
Opposing effects of pre-existing antibody and memory T cell help on the dynamics of recall germinal centers.	Schiepers A, Van't Wout MFL, Hobbs A, Mesin L, Victora GD	Immunity	38838672	Immunity	2024 Jul 9	https://www.ncbi.nlm.nih.gov/pubmed/38838672
Expression of Foxp3 by T follicular helper cells in end-stage germinal centers.	Jacobsen JT, Hu W, R Castro TB, Solem S, Galante A, Lin Z, Allon SJ, Mesin L, Bilate AM, Schiepers A, Shalek AK, Rudensky AY, Victora GD	Science (New York, N.Y.)	34437125	Science	2021 Jul 16	https://www.ncbi.nlm.nih.gov/pubmed/34437125
Clonal replacement sustains long-lived germinal centers primed by respiratory viruses.	de Carvalho RVH, Ersching J, Barbulescu A, Hobbs A, Castro TBR, Mesin L, Jacobsen JT, Phillips BK, Hoffmann HH, Parsa R, Canesso MCC, Nowosad CR, Feng A, Leist SR, Baric RS, Yang E, Utz PJ, Victora GD	Cell	36565697	Cell	2023 Jan 5	https://www.ncbi.nlm.nih.gov/pubmed/36565697
Restricted Clonality and Limited Germinal Center Reentry Characterize Memory B Cell Reactivation by Boosting.	Mesin L, Schiepers A, Ersching J, Barbulescu A, Cavazzoni CB, Angelini A, Okada T, Kurosaki T, Victora GD	Cell	31866068	Cell	2020 Jan 9	https://www.ncbi.nlm.nih.gov/pubmed/31866068
Monitoring the Interaction Between Dendritic Cells and T Cells In Vivo with LIPSTIC.	Pasqual G, Chudnovskiy A, Victora GD	Methods in molecular biology (Clifton, N.J.)	36905509	Methods Mol Biol	2023	https://www.ncbi.nlm.nih.gov/pubmed/36905509
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells.	Pae J, Ersching J, Castro TBR, Schips M, Mesin L, Allon SJ, Ordovas-Montanes J, Mlynarczyk C, Melnick A, Efeyan A, Shalek AK, Meyer-Hermann M, Victora GD	The Journal of experimental medicine	33332554	J Exp Med	2021 Apr 5	https://www.ncbi.nlm.nih.gov/pubmed/33332554
Tunable dynamics of B cell selection in gut germinal centres.	Nowosad CR, Mesin L, Castro TBR, Wichmann C, Donaldson GP, Araki T, Schiepers A, Lockhart AAK, Bilate AM, Mucida D, Victora GD	Nature	33116306	Nature	2020 Dec	https://www.ncbi.nlm.nih.gov/pubmed/33116306
Studying interactions between dendritic cells and T cells in vivo.	Chudnovskiy A, Pasqual G, Victora GD	Current opinion in immunology	30884422	Curr Opin Immunol	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/30884422
Molecular fate-mapping of serum antibody responses to repeat immunization.	Schiepers A, van 't Wout MFL, Greaney AJ, Zang T, Muramatsu H, Lin PJC, Tam YK, Mesin L, Starr TN, Bieniasz PD, Pardi N, Bloom JD, Victora GD	Nature	36646114	Nature	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36646114
Opposing effects of pre-existing antibody and memory T cell help on the dynamics of recall germinal centers.	Schiepers A, van 't Wout MFL, Hobbs A, Mesin L, Victora GD	bioRxiv : the preprint server for biology	38168231	bioRxiv	2023 Dec 15	https://www.ncbi.nlm.nih.gov/pubmed/38168231
Preconceptual Zika virus asymptomatic infection protects against secondary prenatal infection.	Turner LH, Kinder JM, Wilburn A, D'Mello RJ, Braunlin MR, Jiang TT, Pham G, Way SS	PLoS pathogens	29145516	PLoS Pathog	2017 Nov	https://www.ncbi.nlm.nih.gov/pubmed/29145516
Intestinal epithelial HDAC3 and MHC class II coordinate microbiota-specific immunity.	Eshleman EM, Shao TY, Woo V, Rice T, Engleman L, Didriksen BJ, Whitt J, Haslam DB, Way SS, Alenghat T	The Journal of clinical investigation	36602872	J Clin Invest	2023 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/36602872
Kruppel-like factor 2+ CD4 T cells avert microbiota-induced intestinal inflammation.	Shao TY, Jiang TT, Stevens J, Russi AE, Troutman TD, Bernieh A, Pham G, Erickson JJ, Eshleman EM, Alenghat T, Jameson SC, Hogquist KA, Weaver CT, Haslam DB, Deshmukh H, Way SS	Cell reports	37889750	Cell Rep	2023 Nov 28	https://www.ncbi.nlm.nih.gov/pubmed/37889750
Mouse models of neutropenia reveal progenitor-stage-specific defects.	Muench DE, Olsson A, Ferchen K, Pham G, Serafin RA, Chutipongtanate S, Dwivedi P, Song B, Hay S, Chetal K, Trump-Durbin LR, Mookerjee-Basu J, Zhang K, Yu JC, Lutzko C, Myers KC, Nazor KL, Greis KD, Kappes DJ, Way SS, Salomonis N, Grimes HL	Nature	32494068	Nature	2020 Jun	https://www.ncbi.nlm.nih.gov/pubmed/32494068
In situ mapping identifies distinct vascular niches for myelopoiesis.	Zhang J, Wu Q, Johnson CB, Pham G, Kinder JM, Olsson A, Slaughter A, May M, Weinhaus B, D'Alessandro A, Engel JD, Jiang JX, Kofron JM, Huang LF, Prasath VBS, Way SS, Salomonis N, Grimes HL, Lucas D	Nature	33568812	Nature	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/33568812
Immunological implications of pregnancy-induced microchimerism.	Kinder JM, Stelzer IA, Arck PC, Way SS	Nature reviews. Immunology	28480895	Nat Rev Immunol	2017 Aug	https://www.ncbi.nlm.nih.gov/pubmed/28480895
Fungus Among Us: The Frenemies Within.	Aggor FEY, Way SS, Gaffen SL	Trends in immunology	31053496	Trends Immunol	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31053496
Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria.	Jiang TT, Shao TY, Ang WXG, Kinder JM, Turner LH, Pham G, Whitt J, Alenghat T, Way SS	Cell host & microbe	29174402	Cell Host Microbe	2017 Dec 13	https://www.ncbi.nlm.nih.gov/pubmed/29174402
Systematic reconstruction of an effector-gene network reveals determinants of Salmonella cellular and tissue tropism.	Chen D, Burford WB, Pham G, Zhang L, Alto LT, Ertelt JM, Winter MG, Winter SE, Way SS, Alto NM	Cell host & microbe	34536347	Cell Host Microbe	2021 Oct 13	https://www.ncbi.nlm.nih.gov/pubmed/34536347
Pregnancy enables antibody protection against intracellular infection.	Erickson JJ, Archer-Hartmann S, Yarawsky AE, Miller JLC, Seveau S, Shao TY, Severance AL, Miller-Handley H, Wu Y, Pham G, Wasik BR, Parrish CR, Hu YC, Lau JTY, Azadi P, Herr AB, Way SS	Nature	35676476	Nature	2022 Jun	https://www.ncbi.nlm.nih.gov/pubmed/35676476
Friendly fungi: symbiosis with commensal Candida albicans.	Shao TY, Haslam DB, Bennett RJ, Way SS	Trends in immunology	35961916	Trends Immunol	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/35961916
Immune suppression sustained allograft acceptance requires PD1 inhibition of CD8+ T cells.	Miller-Handley H, Harper G, Pham G, Turner LH, Shao TY, Russi AE, Erickson JJ, Ford ML, Araki K, Way SS	Journal of immunology (Baltimore, Md. : 1950)	40073258	J Immunol	2025 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/40073258
TCR Affinity Biases Th Cell Differentiation by Regulating CD25, Eef1e1, and Gbp2.	Kotov DI, Mitchell JS, Pengo T, Ruedl C, Way SS, Langlois RA, Fife BT, Jenkins MK	Journal of immunology (Baltimore, Md. : 1950)	30858199	J Immunol	2019 May 1	https://www.ncbi.nlm.nih.gov/pubmed/30858199
Declining responsiveness to influenza vaccination with progression of human pregnancy.	Schlaudecker EP, Ambroggio L, McNeal MM, Finkelman FD, Way SS	Vaccine	29941326	Vaccine	2018 Jul 25	https://www.ncbi.nlm.nih.gov/pubmed/29941326
Preconceptual Priming Overrides Susceptibility to Escherichia coli Systemic Infection during Pregnancy.	Prasanphanich NS, Gregory EJ, Erickson JJ, Miller-Handley H, Kinder JM, Way SS	mBio	33622714	mBio	2021 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/33622714
Tacrolimus exposure windows responsible for Listeria monocytogenes infection susceptibility.	Miller-Handley H, Erickson JJ, Gregory EJ, Prasanphanich NS, Shao TY, Way SS	Transplant infectious disease : an official journal of the Transplantation Society	34057792	Transpl Infect Dis	2021 Aug	https://www.ncbi.nlm.nih.gov/pubmed/34057792
Epidemiology of Pregnancy Complications Through the Lens of Immunological Memory.	Gregory EJ, Liu J, Miller-Handley H, Kinder JM, Way SS	Frontiers in immunology	34248991	Front Immunol	2021	https://www.ncbi.nlm.nih.gov/pubmed/34248991
Persistent Zika Virus Clinical Susceptibility despite Reduced Viral Burden in Mice with Expanded Virus-Specific CD8(+) T Cells Primed by Recombinant Listeria monocytogenes.	Burg AR, Erickson JJ, Turner LH, Pham G, Kinder JM, Way SS	Journal of immunology (Baltimore, Md. : 1950)	32522837	J Immunol	2020 Jul 15	https://www.ncbi.nlm.nih.gov/pubmed/32522837
Differential IL-2 expression defines developmental fates of follicular versus nonfollicular helper T cells.	DiToro D, Winstead CJ, Pham D, Witte S, Andargachew R, Singer JR, Wilson CG, Zindl CL, Luther RJ, Silberger DJ, Weaver BT, Kolawole EM, Martinez RJ, Turner H, Hatton RD, Moon JJ, Way SS, Evavold BD, Weaver CT	Science (New York, N.Y.)	30213884	Science	2018 Sep 14	https://www.ncbi.nlm.nih.gov/pubmed/30213884
Immunology of the Uterine and Vaginal Mucosae.	Zhou JZ, Way SS, Chen K	Trends in immunology	29433961	Trends Immunol	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29433961
Maternal-fetal conflict averted by progesterone- induced FOXP3+ regulatory T cells.	Severance AL, Kinder JM, Xin L, Burg AR, Shao TY, Pham G, Tilburgs T, Goodman WA, Mesiano S, Way SS	iScience	35637736	iScience	2022 Jun 17	https://www.ncbi.nlm.nih.gov/pubmed/35637736
The induction of preterm labor in rhesus macaques is determined by the strength of immune response to intrauterine infection.	Cappelletti M, Presicce P, Feiyang M, Senthamaraikannan P, Miller LA, Pellegrini M, Sim MS, Jobe AH, Divanovic S, Way SS, Chougnet CA, Kallapur SG	PLoS biology	34495952	PLoS Biol	2021 Sep	https://www.ncbi.nlm.nih.gov/pubmed/34495952
Immunological Basis for Recurrent Fetal Loss and Pregnancy Complications.	Deshmukh H, Way SS	Annual review of pathology	30183507	Annu Rev Pathol	2019 Jan 24	https://www.ncbi.nlm.nih.gov/pubmed/30183507
A disconnect between precursor frequency, expansion potential, and site-specific CD4+ T cell responses in aged mice.	Deshpande NR, Uhrlaub JL, Way SS, Nikolich-Žugich J, Kuhns MS	PloS one	29864157	PLoS One	2018	https://www.ncbi.nlm.nih.gov/pubmed/29864157
IL-17-producing γδ T cells protect against Clostridium difficile infection.	Chen YS, Chen IB, Pham G, Shao TY, Bangar H, Way SS, Haslam DB	The Journal of clinical investigation	31990686	J Clin Invest	2020 May 1	https://www.ncbi.nlm.nih.gov/pubmed/31990686
Vaccination strategies to enhance immunity in neonates.	Kollmann TR, Marchant A, Way SS	Science (New York, N.Y.)	32381718	Science	2020 May 8	https://www.ncbi.nlm.nih.gov/pubmed/32381718
CD8(+) T Cell Functional Exhaustion Overrides Pregnancy-Induced Fetal Antigen Alloimmunization.	Kinder JM, Turner LH, Stelzer IA, Miller-Handley H, Burg A, Shao TY, Pham G, Way SS	Cell reports	32579916	Cell Rep	2020 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/32579916
Commensal Candida albicans Positively Calibrates Systemic Th17 Immunological Responses.	Shao TY, Ang WXG, Jiang TT, Huang FS, Andersen H, Kinder JM, Pham G, Burg AR, Ruff B, Gonzalez T, Khurana Hershey GK, Haslam DB, Way SS	Cell host & microbe	30870622	Cell Host Microbe	2019 Mar 13	https://www.ncbi.nlm.nih.gov/pubmed/30870622
Reproductive outcomes after pregnancy-induced displacement of preexisting microchimeric cells.	Shao TY, Kinder JM, Harper G, Pham G, Peng Y, Liu J, Gregory EJ, Sherman BE, Wu Y, Iten AE, Hu YC, Russi AE, Erickson JJ, Miller-Handley H, Way SS	Science (New York, N.Y.)	37733857	Science	2023 Sep 22	https://www.ncbi.nlm.nih.gov/pubmed/37733857
Candida albicans oscillating UME6 expression during intestinal colonization primes systemic Th17 protective immunity.	Shao TY, Kakade P, Witchley JN, Frazer C, Murray KL, Ene IV, Haslam DB, Hagan T, Noble SM, Bennett RJ, Way SS	Cell reports	35584674	Cell Rep	2022 May 17	https://www.ncbi.nlm.nih.gov/pubmed/35584674
Maternal Vaccination to Prevent Adverse Pregnancy Outcomes: An Underutilized Molecular Immunological Intervention?	Giles ML, Way SS, Marchant A, Aghaepour N, James T, Schaltz-Buchholzer F, Zazara D, Arck P, Kollmann TR	Journal of molecular biology	37080422	J Mol Biol	2023 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/37080422
Mycobacterium tuberculosis-specific CD4+ and CD8+ T cells differ in their capacity to recognize infected macrophages.	Yang JD, Mott D, Sutiwisesak R, Lu YJ, Raso F, Stowell B, Babunovic GH, Lee J, Carpenter SM, Way SS, Fortune SM, Behar SM	PLoS pathogens	29782535	PLoS Pathog	2018 Feb	https://www.ncbi.nlm.nih.gov/pubmed/29782535
Immunology of Uterine and Vaginal Mucosae: (Trends in Immunology 39, 302-314, 2018).	Zhou JZ, Way SS, Chen K	Trends in immunology	29530651	Trends Immunol	2018 Apr	https://www.ncbi.nlm.nih.gov/pubmed/29530651
Resilient anatomy and local plasticity of naive and stress haematopoiesis.	Wu Q, Zhang J, Kumar S, Shen S, Kincaid M, Johnson CB, Zhang YS, Turcotte R, Alt C, Ito K, Homan S, Sherman BE, Shao TY, Slaughter A, Weinhaus B, Song B, Filippi MD, Grimes HL, Lin CP, Ito K, Way SS, Kofron JM, Lucas D	Nature	38509363	Nature	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38509363
Human CTP synthase filament structure reveals the active enzyme conformation.	Lynch EM, Hicks DR, Shepherd M, Endrizzi JA, Maker A, Hansen JM, Barry RM, Gitai Z, Baldwin EP, Kollman JM	Nature structural & molecular biology	28459447	Nat Struct Mol Biol	2017 Jun	https://www.ncbi.nlm.nih.gov/pubmed/28459447
Global and gene-specific translational regulation in Escherichia coli across different conditions.	Zhang D, Li SH, King CG, Wingreen NS, Gitai Z, Li Z	PLoS computational biology	36264977	PLoS Comput Biol	2022 Oct	https://www.ncbi.nlm.nih.gov/pubmed/36264977
Pseudomonas aeruginosa distinguishes surfaces by stiffness using retraction of type IV pili.	Koch MD, Black ME, Han E, Shaevitz JW, Gitai Z	Proceedings of the National Academy of Sciences of the United States of America	35561220	Proc Natl Acad Sci U S A	2022 May 17	https://www.ncbi.nlm.nih.gov/pubmed/35561220
Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus.	Fröhlich KS, Förstner KU, Gitai Z	Nucleic acids research	30165530	Nucleic Acids Res	2018 Nov 16	https://www.ncbi.nlm.nih.gov/pubmed/30165530
Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink.	Wilson MZ, Wang R, Gitai Z, Seyedsayamdost MR	Proceedings of the National Academy of Sciences of the United States of America	26802120	Proc Natl Acad Sci U S A	2016 Feb 9	https://www.ncbi.nlm.nih.gov/pubmed/26802120
Pseudomonas aeruginosa detachment from surfaces via a self-made small molecule.	Scheffler RJ, Sugimoto Y, Bratton BP, Ellison CK, Koch MD, Donia MS, Gitai Z	The Journal of biological chemistry	33450229	J Biol Chem	2021 Jan-Jun	https://www.ncbi.nlm.nih.gov/pubmed/33450229
Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili.	Koch MD, Fei C, Wingreen NS, Shaevitz JW, Gitai Z	Proceedings of the National Academy of Sciences of the United States of America	33593905	Proc Natl Acad Sci U S A	2021 Feb 23	https://www.ncbi.nlm.nih.gov/pubmed/33593905
Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection.	Wang B, Lin AE, Yuan J, Novak KE, Koch MD, Wingreen NS, Adamson B, Gitai Z	Nature microbiology	37653008	Nat Microbiol	2023 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37653008
A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.	Bartlett TM, Bratton BP, Duvshani A, Miguel A, Sheng Y, Martin NR, Nguyen JP, Persat A, Desmarais SM, VanNieuwenhze MS, Huang KC, Zhu J, Shaevitz JW, Gitai Z	Cell	28086090	Cell	2017 Jan 12	https://www.ncbi.nlm.nih.gov/pubmed/28086090
A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa.	Inclan YF, Persat A, Greninger A, Von Dollen J, Johnson J, Krogan N, Gitai Z, Engel JN	Molecular microbiology	27145134	Mol Microbiol	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27145134
Modeling microbial metabolic trade-offs in a chemostat.	Li Z, Liu B, Li SH, King CG, Gitai Z, Wingreen NS	PLoS computational biology	32857772	PLoS Comput Biol	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32857772
A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance.	Martin JK 2nd, Sheehan JP, Bratton BP, Moore GM, Mateus A, Li SH, Kim H, Rabinowitz JD, Typas A, Savitski MM, Wilson MZ, Gitai Z	Cell	32497502	Cell	2020 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/32497502
How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction.	Shi H, Bratton BP, Gitai Z, Huang KC	Cell	29522748	Cell	2018 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/29522748
Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma.	Ducker GS, Ghergurovich JM, Mainolfi N, Suri V, Jeong SK, Hsin-Jung Li S, Friedman A, Manfredi MG, Gitai Z, Kim H, Rabinowitz JD	Proceedings of the National Academy of Sciences of the United States of America	29073064	Proc Natl Acad Sci U S A	2017 Oct 24	https://www.ncbi.nlm.nih.gov/pubmed/29073064
CrvA and CrvB form a curvature-inducing module sufficient to induce cell-shape complexity in Gram-negative bacteria.	Martin NR, Blackman E, Bratton BP, Chase KJ, Bartlett TM, Gitai Z	Nature microbiology	34183815	Nat Microbiol	2021 Jul	https://www.ncbi.nlm.nih.gov/pubmed/34183815
Subcellular localization of type IV pili regulates bacterial multicellular development.	Ellison CK, Fei C, Dalia TN, Wingreen NS, Dalia AB, Shaevitz JW, Gitai Z	Nature communications	36284096	Nat Commun	2022 Oct 25	https://www.ncbi.nlm.nih.gov/pubmed/36284096
Bacterial viability in the built environment of the home.	Xie J, Acosta EM, Gitai Z	PloS one	37939059	PLoS One	2023	https://www.ncbi.nlm.nih.gov/pubmed/37939059
Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.	Li SH, Li Z, Park JO, King CG, Rabinowitz JD, Wingreen NS, Gitai Z	Nature microbiology	30038306	Nat Microbiol	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/30038306
Surface association sensitizes Pseudomonas aeruginosa to quorum sensing.	Chuang SK, Vrla GD, Fröhlich KS, Gitai Z	Nature communications	31511506	Nat Commun	2019 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/31511506
Type IV pili mechanochemically regulate virulence factors in Pseudomonas aeruginosa.	Persat A, Inclan YF, Engel JN, Stone HA, Gitai Z	Proceedings of the National Academy of Sciences of the United States of America	26041805	Proc Natl Acad Sci U S A	2015 Jun 16	https://www.ncbi.nlm.nih.gov/pubmed/26041805
The mechanical world of bacteria.	Persat A, Nadell CD, Kim MK, Ingremeau F, Siryaporn A, Drescher K, Wingreen NS, Bassler BL, Gitai Z, Stone HA	Cell	26000479	Cell	2015 May 21	https://www.ncbi.nlm.nih.gov/pubmed/26000479
Cytotoxic alkyl-quinolones mediate surface-induced virulence in Pseudomonas aeruginosa.	Vrla GD, Esposito M, Zhang C, Kang Y, Seyedsayamdost MR, Gitai Z	PLoS pathogens	32925969	PLoS Pathog	2020 Sep	https://www.ncbi.nlm.nih.gov/pubmed/32925969
Colonization, competition, and dispersal of pathogens in fluid flow networks.	Siryaporn A, Kim MK, Shen Y, Stone HA, Gitai Z	Current biology : CB	25843031	Curr Biol	2015 May 4	https://www.ncbi.nlm.nih.gov/pubmed/25843031
The curved shape of Caulobacter crescentus enhances surface colonization in flow.	Persat A, Stone HA, Gitai Z	Nature communications	24806788	Nat Commun	2014 May 8	https://www.ncbi.nlm.nih.gov/pubmed/24806788
Pseudomonas aeruginosa clinical blood isolates display significant phenotypic variability.	Scheffler RJ, Bratton BP, Gitai Z	PloS one	35793311	PLoS One	2022	https://www.ncbi.nlm.nih.gov/pubmed/35793311
Acinetobacter baylyi regulates type IV pilus synthesis by employing two extension motors and a motor protein inhibitor.	Ellison CK, Dalia TN, Klancher CA, Shaevitz JW, Gitai Z, Dalia AB	Nature communications	34145281	Nat Commun	2021 Jun 18	https://www.ncbi.nlm.nih.gov/pubmed/34145281
Algal p-coumaric acid induces oxidative stress and siderophore biosynthesis in the bacterial symbiont Phaeobacter inhibens.	Wang R, Gallant É, Wilson MZ, Wu Y, Li A, Gitai Z, Seyedsayamdost MR	Cell chemical biology	34437838	Cell Chem Biol	2022 Apr 21	https://www.ncbi.nlm.nih.gov/pubmed/34437838
Mechanical Genomic Studies Reveal the Role of d-Alanine Metabolism in Pseudomonas aeruginosa Cell Stiffness.	Trivedi RR, Crooks JA, Auer GK, Pendry J, Foik IP, Siryaporn A, Abbott NL, Gitai Z, Weibel DB	mBio	30206169	mBio	2018 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/30206169
The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane.	Liu GS, Bratton BP, Gitai Z, Shaevitz JW	PloS one	28977034	PLoS One	2017	https://www.ncbi.nlm.nih.gov/pubmed/28977034
Bacterial DNA on the skin surface overrepresents the viable skin microbiome.	Acosta EM, Little KA, Bratton BP, Lopez JG, Mao X, Payne AS, Donia M, Devenport D, Gitai Z	eLife	37389570	Elife	2023 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/37389570
Microfluidic-based transcriptomics reveal force-independent bacterial rheosensing.	Sanfilippo JE, Lorestani A, Koch MD, Bratton BP, Siryaporn A, Stone HA, Gitai Z	Nature microbiology	31086313	Nat Microbiol	2019 Aug	https://www.ncbi.nlm.nih.gov/pubmed/31086313
Light-based control of metabolic flux through assembly of synthetic organelles.	Zhao EM, Suek N, Wilson MZ, Dine E, Pannucci NL, Gitai Z, Avalos JL, Toettcher JE	Nature chemical biology	31086330	Nat Chem Biol	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31086330
Both clinical and environmental Caulobacter species are virulent in the Galleria mellonella infection model.	Moore GM, Gitai Z	PloS one	32163465	PLoS One	2020	https://www.ncbi.nlm.nih.gov/pubmed/32163465
Ribosome Rescue Inhibitors Kill Actively Growing and Nonreplicating Persister Mycobacterium tuberculosis Cells.	Alumasa JN, Manzanillo PS, Peterson ND, Lundrigan T, Baughn AD, Cox JS, Keiler KC	ACS infectious diseases	28762275	ACS Infect Dis	2017 Sep 8	https://www.ncbi.nlm.nih.gov/pubmed/28762275
Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages.	Chin J, Abeydeera N, Repasy T, Rivera-Lugo R, Mitchell G, Nguyen VQ, Zheng W, Richards A, Swaney DL, Krogan NJ, Ernst JD, Cox JS, Budzik JM	bioRxiv : the preprint server for biology	39763950	bioRxiv	2024 Dec 16	https://www.ncbi.nlm.nih.gov/pubmed/39763950
Cas9(+) conditionally-immortalized macrophages as a tool for bacterial pathogenesis and beyond.	Roberts AW, Popov LM, Mitchell G, Ching KL, Licht DJ, Golovkine G, Barton GM, Cox JS	eLife	31204998	Elife	2019 Jun 17	https://www.ncbi.nlm.nih.gov/pubmed/31204998
An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses.	Penn BH, Netter Z, Johnson JR, Von Dollen J, Jang GM, Johnson T, Ohol YM, Maher C, Bell SL, Geiger K, Golovkine G, Du X, Choi A, Parry T, Mohapatra BC, Storck MD, Band H, Chen C, Jäger S, Shales M, Portnoy DA, Hernandez R, Coscoy L, Cox JS, Krogan NJ	Molecular cell	30118682	Mol Cell	2018 Aug 16	https://www.ncbi.nlm.nih.gov/pubmed/30118682
Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages.	Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS	eLife	31951200	Elife	2020 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/31951200
TRIM14 Is a Key Regulator of the Type I IFN Response during Mycobacterium tuberculosis Infection.	Hoffpauir CT, Bell SL, West KO, Jing T, Wagner AR, Torres-Odio S, Cox JS, West AP, Li P, Patrick KL, Watson RO	Journal of immunology (Baltimore, Md. : 1950)	32404352	J Immunol	2020 Jul 1	https://www.ncbi.nlm.nih.gov/pubmed/32404352
Neuromodulation of Courtship Drive through Tyramine-Responsive Neurons in the Drosophila Brain.	Huang J, Liu W, Qi YX, Luo J, Montell C	Current biology : CB	27498566	Curr Biol	2016 Sep 12	https://www.ncbi.nlm.nih.gov/pubmed/27498566
Neuropeptide F regulates courtship in Drosophila through a male-specific neuronal circuit.	Liu W, Ganguly A, Huang J, Wang Y, Ni JD, Gurav AS, Aguilar MA, Montell C	eLife	31403399	Elife	2019 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/31403399
The Role of Y Chromosome Genes in Male Fertility in Drosophila melanogaster.	Zhang J, Luo J, Chen J, Dai J, Montell C	Genetics	32404399	Genetics	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32404399
Elimination of vision-guided target attraction in Aedes aegypti using CRISPR.	Zhan Y, Alonso San Alberto D, Rusch C, Riffell JA, Montell C	Current biology : CB	34331858	Curr Biol	2021 Sep 27	https://www.ncbi.nlm.nih.gov/pubmed/34331858
Suppression of female fertility in Aedes aegypti with a CRISPR-targeted male-sterile mutation.	Chen J, Luo J, Wang Y, Gurav AS, Li M, Akbari OS, Montell C	Proceedings of the National Academy of Sciences of the United States of America	34031258	Proc Natl Acad Sci U S A	2021 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/34031258
Unconventional Roles of Opsins.	Leung NY, Montell C	Annual review of cell and developmental biology	28598695	Annu Rev Cell Dev Biol	2017 Oct 6	https://www.ncbi.nlm.nih.gov/pubmed/28598695
Differential regulation of the Drosophila sleep homeostat by circadian and arousal inputs.	Ni JD, Gurav AS, Liu W, Ogunmowo TH, Hackbart H, Elsheikh A, Verdegaal AA, Montell C	eLife	30719975	Elife	2019 Feb 5	https://www.ncbi.nlm.nih.gov/pubmed/30719975
A Temperature Gradient Assay to Determine Thermal Preferences of Drosophila Larvae.	Liu J, Sokabe T, Montell C	Journal of visualized experiments : JoVE	29985331	J Vis Exp	2018 Jun 25	https://www.ncbi.nlm.nih.gov/pubmed/29985331
Pseudotyping of HIV-1 with Human T-Lymphotropic Virus 1 (HTLV-1) Envelope Glycoprotein during HIV-1-HTLV-1 Coinfection Facilitates Direct HIV-1 Infection of Female Genital Epithelial Cells: Implications for Sexual Transmission of HIV-1.	Tang Y, George AM, Petrechko O, Nouvet FJ, Sweet SD, Tanaka Y, Imbiakha BS, Jiang G, Gao W, Anastos K, Hildreth JEK	mSphere	29624497	mSphere	2018 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/29624497
Reduced removal of waste products from energy metabolism takes center stage in human brain aging.	Mangia S, DiNuzzo M, Ponticorvo S, Dienel GA, Behar KL, Benveniste H, Hyder F, Giove F, Herculano-Houzel S, Petroff OA, Eberly LE, Filip P, Michaeli S, Rothman DL	Scientific reports	40057554	Sci Rep	2025 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/40057554
Cloud Computing to Enable Wearable-Driven Longitudinal Hemodynamic Maps.	Tanade C, Rakestraw E, Ladd W, Draeger E, Randles A	International Conference for High Performance Computing, Networking, Storage and Analysis : [proceedings]. SC (Conference : Supercomputing)	38939612	Int Conf High Perform Comput Netw Storage Anal	2023 Nov	https://www.ncbi.nlm.nih.gov/pubmed/38939612
Optimizing Temporal Waveform Analysis: A Novel Pipeline for Efficient Characterization of Left Coronary Artery Velocity Profiles.	Geddes JR, Randles A	ArXiv	38410654	ArXiv	2024 Feb 15	https://www.ncbi.nlm.nih.gov/pubmed/38410654
Modeling the effect of patient size on cerebral perfusion during veno-arterial extracorporeal membrane oxygenation.	Feiger B, Jensen CW, Bryner BS, Segars WP, Randles A	Perfusion	37395266	Perfusion	2024 Oct	https://www.ncbi.nlm.nih.gov/pubmed/37395266
Investigating the Influence of Heterogeneity Within Cell Types on Microvessel Network Transport.	Nan J, Roychowdhury S, Randles A	Cellular and molecular bioengineering	38099216	Cell Mol Bioeng	2023 Dec	https://www.ncbi.nlm.nih.gov/pubmed/38099216
Neuronal activation of G(αq) EGL-30/GNAQ late in life rejuvenates cognition across species.	Stevenson ME, Bieri G, Kaletsky R, St Ange J, Remesal L, Pratt KJB, Zhou S, Weng Y, Murphy CT, Villeda SA	Cell reports	37713310	Cell Rep	2023 Sep 26	https://www.ncbi.nlm.nih.gov/pubmed/37713310
CeLab, a microfluidic platform for the study of life history traits, reveals metformin and SGK-1 regulation of longevity and reproductive span.	Sohrabi S, Cota V, Murphy CT	Lab on a chip	37221962	Lab Chip	2023 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/37221962
Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer.	Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlov I, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, Amos CI	Nature genetics	35915169	Nat Genet	2022 Aug	https://www.ncbi.nlm.nih.gov/pubmed/35915169
Life, the genome and everything.	Rosenberg SM	Journal of bacteriology	38018999	J Bacteriol	2023 Dec 19	https://www.ncbi.nlm.nih.gov/pubmed/38018999
Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies.	Li Y, Xiao X, Li J, Han Y, Cheng C, Fernandes GF, Slewitzke SE, Rosenberg SM, Zhu M, Byun J, Bossé Y, McKay JD, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeböller H, Wichmann HE, Christiani DC, Rennert G, Arnold SM, Goodman GE, Field JK, Davies MPA, Shete S, Marchand LL, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Sun R, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Cox A, Hong YC, Lazarus P, Schabath MB, Aldrich MC, Schwartz AG, Gorlov I, Purrington KS, Yang P, Liu Y, Bailey-Wilson JE, Pinney SM, Mandal D, Willey JC, Gaba C, Brennan P, Xia J, Shen H, Amos CI	Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology	38180474	Cancer Epidemiol Biomarkers Prev	2024 Mar 1	https://www.ncbi.nlm.nih.gov/pubmed/38180474
Rapid profiling of DNA replication dynamics using mass spectrometry-based analysis of nascent DNA.	Ashour ME, Byrum AK, Meroni A, Xia J, Singh S, Galletto R, Rosenberg SM, Vindigni A, Mosammaparast N	The Journal of cell biology	36795402	J Cell Biol	2023 Apr 3	https://www.ncbi.nlm.nih.gov/pubmed/36795402
Genomic mapping of DNA-repair reaction intermediates in living cells with engineered DNA structure-trap proteins.	Liu J, Mei Q, Nimer S, Fitzgerald DM, Rosenberg SM	Methods in enzymology	34776211	Methods Enzymol	2021	https://www.ncbi.nlm.nih.gov/pubmed/34776211
Biology before the SOS Response-DNA Damage Mechanisms at Chromosome Fragile Sites.	Fitzgerald DM, Rosenberg SM	Cells	34571923	Cells	2021 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/34571923
Drugging evolution of antibiotic resistance at a regulatory network hub.	Zhai Y, Pribis JP, Dooling SW, Garcia-Villada L, Minnick PJ, Xia J, Liu J, Mei Q, Fitzgerald DM, Herman C, Hastings PJ, Costa-Mattioli M, Rosenberg SM	Science advances	37352342	Sci Adv	2023 Jun 23	https://www.ncbi.nlm.nih.gov/pubmed/37352342
Stress-Induced Mutagenesis, Gambler Cells, and Stealth Targeting Antibiotic-Induced Evolution.	Pribis JP, Zhai Y, Hastings PJ, Rosenberg SM	mBio	35658528	mBio	2022 Jun 28	https://www.ncbi.nlm.nih.gov/pubmed/35658528
IRE1α silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer.	Xu L, Peng F, Luo Q, Ding Y, Yuan F, Zheng L, He W, Zhang SS, Fu X, Liu J, Mutlu AS, Wang S, Nehring RB, Li X, Tang Q, Li C, Lv X, Dobrolecki LE, Zhang W, Han D, Zhao N, Jaehnig E, Wang J, Wu W, Graham DA, Li Y, Chen R, Peng W, Chen Y, Catic A, Zhang Z, Zhang B, Mustoe AM, Koong AC, Miles G, Lewis MT, Wang MC, Rosenberg SM, O'Malley BW, Westbrook TF, Xu H, Zhang XH, Osborne CK, Li JB, Ellis MJ, Rimawi MF, Rosen JM, Chen X	Cell	39419025	Cell	2024 Dec 12	https://www.ncbi.nlm.nih.gov/pubmed/39419025
Self-Assembly of Antimicrobial Peptoids Impacts Their Biological Effects on ESKAPE Bacterial Pathogens.	Nielsen JE, Alford MA, Yung DBY, Molchanova N, Fortkort JA, Lin JS, Diamond G, Hancock REW, Jenssen H, Pletzer D, Lund R, Barron AE	ACS infectious diseases	35175731	ACS Infect Dis	2022 Mar 11	https://www.ncbi.nlm.nih.gov/pubmed/35175731
Efficacy of Cathelicidin-Mimetic Antimicrobial Peptoids against Staphylococcus aureus.	Benjamin AB, Moule MG, Didwania MK, Hardy J, Saenkham-Huntsinger P, Sule P, Nielsen JE, Lin JS, Contag CH, Barron AE, Cirillo JD	Microbiology spectrum	35467395	Microbiol Spectr	2022 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/35467395
Targeting Impaired Antimicrobial Immunity in the Brain for the Treatment of Alzheimer's Disease.	Fulop T, Tripathi S, Rodrigues S, Desroches M, Bunt T, Eiser A, Bernier F, Beauregard PB, Barron AE, Khalil A, Plotka A, Hirokawa K, Larbi A, Bocti C, Laurent B, Frost EH, Witkowski JM	Neuropsychiatric disease and treatment	33976546	Neuropsychiatr Dis Treat	2021	https://www.ncbi.nlm.nih.gov/pubmed/33976546
Membrane-acting biomimetic peptoids against visceral leishmaniasis.	Kumar V, Lin JS, Molchanova N, Fortkort JA, Reckmann C, Bräse S, Jenssen H, Barron AE, Chugh A	FEBS open bio	36683396	FEBS Open Bio	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36683396
Pf bacteriophages hinder sputum antibiotic diffusion via electrostatic binding.	Chen Q, Cai P, Chang THW, Burgener E, Kratochvil MJ, Gupta A, Hargil A, Secor PR, Nielsen JE, Barron AE, Milla C, Heilshorn SC, Spakowitz A, Bollyky PL	bioRxiv : the preprint server for biology	38496625	bioRxiv	2024 Mar 10	https://www.ncbi.nlm.nih.gov/pubmed/38496625
The activity of antimicrobial peptoids against multidrug-resistant ocular pathogens.	Sara M, Yasir M, Kalaiselvan P, Hui A, Kuppusamy R, Kumar N, Chakraborty S, Yu TT, Wong EHH, Molchanova N, Jenssen H, Lin JS, Barron AE, Willcox M	Contact lens & anterior eye : the journal of the British Contact Lens Association	38341309	Cont Lens Anterior Eye	2024 Apr	https://www.ncbi.nlm.nih.gov/pubmed/38341309
Author Correction: Peptide-mimetic treatment of Pseudomonas aeruginosa in a mouse model of respiratory infection.	Moule MG, Benjamin AB, Burger ML, Herlan C, Lebedev M, Lin JS, Koster KJ, Wavare N, Adams LG, Bräse S, Munoz-Medina R, Cannon CL, Barron AE, Cirillo JD	Communications biology	39271756	Commun Biol	2024 Sep 13	https://www.ncbi.nlm.nih.gov/pubmed/39271756
Real-Time Monitoring of Multitarget Antimicrobial Mechanisms of Peptoids Using Label-Free Imaging with Optical Diffraction Tomography.	Kim M, Cheon Y, Shin D, Choi J, Nielsen JE, Jeong MS, Nam HY, Kim SH, Lund R, Jenssen H, Barron AE, Lee S, Seo J	Advanced science (Weinheim, Baden-Wurttemberg, Germany)	37341246	Adv Sci (Weinh)	2023 Aug	https://www.ncbi.nlm.nih.gov/pubmed/37341246
The anti-inflammatory effects of photobiomodulation are mediated by cytokines: Evidence from a mouse model of inflammation.	Shamloo S, Defensor E, Ciari P, Ogawa G, Vidano L, Lin JS, Fortkort JA, Shamloo M, Barron AE	Frontiers in neuroscience	37090796	Front Neurosci	2023	https://www.ncbi.nlm.nih.gov/pubmed/37090796
Potent Antiviral Activity against HSV-1 and SARS-CoV-2 by Antimicrobial Peptoids.	Diamond G, Molchanova N, Herlan C, Fortkort JA, Lin JS, Figgins E, Bopp N, Ryan LK, Chung D, Adcock RS, Sherman M, Barron AE	Pharmaceuticals (Basel, Switzerland)	33807248	Pharmaceuticals (Basel)	2021 Mar 31	https://www.ncbi.nlm.nih.gov/pubmed/33807248
Anti-persister and Anti-biofilm Activity of Self-Assembled Antimicrobial Peptoid Ellipsoidal Micelles.	Lin JS, Bekale LA, Molchanova N, Nielsen JE, Wright M, Bacacao B, Diamond G, Jenssen H, Santa Maria PL, Barron AE	ACS infectious diseases	36018039	ACS Infect Dis	2022 Sep 9	https://www.ncbi.nlm.nih.gov/pubmed/36018039
Peptide-mimetic treatment of Pseudomonas aeruginosa in a mouse model of respiratory infection.	Moule MG, Benjamin AB, Burger ML, Herlan C, Lebedev M, Lin JS, Koster KJ, Wavare N, Adams LG, Bräse S, Munoz-Medina R, Cannon CL, Barron AE, Cirillo JD	Communications biology	39174819	Commun Biol	2024 Aug 22	https://www.ncbi.nlm.nih.gov/pubmed/39174819
Antiviral Effect of Antimicrobial Peptoid TM9 and Murine Model of Respiratory Coronavirus Infection.	Lebedev M, Benjamin AB, Kumar S, Molchanova N, Lin JS, Koster KJ, Leibowitz JL, Barron AE, Cirillo JD	Pharmaceutics	38675125	Pharmaceutics	2024 Mar 27	https://www.ncbi.nlm.nih.gov/pubmed/38675125
Ethylene oxide graft copolymers reduce the immunogenicity of lipid nanoparticles.	Qi Y, Han H, Liu A, Zhao S, Lawanprasert A, Nielsen JE, Choudhary H, Liang D, Barron AE, Murthy N	RSC advances	39309654	RSC Adv	2024 Sep 18	https://www.ncbi.nlm.nih.gov/pubmed/39309654
Antiviral effect of peptoids on hepatitis B virus infection in cell culture.	Murayama A, Igarashi H, Yamada N, Aly HH, Molchanova N, Lin JS, Nishitsuji H, Shimotohno K, Muramatsu M, Barron AE, Kato T	Antiviral research	38272318	Antiviral Res	2024 Mar	https://www.ncbi.nlm.nih.gov/pubmed/38272318
Targeting Infectious Agents as a Therapeutic Strategy in Alzheimer's Disease.	Fülöp T, Munawara U, Larbi A, Desroches M, Rodrigues S, Catanzaro M, Guidolin A, Khalil A, Bernier F, Barron AE, Hirokawa K, Beauregard PB, Dumoulin D, Bellenger JP, Witkowski JM, Frost E	CNS drugs	32458360	CNS Drugs	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32458360
Hyperactivation of monocytes and macrophages in MCI patients contributes to the progression of Alzheimer's disease.	Munawara U, Catanzaro M, Xu W, Tan C, Hirokawa K, Bosco N, Dumoulin D, Khalil A, Larbi A, Lévesque S, Ramassamy C, Barron AE, Cunnane S, Beauregard PB, Bellenger JP, Rodrigues S, Desroches M, Witkowski JM, Laurent B, Frost EH, Fulop T	Immunity & ageing : I & A	34154615	Immun Ageing	2021 Jun 21	https://www.ncbi.nlm.nih.gov/pubmed/34154615
Supramolecular Peptoid Structure Strengthens Complexation with Polyacrylic Acid Microgels.	Zhao W, Lin JS, Nielsen JE, Sørensen K, Wadurkar AS, Ji J, Barron AE, Nangia S, Libera MR	Biomacromolecules	38240722	Biomacromolecules	2024 Feb 12	https://www.ncbi.nlm.nih.gov/pubmed/38240722
Acid-degradable lipid nanoparticles enhance the delivery of mRNA.	Zhao S, Gao K, Han H, Stenzel M, Yin B, Song H, Lawanprasert A, Nielsen JE, Sharma R, Arogundade OH, Pimcharoen S, Chen YJ, Paul A, Tuma J, Collins MG, Wyle Y, Cranick MG, Burgstone BW, Perez BS, Barron AE, Smith AM, Lee HY, Wang A, Murthy N	Nature nanotechnology	39179796	Nat Nanotechnol	2024 Nov	https://www.ncbi.nlm.nih.gov/pubmed/39179796
From Global to Nano: A Geographical Perspective of Aggregatibacter actinomycetemcomitans.	Ryder MI, Fine DH, Barron AE	Pathogens (Basel, Switzerland)	39452709	Pathogens	2024 Sep 27	https://www.ncbi.nlm.nih.gov/pubmed/39452709
Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks.	Yamamoto T, Cockburn K, Greco V, Kawaguchi K	PLoS computational biology	36067226	PLoS Comput Biol	2022 Sep	https://www.ncbi.nlm.nih.gov/pubmed/36067226
Organ function is preserved despite reorganization of niche architecture in the hair follicle.	Wei H, Du S, Parksong J, Pasolli HA, Matte-Martone C, Regot S, Gonzalez LE, Xin T, Greco V	Cell stem cell	37419106	Cell Stem Cell	2023 Jul 6	https://www.ncbi.nlm.nih.gov/pubmed/37419106
Selective utilization of glucose metabolism guides mammalian gastrulation.	Cao D, Bergmann J, Zhong L, Hemalatha A, Dingare C, Jensen T, Cox AL, Greco V, Steventon B, Sozen B	Nature	39415005	Nature	2024 Oct	https://www.ncbi.nlm.nih.gov/pubmed/39415005
Skin-resident immune cells actively coordinate their distribution with epidermal cells during homeostasis.	Park S, Matte-Martone C, Gonzalez DG, Lathrop EA, May DP, Pineda CM, Moore JL, Boucher JD, Marsh E, Schmitter-Sánchez A, Cockburn K, Markova O, Bellaïche Y, Greco V	Nature cell biology	33958758	Nat Cell Biol	2021 May	https://www.ncbi.nlm.nih.gov/pubmed/33958758
Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo.	May D, Yun S, Gonzalez DG, Park S, Chen Y, Lathrop E, Cai B, Xin T, Zhao H, Wang S, Gonzalez LE, Cockburn K, Greco V	eLife	36880644	Elife	2023 Mar 7	https://www.ncbi.nlm.nih.gov/pubmed/36880644
Cell cycle controls long-range calcium signaling in the regenerating epidermis.	Moore JL, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Campamà Sanz N, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V	The Journal of cell biology	37102999	J Cell Biol	2023 Jul 3	https://www.ncbi.nlm.nih.gov/pubmed/37102999
Metabolic rewiring in skin epidermis drives tolerance to oncogenic mutations.	Hemalatha A, Li Z, Gonzalez DG, Matte-Martone C, Tai K, Lathrop E, Gil D, Ganesan S, Gonzalez LE, Skala M, Perry RJ, Greco V	Nature cell biology	39762578	Nat Cell Biol	2025 Feb	https://www.ncbi.nlm.nih.gov/pubmed/39762578
Functional cell death, corneoptosis, requires temporally controlled intracellular acidification.	Moore JL, Greco V	Proceedings of the National Academy of Sciences of the United States of America	33986147	Proc Natl Acad Sci U S A	2021 Jun 1	https://www.ncbi.nlm.nih.gov/pubmed/33986147
Injury prevents Ras mutant cell expansion in mosaic skin.	Gallini S, Annusver K, Rahman NT, Gonzalez DG, Yun S, Matte-Martone C, Xin T, Lathrop E, Suozzi KC, Kasper M, Greco V	Nature	37344586	Nature	2023 Jul	https://www.ncbi.nlm.nih.gov/pubmed/37344586
Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation.	Xin T, Gallini S, Wei H, Gonzalez DG, Matte-Martone C, Machida H, Fujiwara H, Pasolli HA, Suozzi KC, Gonzalez LE, Regot S, Greco V	Nature cell biology	38689013	Nat Cell Biol	2024 Jun	https://www.ncbi.nlm.nih.gov/pubmed/38689013
From start to finish-a molecular link in wound repair.	Yun S, Greco V	Science (New York, N.Y.)	35143296	Science	2022 Feb 11	https://www.ncbi.nlm.nih.gov/pubmed/35143296
Gradual differentiation uncoupled from cell cycle exit generates heterogeneity in the epidermal stem cell layer.	Cockburn K, Annusver K, Gonzalez DG, Ganesan S, May DP, Mesa KR, Kawaguchi K, Kasper M, Greco V	Nature cell biology	36357619	Nat Cell Biol	2022 Dec	https://www.ncbi.nlm.nih.gov/pubmed/36357619
A Spatiotemporal Compartmentalization of Glucose Metabolism Guides Mammalian Gastrulation Progression.	Cao D, Zhong L, Hemalatha A, Bergmann J, Cox AL, Greco V, Sozen B	bioRxiv : the preprint server for biology	37333168	bioRxiv	2023 Jun 8	https://www.ncbi.nlm.nih.gov/pubmed/37333168
Mechanisms of skin vascular maturation and maintenance captured by longitudinal imaging of live mice.	Kam CY, Singh ID, Gonzalez DG, Matte-Martone C, Solá P, Solanas G, Bonjoch J, Marsh E, Hirschi KK, Greco V	Cell	37167971	Cell	2023 May 25	https://www.ncbi.nlm.nih.gov/pubmed/37167971
Correction: Cell cycle controls long-range calcium signaling in the regenerating epidermis.	Moore JL, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Sanz NC, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V	The Journal of cell biology	38477880	J Cell Biol	2024 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/38477880
In Situ Modification of Tissue Stem and Progenitor Cell Genomes.	Goldstein JM, Tabebordbar M, Zhu K, Wang LD, Messemer KA, Peacker B, Ashrafi Kakhki S, Gonzalez-Celeiro M, Shwartz Y, Cheng JKW, Xiao R, Barungi T, Albright C, Hsu YC, Vandenberghe LH, Wagers AJ	Cell reports	31018138	Cell Rep	2019 Apr 23	https://www.ncbi.nlm.nih.gov/pubmed/31018138
Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species.	Tabebordbar M, Lagerborg KA, Stanton A, King EM, Ye S, Tellez L, Krunnfusz A, Tavakoli S, Widrick JJ, Messemer KA, Troiano EC, Moghadaszadeh B, Peacker BL, Leacock KA, Horwitz N, Beggs AH, Wagers AJ, Sabeti PC	Cell	34506722	Cell	2021 Sep 16	https://www.ncbi.nlm.nih.gov/pubmed/34506722
Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells.	Yagi M, Ji F, Charlton J, Cristea S, Messemer K, Horwitz N, Di Stefano B, Tsopoulidis N, Hoetker MS, Huebner AJ, Bar-Nur O, Almada AE, Yamamoto M, Patelunas A, Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI, Hochedlinger K	Genes & development	34413137	Genes Dev	2021 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/34413137
High-efficiency purification of divergent AAV serotypes using AAVX affinity chromatography.	Florea M, Nicolaou F, Pacouret S, Zinn EM, Sanmiguel J, Andres-Mateos E, Unzu C, Wagers AJ, Vandenberghe LH	Molecular therapy. Methods & clinical development	36654797	Mol Ther Methods Clin Dev	2023 Mar 9	https://www.ncbi.nlm.nih.gov/pubmed/36654797
Harvard HIV and Aging Workshop: Perspectives and Priorities from Claude D. Pepper Centers and Centers for AIDS Research.	Montano M, Bhasin S, D'Aquila RT, Erlandson KM, Evans WJ, Funderburg NT, Justice A, Ndhlovu LC, Ojikutu B, Pahor M, Pahwa S, Ryan AS, Schrack J, Schultz MB, Sebastiani P, Sinclair DA, Tripp J, Walker B, Womack JA, Yung R, Reeves RK	AIDS research and human retroviruses	31456412	AIDS Res Hum Retroviruses	2019 Nov-Dec	https://www.ncbi.nlm.nih.gov/pubmed/31456412
NAD(+) Repletion Rescues Female Fertility during Reproductive Aging.	Bertoldo MJ, Listijono DR, Ho WJ, Riepsamen AH, Goss DM, Richani D, Jin XL, Mahbub S, Campbell JM, Habibalahi A, Loh WN, Youngson NA, Maniam J, Wong ASA, Selesniemi K, Bustamante S, Li C, Zhao Y, Marinova MB, Kim LJ, Lau L, Wu RM, Mikolaizak AS, Araki T, Le Couteur DG, Turner N, Morris MJ, Walters KA, Goldys E, O'Neill C, Gilchrist RB, Sinclair DA, Homer HA, Wu LE	Cell reports	32049001	Cell Rep	2020 Feb 11	https://www.ncbi.nlm.nih.gov/pubmed/32049001
Longitudinal analysis of biomarker data from a personalized nutrition platform in healthy subjects.	Westerman K, Reaver A, Roy C, Ploch M, Sharoni E, Nogal B, Sinclair DA, Katz DL, Blumberg JB, Blander G	Scientific reports	30279436	Sci Rep	2018 Oct 2	https://www.ncbi.nlm.nih.gov/pubmed/30279436
Impairment of an Endothelial NAD(+)-H(2)S Signaling Network Is a Reversible Cause of Vascular Aging.	Das A, Huang GX, Bonkowski MS, Longchamp A, Li C, Schultz MB, Kim LJ, Osborne B, Joshi S, Lu Y, Treviño-Villarreal JH, Kang MJ, Hung TT, Lee B, Williams EO, Igarashi M, Mitchell JR, Wu LE, Turner N, Arany Z, Guarente L, Sinclair DA	Cell	29570999	Cell	2018 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/29570999
Multiple basal cell carcinomas in a patient with myotonic dystrophy type 1.	Feng J, LaChance A, Sinclair DA, Asgari MM	BMJ case reports	30852496	BMJ Case Rep	2019 Mar 8	https://www.ncbi.nlm.nih.gov/pubmed/30852496
Skeletal muscle overexpression of nicotinamide phosphoribosyl transferase in mice coupled with voluntary exercise augments exercise endurance.	Costford SR, Brouwers B, Hopf ME, Sparks LM, Dispagna M, Gomes AP, Cornnell HH, Petucci C, Phelan P, Xie H, Yi F, Walter GA, Osborne TF, Sinclair DA, Mynatt RL, Ayala JE, Gardell SJ, Smith SR	Molecular metabolism	29146412	Mol Metab	2018 Jan	https://www.ncbi.nlm.nih.gov/pubmed/29146412
Resveratrol Improves Vascular Function and Mitochondrial Number but Not Glucose Metabolism in Older Adults.	Pollack RM, Barzilai N, Anghel V, Kulkarni AS, Golden A, O'Broin P, Sinclair DA, Bonkowski MS, Coleville AJ, Powell D, Kim S, Moaddel R, Stein D, Zhang K, Hawkins M, Crandall JP	The journals of gerontology. Series A, Biological sciences and medical sciences	28329397	J Gerontol A Biol Sci Med Sci	2017 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/28329397
Multigenerational obesity-induced perturbations in oocyte-secreted factor signalling can be ameliorated by exercise and nicotinamide mononucleotide.	Bertoldo MJ, Uddin GM, Youngson NA, Agapiou D, Walters KA, Sinclair DA, Morris MJ, Gilchrist RB	Human reproduction open	30895251	Hum Reprod Open	2018	https://www.ncbi.nlm.nih.gov/pubmed/30895251
Comparing the Effects of Low-Protein and High-Carbohydrate Diets and Caloric Restriction on Brain Aging in Mice.	Wahl D, Solon-Biet SM, Wang QP, Wali JA, Pulpitel T, Clark X, Raubenheimer D, Senior AM, Sinclair DA, Cooney GJ, de Cabo R, Cogger VC, Simpson SJ, Le Couteur DG	Cell reports	30463018	Cell Rep	2018 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/30463018
Publisher Correction: Longitudinal analysis of biomarker data from a personalized nutrition platform in healthy subjects.	Westerman K, Reaver A, Roy C, Ploch M, Sharoni E, Nogal B, Sinclair DA, Katz DL, Blumberg JB, Blander G	Scientific reports	30405144	Sci Rep	2018 Nov 8	https://www.ncbi.nlm.nih.gov/pubmed/30405144
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice.	Ross JM, Coppotelli G, Branca RM, Kim KM, Lehtiö J, Sinclair DA, Olson L	Aging cell	31489782	Aging Cell	2019 Dec	https://www.ncbi.nlm.nih.gov/pubmed/31489782
Barrier-to-autointegration factor 1 (Banf1) regulates poly [ADP-ribose] polymerase 1 (PARP1) activity following oxidative DNA damage.	Bolderson E, Burgess JT, Li J, Gandhi NS, Boucher D, Croft LV, Beard S, Plowman JJ, Suraweera A, Adams MN, Naqi A, Zhang SD, Sinclair DA, O'Byrne KJ, Richard DJ	Nature communications	31796734	Nat Commun	2019 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/31796734
Epigenetic changes during aging and their reprogramming potential.	Kane AE, Sinclair DA	Critical reviews in biochemistry and molecular biology	30822165	Crit Rev Biochem Mol Biol	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30822165
Sirtuin activators and inhibitors: Promises, achievements, and challenges.	Dai H, Sinclair DA, Ellis JL, Steegborn C	Pharmacology & therapeutics	29577959	Pharmacol Ther	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29577959
Targeting mitochondria for cardiovascular disorders: therapeutic potential and obstacles.	Bonora M, Wieckowski MR, Sinclair DA, Kroemer G, Pinton P, Galluzzi L	Nature reviews. Cardiology	30177752	Nat Rev Cardiol	2019 Jan	https://www.ncbi.nlm.nih.gov/pubmed/30177752
Therapeutic Potential of NAD-Boosting Molecules: The In Vivo Evidence.	Rajman L, Chwalek K, Sinclair DA	Cell metabolism	29514064	Cell Metab	2018 Mar 6	https://www.ncbi.nlm.nih.gov/pubmed/29514064
Nicotinamide Improves Aspects of Healthspan, but Not Lifespan, in Mice.	Mitchell SJ, Bernier M, Aon MA, Cortassa S, Kim EY, Fang EF, Palacios HH, Ali A, Navas-Enamorado I, Di Francesco A, Kaiser TA, Waltz TB, Zhang N, Ellis JL, Elliott PJ, Frederick DW, Bohr VA, Schmidt MS, Brenner C, Sinclair DA, Sauve AA, Baur JA, de Cabo R	Cell metabolism	29514072	Cell Metab	2018 Mar 6	https://www.ncbi.nlm.nih.gov/pubmed/29514072
Mitohormesis and metabolic health: The interplay between ROS, cAMP and sirtuins.	Palmeira CM, Teodoro JS, Amorim JA, Steegborn C, Sinclair DA, Rolo AP	Free radical biology & medicine	31349039	Free Radic Biol Med	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31349039
Sirtuins and NAD(+) in the Development and Treatment of Metabolic and Cardiovascular Diseases.	Kane AE, Sinclair DA	Circulation research	30355082	Circ Res	2018 Sep 14	https://www.ncbi.nlm.nih.gov/pubmed/30355082
NAD(+) in Brain Aging and Neurodegenerative Disorders.	Lautrup S, Sinclair DA, Mattson MP, Fang EF	Cell metabolism	31577933	Cell Metab	2019 Oct 1	https://www.ncbi.nlm.nih.gov/pubmed/31577933
Molecular and Cellular Characterization of SIRT1 Allosteric Activators.	Schultz MB, Rinaldi C, Lu Y, Amorim JA, Sinclair DA	Methods in molecular biology (Clifton, N.J.)	31087296	Methods Mol Biol	2019	https://www.ncbi.nlm.nih.gov/pubmed/31087296
Telomere Dysfunction Induces Sirtuin Repression that Drives Telomere-Dependent Disease.	Amano H, Chaudhury A, Rodriguez-Aguayo C, Lu L, Akhanov V, Catic A, Popov YV, Verdin E, Johnson H, Stossi F, Sinclair DA, Nakamaru-Ogiso E, Lopez-Berestein G, Chang JT, Neilson JR, Meeker A, Finegold M, Baur JA, Sahin E	Cell metabolism	30930169	Cell Metab	2019 Jun 4	https://www.ncbi.nlm.nih.gov/pubmed/30930169
Nicotinamide mononucleotide (NMN) supplementation ameliorates the impact of maternal obesity in mice: comparison with exercise.	Uddin GM, Youngson NA, Doyle BM, Sinclair DA, Morris MJ	Scientific reports	29118320	Sci Rep	2017 Nov 8	https://www.ncbi.nlm.nih.gov/pubmed/29118320
Assays for NAD(+)-Dependent Reactions and NAD(+) Metabolites.	Schultz MB, Lu Y, Braidy N, Sinclair DA	Methods in molecular biology (Clifton, N.J.)	30097862	Methods Mol Biol	2018	https://www.ncbi.nlm.nih.gov/pubmed/30097862
Quantitative proteomic analysis of extracellular vesicle subgroups isolated by an optimized method combining polymer-based precipitation and size exclusion chromatography.	Martínez-Greene JA, Hernández-Ortega K, Quiroz-Baez R, Resendis-Antonio O, Pichardo-Casas I, Sinclair DA, Budnik B, Hidalgo-Miranda A, Uribe-Querol E, Ramos-Godínez MDP, Martínez-Martínez E	Journal of extracellular vesicles	33936570	J Extracell Vesicles	2021 Apr	https://www.ncbi.nlm.nih.gov/pubmed/33936570
Amino Acid Restriction Triggers Angiogenesis via GCN2/ATF4 Regulation of VEGF and H(2)S Production.	Longchamp A, Mirabella T, Arduini A, MacArthur MR, Das A, Treviño-Villarreal JH, Hine C, Ben-Sahra I, Knudsen NH, Brace LE, Reynolds J, Mejia P, Tao M, Sharma G, Wang R, Corpataux JM, Haefliger JA, Ahn KH, Lee CH, Manning BD, Sinclair DA, Chen CS, Ozaki CK, Mitchell JR	Cell	29570992	Cell	2018 Mar 22	https://www.ncbi.nlm.nih.gov/pubmed/29570992
Dynamic Acetylation of Phosphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions.	Latorre-Muro P, Baeza J, Armstrong EA, Hurtado-Guerrero R, Corzana F, Wu LE, Sinclair DA, López-Buesa P, Carrodeguas JA, Denu JM	Molecular cell	30193097	Mol Cell	2018 Sep 6	https://www.ncbi.nlm.nih.gov/pubmed/30193097
Impacts of obesity, maternal obesity and nicotinamide mononucleotide supplementation on sperm quality in mice.	Youngson NA, Uddin GM, Das A, Martinez C, Connaughton HS, Whiting S, Yu J, Sinclair DA, Aitken RJ, Morris MJ	Reproduction (Cambridge, England)	31226694	Reproduction	2019 Aug 1	https://www.ncbi.nlm.nih.gov/pubmed/31226694
Frailty biomarkers in humans and rodents: Current approaches and future advances.	Kane AE, Sinclair DA	Mechanisms of ageing and development	31002925	Mech Ageing Dev	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31002925
Nicotinamide mononucleotide (NMN) supplementation rescues cerebromicrovascular endothelial function and neurovascular coupling responses and improves cognitive function in aged mice.	Tarantini S, Valcarcel-Ares MN, Toth P, Yabluchanskiy A, Tucsek Z, Kiss T, Hertelendy P, Kinter M, Ballabh P, Süle Z, Farkas E, Baur JA, Sinclair DA, Csiszar A, Ungvari Z	Redox biology	31015147	Redox Biol	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31015147
Transcriptional profiling of isogenic Friedreich ataxia neurons and effect of an HDAC inhibitor on disease signatures.	Lai JI, Nachun D, Petrosyan L, Throesch B, Campau E, Gao F, Baldwin KK, Coppola G, Gottesfeld JM, Soragni E	The Journal of biological chemistry	30552117	J Biol Chem	2019 Feb 8	https://www.ncbi.nlm.nih.gov/pubmed/30552117
Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing.	Lo Sardo V, Chubukov P, Ferguson W, Kumar A, Teng EL, Duran M, Zhang L, Cost G, Engler AJ, Urnov F, Topol EJ, Torkamani A, Baldwin KK	Cell	30528432	Cell	2018 Dec 13	https://www.ncbi.nlm.nih.gov/pubmed/30528432
Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program.	Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA	Stem cell research	32442913	Stem Cell Res	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32442913
Influence of donor age on induced pluripotent stem cells.	Lo Sardo V, Ferguson W, Erikson GA, Topol EJ, Baldwin KK, Torkamani A	Nature biotechnology	27941802	Nat Biotechnol	2017 Jan	https://www.ncbi.nlm.nih.gov/pubmed/27941802
Rates of contributory de novo mutation in high and low-risk autism families.	Yoon S, Munoz A, Yamrom B, Lee YH, Andrews P, Marks S, Wang Z, Reeves C, Winterkorn L, Krieger AM, Buja A, Pradhan K, Ronemus M, Baldwin KK, Levy D, Wigler M, Iossifov I	Communications biology	34471188	Commun Biol	2021 Sep 1	https://www.ncbi.nlm.nih.gov/pubmed/34471188
Diverse reprogramming codes for neuronal identity.	Tsunemoto R, Lee S, Szűcs A, Chubukov P, Sokolova I, Blanchard JW, Eade KT, Bruggemann J, Wu C, Torkamani A, Sanna PP, Baldwin KK	Nature	29743677	Nature	2018 May	https://www.ncbi.nlm.nih.gov/pubmed/29743677
Physiological blood-brain transport is impaired with age by a shift in transcytosis.	Yang AC, Stevens MY, Chen MB, Lee DP, Stähli D, Gate D, Contrepois K, Chen W, Iram T, Zhang L, Vest RT, Chaney A, Lehallier B, Olsson N, du Bois H, Hsieh R, Cropper HC, Berdnik D, Li L, Wang EY, Traber GM, Bertozzi CR, Luo J, Snyder MP, Elias JE, Quake SR, James ML, Wyss-Coray T	Nature	32612231	Nature	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32612231
Brain Endothelial Cells Are Exquisite Sensors of Age-Related Circulatory Cues.	Chen MB, Yang AC, Yousef H, Lee D, Chen W, Schaum N, Lehallier B, Quake SR, Wyss-Coray T	Cell reports	32234477	Cell Rep	2020 Mar 31	https://www.ncbi.nlm.nih.gov/pubmed/32234477
Undulating changes in human plasma proteome profiles across the lifespan.	Lehallier B, Gate D, Schaum N, Nanasi T, Lee SE, Yousef H, Moran Losada P, Berdnik D, Keller A, Verghese J, Sathyan S, Franceschi C, Milman S, Barzilai N, Wyss-Coray T	Nature medicine	31806903	Nat Med	2019 Dec	https://www.ncbi.nlm.nih.gov/pubmed/31806903
A neuronal blood marker is associated with mortality in old age.	Kaeser SA, Lehallier B, Thinggaard M, Häsler LM, Apel A, Bergmann C, Berdnik D, Jeune B, Christensen K, Grönke S, Partridge L, Wyss-Coray T, Mengel-From J, Jucker M	Nature aging	37118632	Nat Aging	2021 Feb	https://www.ncbi.nlm.nih.gov/pubmed/37118632
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse.	Tabula Muris Consortium	Nature	32669714	Nature	2020 Jul	https://www.ncbi.nlm.nih.gov/pubmed/32669714
Eosinophils regulate adipose tissue inflammation and sustain physical and immunological fitness in old age.	Brigger D, Riether C, van Brummelen R, Mosher KI, Shiu A, Ding Z, Zbären N, Gasser P, Guntern P, Yousef H, Castellano JM, Storni F, Graff-Radford N, Britschgi M, Grandgirard D, Hinterbrandner M, Siegrist M, Moullan N, Hofstetter W, Leib SL, Villiger PM, Auwerx J, Villeda SA, Wyss-Coray T, Noti M, Eggel A	Nature metabolism	32694825	Nat Metab	2020 Aug	https://www.ncbi.nlm.nih.gov/pubmed/32694825
Lipid-droplet-accumulating microglia represent a dysfunctional and proinflammatory state in the aging brain.	Marschallinger J, Iram T, Zardeneta M, Lee SE, Lehallier B, Haney MS, Pluvinage JV, Mathur V, Hahn O, Morgens DW, Kim J, Tevini J, Felder TK, Wolinski H, Bertozzi CR, Bassik MC, Aigner L, Wyss-Coray T	Nature neuroscience	31959936	Nat Neurosci	2020 Feb	https://www.ncbi.nlm.nih.gov/pubmed/31959936
CD22 blockade restores homeostatic microglial phagocytosis in ageing brains.	Pluvinage JV, Haney MS, Smith BAH, Sun J, Iram T, Bonanno L, Li L, Lee DP, Morgens DW, Yang AC, Shuken SR, Gate D, Scott M, Khatri P, Luo J, Bertozzi CR, Bassik MC, Wyss-Coray T	Nature	30944478	Nature	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30944478
Human umbilical cord plasma proteins revitalize hippocampal function in aged mice.	Castellano JM, Mosher KI, Abbey RJ, McBride AA, James ML, Berdnik D, Shen JC, Zou B, Xie XS, Tingle M, Hinkson IV, Angst MS, Wyss-Coray T	Nature	28424512	Nature	2017 Apr 27	https://www.ncbi.nlm.nih.gov/pubmed/28424512
Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics.	Yang AC, du Bois H, Olsson N, Gate D, Lehallier B, Berdnik D, Brewer KD, Bertozzi CR, Elias JE, Wyss-Coray T	Journal of the American Chemical Society	29775058	J Am Chem Soc	2018 Jun 13	https://www.ncbi.nlm.nih.gov/pubmed/29775058
Papain-based Single Cell Isolation of Primary Murine Brain Endothelial Cells Using Flow Cytometry.	Yousef H, Czupalla CJ, Lee D, Butcher EC, Wyss-Coray T	Bio-protocol	31032379	Bio Protoc	2018 Nov 20	https://www.ncbi.nlm.nih.gov/pubmed/31032379
Aged blood impairs hippocampal neural precursor activity and activates microglia via brain endothelial cell VCAM1.	Yousef H, Czupalla CJ, Lee D, Chen MB, Burke AN, Zera KA, Zandstra J, Berber E, Lehallier B, Mathur V, Nair RV, Bonanno LN, Yang AC, Peterson T, Hadeiba H, Merkel T, Körbelin J, Schwaninger M, Buckwalter MS, Quake SR, Butcher EC, Wyss-Coray T	Nature medicine	31086348	Nat Med	2019 Jun	https://www.ncbi.nlm.nih.gov/pubmed/31086348
Molecular hallmarks of heterochronic parabiosis at single-cell resolution.	Pálovics R, Keller A, Schaum N, Tan W, Fehlmann T, Borja M, Kern F, Bonanno L, Calcuttawala K, Webber J, McGeever A, Tabula Muris Consortium, Luo J, Pisco AO, Karkanias J, Neff NF, Darmanis S, Quake SR, Wyss-Coray T	Nature	35236985	Nature	2022 Mar	https://www.ncbi.nlm.nih.gov/pubmed/35236985
Organization of the Mammalian Ionome According to Organ Origin, Lineage Specialization, and Longevity.	Ma S, Lee SG, Kim EB, Park TJ, Seluanov A, Gorbunova V, Buffenstein R, Seravalli J, Gladyshev VN	Cell reports	26549444	Cell Rep	2015 Nov 17	https://www.ncbi.nlm.nih.gov/pubmed/26549444
Defining Molecular Basis for Longevity Traits in Natural Yeast Isolates.	Kaya A, Ma S, Wasko B, Lee M, Kaeberlein M, Gladyshev VN	NPJ aging and mechanisms of disease	27030810	NPJ Aging Mech Dis	2015	https://www.ncbi.nlm.nih.gov/pubmed/27030810
Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity.	Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN	Aging cell	29671950	Aging Cell	2018 Aug	https://www.ncbi.nlm.nih.gov/pubmed/29671950
Naked mole rats can undergo developmental, oncogene-induced and DNA damage-induced cellular senescence.	Zhao Y, Tyshkovskiy A, Muñoz-Espín D, Tian X, Serrano M, de Magalhaes JP, Nevo E, Gladyshev VN, Seluanov A, Gorbunova V	Proceedings of the National Academy of Sciences of the United States of America	29432174	Proc Natl Acad Sci U S A	2018 Feb 20	https://www.ncbi.nlm.nih.gov/pubmed/29432174
INK4 locus of the tumor-resistant rodent, the naked mole rat, expresses a functional p15/p16 hybrid isoform.	Tian X, Azpurua J, Ke Z, Augereau A, Zhang ZD, Vijg J, Gladyshev VN, Gorbunova V, Seluanov A	Proceedings of the National Academy of Sciences of the United States of America	25550505	Proc Natl Acad Sci U S A	2015 Jan 27	https://www.ncbi.nlm.nih.gov/pubmed/25550505
Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes.	Fang X, Seim I, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, Zhu Y, Lobanov AV, Fan D, Yim SH, Yao X, Ma S, Yang L, Lee SG, Kim EB, Bronson RT, Šumbera R, Buffenstein R, Zhou X, Krogh A, Park TJ, Zhang G, Wang J, Gladyshev VN	Cell reports	25176646	Cell Rep	2014 Sep 11	https://www.ncbi.nlm.nih.gov/pubmed/25176646
Integrating cellular senescence with the concept of damage accumulation in aging: Relevance for clearance of senescent cells.	Ogrodnik M, Salmonowicz H, Gladyshev VN	Aging cell	30346102	Aging Cell	2019 Feb	https://www.ncbi.nlm.nih.gov/pubmed/30346102
Gene expression defines natural changes in mammalian lifespan.	Fushan AA, Turanov AA, Lee SG, Kim EB, Lobanov AV, Yim SH, Buffenstein R, Lee SR, Chang KT, Rhee H, Kim JS, Yang KS, Gladyshev VN	Aging cell	25677554	Aging Cell	2015 Jun	https://www.ncbi.nlm.nih.gov/pubmed/25677554
Convergent evolution of marine mammals is associated with distinct substitutions in common genes.	Zhou X, Seim I, Gladyshev VN	Scientific reports	26549748	Sci Rep	2015 Nov 9	https://www.ncbi.nlm.nih.gov/pubmed/26549748
Deficiency of the 15-kDa selenoprotein led to cytoskeleton remodeling and non-apoptotic membrane blebbing through a RhoA/ROCK pathway.	Bang J, Jang M, Huh JH, Na JW, Shim M, Carlson BA, Tobe R, Tsuji PA, Gladyshev VN, Hatfield DL, Lee BJ	Biochemical and biophysical research communications	25529450	Biochem Biophys Res Commun	2015 Jan 24	https://www.ncbi.nlm.nih.gov/pubmed/25529450
A Disease or Not a Disease? Aging As a Pathology.	Gladyshev TV, Gladyshev VN	Trends in molecular medicine	27793599	Trends Mol Med	2016 Dec	https://www.ncbi.nlm.nih.gov/pubmed/27793599
Age-associated molecular changes are deleterious and may modulate life span through diet.	Lee SG, Kaya A, Avanesov AS, Podolskiy DI, Song EJ, Go DM, Jin GD, Hwang JY, Kim EB, Kim DY, Gladyshev VN	Science advances	28232953	Sci Adv	2017 Feb	https://www.ncbi.nlm.nih.gov/pubmed/28232953
Non-enzymatic molecular damage as a prototypic driver of aging.	Golubev A, Hanson AD, Gladyshev VN	The Journal of biological chemistry	28264930	J Biol Chem	2017 Apr 14	https://www.ncbi.nlm.nih.gov/pubmed/28264930
Aging: progressive decline in fitness due to the rising deleteriome adjusted by genetic, environmental, and stochastic processes.	Gladyshev VN	Aging cell	27060562	Aging Cell	2016 Aug	https://www.ncbi.nlm.nih.gov/pubmed/27060562
Germline burden of rare damaging variants negatively affects human healthspan and lifespan.	Shindyapina AV, Zenin AA, Tarkhov AE, Santesmasses D, Fedichev PO, Gladyshev VN	eLife	32254024	Elife	2020 Apr 7	https://www.ncbi.nlm.nih.gov/pubmed/32254024
SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species.	Tian X, Firsanov D, Zhang Z, Cheng Y, Luo L, Tombline G, Tan R, Simon M, Henderson S, Steffan J, Goldfarb A, Tam J, Zheng K, Cornwell A, Johnson A, Yang JN, Mao Z, Manta B, Dang W, Zhang Z, Vijg J, Wolfe A, Moody K, Kennedy BK, Bohmann D, Gladyshev VN, Seluanov A, Gorbunova V	Cell	31002797	Cell	2019 Apr 18	https://www.ncbi.nlm.nih.gov/pubmed/31002797
DNA methylation aging clocks: challenges and recommendations.	Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK	Genome biology	31767039	Genome Biol	2019 Nov 25	https://www.ncbi.nlm.nih.gov/pubmed/31767039
Naked Mole Rat Induced Pluripotent Stem Cells and Their Contribution to Interspecific Chimera.	Lee SG, Mikhalchenko AE, Yim SH, Lobanov AV, Park JK, Choi KH, Bronson RT, Lee CK, Park TJ, Gladyshev VN	Stem cell reports	29107591	Stem Cell Reports	2017 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/29107591
Molecular signatures of longevity: Insights from cross-species comparative studies.	Ma S, Gladyshev VN	Seminars in cell & developmental biology	28800931	Semin Cell Dev Biol	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28800931
Selenocysteine tRNA([Ser]Sec), the Central Component of Selenoprotein Biosynthesis: Isolation, Identification, Modification, and Sequencing.	Carlson BA, Lee BJ, Tsuji PA, Copeland PR, Schweizer U, Gladyshev VN, Hatfield DL	Methods in molecular biology (Clifton, N.J.)	28917036	Methods Mol Biol	2018	https://www.ncbi.nlm.nih.gov/pubmed/28917036
Biological age is increased by stress and restored upon recovery.	Poganik JR, Zhang B, Baht GS, Tyshkovskiy A, Deik A, Kerepesi C, Yim SH, Lu AT, Haghani A, Gong T, Hedman AM, Andolf E, Pershagen G, Almqvist C, Clish CB, Horvath S, White JP, Gladyshev VN	Cell metabolism	37086720	Cell Metab	2023 May 2	https://www.ncbi.nlm.nih.gov/pubmed/37086720
Systematic age-, organ-, and diet-associated ionome remodeling and the development of ionomic aging clocks.	Zhang B, Podolskiy DI, Mariotti M, Seravalli J, Gladyshev VN	Aging cell	32323920	Aging Cell	2020 May	https://www.ncbi.nlm.nih.gov/pubmed/32323920
Gene expression signatures of human cell and tissue longevity.	Seim I, Ma S, Gladyshev VN	NPJ aging and mechanisms of disease	28721269	NPJ Aging Mech Dis	2016	https://www.ncbi.nlm.nih.gov/pubmed/28721269
Multifaceted deregulation of gene expression and protein synthesis with age.	Anisimova AS, Meerson MB, Gerashchenko MV, Kulakovskiy IV, Dmitriev SE, Gladyshev VN	Proceedings of the National Academy of Sciences of the United States of America	32576685	Proc Natl Acad Sci U S A	2020 Jul 7	https://www.ncbi.nlm.nih.gov/pubmed/32576685
Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity.	Zhou X, Dou Q, Fan G, Zhang Q, Sanderford M, Kaya A, Johnson J, Karlsson EK, Tian X, Mikhalchenko A, Kumar S, Seluanov A, Zhang ZD, Gorbunova V, Liu X, Gladyshev VN	Cell reports	32726638	Cell Rep	2020 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/32726638
Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human.	MacRae SL, Zhang Q, Lemetre C, Seim I, Calder RB, Hoeijmakers J, Suh Y, Gladyshev VN, Seluanov A, Gorbunova V, Vijg J, Zhang ZD	Aging cell	25645816	Aging Cell	2015 Apr	https://www.ncbi.nlm.nih.gov/pubmed/25645816
Comparative genetics of longevity and cancer: insights from long-lived rodents.	Gorbunova V, Seluanov A, Zhang Z, Gladyshev VN, Vijg J	Nature reviews. Genetics	24981598	Nat Rev Genet	2014 Aug	https://www.ncbi.nlm.nih.gov/pubmed/24981598
Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity.	Ma S, Upneja A, Galecki A, Tsai YM, Burant CF, Raskind S, Zhang Q, Zhang ZD, Seluanov A, Gorbunova V, Clish CB, Miller RA, Gladyshev VN	eLife	27874830	Elife	2016 Nov 22	https://www.ncbi.nlm.nih.gov/pubmed/27874830
Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction.	Sziráki A, Tyshkovskiy A, Gladyshev VN	Aging cell	29575528	Aging Cell	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29575528
Glutathione peroxidase 4 and vitamin E cooperatively prevent hepatocellular degeneration.	Carlson BA, Tobe R, Yefremova E, Tsuji PA, Hoffmann VJ, Schweizer U, Gladyshev VN, Hatfield DL, Conrad M	Redox biology	27262435	Redox Biol	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27262435
Analysis of cancer genomes reveals basic features of human aging and its role in cancer development.	Podolskiy DI, Lobanov AV, Kryukov GV, Gladyshev VN	Nature communications	27515585	Nat Commun	2016 Aug 12	https://www.ncbi.nlm.nih.gov/pubmed/27515585
Intrinsic Versus Extrinsic Cancer Risk Factors and Aging.	Podolskiy DI, Gladyshev VN	Trends in molecular medicine	27544777	Trends Mol Med	2016 Oct	https://www.ncbi.nlm.nih.gov/pubmed/27544777
Organization of the Mammalian Metabolome according to Organ Function, Lineage Specialization, and Longevity.	Ma S, Yim SH, Lee SG, Kim EB, Lee SR, Chang KT, Buffenstein R, Lewis KN, Park TJ, Miller RA, Clish CB, Gladyshev VN	Cell metabolism	26244935	Cell Metab	2015 Aug 4	https://www.ncbi.nlm.nih.gov/pubmed/26244935
The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal.	Seim I, Ma S, Zhou X, Gerashchenko MV, Lee SG, Suydam R, George JC, Bickham JW, Gladyshev VN	Aging	25411232	Aging (Albany NY)	2014 Oct	https://www.ncbi.nlm.nih.gov/pubmed/25411232
LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation.	Simon M, Van Meter M, Ablaeva J, Ke Z, Gonzalez RS, Taguchi T, De Cecco M, Leonova KI, Kogan V, Helfand SL, Neretti N, Roichman A, Cohen HY, Meer MV, Gladyshev VN, Antoch MP, Gudkov AV, Sedivy JM, Seluanov A, Gorbunova V	Cell metabolism	30853213	Cell Metab	2019 Apr 2	https://www.ncbi.nlm.nih.gov/pubmed/30853213
Identification and Application of Gene Expression Signatures Associated with Lifespan Extension.	Tyshkovskiy A, Bozaykut P, Borodinova AA, Gerashchenko MV, Ables GP, Garratt M, Khaitovich P, Clish CB, Miller RA, Gladyshev VN	Cell metabolism	31353263	Cell Metab	2019 Sep 3	https://www.ncbi.nlm.nih.gov/pubmed/31353263
Extrarenal expression of α-klotho, the kidney related longevity gene, in Heterocephalus glaber, the long living Naked Mole Rat.	Morevati M, Mace ML, Egstrand S, Nordholm A, Doganli C, Strand J, Rukov JL, Torsetnes SB, Gorbunova V, Olgaard K, Lewin E	Scientific reports	34321565	Sci Rep	2021 Jul 28	https://www.ncbi.nlm.nih.gov/pubmed/34321565
Translation fidelity coevolves with longevity.	Ke Z, Mallik P, Johnson AB, Luna F, Nevo E, Zhang ZD, Gladyshev VN, Seluanov A, Gorbunova V	Aging cell	28707419	Aging Cell	2017 Oct	https://www.ncbi.nlm.nih.gov/pubmed/28707419
Mechanisms of cancer resistance in long-lived mammals.	Seluanov A, Gladyshev VN, Vijg J, Gorbunova V	Nature reviews. Cancer	29622806	Nat Rev Cancer	2018 Jul	https://www.ncbi.nlm.nih.gov/pubmed/29622806
A whole lifespan mouse multi-tissue DNA methylation clock.	Meer MV, Podolskiy DI, Tyshkovskiy A, Gladyshev VN	eLife	30427307	Elife	2018 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/30427307
Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions.	Petkovich DA, Podolskiy DI, Lobanov AV, Lee SG, Miller RA, Gladyshev VN	Cell metabolism	28380383	Cell Metab	2017 Apr 4	https://www.ncbi.nlm.nih.gov/pubmed/28380383
Stress weakens prefrontal networks: molecular insults to higher cognition.	Arnsten AF	Nature neuroscience	26404712	Nat Neurosci	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26404712
Classical complement cascade initiating C1q protein within neurons in the aged rhesus macaque dorsolateral prefrontal cortex.	Datta D, Leslie SN, Morozov YM, Duque A, Rakic P, van Dyck CH, Nairn AC, Arnsten AFT	Journal of neuroinflammation	31906973	J Neuroinflammation	2020 Jan 6	https://www.ncbi.nlm.nih.gov/pubmed/31906973
Interrogating the Etiology of Sporadic Alzheimer's Disease Using Aging Rhesus Macaques: Cellular, Molecular, and Cortical Circuitry Perspectives.	Datta D	The journals of gerontology. Series A, Biological sciences and medical sciences	37279946	J Gerontol A Biol Sci Med Sci	2023 Aug 27	https://www.ncbi.nlm.nih.gov/pubmed/37279946
cAMP-PKA phosphorylation of tau confers risk for degeneration in aging association cortex.	Carlyle BC, Nairn AC, Wang M, Yang Y, Jin LE, Simen AA, Ramos BP, Bordner KA, Craft GE, Davies P, Pletikos M, Šestan N, Arnsten AF, Paspalas CD	Proceedings of the National Academy of Sciences of the United States of America	24707050	Proc Natl Acad Sci U S A	2014 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/24707050
The aged rhesus macaque manifests Braak stage III/IV Alzheimer's-like pathology.	Paspalas CD, Carlyle BC, Leslie S, Preuss TM, Crimins JL, Huttner AJ, van Dyck CH, Rosene DL, Nairn AC, Arnsten AFT	Alzheimer's & dementia : the journal of the Alzheimer's Association	29241829	Alzheimers Dement	2018 May	https://www.ncbi.nlm.nih.gov/pubmed/29241829
Ameliorating treatment-refractory depression with intranasal ketamine: potential NMDA receptor actions in the pain circuitry representing mental anguish.	Opler LA, Opler MG, Arnsten AF	CNS spectrums	25619798	CNS Spectr	2016 Feb	https://www.ncbi.nlm.nih.gov/pubmed/25619798
Ultrastructural evidence for impaired mitochondrial fission in the aged rhesus monkey dorsolateral prefrontal cortex.	Morozov YM, Datta D, Paspalas CD, Arnsten AFT	Neurobiology of aging	28027494	Neurobiol Aging	2017 Mar	https://www.ncbi.nlm.nih.gov/pubmed/28027494
Noradrenergic α1-Adrenoceptor Actions in the Primate Dorsolateral Prefrontal Cortex.	Datta D, Yang ST, Galvin VC, Solder J, Luo F, Morozov YM, Arellano J, Duque A, Rakic P, Arnsten AFT, Wang M	The Journal of neuroscience : the official journal of the Society for Neuroscience	30755491	J Neurosci	2019 Apr 3	https://www.ncbi.nlm.nih.gov/pubmed/30755491
Persistent Spiking Activity Underlies Working Memory.	Constantinidis C, Funahashi S, Lee D, Murray JD, Qi XL, Wang M, Arnsten AFT	The Journal of neuroscience : the official journal of the Society for Neuroscience	30089641	J Neurosci	2018 Aug 8	https://www.ncbi.nlm.nih.gov/pubmed/30089641
Core Differences in Synaptic Signaling Between Primary Visual and Dorsolateral Prefrontal Cortex.	Yang ST, Wang M, Paspalas CD, Crimins JL, Altman MT, Mazer JA, Arnsten AFT	Cerebral cortex (New York, N.Y. : 1991)	29351585	Cereb Cortex	2018 Apr 1	https://www.ncbi.nlm.nih.gov/pubmed/29351585
Evolution in Neuromodulation-The Differential Roles of Acetylcholine in Higher Order Association vs. Primary Visual Cortices.	Galvin VC, Arnsten AFT, Wang M	Frontiers in neural circuits	30210306	Front Neural Circuits	2018	https://www.ncbi.nlm.nih.gov/pubmed/30210306
A novel dopamine D1 receptor agonist excites delay-dependent working memory-related neuronal firing in primate dorsolateral prefrontal cortex.	Wang M, Datta D, Enwright J, Galvin V, Yang ST, Paspalas C, Kozak R, Gray DL, Lewis DA, Arnsten AFT	Neuropharmacology	30858103	Neuropharmacology	2019 May 15	https://www.ncbi.nlm.nih.gov/pubmed/30858103
Dopamine's Actions in Primate Prefrontal Cortex: Challenges for Treating Cognitive Disorders.	Arnsten AF, Wang M, Paspalas CD	Pharmacological reviews	26106146	Pharmacol Rev	2015 Jul	https://www.ncbi.nlm.nih.gov/pubmed/26106146
Alzheimer's-like pathology in aging rhesus macaques: Unique opportunity to study the etiology and treatment of Alzheimer's disease.	Arnsten AFT, Datta D, Leslie S, Yang ST, Wang M, Nairn AC	Proceedings of the National Academy of Sciences of the United States of America	31871209	Proc Natl Acad Sci U S A	2019 Dec 26	https://www.ncbi.nlm.nih.gov/pubmed/31871209
The 7q11.23 Protein DNAJC30 Interacts with ATP Synthase and Links Mitochondria to Brain Development.	Tebbenkamp ATN, Varela L, Choi J, Paredes MI, Giani AM, Song JE, Sestan-Pesa M, Franjic D, Sousa AMM, Liu ZW, Li M, Bichsel C, Koch M, Szigeti-Buck K, Liu F, Li Z, Kawasawa YI, Paspalas CD, Mineur YS, Prontera P, Merla G, Picciotto MR, Arnsten AFT, Horvath TL, Sestan N	Cell	30318146	Cell	2018 Nov 1	https://www.ncbi.nlm.nih.gov/pubmed/30318146
Unique Molecular Regulation of Higher-Order Prefrontal Cortical Circuits: Insights into the Neurobiology of Schizophrenia.	Datta D, Arnsten AFT	ACS chemical neuroscience	29470055	ACS Chem Neurosci	2018 Sep 19	https://www.ncbi.nlm.nih.gov/pubmed/29470055
Novel Dopamine Therapeutics for Cognitive Deficits in Schizophrenia.	Arnsten AF, Girgis RR, Gray DL, Mailman RB	Biological psychiatry	26946382	Biol Psychiatry	2017 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/26946382
Ketamine's Antidepressant Actions: Potential Mechanisms in the Primate Medial Prefrontal Circuits That Represent Aversive Experience.	Arnsten AF, Murray JD, Seo H, Lee D	Biological psychiatry	27079495	Biol Psychiatry	2016 May 1	https://www.ncbi.nlm.nih.gov/pubmed/27079495
Targeting Prefrontal Cortical Systems for Drug Development: Potential Therapies for Cognitive Disorders.	Arnsten AF, Wang M	Annual review of pharmacology and toxicology	26738476	Annu Rev Pharmacol Toxicol	2016	https://www.ncbi.nlm.nih.gov/pubmed/26738476
Mapping Phosphodiesterase 4D (PDE4D) in Macaque Dorsolateral Prefrontal Cortex: Postsynaptic Compartmentalization in Layer III Pyramidal Cell Circuits.	Datta D, Enwright JF, Arion D, Paspalas CD, Morozov YM, Lewis DA, Arnsten AFT	Frontiers in neuroanatomy	33328902	Front Neuroanat	2020	https://www.ncbi.nlm.nih.gov/pubmed/33328902
Hypothesis: Tau pathology is an initiating factor in sporadic Alzheimer's disease.	Arnsten AFT, Datta D, Del Tredici K, Braak H	Alzheimer's & dementia : the journal of the Alzheimer's Association	33075193	Alzheimers Dement	2021 Jan	https://www.ncbi.nlm.nih.gov/pubmed/33075193
The Effects of Stress Exposure on Prefrontal Cortex: Translating Basic Research into Successful Treatments for Post-Traumatic Stress Disorder.	Arnsten AF, Raskind MA, Taylor FB, Connor DF	Neurobiology of stress	25436222	Neurobiol Stress	2015 Jan 1	https://www.ncbi.nlm.nih.gov/pubmed/25436222
Role of KCNQ potassium channels in stress-induced deficit of working memory.	Arnsten AFT, Jin LE, Gamo NJ, Ramos B, Paspalas CD, Morozov YM, Kata A, Bamford NS, Yeckel MF, Kaczmarek LK, El-Hassar L	Neurobiology of stress	31832507	Neurobiol Stress	2019 Nov	https://www.ncbi.nlm.nih.gov/pubmed/31832507
Interaction Between HCN and Slack Channels Regulates mPFC Pyramidal Cell Excitability and Working Memory.	Wu J, El-Hassar L, Datta D, Thomas M, Zhang Y, Jenkins DP, DeLuca NJ, Chatterjee M, Gribkoff VK, Arnsten AFT, Kaczmarek LK	Research square	37205397	Res Sq	2023 May 4	https://www.ncbi.nlm.nih.gov/pubmed/37205397
Phosphodiesterase PDE4D Is Decreased in Frontal Cortex of Aged Rats and Positively Correlated With Working Memory Performance and Inversely Correlated With PKA Phosphorylation of Tau.	Leslie SN, Datta D, Christensen KR, van Dyck CH, Arnsten AFT, Nairn AC	Frontiers in aging neuroscience	33192469	Front Aging Neurosci	2020	https://www.ncbi.nlm.nih.gov/pubmed/33192469
Age-related calcium dysregulation linked with tau pathology and impaired cognition in non-human primates.	Datta D, Leslie SN, Wang M, Morozov YM, Yang S, Mentone S, Zeiss C, Duque A, Rakic P, Horvath TL, van Dyck CH, Nairn AC, Arnsten AFT	Alzheimer's & dementia : the journal of the Alzheimer's Association	33829643	Alzheimers Dement	2021 Jun	https://www.ncbi.nlm.nih.gov/pubmed/33829643
Studies of aging nonhuman primates illuminate the etiology of early-stage Alzheimer's-like neuropathology: An evolutionary perspective.	Arnsten AFT, Datta D, Preuss TM	American journal of primatology	33960505	Am J Primatol	2021 Nov	https://www.ncbi.nlm.nih.gov/pubmed/33960505
Mono-unsaturated fatty acids link H3K4me3 modifiers to C. elegans lifespan.	Han S, Schroeder EA, Silva-García CG, Hebestreit K, Mair WB, Brunet A	Nature	28379943	Nature	2017 Apr 13	https://www.ncbi.nlm.nih.gov/pubmed/28379943
The impact of common dopamine D2 receptor gene polymorphisms on D2/3 receptor availability: C957T as a key determinant in putamen and ventral striatum.	Smith CT, Dang LC, Buckholtz JW, Tetreault AM, Cowan RL, Kessler RM, Zald DH	Translational psychiatry	28398340	Transl Psychiatry	2017 Apr 11	https://www.ncbi.nlm.nih.gov/pubmed/28398340
Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.	Dulken BW, Leeman DS, Boutet SC, Hebestreit K, Brunet A	Cell reports	28099854	Cell Rep	2017 Jan 17	https://www.ncbi.nlm.nih.gov/pubmed/28099854
Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans.	Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A	Genome research	29141961	Genome Res	2017 Dec	https://www.ncbi.nlm.nih.gov/pubmed/29141961
Lipid Profiles and Signals for Long Life.	Schroeder EA, Brunet A	Trends in endocrinology and metabolism: TEM	26439976	Trends Endocrinol Metab	2015 Nov	https://www.ncbi.nlm.nih.gov/pubmed/26439976
H3K4me3 breadth is linked to cell identity and transcriptional consistency.	Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A	Cell	25083876	Cell	2014 Jul 31	https://www.ncbi.nlm.nih.gov/pubmed/25083876
Bridging the transgenerational gap with epigenetic memory.	Lim JP, Brunet A	Trends in genetics : TIG	23410786	Trends Genet	2013 Mar	https://www.ncbi.nlm.nih.gov/pubmed/23410786
The African turquoise killifish: A research organism to study vertebrate aging and diapause.	Hu CK, Brunet A	Aging cell	29573324	Aging Cell	2018 Jun	https://www.ncbi.nlm.nih.gov/pubmed/29573324
The Genetics of Aging: A Vertebrate Perspective.	Singh PP, Demmitt BA, Nath RD, Brunet A	Cell	30901541	Cell	2019 Mar 21	https://www.ncbi.nlm.nih.gov/pubmed/30901541
Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses.	Benayoun BA, Pollina EA, Singh PP, Mahmoudi S, Harel I, Casey KM, Dulken BW, Kundaje A, Brunet A	Genome research	30858345	Genome Res	2019 Apr	https://www.ncbi.nlm.nih.gov/pubmed/30858345
Vertebrate diapause preserves organisms long term through Polycomb complex members.	Hu CK, Wang W, Brind'Amour J, Singh PP, Reeves GA, Lorincz MC, Alvarado AS, Brunet A	Science (New York, N.Y.)	32079766	Science	2020 Feb 21	https://www.ncbi.nlm.nih.gov/pubmed/32079766
Non-model model organisms.	Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A	BMC biology	28662661	BMC Biol	2017 Jun 29	https://www.ncbi.nlm.nih.gov/pubmed/28662661
A platform for rapid exploration of aging and diseases in a naturally short-lived vertebrate.	Harel I, Benayoun BA, Machado B, Singh PP, Hu CK, Pech MF, Valenzano DR, Zhang E, Sharp SC, Artandi SE, Brunet A	Cell	25684364	Cell	2015 Feb 26	https://www.ncbi.nlm.nih.gov/pubmed/25684364
The Aging Epigenome.	Booth LN, Brunet A	Molecular cell	27259204	Mol Cell	2016 Jun 2	https://www.ncbi.nlm.nih.gov/pubmed/27259204
Shockingly Early: Chromatin-Mediated Loss of the Heat Shock Response.	Booth LN, Brunet A	Molecular cell	26295957	Mol Cell	2015 Aug 20	https://www.ncbi.nlm.nih.gov/pubmed/26295957
The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan.	Valenzano DR, Benayoun BA, Singh PP, Zhang E, Etter PD, Hu CK, Clément-Ziza M, Willemsen D, Cui R, Harel I, Machado BE, Yee MC, Sharp SC, Bustamante CD, Beyer A, Johnson EA, Brunet A	Cell	26638078	Cell	2015 Dec 3	https://www.ncbi.nlm.nih.gov/pubmed/26638078
Variability in paralimbic dopamine signaling correlates with subjective responses to d-amphetamine.	Smith CT, Dang LC, Cowan RL, Kessler RM, Zald DH	Neuropharmacology	27174408	Neuropharmacology	2016 Sep	https://www.ncbi.nlm.nih.gov/pubmed/27174408
Epigenetic regulation of ageing: linking environmental inputs to genomic stability.	Benayoun BA, Pollina EA, Brunet A	Nature reviews. Molecular cell biology	26373265	Nat Rev Mol Cell Biol	2015 Oct	https://www.ncbi.nlm.nih.gov/pubmed/26373265
Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates.	Wang W, Hu CK, Zeng A, Alegre D, Hu D, Gotting K, Ortega Granillo A, Wang Y, Robb S, Schnittker R, Zhang S, Alegre D, Li H, Ross E, Zhang N, Brunet A, Sánchez Alvarado A	Science (New York, N.Y.)	32883834	Science	2020 Sep 4	https://www.ncbi.nlm.nih.gov/pubmed/32883834
Males shorten the life span of C. elegans hermaphrodites via secreted compounds.	Maures TJ, Booth LN, Benayoun BA, Izrayelit Y, Schroeder FC, Brunet A	Science (New York, N.Y.)	24292626	Science	2014 Jan 31	https://www.ncbi.nlm.nih.gov/pubmed/24292626
C. elegans ADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway.	Reich DP, Tyc KM, Bass BL	Genes & development	29483152	Genes Dev	2018 Feb 1	https://www.ncbi.nlm.nih.gov/pubmed/29483152
PKR activation by noncanonical ligands: a 5'-triphosphate requirement versus antisense contamination.	Safran SA, Eckert DM, Leslie EA, Bass BL	RNA (New York, N.Y.)	31239298	RNA	2019 Sep	https://www.ncbi.nlm.nih.gov/pubmed/31239298
Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms.	Reich DP, Bass BL	RNA (New York, N.Y.)	30190375	RNA	2018 Dec	https://www.ncbi.nlm.nih.gov/pubmed/30190375
Neural mechanisms of ageing and cognitive decline.	Bishop NA, Lu T, Yankner BA	Nature	20336135	Nature	2010 Mar 25	https://www.ncbi.nlm.nih.gov/pubmed/20336135
Altered social behavior and neuronal development in mice lacking the Uba6-Use1 ubiquitin transfer system.	Lee PC, Dodart JC, Aron L, Finley LW, Bronson RT, Haigis MC, Yankner BA, Harper JW	Molecular cell	23499007	Mol Cell	2013 Apr 25	https://www.ncbi.nlm.nih.gov/pubmed/23499007
Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease.	Lipinski MM, Zheng B, Lu T, Yan Z, Py BF, Ng A, Xavier RJ, Li C, Yankner BA, Scherzer CR, Yuan J	Proceedings of the National Academy of Sciences of the United States of America	20660724	Proc Natl Acad Sci U S A	2010 Aug 10	https://www.ncbi.nlm.nih.gov/pubmed/20660724
Sustained axon regeneration induced by co-deletion of PTEN and SOCS3.	Sun F, Park KK, Belin S, Wang D, Lu T, Chen G, Zhang K, Yeung C, Feng G, Yankner BA, He Z	Nature	22056987	Nature	2011 Nov 6	https://www.ncbi.nlm.nih.gov/pubmed/22056987
Negative regulation of Vps34 by Cdk mediated phosphorylation.	Furuya T, Kim M, Lipinski M, Li J, Kim D, Lu T, Shen Y, Rameh L, Yankner B, Tsai LH, Yuan J	Molecular cell	20513426	Mol Cell	2010 May 28	https://www.ncbi.nlm.nih.gov/pubmed/20513426
Sorting Out Presenilins in Alzheimer's Disease.	Wolfe MS, Yankner BA	Cell	27368096	Cell	2016 Jun 30	https://www.ncbi.nlm.nih.gov/pubmed/27368096
Slowing Down Aging.	Meyer K, Yankner BA	Cell metabolism	28978424	Cell Metab	2017 Oct 3	https://www.ncbi.nlm.nih.gov/pubmed/28978424
The histone demethylase LSD1/KDM1A promotes the DNA damage response.	Mosammaparast N, Kim H, Laurent B, Zhao Y, Lim HJ, Majid MC, Dango S, Luo Y, Hempel K, Sowa ME, Gygi SP, Steen H, Harper JW, Yankner B, Shi Y	The Journal of cell biology	24217620	J Cell Biol	2013 Nov 11	https://www.ncbi.nlm.nih.gov/pubmed/24217620
Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput.	Eberwine J, Kim J, Anafi RC, Brem S, Bucan M, Fisher SA, Grady MS, Herr AE, Issadore D, Jeong H, Kim H, Lee D, Rubakhin S, Sul JY, Sweedler JV, Wolf JA, Zaret KS, Zou J	Nature methods	36899160	Nat Methods	2023 Mar	https://www.ncbi.nlm.nih.gov/pubmed/36899160
CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.	Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, Eberwine J	Nature communications	37963886	Nat Commun	2023 Nov 14	https://www.ncbi.nlm.nih.gov/pubmed/37963886
Caspase-Activated Oligonucleotide Probe.	Yang L, Eberwine JH, Dmochowski IJ	Bioconjugate chemistry	32786369	Bioconjug Chem	2020 Sep 16	https://www.ncbi.nlm.nih.gov/pubmed/32786369

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