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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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Tolerance of infections. | Ayres JS, Schneider DS | Annual review of immunology | 22224770 | Annu Rev Immunol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22224770 |
| 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 |
| Tracing personalized health curves during infections. | Schneider DS | PLoS biology | 21957398 | PLoS Biol | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21957398 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| Discovery of BI-2493, a Pan-KRAS Inhibitor Showing In Vivo Efficacy. | Bröker J, Waterson AG, Hodges TR, Abbott JR, Arnold A, Böttcher J, Braun N, Cui J, Fuchs JE, Gerstberger T, Gogg S, Hanner S, Herdeis L, Howell LW, Mantoulidis A, Mayer M, Phan J, Rocchetti F, Sankar K, Sarkar D, Schaaf O, Sensintaffar JL, Sun Q, Wunberg T, Fesik SW | Journal of medicinal chemistry | 40709733 | J Med Chem | 2025 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/40709733 |
| 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 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 |
| 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 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 |
| 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 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 |
| 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 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 |
| 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 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Transgenerational genetic effects. | Nelson VR, Nadeau JH | Epigenomics | 22122083 | Epigenomics | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22122083 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| In vitro human corticogenesis. | Wang Y, Dolmetsch R | Neuron | 23395367 | Neuron | 2013 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/23395367 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Modelling to contain pandemics. | Epstein JM | Nature | 19661897 | Nature | 2009 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/19661897 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Free-Breathing and Ungated Dynamic MRI Using Navigator-Less Spiral SToRM. | Ahmed AH, Zhou R, Yang Y, Nagpal P, Salerno M, Jacob M | IEEE transactions on medical imaging | 32746136 | IEEE Trans Med Imaging | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32746136 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Oligonucleotide-based tools for studying zebrafish development. | Shestopalov IA, Chen JK | Zebrafish | 20392138 | Zebrafish | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20392138 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior. | Freddolino L, Tavazoie S | Annual review of cell and developmental biology | 22559263 | Annu Rev Cell Dev Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22559263 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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- 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Bacteria as control engineers. | Allison KR, Collins JJ | Molecular cell | 21211717 | Mol Cell | 2011 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/21211717 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 bundles. | Thoresen T, Lenz M, Gardel ML | Biophysical journal | 21641315 | Biophys J | 2011 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/21641315 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| "Utilizing" signal detection theory. | Lynn SK, Barrett LF | Psychological science | 25097061 | Psychol Sci | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25097061 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Emotions are real. | Barrett LF | Emotion (Washington, D.C.) | 22642358 | Emotion | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22642358 |
| 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 |
| 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 |
| 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 |
| Deficits in Face Recognition and Consequent Quality-of-Life Factors in Individuals with Cerebral Visual Impairment. | Bauer CM, Manley CE, Ravenscroft J, Cabral H, Dilks DD, Bex PJ | Vision (Basel, Switzerland) | 36810313 | Vision (Basel) | 2023 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/36810313 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Reduced stereotypicality and spared use of facial expression predictions for social evaluation in autism. | Robles M, Ramos-Grille I, Hervás A, Duran-Tauleria E, Galiano-Landeira J, Wormwood JB, Falter-Wagner CM, Chanes L | International journal of clinical and health psychology : IJCHP | 38426036 | Int J Clin Health Psychol | 2024 Apr-Jun | https://www.ncbi.nlm.nih.gov/pubmed/38426036 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| "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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| '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 |
| 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 |
| 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 |
| 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 |
| The human microbiome: ecosystem resilience and health. | Relman DA | Nutrition reviews | 22861804 | Nutr Rev | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22861804 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The Picornaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens. | Andino R, Kirkegaard K, Macadam A, Racaniello VR, Rosenfeld AB | The Journal of infectious diseases | 37849401 | J Infect Dis | 2023 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/37849401 |
| 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 spread of naked viruses. | Bird SW, Kirkegaard K | Autophagy | 25680079 | Autophagy | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25680079 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The pharmacophore of a peptoid VEGF receptor 2 antagonist includes both side chain and main chain residues. | Udugamasooriya DG, Dunham G, Ritchie C, Brekken RA, Kodadek T | Bioorganic & medicinal chemistry letters | 18653335 | Bioorg Med Chem Lett | 2008 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/18653335 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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-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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The Dynamics of Inducible Genetic Circuits(). | Yang Z, Rousseau RJ, Mahdavi SD, Garcia HG, Phillips R | bioRxiv : the preprint server for biology | 40463218 | bioRxiv | 2025 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/40463218 |
| Biological Processes as Exploratory Dynamics. | Kondev J, Kirschner M, Garcia HG, Salmon GL, Phillips R | bioRxiv : the preprint server for biology | 40661560 | bioRxiv | 2025 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/40661560 |
| Many Will Enter, Few Will Win: Cost and Sensitivity of Exploratory Dynamics. | Koslover EF, Lin MM, Phillips R | ArXiv | 40909154 | ArXiv | 2025 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/40909154 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The Environment-Dependent Regulatory Landscape of the E. coli Genome. | Röschinger T, Lee HJ, Pan RW, Solini G, Faizi K, Quan B, Chou TF, Mani M, Quake S, Phillips R | ArXiv | 40463697 | ArXiv | 2025 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/40463697 |
| Biological Processes as Exploratory Dynamics. | Kondev J, Kirschner M, Garcia HG, Salmon GL, Phillips R | ArXiv | 40503020 | ArXiv | 2025 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/40503020 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Seeing with an extra sense. | Phillips R | Current biology : CB | 39437733 | Curr Biol | 2024 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/39437733 |
| Many will enter, few will win: Cost and sensitivity of exploratory dynamics. | Koslover EF, Lin MM, Phillips R | Biophysical journal | 40931529 | Biophys J | 2026 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/40931529 |
| Biological processes as exploratory dynamics. | Kondev J, Kirschner M, Garcia HG, Salmon GL, Phillips R | Biophysical journal | 40936266 | Biophys J | 2026 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/40936266 |
| Bifurcations and multistability in inducible three-gene toggle switch networks. | Rousseau RJ, Phillips R | ArXiv | 41256887 | ArXiv | 2025 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/41256887 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Approximating the living. | Phillips R | Seminars in cell & developmental biology | 40896889 | Semin Cell Dev Biol | 2025 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/40896889 |
| Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome. | Tadmor AD, Mahmoudabadi G, Foley HB, Phillips R | Frontiers in microbiomes | 41852816 | Front Microbiomes | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/41852816 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Dynamical Mechanisms for Coordinating Long-term Working Memory Based on the Precision of Spike-timing in Cortical Neurons. | Sejnowski TJ | ArXiv | 41445814 | ArXiv | 2026 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/41445814 |
| Pseudouridine selects RNAs for extracellular transport. | Scacchetti A, Shields EJ, Reich LN, Doherty JF, Tasca JA, Lee GE, Lauman R, Chanaday NL, Garcia BA, Conine CC, Bonasio R | bioRxiv : the preprint server for biology | 41280092 | bioRxiv | 2025 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/41280092 |
| Astrocyte CCN1 stabilizes neural circuits in the adult brain. | Sancho L, Boisvert MM, Eddy T, Burgado J, Contreras M, Labarta-Bajo L, Wang E, Tatsumi L, Allen NJ | Nature | 41407862 | Nature | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41407862 |
| 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 |
| 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 control of spatial transcriptome in live cells and neurons. | Han M, Fu ML, Zhu Y, Choi AA, Li E, Bezney J, Cai S, Miles L, Ma Y, Qi LS | Nature | 40399675 | Nature | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40399675 |
| 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 |
| High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH. | Zhu Y, Balaji A, Han M, Andronov L, Roy AR, Wei Z, Chen C, Miles L, Cai S, Gu Z, Tse A, Yu BC, Uenaka T, Lin X, Spakowitz AJ, Moerner WE, Qi LS | Cell | 40239646 | Cell | 2025 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/40239646 |
| CRISPR-Cas13d-Mediated Targeting of a Context-Specific Essential Gene Enables Selective Elimination of Uveal Melanoma. | Stauber D, Sosnick L, Ma Y, Pimcharoen S, Lawanprasert A, Murthy N, Myung D, Qi LS | bioRxiv : the preprint server for biology | 40894775 | bioRxiv | 2025 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/40894775 |
| Precision Transcriptome Editing. | Chen C, Qi LS | ACS synthetic biology | 39435985 | ACS Synth Biol | 2024 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/39435985 |
| 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 |
| Next-generation hybridization chain reaction tools with enhanced sensitivities to detect challenging targets. | Singh C, Bali N, Coughlin GM, Xu J, Polansky JY, Herget U, Gilbert MS, Cammidge T, Spigolon G, Smirnova Y, Gradinaru V, Zinn K, Prober DA | bioRxiv : the preprint server for biology | 40964373 | bioRxiv | 2025 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/40964373 |
| 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 |
| Structural basis of liver de-targeting and neuronal tropism of CNS-targeted AAV capsids. | Brittain TJ, Jang S, Coughlin GM, Barcelona BH, Giriat I, Ristic F, Appling N, Chossis CP, Shay TF, Gradinaru V | bioRxiv : the preprint server for biology | 40501988 | bioRxiv | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/40501988 |
| Fast, accurate ranking of engineered proteins by target-binding propensity using structure modeling. | Ding X, Chen X, Sullivan EE, Shay TF, Gradinaru V | Molecular therapy : the journal of the American Society of Gene Therapy | 38582966 | Mol Ther | 2024 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/38582966 |
| AAVs targeting human carbonic anhydrase IV enhance gene delivery to the brain. | Lin C, Chen X, Hoang JD, Ristic F, Fan Y, Jang S, Chung JHA, Sullivan EE, Gawda T, Kavvathas B, Tran I, Li Y, Steele AD, Shay TF, Gradinaru V | Cell reports | 41175373 | Cell Rep | 2025 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/41175373 |
| 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 genomics of AAV vectors reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo. | Coughlin GM, Borsos M, Barcelona BH, Appling N, Mayfield AMH, Mackey ED, Eser RA, Jackson CR, Chen X, Kumar SR, Gradinaru V | Nature biotechnology | 40113953 | Nat Biotechnol | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/40113953 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cholinergic neuronal activity promotes diffuse midline glioma growth through muscarinic signaling. | Drexler R, Drinnenberg A, Gavish A, Yalçin B, Shamardani K, Rogers AE, Mancusi R, Trivedi V, Taylor KR, Kim YS, Woo PJ, Soni N, Su M, Ravel A, Tatlock E, Midler A, Wu SH, Ramakrishnan C, Chen R, Ayala-Sarmiento AE, Fernandez Pacheco DR, Siverts L, Daigle TL, Tasic B, Zeng H, Breunig JJ, Deisseroth K, Monje M | Cell | 40541184 | Cell | 2025 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/40541184 |
| 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 |
| 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 |
| Dysregulated Microglial Synaptic Engulfment in Diffuse Midline Glioma. | Mancusi R, Tatlock E, Shamardani K, Acosta-Alvarez L, Drexler R, Trivedi V, Gavish A, Niizuma K, Soni N, Woo P, Mulinyawe S, Jahan S, Logan N, Malacon K, Byun YG, Geraghty A, Barron T, Taylor K, Monje M | bioRxiv : the preprint server for biology | 41497590 | bioRxiv | 2025 Dec 25 | https://www.ncbi.nlm.nih.gov/pubmed/41497590 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Synaptic Communication in Brain Cancer. | Monje M | Cancer research | 32381657 | Cancer Res | 2020 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/32381657 |
| 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 |
| Response to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect. | Takahashi T, Stoiljkovic M, Song E, Gao XB, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu ZW, Kristant A, Zhang Y, Sulkowski P, Glazer PM, Kaczmarek LK, Horvath TL, Iwasaki A | Neuron | 36863323 | Neuron | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36863323 |
| The neuroscience of cancer. | Mancusi R, Monje M | Nature | 37316719 | Nature | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37316719 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Immunotherapy-related cognitive impairment after CAR T cell therapy in mice. | Geraghty AC, Acosta-Alvarez L, Rotiroti MC, Dutton S, O'Dea MR, Kim W, Trivedi V, Mancusi R, Shamardani K, Malacon K, Woo PJ, Martinez-Velez N, Pham T, Reche-Ley NN, Otubu G, Castenada EH, Nwangwu K, Xu H, Mulinyawe SB, Zamler DB, Ni L, Cross K, Rustenhoven J, Kipnis J, Liddelow SA, Mackall CL, Majzner RG, Monje M | Cell | 40359942 | Cell | 2025 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/40359942 |
| Neuroligin-3 interaction with CSPG4 regulates normal and malignant glial precursors through PIEZO1. | Gillespie SM, Seok Kim Y, Geraghty AC, Yalçın B, Mancusi R, Hysinger J, English Ivec A, Reed J, Drexler R, Quezada M, Malacon K, Woo P, Mount C, Yang A, Lam M, Pan Y, Bradley Zuchero J, Trotter J, Monje M | bioRxiv : the preprint server for biology | 40791371 | bioRxiv | 2025 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/40791371 |
| Serotonergic neuron-glioma interactions drive high-grade glioma pathophysiology. | Drexler R, Yalçın B, Mancusi R, Rogers A, Shamardani K, Woo PJ, Ravel A, Wu S, Yabo YA, Steger L, de Biagi-Junior CAO, Cascio CL, Malenka R, Heifets BD, Filbin MG, Heiland DH, Deisseroth K, Monje M | bioRxiv : the preprint server for biology | 41427306 | bioRxiv | 2025 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/41427306 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| The neurobiology of long COVID. | Monje M, Iwasaki A | Neuron | 36288726 | Neuron | 2022 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/36288726 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Neuronal activity-dependent mechanisms of small cell lung cancer pathogenesis. | Savchuk S, Gentry KM, Wang W, Carleton E, Biagi-Junior CAO, Luthria K, Yalçın B, Ni L, Farnsworth HC, Davis RA, Drexler R, Melms JC, Liu Y, Acosta-Alvarez L, Hartmann GG, Pavarino EC, LaBelle J, Woo PJ, Toland AM, Qu F, Kim YS, Filbin MG, Krasnow MA, Ligon KL, Izar B, Sage J, Sabatini BL, Monje M, Venkatesh HS | Nature | 40931074 | Nature | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40931074 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Association of Brain Age, Lesion Volume, and Functional Outcome in Patients With Stroke. | Liew SL, Schweighofer N, Cole JH, Zavaliangos-Petropulu A, Tavenner BP, Han LKM, Hahn T, Schmaal L, Donnelly MR, Jeong JN, Wang Z, Abdullah A, Kim JH, Hutton A, Barisano G, Borich MR, Boyd LA, Brodtmann A, Buetefisch CM, Byblow WD, Cassidy JM, Charalambous CC, Ciullo V, Conforto AB, Dacosta-Aguayo R, DiCarlo JA, Domin M, Dula AN, Egorova-Brumley N, Feng W, Geranmayeh F, Gregory CM, Hanlon CA, Hayward K, Holguin JA, Hordacre B, Jahanshad N, Kautz SA, Khlif MS, Kim H, Kuceyeski A, Lin DJ, Liu J, Lotze M, MacIntosh BJ, Margetis JL, Mataro M, Mohamed FB, Olafson ER, Park G, Piras F, Revill KP, Roberts P, Robertson AD, Sanossian N, Schambra HM, Seo NJ, Soekadar SR, Spalletta G, Stinear CM, Taga M, Tang WK, Thielman GT, Vecchio D, Ward NS, Westlye LT, Winstein CJ, Wittenberg GF, Wolf SL, Wong KA, Yu C, Cramer SC, Thompson PM | Neurology | 37015818 | Neurology | 2023 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/37015818 |
| 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 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 |
| 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 |
| 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 | Nature neuroscience | 41461932 | Nat Neurosci | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41461932 |
| Sequestration of growth cone surface proteins by cytoplasmic Lrrtm2 induces de novo amygdala innervation by cerebral cortex associative neurons. | Tillman DE, Durak O, Veeraraghavan P, Froberg JE, Wheeler G, Budnik B, Macklis JD | bioRxiv : the preprint server for biology | 41993341 | bioRxiv | 2026 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/41993341 |
| 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 |
| 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 |
| 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 |
| 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 | 2025 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/38712174 |
| 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 |
| 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 |
| 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 | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/39763931 |
| 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 | eLife | 41589677 | Elife | 2026 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/41589677 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Molecular Gold Nanoclusters for Advanced NIR-II Bioimaging and Therapy. | Baghdasaryan A, Dai H | Chemical reviews | 40435324 | Chem Rev | 2025 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/40435324 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Plasticity of Spine Structure: Local Signaling, Translation and Cytoskeletal Reorganization. | Nakahata Y, Yasuda R | Frontiers in synaptic neuroscience | 30210329 | Front Synaptic Neurosci | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30210329 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Rab10 inactivation promotes AMPAR trafficking and spine enlargement during long-term potentiation. | Wang J, Nishiyama J, Parra-Bueno P, Okaz E, Oz G, Liu X, Watabe T, Suponitsky-Kroyter I, McGraw TE, Szatmari EM, Yasuda R | bioRxiv : the preprint server for biology | 40501544 | bioRxiv | 2025 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/40501544 |
| Rab10 inactivation promotes AMPAR trafficking and spine enlargement during long-term potentiation. | Wang J, Nishiyama J, Parra-Bueno P, Okaz E, Oz G, Liu X, Watabe T, Suponitsky-Kroyter I, McGraw TE, Szatmari EM, Yasuda R | eLife | 40986440 | Elife | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/40986440 |
| 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 |
| Canonical Wnt Signaling Suppresses Brain Endothelial Cell Transcytosis to Maintain Blood-Brain Barrier Integrity. | du Maine X, Gu C | bioRxiv : the preprint server for biology | 40161584 | bioRxiv | 2025 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/40161584 |
| HaloTrace: A spatiotemporally precise fluorescent readout of blood-brain barrier permeability in mice. | Zucker HL, Konshina E, Mitchell P, Gu C | bioRxiv : the preprint server for biology | 41279380 | bioRxiv | 2025 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/41279380 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nanoscale Resolution Imaging of Whole Mouse Embryos Using Expansion Microscopy. | Sim J, Park CE, Cho I, Min K, Eom M, Han S, Jeon H, Cho ES, Lee Y, Yun YH, Lee S, Cheon DH, Kim J, Kim M, Cho HJ, Park JW, Kumar A, Chong Y, Kang JS, Piatkevich KD, Jung EE, Kang DS, Kwon SK, Kim J, Yoon KJ, Lee JS, Kim CH, Choi M, Kim JW, Song MR, Choi HJ, Boyden ES, Yoon YG, Chang JB | ACS nano | 39964913 | ACS Nano | 2025 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/39964913 |
| 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 |
| 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 |
| Large-scale high-density brain-wide neural recording in nonhuman primates. | Trautmann EM, Hesse JK, Stine GM, Xia R, Zhu S, O'Shea DJ, Karsh B, Colonell J, Lanfranchi FF, Vyas S, Zimnik A, Amematsro E, Steinemann NA, Wagenaar DA, Pachitariu M, Andrei A, Lopez CM, O'Callaghan J, Putzeys J, Raducanu BC, Welkenhuysen M, Churchland M, Moore T, Shadlen M, Shenoy K, Tsao D, Dutta B, Harris T | Nature neuroscience | 40551025 | Nat Neurosci | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40551025 |
| A compressed hierarchy for visual form processing in the tree shrew. | Lanfranchi FF, Wekselblatt J, Wagenaar DA, Tsao DY | Nature | 40866712 | Nature | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40866712 |
| Mapping function in the tree shrew visual system using functional ultrasound imaging. | Wekselblatt JB, Nayak R, Lanfranchi FF, Luongo F | bioRxiv : the preprint server for biology | 41256461 | bioRxiv | 2025 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/41256461 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| The big data problem: turning maps into knowledge. | Engert F | Neuron | 25233305 | Neuron | 2014 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/25233305 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| Engineering brain activity patterns by neuromodulator polytherapy for treatment of disorders. | Ghannad-Rezaie M, Eimon PM, Wu Y, Yanik MF | Nature communications | 31197165 | Nat Commun | 2019 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/31197165 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A neuroimmune circuit mediates cancer cachexia-associated apathy. | Zhu XA, Starosta S, Ferrer M, Hou J, Chevy Q, Lucantonio F, Muñoz-Castañeda R, Zhang F, Zang K, Zhao X, Fiocchi FR, Bergstrom M, Siebels AA, Upin T, Wulf M, Evans S, Kravitz AV, Osten P, Janowitz T, Pignatelli M, Kepecs A | Science (New York, N.Y.) | 40208971 | Science | 2025 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/40208971 |
| A cortical circuit for orchestrating oromanual food manipulation. | An X, Li Y, Matho K, Mohan H, Xu XH, Boato F, Whishaw IQ, Kepecs A, Huang ZJ | Neuron | 41895264 | Neuron | 2026 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/41895264 |
| 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 |
| VTA dopamine neuron activity produces spatially organized value representations. | Pan-Vazquez A, Zimmerman CA, McMannon B, Fabre JMJ, Louka M, Jia T, Sagiv Y, West SJ, Faulkner M, International Brain Laboratory, Dayan P, Witten IB | bioRxiv : the preprint server for biology | 41279742 | bioRxiv | 2025 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/41279742 |
| Stress resilience is associated with transcriptional remodeling in the VTA. | Minerva AR, McMannon B, Lin R, Zhukovskaya A, Witten IB, Peña CJ | bioRxiv : the preprint server for biology | 41292885 | bioRxiv | 2025 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/41292885 |
| 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 | Nature | 40175547 | Nature | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40175547 |
| Between planning and map building: Prioritizing replay when future goals are uncertain. | Sagiv Y, Akam T, Witten IB, Daw ND | Neuron | 41151586 | Neuron | 2025 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/41151586 |
| Stress resilience is associated with transcriptional remodeling in the VTA. | Minerva AR, McMannon B, Lin R, Zhukovskaya A, Witten IB, Peña CJ | Cell reports | 41575858 | Cell Rep | 2026 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/41575858 |
| Striatal pathways oppositely shift cortical activity along the decision axis. | Cho JR, Bolkan SS, Brown LS, Skuza M, El-Jayyousi Y, Midler B, Fetcho RN, Zimmerman CA, Pan-Vazquez A, Schottdorf M, Bondy AG, Sanchez MA, Lopez Luna JF, Luna A, Eilers T, Kalmbach AS, Lu Y, Lynch LA, Witten IB | bioRxiv : the preprint server for biology | 40766374 | bioRxiv | 2025 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/40766374 |
| Synaptic editing of frontostriatal circuitry prevents excessive grooming in SAPAP3-deficient mice. | Walder-Christensen KK, Soliman HA, Calakos N, Dzirasa K | bioRxiv : the preprint server for biology | 40196561 | bioRxiv | 2025 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/40196561 |
| 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 |
| 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 | Cell genomics | 38991604 | Cell Genom | 2024 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/38991604 |
| 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 |
| FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data. | Patel R, Pham K, Chandrashekar H, Phillips-Cremins JE | Nature methods | 40355724 | Nat Methods | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40355724 |
| 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 |
| Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons. | Paranjapye A, Ahmad R, Su S, Waldman AJ, Philips-Cremins J, Zhang S, Korb E | bioRxiv : the preprint server for biology | 40196547 | bioRxiv | 2025 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/40196547 |
| 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 |
| 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 |
| 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 |
| Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons. | Waldman AJ, Pham K, Titus KR, Nikish A, Liu C, Ryu HS, Muppidi SS, Chandradoss KR, Xu P, Patel R, Boya R, Phillips-Cremins JE | bioRxiv : the preprint server for biology | 41256638 | bioRxiv | 2025 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/41256638 |
| 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 |
| 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 |
| B cell stimulation changes the structure and higher-order organization of the inactive X chromosome. | Sierra I, Toothacre NE, van der Weide RH, Lovell CD, Nguyen SC, Jordan Barnett R, Cook AL, Ryu HS, Pyfrom S, Wang H, Beiting D, Philips-Cremins JE, Joyce EF, Anguera MC | bioRxiv : the preprint server for biology | 39975382 | bioRxiv | 2025 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/39975382 |
| B cell stimulation changes the structure and higher-order organization of the inactive X chromosome. | Sierra I, Toothacre NE, van der Weide RH, Lovell CD, Nguyen SC, Barnett RJ, Cook AL, Ryu HS, Pyfrom S, Wang H, Beiting D, Philips-Cremins JE, Joyce EF, Anguera MC | Cell reports | 40014450 | Cell Rep | 2025 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/40014450 |
| 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 |
| Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons. | Paranjapye A, Ahmad R, Su S, Waldman AJ, Phillips-Cremins JE, Zhang S, Korb E | Genome research | 41115806 | Genome Res | 2025 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/41115806 |
| 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 |
| 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 |
| Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity. | Pham K, Malachowski T, Zhou L, Kim JH, Su C, Phillips-Cremins JE | bioRxiv : the preprint server for biology | 40166285 | bioRxiv | 2025 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/40166285 |
| 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 |
| Learning induces persistent chromatin loops underlying robust gene expression during memory recall. | Xu P, Raanin Chandradoss K, Lukasak B, Paranjapye A, Waldman AJ, Pham K, Ryu HS, Liu C, Titus KR, Sureka R, Shepherd J, Korb E, Phillips-Cremins JE | bioRxiv : the preprint server for biology | 41256431 | bioRxiv | 2025 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/41256431 |
| Cortico-thalamic communication for action coordination in a skilled motor sequence. | Li Y, An X, Mulcahey PJ, Qian Y, Xu XH, Zhao S, Mohan H, Suryanarayana SM, Bachschmid-Romano L, Brunel N, Whishaw IQ, Huang ZJ | bioRxiv : the preprint server for biology | 37961483 | bioRxiv | 2024 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/37961483 |
| 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 | eLife | 39012795 | Elife | 2024 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/39012795 |
| Distinct neurogenic pathways shape the diversification and mosaic organization of cortical output channels. | Suryanarayana SM, An X, Qian Y, Zhao S, Mohan H, Huang ZJ | Neuron | 41887213 | Neuron | 2026 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/41887213 |
| 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 |
| 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, Huang ZJ, Southwell DG | bioRxiv : the preprint server for biology | 39677799 | bioRxiv | 2025 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/39677799 |
| 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 |
| 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 M, Huang ZJ, Southwell D | Cell reports | 40700016 | Cell Rep | 2025 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/40700016 |
| Distinct neurogenic pathways shape the diversification and mosaic organization of cortical output channels. | Suryanarayana SM, An X, Qian Y, Zhao S, Mohan H, Huang ZJ | bioRxiv : the preprint server for biology | 40777408 | bioRxiv | 2025 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/40777408 |
| Orderly specification and precise laminar deployment of mouse cortical projection neuron types through intermediate progenitors. | Huilgol D, Levine JM, Galbavy W, Wang BS, Huang ZJ | Developmental cell | 40068685 | Dev Cell | 2025 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/40068685 |
| 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 |
| Motor Cortical Output Integrates Distorted Proprioceptive Feedback. | Li Y, Xu XH, Pan S, An X, Mulcahey PJ, Qiu Z, Zhao S, Li N, Pearson J, Huang ZJ | bioRxiv : the preprint server for biology | 41292794 | bioRxiv | 2025 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/41292794 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Specialized structure of neural population codes in parietal cortex outputs. | Safaai H, Wang AY, Kira S, Blanco Malerba S, Panzeri S, Harvey CD | Nature neuroscience | 41174169 | Nat Neurosci | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41174169 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Intercellular communication in the brain through a dendritic nanotubular network. | Chang M, Krüssel S, Parajuli LK, Kim J, Lee D, Merodio A, Kwon J, Okabe S, Kwon HB | Science (New York, N.Y.) | 41037599 | Science | 2025 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/41037599 |
| 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 |
| Serotonin in the orbitofrontal cortex enhances cognitive flexibility. | Hyun JH, Hannan P, Iwamoto H, Blakely RD, Kwon HB | bioRxiv : the preprint server for biology | 36945634 | bioRxiv | 2023 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/36945634 |
| Cutting-edge methodologies for tagging and tracing active neuronal coding in the brain. | Nagahama K, Jung VH, Kwon HB | Current opinion in neurobiology | 40056794 | Curr Opin Neurobiol | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40056794 |
| Intercellular communication in the brain via dendritic nanotubular network. | Chang M, Krüssel S, Parajuli LK, Kim J, Lee D, Merodio A, Kwon J, Okabe S, Kwon HB | bioRxiv : the preprint server for biology | 40475405 | bioRxiv | 2025 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/40475405 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Parasitoid Wasp Culturing and Assay to Study Parasitoid-induced Reproductive Modifications in Drosophila. | Sadanandappa MK, Sathyanarayana SH, Bosco G | Bio-protocol | 36789084 | Bio Protoc | 2023 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/36789084 |
| 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 |
| Protocol for studying parasitoid-induced long-term effects in Drosophila. | Sadanandappa MK, Bosco G | STAR protocols | 39499614 | STAR Protoc | 2024 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/39499614 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Identifying Parabrachial Neurons Selectively Regulating Satiety for Highly Palatable Food in Mice. | Rodriguez E, Ryu D, Zhao S, Han BX, Wang F | eNeuro | 31662323 | eNeuro | 2019 Nov/Dec | https://www.ncbi.nlm.nih.gov/pubmed/31662323 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| CRISPR-Cas9: Prospects and Challenges. | Zhang F | Human gene therapy | 26176430 | Hum Gene Ther | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26176430 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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-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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Concurrent presentation of memory-related odors and sounds nullified sleep reactivation benefits. | Subramanian G, Zelano C, Paller KA, Schechtman E | bioRxiv : the preprint server for biology | 40766463 | bioRxiv | 2025 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/40766463 |
| Using Real-time Reporting to Investigate Visual Experiences in Dreams. | Konkoly KR, Al-Youssef S, Mazurek CY, Mallett R, Morris DJ, Gales A, Arnulf I, Oudiette D, Paller KA | Journal of cognitive neuroscience | 41026873 | J Cogn Neurosci | 2026 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/41026873 |
| 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 |
| Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals. | Hassan NT, Van Treeck B, Rodríguez-Vargas A, Sheppard AE, Collins K, Adelson DL | bioRxiv : the preprint server for biology | 40654615 | bioRxiv | 2025 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/40654615 |
| Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs. | Manning AC, Bashir MM, Rapchak K, Huff CJ, Jimenez AR, Gonzalez S, Woodruff CL, Upton HE, Collins K, Lowe TM, Tucker JM | mBio | 40444975 | mBio | 2025 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/40444975 |
| 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 | Science advances | 40540573 | Sci Adv | 2025 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/40540573 |
| 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 |
| 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 |
| Structural and biochemical studies of mobile retrotransposon proteins in action. | Thawani A, Collins K, Nogales E | Current opinion in structural biology | 40334519 | Curr Opin Struct Biol | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40334519 |
| Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies. | Singh J, Williams JK, Elliott Q, Jhawar R, Ferguson L, Collins K, Schekman R | Proceedings of the National Academy of Sciences of the United States of America | 41060753 | Proc Natl Acad Sci U S A | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41060753 |
| 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 |
| 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 | bioRxiv : the preprint server for biology | 39574714 | bioRxiv | 2024 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/39574714 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Template and target-site recognition by human LINE-1 in retrotransposition. | Thawani A, Florez Ariza AJ, Nogales E, Collins K | Nature | 38096901 | Nature | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38096901 |
| miRNA-Mediated Regulation of Gene Expression During Early Activation in Jurkat Cells. | Mukherjee P, Leal-Calvo T, Ferguson L, Cate JHD | bioRxiv : the preprint server for biology | 40667200 | bioRxiv | 2025 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/40667200 |
| 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 |
| 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 |
| 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 |
| Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR. | Gustafsson HT, Ferguson L, Galan C, Yu T, Upton H, Kaymak E, Weng Z, Collins K, Rando OJ | eLife | 40277192 | Elife | 2025 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/40277192 |
| Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies. | Singh J, Williams JK, Elliott Q, Jhawar R, Ferguson L, Collins K, Schekman R | bioRxiv : the preprint server for biology | 40475654 | bioRxiv | 2025 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/40475654 |
| Translational Downregulation of 5' TOP mRNAs During T Cell Exhaustion. | Pledger ES, Ambavaram N, Ferguson L, Cate JHD | bioRxiv : the preprint server for biology | 41473299 | bioRxiv | 2025 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/41473299 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| "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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Universal atrial coordinates applied to visualisation, registration and construction of patient specific meshes. | Roney CH, Pashaei A, Meo M, Dubois R, Boyle PM, Trayanova NA, Cochet H, Niederer SA, Vigmond EJ | Medical image analysis | 31026761 | Med Image Anal | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31026761 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Patterns of Mitochondrial ATP Predict Tissue Folding. | Lemma B, Rothstein M, Zhang P, Waas B, Kilwein M, Topiwala S, Zhang SX, Sudhakar A, Goodwin K, Gavis ER, Mallarino R, Kosmrlj A, Nelson CM | bioRxiv : the preprint server for biology | 40909554 | bioRxiv | 2025 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/40909554 |
| 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 |
| Biophysical mechanisms of morphogenesis in lizard lungs. | Hill K, Griffing AH, Palmer MA, Lemma B, Lupo A, Gamble T, Shylo NA, Košmrlj A, Trainor PA, Nelson CM | bioRxiv : the preprint server for biology | 40950153 | bioRxiv | 2025 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/40950153 |
| 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 |
| 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 |
| Fuel, form, and memory: The motility-driven journey of cancer cells. | Trenado-Yuste C, Nelson CM | Current opinion in biomedical engineering | 41306346 | Curr Opin Biomed Eng | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41306346 |
| Mapping embryonic mouse lung development using enhanced spatial transcriptomics. | Zhang P, Law BK, Goodwin K, Chan MM, Nelson CM | bioRxiv : the preprint server for biology | 41394655 | bioRxiv | 2025 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/41394655 |
| Biophysical processes of morphogenesis in lizard lungs. | Hill K, Griffing AH, Palmer MA, Lemma B, Lupo AS, Gamble T, Shylo NA, Košmrlj A, Trainor PA, Nelson CM | Developmental dynamics : an official publication of the American Association of Anatomists | 41235677 | Dev Dyn | 2025 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/41235677 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Scientific data | 40610484 | Sci Data | 2025 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/40610484 |
| Emergence of a temporal processing gradient from naturalistic inputs and network connectivity. | Chang CHC, Nastase SA, Hasson U, Dominey PF | Proceedings of the National Academy of Sciences of the United States of America | 40632567 | Proc Natl Acad Sci U S A | 2025 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/40632567 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A unified acoustic-to-speech-to-language embedding space captures the neural basis of natural language processing in everyday conversations. | Goldstein A, Wang H, Niekerken L, Schain M, Zada Z, Aubrey B, Sheffer T, Nastase SA, Gazula H, Singh A, Rao A, Choe G, Kim C, Doyle W, Friedman D, Devore S, Dugan P, Hassidim A, Brenner M, Matias Y, Devinsky O, Flinker A, Hasson U | Nature human behaviour | 40055549 | Nat Hum Behav | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40055549 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Mechanism of ubiquitin transfer promoted by TRAF6. | Fu TM, Shen C, Li Q, Zhang P, Wu H | Proceedings of the National Academy of Sciences of the United States of America | 29432170 | Proc Natl Acad Sci U S A | 2018 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/29432170 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| CIDE domains form functionally important higher-order assemblies for DNA fragmentation. | Choi JY, Qiao Q, Hong SH, Kim CM, Jeong JH, Kim YG, Jung YK, Wu H, Park HH | Proceedings of the National Academy of Sciences of the United States of America | 28652364 | Proc Natl Acad Sci U S A | 2017 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/28652364 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A Systematic Review of Human Paenibacillus Infections and Comparison of Adult and Pediatric Cases. | Smith D, Bastug K, Burgoine K, Broach JR, Hammershaimb EA, Hehnly C, Morton SU, Osman M, Schiff SJ, Ericson JE | The Pediatric infectious disease journal | 39705610 | Pediatr Infect Dis J | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/39705610 |
| 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 |
| 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 |
| 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 |
| CLIF-Net: Intersection-guided Cross-view Fusion Network for Infection Detection from Cranial Ultrasound. | Yu M, Peterson MR, Burgoine K, Harbaugh T, Olupot-Olupot P, Gladstone M, Hagmann C, Cowan FM, Weeks A, Morton SU, Mulondo R, Mbabazi-Kabachelor E, Schiff SJ, Monga V | medRxiv : the preprint server for health sciences | 40778164 | medRxiv | 2025 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/40778164 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | |
| 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 |
| CLIF-Net: Intersection-Guided Cross-View Fusion Network for Infection Detection From Cranial Ultrasound. | Yu M, Peterson MR, Burgoine K, Harbaugh T, Olupot-Olupot P, Gladstone M, Hagmann C, Cowan FM, Weeks A, Morton SU, Mulondo R, Mbabazi-Kabachelor E, Schiff SJ, Monga V | IEEE transactions on medical imaging | 40372847 | IEEE Trans Med Imaging | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40372847 |
| 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 |
| Poor Surgical Outcomes Following Paenibacillus Infant Infectious Hydrocephalus. | Ericson JE, Natukwatsa D, Ssenyonga P, Onen J, Mugamba J, Mulondo R, Morton SU, Movassagh M, Templeton K, Hehnly C, Mbabazi-Kabachelor E, Kulkarni AV, Warf BC, Broach JR, Paulson JN, Schiff SJ | medRxiv : the preprint server for health sciences | 40385433 | medRxiv | 2025 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/40385433 |
| 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 |
| 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 |
| 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 |
| 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 |
| Poor surgical outcomes following Paenibacillus infant infectious hydrocephalus. | Ericson JE, Natukwatsa D, Ssenyonga P, Onen J, Mugamba J, Mulondo R, Morton SU, Movassagh M, Templeton K, Hehnly C, Mbabazi-Kabachelor E, Kulkarni AV, Warf BC, Broach JR, Paulson JN, Schiff SJ | Journal of neurosurgery. Pediatrics | 40378477 | J Neurosurg Pediatr | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/40378477 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| High-fidelity musculoskeletal modeling reveals that motor planning variability contributes to the speed-accuracy tradeoff. | Al Borno M, Vyas S, Shenoy KV, Delp SL | eLife | 33325369 | Elife | 2020 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/33325369 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Phagosome Maturation in Macrophages is Enhanced by p38α MAPK Signaling. | Shah M, Kirthivasan N, Chakraborty S, Krishnan Y, Jhunjhunwala S | bioRxiv : the preprint server for biology | 40631207 | bioRxiv | 2025 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/40631207 |
| 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 |
| Phagosome Maturation in Macrophages is Enhanced by p38α MAPK Signaling. | Shah M, Kirthivasan N, Chakraborty S, Krishnan Y, Jhunjhunwala S | Small (Weinheim an der Bergstrasse, Germany) | 40968501 | Small | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40968501 |
| 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 |
| A nucleic acid labeling chemistry reveals surface DNA on exosomes. | Boskovic F, Gupta PD, Zhang J, Krishnan Y, Szostak JW | bioRxiv : the preprint server for biology | 41332572 | bioRxiv | 2025 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/41332572 |
| 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 |
| 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 |
| An SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity. | Levin-Konigsberg R, Mitra K, Spees K, Nigam A, Liu K, Januel C, Hivare P, Arana SM, Prolo LM, Kundaje A, Leonetti MD, Krishnan Y, Bassik MC | Developmental cell | 39476838 | Dev Cell | 2025 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/39476838 |
| Organelles harbour pH gradients. | Lee S, Chakraborty S, Kim S, Ali A, Mitra K, Zajac M, Brown A, Pincus D, Krishnan Y | bioRxiv : the preprint server for biology | 41446184 | bioRxiv | 2025 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/41446184 |
| Organelles harbour pH gradients. | Lee S, Chakraborty S, Kim S, Ali A, Mitra K, Zajac M, Brown A, Pincus D, Krishnan Y | Research square | 41646419 | Res Sq | 2026 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/41646419 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Identification of an on-pathway intermediate illuminates the kinetic competition between protein folding and misfolding. | Luan Q, Clark PL | Proceedings of the National Academy of Sciences of the United States of America | 40737324 | Proc Natl Acad Sci U S A | 2025 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/40737324 |
| 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 |
| 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 |
| Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). | Loughran G, Andreev DE, Terenin IM, Namy O, Mikl M, Yordanova MM, McManus CJ, Firth AE, Atkins JF, Fraser CS, Ignatova Z, Iwasaki S, Kufel J, Larsson O, Leidel SA, Mankin AS, Mariotti M, Tanenbaum ME, Topisirovic I, Vázquez-Laslop N, Viero G, Caliskan N, Chen Y, Clark PL, Dinman JD, Farabaugh PJ, Gilbert WV, Ivanov P, Kieft JS, Mühlemann O, Sachs MS, Shatsky IN, Sonenberg N, Steckelberg AL, Willis AE, Woodside MT, Valasek LS, Dmitriev SE, Baranov PV | Nature structural & molecular biology | 40033152 | Nat Struct Mol Biol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40033152 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Programmable initiation of mRNA translation by trans-RNA. | Jia L, Nguyen TT, Uematsu S, Gu Y, Shi S, Hashem Y, Qian SB | Nature biotechnology | 41272315 | Nat Biotechnol | 2025 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/41272315 |
| 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 |
| Profiling of terminating ribosomes reveals translational control at stop codons. | Jia L, Mao Y, Uematsu S, Liu XA, Dong L, de Lima LHF, Qian SB | bioRxiv : the preprint server for biology | 41000726 | bioRxiv | 2025 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/41000726 |
| 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 |
| Interpreting ribosome dynamics during mRNA translation. | Uematsu S, Qian SB | The Journal of biological chemistry | 40651611 | J Biol Chem | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40651611 |
| Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane. | Huang S, Kim YJ, Cao X, Bumpus TW, Sohn M, Menold MT, Dale RS, Kang JJ, Uematsu S, Gupta S, Qian SB, Yu H, Balla T, Baskin JM | bioRxiv : the preprint server for biology | 41256676 | bioRxiv | 2025 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/41256676 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39075149 |
| 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 |
| 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 |
| 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 | Proceedings of the National Academy of Sciences of the United States of America | 40773232 | Proc Natl Acad Sci U S A | 2025 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/40773232 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Phage induction of Staphylococcus aureus pathogenicity islands promotes the CRISPR-Cas adaptive immune response. | Banh DV, Goldberg GW, Marraffini LA | Cell reports | 41474623 | Cell Rep | 2026 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/41474623 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| (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 |
| 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 |
| 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 |
| 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 |
| 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 |
| mRNA 3'UTRs chaperone intrinsically disordered regions to control protein activity. | Luo Y, Zhong Y, Basu S, Mayr C | bioRxiv : the preprint server for biology | 40631257 | bioRxiv | 2025 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/40631257 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| C. elegans cognitive decline with age: more than just wiggling forward and backward. | Sengupta T, Murphy CT | Genes & development | 40645666 | Genes Dev | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/40645666 |
| 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 |
| 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 |
| 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 |
| 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 |
| Single-nucleus neuronal transcriptional profiling of male C. elegans uncovers regulators of sex-specific and sex-shared behaviors. | Morillo KS, St Ange J, Weng Y, Kaletsky R, Murphy CT | Cell reports | 40682776 | Cell Rep | 2025 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/40682776 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Molecular requirements for C. elegans transgenerational epigenetic inheritance of pathogen avoidance. | Kaletsky R, Moore RS, Sengupta T, Seto R, Ceballos-Llera B, Murphy CT | eLife | 40372780 | Elife | 2025 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/40372780 |
| 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 |
| Biological sex matters in brain aging. | Dubal DB, Murphy CT, Suh Y, Benayoun BA | Neuron | 39788086 | Neuron | 2025 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/39788086 |
| 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 |
| Strategies for studying sex differences in brain aging. | Ansere VA, Kim SS, Marino F, Morillo K, Dubal DB, Murphy CT, Suh Y, Benayoun BA | Trends in genetics : TIG | 40037936 | Trends Genet | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40037936 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Adult single-nucleus neuronal transcriptomes of insulin signaling mutants reveal regulators of behavior and learning. | St Ange J, Weng Y, Kaletsky R, Stevenson ME, Moore RS, Zhou S, Murphy CT | Cell genomics | 39637862 | Cell Genom | 2024 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/39637862 |
| 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 |
| C. elegans transgenerational avoidance of P. fluorescens is mediated by the Pfs1 sRNA and vab-1. | Seto RJ, Brown R, Kaletsky R, Parsons LR, Moore RS, Balch JM, Gitai Z, Murphy CT | Science advances | 40267186 | Sci Adv | 2025 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/40267186 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Protocol for measuring cell cycle Zn(2+) dynamics using a FRET-based biosensor. | Holtzen SE, Rakshit A, Palmer AE | STAR protocols | 38861382 | STAR Protoc | 2024 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/38861382 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The mechanism of the phage-encoded protein antibiotic from ΦX174. | Orta AK, Riera N, Li YE, Tanaka S, Yun HG, Klaic L, Clemons WM Jr | Science (New York, N.Y.) | 37440661 | Science | 2023 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/37440661 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nano-Bioelectronics. | Zhang A, Lieber CM | Chemical reviews | 26691648 | Chem Rev | 2016 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/26691648 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| "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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Correcting for bias due to mismeasured exposure in mediation analysis with a survival outcome. | Cheng C, Spiegelman D, Li F | Journal of the Royal Statistical Society. Series C, Applied statistics | 40837827 | J R Stat Soc Ser C Appl Stat | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40837827 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Spiegelman Responds. | Spiegelman D | American journal of public health | 27153027 | Am J Public Health | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27153027 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Effects of a dietary intervention on cardiometabolic risk and food consumption in a workplace. | Shrestha A, Tamrakar D, Ghinanju B, Shrestha D, Khadka P, Adhikari B, Shrestha J, Waiwa S, Pyakurel P, Bhandari N, Karmacharya BM, Shrestha A, Shrestha R, Bhatta RD, Malik V, Mattei J, Spiegelman D | PloS one | 38656951 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38656951 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Bacterial adaptation through loss of function. | Hottes AK, Freddolino L, Khare A, Donnell ZN, Liu JC, Tavazoie S | PLoS genetics | 23874220 | PLoS Genet | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23874220 |
| Principles of Systems Biology, No. 29. | Cell systems | 29792823 | Cell Syst | 2018 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/29792823 | |
| 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 |
| The dawn of virtual cell biology. | Freddolino L, Tavazoie S | Cell | 22817888 | Cell | 2012 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/22817888 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Comprehensive Measurement of Inter-Individual Variation in DNA Repair Capacity in Healthy Individuals. | Zhai T, Mazzucato P, Ricciardi C, Christiani DC, Liang L, Samson LD, Chaim IA, Nagel ZD | medRxiv : the preprint server for health sciences | 40585106 | medRxiv | 2025 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/40585106 |
| 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 |
| Comprehensive Measurement of Inter-Individual Variation in DNA Repair Capacity in Healthy Individuals. | Zhai T, Mazzucato P, Ricciardi C, Christiani DC, Liang L, Samson LD, Chaim IA, Nagel ZD | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 41058006 | Adv Sci (Weinh) | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41058006 |
| 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 |
| Thermally Controlled State Switches for Engineered Macrophages. | Liu A, Farooq AS, Abedi MH, Criado-Hidalgo E, Smith CAB, Wu D, Shapiro MG | ACS synthetic biology | 41075299 | ACS Synth Biol | 2025 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/41075299 |
| Modulating Protein Function through Genetically Encoded Oxidative Chemistry. | Li H, Pavlič A, Ibrahim NE, Wu D, Shapiro MG | Journal of the American Chemical Society | 42231837 | J Am Chem Soc | 2026 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/42231837 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nanowire-Enabled Bioelectronics. | Zhang A, Lee JH, Lieber CM | Nano today | 36970717 | Nano Today | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36970717 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nanowired Bioelectric Interfaces. | Tian B, Lieber CM | Chemical reviews | 30995019 | Chem Rev | 2019 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/30995019 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Sensitivity of photoacoustic microscopy. | Yao J, Wang LV | Photoacoustics | 25302158 | Photoacoustics | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25302158 |
| 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 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Single-shot ultrafast optical imaging. | Liang J, Wang LV | Optica | 30820445 | Optica | 2018 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/30820445 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Intranasal versus intravenous AAV delivery: A comparative analysis of brain-targeting efficiency and peripheral exposure in mice. | Chukwu C, Yuan J, Chen H | Gene therapy | 41361083 | Gene Ther | 2025 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/41361083 |
| Sonobiopsy for sensitive and spatially targeted molecular diagnosis through integrating ultrasound with liquid biopsy. | Yuan J, Chen H | NPJ acoustics | 40620711 | NPJ Acoust | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40620711 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Many circulating indole and phenol metabolites are host derived. | AbuSalim JE, Olszewski K, Youssef S, Hunter CJ, MacArthur MR, Henneberg A, Ryseck RP, Opitz CA, Donia MS, Rabinowitz JD | bioRxiv : the preprint server for biology | 41279320 | bioRxiv | 2025 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/41279320 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Microbiome metabolism of dietary phytochemicals controls the anticancer activity of PI3K inhibitors. | Roichman A, Zuo Q, Hwang S, Lu W, Cordova RA, MacArthur MR, Boyer JA, Mitchell SJ, Powers J, Koval SA, Hunter CJ, Rijmers J, Ryseck RP, AbuSalim JE, Chatterjee S, Lee WD, Xu X, Xing X, Chen Z, Zeng X, Marwaha S, McBride MJ, Guo JY, Kang Y, Donia MS, Rabinowitz JD | Cell | 40393457 | Cell | 2025 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/40393457 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| One-carbon unit supplementation fuels purine synthesis in tumor-infiltrating T cells and augments checkpoint blockade. | Xu X, Chen Z, Bartman CR, Xing X, Olszewski K, Rabinowitz JD | Cell chemical biology | 38759619 | Cell Chem Biol | 2024 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/38759619 |
| 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 |
| 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 |
| 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 |
| Reprogramming neuroblastoma by diet-enhanced polyamine depletion. | Cherkaoui S, Turn CS, Yuan Y, Lu W, Yang L, McBride MJ, Eigenmann C, Allen GE, Panasenko OO, Zhang L, Vu A, Liu K, Li Y, Gandhi OH, Surrey LF, Kienast SD, Leidel SA, Wierer M, White E, Rabinowitz JD, Hogarty MD, Morscher RJ | Nature | 40993392 | Nature | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40993392 |
| 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 |
| 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 |
| 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 |
| 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 |
| Protocol for the generation of blastocyst-like structures from mouse extended pluripotent stem cells. | Li R, Izpisua Belmonte JC | STAR protocols | 34430918 | STAR Protoc | 2021 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/34430918 |
| 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 |
| 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 |
| 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 |
| Microbiome: Focus on Causation and Mechanism. | Fischbach MA | Cell | 30096310 | Cell | 2018 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/30096310 |
| 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 |
| Skin microbiota-host interactions. | Chen YE, Fischbach MA, Belkaid Y | Nature | 29364286 | Nature | 2018 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/29364286 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Phosphoribosomes for fingerprinting neurons. | Dietrich MO, Horvath TL | Cell | 23178116 | Cell | 2012 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/23178116 |
| 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 |
| 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 |
| 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 |
| 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 |
| Creation of true interspecies hybrids: Rescue of hybrid class with hybrid cytoplasm affecting growth and metabolism. | Sati L, Varela L, Horvath TL, McGrath J | Science advances | 39441922 | Sci Adv | 2024 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/39441922 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | |
| 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 |
| 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 |
| 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 |
| 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 |
| The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour. | Yoshida TM, Nguyen M, Zhang L, Lu BY, Zhu B, Murray KN, Mineur YS, Zhang C, Xu D, Lin E, Luchsinger J, Bhatta S, Waizman DA, Coden ME, Ma Y, Israni-Winger K, Russo A, Wang H, Song W, Al Souz J, Zhao H, Craft JE, Picciotto MR, Grutzendler J, Distasio M, Palm NW, Hafler DA, Wang A | Nature | 40437096 | Nature | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40437096 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| CD47 inhibits phagocytosis through Vav dephosphorylation. | Miller WD, Manion A, Mishra AK, Sheedy CJ, Bond A, Gardner BM, Montell DJ, Morrissey MA | The Journal of cell biology | 41100219 | J Cell Biol | 2025 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/41100219 |
| A kinome inhibitor screen implicates adhesion and growth factor signaling in cellular recovery after caspase activation. | Nano M, Harwood J, Lukaszewicz G, Kagan A, Peshkin L, Montell DJ | bioRxiv : the preprint server for biology | 41542583 | bioRxiv | 2026 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/41542583 |
| The Perils and Promise of Cellular Cannibalism in Development, Homeostasis, and Disease. | Rodriguez M, Mishra AK, Montell DJ | Annual review of cell and developmental biology | 40769506 | Annu Rev Cell Dev Biol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40769506 |
| ADAPT-M: A workflow for rapid, quantitative in vitro measurements of enriched protein libraries. | Perez CP, DelRosso NV, Noland CL, Parekh U, Choe CA, Eguchi RR, Wen Q, Fordyce PM, Huang PS | bioRxiv : the preprint server for biology | 41279512 | bioRxiv | 2025 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/41279512 |
| Continuous FACS sorting of double emulsion picoreactors with a 3D printed vertical mixer. | Yang Z, Thompson S, Zhang Y, Rutten I, Van Duyse J, Van Isterdael G, Nichols L, Lammertyn J, Soh HT, Fordyce P | bioRxiv : the preprint server for biology | 40161623 | bioRxiv | 2025 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/40161623 |
| FACS-Sortable Triple Emulsion Picoreactors for Screening Reactions in Biphasic Environments. | Thompson S, Zhang Y, Yang Z, Nichols L, Fordyce PM | Advanced materials interfaces | 40831677 | Adv Mater Interfaces | 2025 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/40831677 |
| Continuous FACS Sorting of Double Emulsion Picoreactors with a 3D-Printed Vertical Mixer. | Yang Z, Thompson S, Zhang Y, Rutten I, Van Duyse J, Van Isterdael G, Nichols L, Lammertyn J, Soh HT, Fordyce P | Analytical chemistry | 40602756 | Anal Chem | 2025 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/40602756 |
| Large field of view fluorescence imaging of microfluidic devices with a tandem-lens macroscope(†). | Mokhtari DA, Lashkaripour A, Fordyce PM | bioRxiv : the preprint server for biology | 41279154 | bioRxiv | 2025 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/41279154 |
| Sensitizing solid tumors to CAR-mediated cytotoxicity by lipid nanoparticle delivery of synthetic antigens. | Gamboa L, Zamat AH, Thiveaud CA, Lee HJ, Kulaksizoglu E, Zha Z, Campbell NS, Chan CS, Fábrega S, Oliver SA, Su FY, Phuengkham H, Vanover D, Peck HE, Sivakumar A, Dahotre SN, Harris AM, Santangelo PJ, Kwong GA | Nature cancer | 40379831 | Nat Cancer | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40379831 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Polyclonal origins of human premalignant colorectal lesions. | Van Egeren D, Schenck RO, Khan A, Horning AM, Mo S, Weiß CL, Esplin ED, Becker WR, Wu S, Hanson C, Barapour N, Jiang L, Contrepois K, Lee H, Nevins SA, Guha TK, Zhang H, He Z, Ma Z, Monte E, Karathanos TV, Laquindanum R, Mills MA, Chaib H, Chiu R, Jian R, Chan J, Ellenberger M, Bahmani B, Michael B, Weimer AK, Esplin DG, Lancaster S, Shen J, Ladabaum U, Longacre TA, Kundaje A, Greenleaf WJ, Hu Z, Ford JM, Snyder MP, Curtis C | bioRxiv : the preprint server for biology | 41292759 | bioRxiv | 2025 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/41292759 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| NACK and INTEGRATOR act coordinately to activate Notch-mediated transcription in tumorigenesis. | Shersher E, Lahiry M, Alvarez-Trotta A, Diluvio G, Robbins DJ, Shiekhattar R, Capobianco AJ | Cell communication and signaling : CCS | 34551776 | Cell Commun Signal | 2021 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/34551776 |
| Integrator enforces the fidelity of transcriptional termination at protein-coding genes. | Dasilva LF, Blumenthal E, Beckedorff F, Cingaram PR, Gomes Dos Santos H, Edupuganti RR, Zhang A, Dokaneheifard S, Aoi Y, Yue J, Kirstein N, Tayari MM, Shilatifard A, Shiekhattar R | Science advances | 34730992 | Sci Adv | 2021 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/34730992 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes. | Chen XD, Chen Z, Wythes G, Zhang Y, Orr BC, Sun G, Chao YK, Navarro Torres A, Thao K, Vallurupalli M, Sun J, Borji M, Tkacik E, Chen H, Bernstein BE, Chen F | Science (New York, N.Y.) | 39388570 | Science | 2024 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/39388570 |
| Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas. | Miller TE, El Farran CA, Couturier CP, Chen Z, D'Antonio JP, Verga J, Villanueva MA, Castro LNG, Tong YE, Saadi TA, Chiocca AN, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE | bioRxiv : the preprint server for biology | 37961527 | bioRxiv | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37961527 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Programs, origins and immunomodulatory functions of myeloid cells in glioma. | Miller TE, El Farran CA, Couturier CP, Chen Z, D'Antonio JP, Verga J, Villanueva MA, Gonzalez Castro LN, Tong YE, Saadi TA, Chiocca AN, Zhang Y, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE | Nature | 40011771 | Nature | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40011771 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Single molecules meet genomics: pinpointing precision medicine. | Xie XS | JAMA | 25974149 | JAMA | 2015 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/25974149 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Next-Generation GLUT Inhibitors: Lactone to Lactam Conversion in Rapaglutin A Confers Resistance to Plasma Esterases. | Rao AVS, Kotlyar M, Peng H, Liu JO | ACS medicinal chemistry letters | 41257007 | ACS Med Chem Lett | 2025 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/41257007 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Molecular imaging: exploring the next frontier. | Weissleder R | Radiology | 10478223 | Radiology | 1999 Sep | https://www.ncbi.nlm.nih.gov/pubmed/10478223 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Neurons, Muscles, and Venom: Identifying Drivers of Cephalopod Predation. | Kirchhoff KN, Williams M, Stambouli B, Pardos-Blas JR, Courtney A, Sugarman AL, Vanselow DJ, Carrasco C, Cuddy C, Schafer WR, Cheng KC, Seuntjens E, Holford M | bioRxiv : the preprint server for biology | 40661549 | bioRxiv | 2025 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/40661549 |
| 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 |
| Shank3 mutation manifests in abnormal gastrointestinal morphology and function in mice. | Eberly GL, Manthey M, Pang KKL, Hussein H, Vargas Paniagua E, Machen S, Klingensmith SM, Anikeeva P | Frontiers in neuroscience | 40313537 | Front Neurosci | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40313537 |
| Accessing the viscera: Technologies for interoception research. | Pang KKL, Mondal R, Sahasrabudhe A, Anikeeva P | Current opinion in neurobiology | 40383048 | Curr Opin Neurobiol | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40383048 |
| 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 |
| Adeno-associated viruses escort nanomaterials to specific cells and tissues. | Nagao K, Paniagua EV, Lei K, Beckham JL, Worthington P, Manthey M, Ye M, Koehler F, Kim YJ, Malkin E, Onoda M, Kent N, Michida S, Guerra EC, Macfarlane RJ, Anikeeva P | bioRxiv : the preprint server for biology | 40291644 | bioRxiv | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/40291644 |
| Correction to "Magnetite Nanodiscs Activate Mechanotransductive Calcium Signaling in Diverse Cell Types". | Beckham JL, Kim YJ, Vargas Paniagua E, Kent N, Nagao K, Selvaraji S, Koehler F, Malkin E, Smith X, Tabet A, Kang S, Anikeeva P | Journal of the American Chemical Society | 40492674 | J Am Chem Soc | 2025 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/40492674 |
| Multifunctional bioelectronics for brain-body circuits. | Sahasrabudhe A, Cea C, Anikeeva P | Nature reviews bioengineering | 40880897 | Nat Rev Bioeng | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40880897 |
| 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 | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39506430 |
| 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 |
| Magnetoelectric nanodiscs diminish motor deficits in a model of Parkinson's disease. | Kim YJ, De Comite A, Paniagua EV, Selvaraji S, Frey E, Mondal R, Seethapathi N, Anikeeva P | bioRxiv : the preprint server for biology | 40661492 | bioRxiv | 2025 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/40661492 |
| 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 |
| Magnetite Nanodiscs Activate Mechanotransductive Calcium Signaling in Diverse Cell Types. | Beckham JL, Kim YJ, Vargas Paniagua E, Kent N, Nagao K, Selvaraji S, Koehler F, Malkin E, Smith X, Tabet A, Kang S, Anikeeva P | Journal of the American Chemical Society | 40215485 | J Am Chem Soc | 2025 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/40215485 |
| Stretchable thin-film metal electronics enabled by multilayered nanomembranes. | Jung D, Cunin CE, Mondal R, Pang KKL, Kim Y, Frey E, Winther S, Beckham J, Cannon TM, Cea C, Gumyusenge A, Anikeeva P | bioRxiv : the preprint server for biology | 41279141 | bioRxiv | 2025 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/41279141 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Stochastic neuropeptide signals compete to calibrate the rate of satiation. | Zhang SX, Kim A, Madara JC, Zhu PK, Christenson LF, Lutas A, Kalugin PN, Sunkavalli PS, Jin Y, Pal A, Tian L, Lowell BB, Andermann ML | Nature | 39506113 | Nature | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39506113 |
| 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 |
| 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 |
| 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 |
| Obesity dysregulates feeding-evoked response dynamics in hypothalamic satiety neurons. | Porniece M, Baker J, Ausfahl CD, Zhang SX, Andermann ML | Scientific reports | 41087441 | Sci Rep | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41087441 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Obesity dysregulates feeding-evoked response dynamics in hypothalamic satiety neurons. | Porniece M, Baker J, Ausfahl CD, Zhang SX, Andermann ML | bioRxiv : the preprint server for biology | 40502019 | bioRxiv | 2025 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/40502019 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes. | Brennan C, Shaffer JP, Belda-Ferre P, Mohanty I, Weng Y, Cantrell K, Ackermann G, Allaband C, Bryant M, Farmer S, González A, McDonald D, Martino C, Meehan MJ, Rahman G, Salido RA, Schwartz T, Song SJ, Tribelhorn C, Tubb HM, Dorrestein PC, Knight R | Microbiology spectrum | 41070991 | Microbiol Spectr | 2025 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/41070991 |
| The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns. | Salido RA, Zhao HN, McDonald D, Mannochio-Russo H, Zuffa S, Oles RE, Aron AT, El Abiead Y, Farmer S, González A, Martino C, Mohanty I, Parker CW, Patel L, Portal Gomes PW, Schmid R, Schwartz T, Zhu J, Barratt MR, Rubins KH, Chu H, Karouia F, Venkateswaran K, Dorrestein PC, Knight R | Cell | 40020666 | Cell | 2025 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/40020666 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Bayesian multivariate sparse functional principal components analysis with application to longitudinal microbiome multiomics data. | Jiang L, Elrod C, Kim JJ, Swafford AD, Knight R, Thompson WK | The annals of applied statistics | 40969773 | Ann Appl Stat | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/40969773 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 infectivity can be modulated through bacterial grooming of the glycocalyx. | Martino C, Kellman BP, Sandoval DR, Clausen TM, Cooper R, Benjdia A, Soualmia F, Clark AE, Garretson AF, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Das P, Ali F, Liang C, Zhang Y, Schifanella L, Covizzi A, Lai A, Riva A, Basting C, Broedlow CA, Havulinna AS, Jousilahti P, Estaki M, Kosciolek T, Kuplicki R, Victor TA, Paulus MP, Savage KE, Benbow JL, Spielfogel ES, Anderson CAM, Martinez ME, Lacey JV Jr, Huang S, Haiminen N, Parida L, Kim H-C, Gilbert JA, Sweeney DA, Allard SM, Swafford AD, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Zengler K, Klatt NR, Hasty J, Berteau O, Carlin AF, Esko JD, Lewis NE, Knight R | mBio | 39998226 | mBio | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/39998226 |
| Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2. | Levy JI, Gangavarapu P, Pilz DA, Jesvaghane MA, Steedman A, Zeller M, Gangavarapu K, McDonald D, Libuit K, Kapsak C, Young EL, Agrawal S, Orschler L, Hölzer M, Stachler E, Park DJ, Hinrichs AS, Laurent LC, Knight R, Andersen KG | medRxiv : the preprint server for health sciences | 40778124 | medRxiv | 2025 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/40778124 |
| Calculating fast differential genome coverages among metagenomic sources using micov. | Weng Y, Guccione C, McDonald D, Oles R, Devkota S, Kopylova E, Sepich-Poore GD, Salido RA, Din MO, Song SJ, Curtius K, Chu H, Bartko A, Hasty J, Knight R | Communications biology | 41266796 | Commun Biol | 2025 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/41266796 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. | Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC | Nature reviews. Gastroenterology & hepatology | 38575682 | Nat Rev Gastroenterol Hepatol | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38575682 |
| Blood microbial DNA signature differentiates hepatocellular carcinoma from metastatic lesions. | Guccione C, Dantas Machado AC, Youssef F, Angeli-Pahim I, Duarte S, Warren C, Farmer S, Humphrey G, Richter RA, McDonald D, Weng Y, Burgoyne A, Loomba R, Curtius K, Zarrinpar A, Knight R, Zarrinpar A | eGastroenterology | 40843454 | eGastroenterology | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40843454 |
| Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects. | Ramos SF, Siguenza N, Zhong W, Mohanty I, Lingaraju A, Richter RA, Karthikeyan S, Lukowski AL, Zhu Q, Nunes WDG, Zemlin J, Xu ZZ, Hasty J, Dorrestein PC, Panda S, Knight R, Zarrinpar A | Cell host & microbe | 40777923 | Cell Host Microbe | 2025 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/40777923 |
| Temporal nutrition analysis associates dietary regularity and quality with gut microbiome diversity: insights from the Food & You digital cohort. | Singh R, McDonald D, Hernandez AR, Song SJ, Bartko A, Knight R, Salathé M | Nature communications | 41028733 | Nat Commun | 2025 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/41028733 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Septin higher-order structure on yeast membranes in vitro. | Goodchild JA, Curtis BN, Pan Y, Jiang Y, Jiao F, Gladfelter AS, Scheuring S | Nature communications | 40447632 | Nat Commun | 2025 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/40447632 |
| 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 |
| 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 |
| 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 |
| 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 |
| Structural dynamics and permeability of the TRPV3 pentamer. | Lansky S, Wang Z, Clarke OB, Chipot C, Scheuring S | Nature communications | 40374654 | Nat Commun | 2025 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/40374654 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Social Exclusion Amplifies Behavioral Responses to Physical Pain via Insular Neuromodulation. | Tye K, Jia C, Tran A, Aloboudi F, Say E, Thao N, Lee C, Batra K, Nguyen A, Bal A, Delahanty J, Chan M, Keyes L, Patel R, Wichmann R, Taschbach F, Li Y, Benna M, Pereira T, Li H, Nono N | Research square | 40502764 | Res Sq | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/40502764 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Social Exclusion Amplifies Behavioral Responses to Physical Pain via Insular Neuromodulation. | Jia C, Tran A, Aloboudi F, Say E, Thao N, Lee CR, Batra K, Nguyen A, Bal A, Nono NN, Delahanty J, Chan MG, Keyes LR, Patel RR, Wichmann R, Taschbach F, Li Y, Benna M, Pereira TD, Li H, Tye K | bioRxiv : the preprint server for biology | 40463290 | bioRxiv | 2025 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/40463290 |
| Separable dorsal raphe dopamine projections mimic the facets of a loneliness-like state. | Lee CR, Matthews GA, Lemieux ME, Wasserlein EM, Borio M, Miranda RL, Keyes LR, Schneider GP, Jia C, Tran A, Aloboudi F, Chan MG, Peroni E, Pereira G, López-Moraga A, Pallé A, Kimchi EY, Padilla-Coreano N, Wichmann R, Tye KM | eLife | 40747785 | Elife | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/40747785 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Research square | 40166035 | Res Sq | 2025 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/40166035 |
| 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 |
| Control of innate olfactory valence by segregated cortical amygdala circuits. | Howe JR, Chan CL, Lee D, Blanquart M, Lee JH, Decoster L, Romero HK, Zadina AN, Lemieux ME, Mills F, Desplats PA, Tye KM, Root CM | eLife | 41870253 | Elife | 2026 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/41870253 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| High-throughput identification of gut microbiome-dependent metabolites. | Han S, Guiberson ER, Li Y, Sonnenburg JL | Nature protocols | 38740909 | Nat Protoc | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38740909 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Internal senses of the vagus nerve. | Prescott SL, Liberles SD | Neuron | 35051375 | Neuron | 2022 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/35051375 |
| Vagal blood volume receptors compensate for haemorrhage and posture change. | Liu Z, Lu S, Haskell IA, Schappe MS, Josipović M, Min S, Alabi AA, Chi J, Kim M, Liberles SD | Nature | 41606321 | Nature | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41606321 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Biosynthesis of medicinal tropane alkaloids in yeast. | Srinivasan P, Smolke CD | Nature | 32879484 | Nature | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32879484 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Age-associated Senescent - T Cell Signaling Promotes Type 3 Immunity that Inhibits the Biomaterial Regenerative Response. | Han J, Cherry C, Mejías JC, Krishnan K, Ruta A, Maestas DR Jr, Peña AN, Nguyen HH, Nagaraj S, Yang B, Gray-Gaillard EF, Rutkowski N, Browne M, Tam AJ, Fertig EJ, Housseau F, Ganguly S, Moore EM, Pardoll DM, Elisseeff JH | Advanced materials (Deerfield Beach, Fla.) | 38087458 | Adv Mater | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38087458 |
| 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 |
| 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 |
| 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 |
| 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 |
| Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal. | Mitchell JT, Stapleton O, Krishnan K, Nagaraj S, Lvovs D, Cherry C, Poissonnier A, Horton W, Adey A, Rao V, Huff A, Zimmerman JW, Kagohara LT, Zaidi N, Coussens LM, Jaffee EM, Elisseeff JH, Fertig EJ | bioRxiv : the preprint server for biology | 40654902 | bioRxiv | 2025 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/40654902 |
| Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant. | Yang B, Rutkowski N, Ruta A, Gray-Gaillard E, Maestas DR Jr, Kelly SH, Krishnan K, Wu X, Wu S, Chen A, Mejías JC, Hooks JST, Vanderzee I, Mensah P, Celik N, Eric M, Abraham P, Tam A, Housseau F, Pardoll DM, Sears CL, Elisseeff JH | Proceedings of the National Academy of Sciences of the United States of America | 40354538 | Proc Natl Acad Sci U S A | 2025 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/40354538 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 for Regenerative Engineering. | Ogueri KS, Laurencin CT | ACS nano | 32678581 | ACS Nano | 2020 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/32678581 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| CauloKO: an ordered transposon mutant library in Caulobacter crescentus. | Moore GM, Ramos JG, Sheehan JP, Bratton BP, Gitai Z | Journal of bacteriology | 41757907 | J Bacteriol | 2026 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/41757907 |
| Sensing the shape of a surface by tightly surface-bound filaments. | Shi H, Nguyen J, Huang JA, Gitai Z, Shaevitz J, Bratton BP, Gopinathan A, Grason G, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 41428884 | Proc Natl Acad Sci U S A | 2025 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/41428884 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses. | Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell A, Dirasantha O, Yang Q, Sawyer SL | eLife | 40366257 | Elife | 2025 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/40366257 |
| Reverse genetics rescue of sylvatic dengue viruses. | Gendler P, Barbachano-Guerrero A, Chappell SD, Ratnayake OC, Pinto SM, Perera R, Sawyer SL | Journal of virology | 40464564 | J Virol | 2025 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/40464564 |
| 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 |
| 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 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/37209094 |
| 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 |
| 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 |
| 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 |
| Future threats: Animal orthoflaviviruses that currently infect fewer than 100 people per year. | Worden-Sapper ER, Gendler P, Lange RE, Kuhn JH, Sawyer SL | Cell reports | 40440170 | Cell Rep | 2025 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/40440170 |
| 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 |
| 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 |
| The RIG-I-like receptor family of immune proteins. | van Huizen M, Gack MU | Molecular cell | 41106369 | Mol Cell | 2025 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/41106369 |
| Inhibition of coronaviral exonuclease activity by TRIM-mediated SUMOylation. | Balakrishnan K, Chakraborty S, Chiang C, Stratton C, Tumanova AA, Olsen SK, Gack MU | bioRxiv : the preprint server for biology | 40766373 | bioRxiv | 2025 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/40766373 |
| The Flavivirus NS3 Protein: Its Multifaceted Roles and Therapeutic Potential. | Lee H, Cho H, Gack MU | Journal of medical virology | 41910366 | J Med Virol | 2026 Apr | https://www.ncbi.nlm.nih.gov/pubmed/41910366 |
| 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 |
| 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 |
| Tearing down the house of mosquito-transmitted viruses. | Pandey S, Gack MU | Proceedings of the National Academy of Sciences of the United States of America | 40228137 | Proc Natl Acad Sci U S A | 2025 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/40228137 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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, Harkema JR, Baric RS, Baker D, Veesler D | Cell reports | 40450691 | Cell Rep | 2025 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/40450691 |
| Computationally designed mRNA-launched protein nanoparticle immunogens elicit protective antibody and T cell responses in mice. | 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, Zepeda SK, Ols S, 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 | Science translational medicine | 41091918 | Sci Transl Med | 2025 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/41091918 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses. | Park YJ, Liu C, Lee J, Brown JT, Ma CB, Liu P, Gen R, Xiong Q, Zepeda SK, Stewart C, Addetia A, Craig CJ, Tortorici MA, Alshukairi AN, Starr TN, Yan H, Veesler D | Cell | 39922192 | Cell | 2025 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/39922192 |
| The computationally designed TRI2-2 miniprotein inhibitor protects against multiple SARS-CoV-2 Omicron 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 | Communications biology | 41519898 | Commun Biol | 2026 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/41519898 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Design of customized coronavirus receptors. | Liu P, Huang ML, Guo H, McCallum M, Si JY, Chen YM, Wang CL, Yu X, Shi LL, Xiong Q, Ma CB, Bowen JE, Tong F, Liu C, Sun YH, Yang X, Chen J, Guo M, Li J, Corti D, Veesler D, Shi ZL, Yan H | Nature | 39478224 | Nature | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39478224 |
| Potent neutralization of Marburg virus by a vaccine-elicited monoclonal antibody. | Addetia A, Perruzza L, Park YJ, McCallum M, Stewart C, Brown JT, Donati A, Culap K, Balmelli A, Gazi M, Carrion R Jr, Corti D, Benigni F, Veesler D | bioRxiv : the preprint server for biology | 40463027 | bioRxiv | 2025 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/40463027 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 AN, Veesler D | Cell reports | 39058596 | Cell Rep | 2024 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/39058596 |
| 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 |
| 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 | Research square | 37503272 | Res Sq | 2023 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/37503272 |
| Functional and antigenic constraints on the Nipah virus fusion protein. | Larsen BB, Harari S, Gen R, Stewart C, Veesler D, Bloom JD | bioRxiv : the preprint server for biology | 41279479 | bioRxiv | 2026 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/41279479 |
| Repeated COVID-19 vaccine boosters elicit variant-specific memory B cells in humans. | Tortorici MA, Sprouse KR, Addetia A, Brown JT, Harteloo A, Elias-Warren A, Chu HY, Veesler D | bioRxiv : the preprint server for biology | 41279737 | bioRxiv | 2025 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/41279737 |
| 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 | Research square | 40162213 | Res Sq | 2025 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/40162213 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses. | Ma CB, Liu C, Park YJ, Tang J, Chen J, Xiong Q, Lee J, Stewart C, Asarnow D, Brown J, Tortorici MA, Yang X, Sun YH, Chen YM, Yu X, Si JY, Liu P, Tong F, Huang ML, Li J, Shi ZL, Deng Z, Veesler D, Yan H | Cell | 39922191 | Cell | 2025 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/39922191 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Cell reports | 40359110 | Cell Rep | 2025 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/40359110 |
| Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics. | Tortorici MA, Choi A, Gibson CA, Lee J, Brown JT, Stewart C, Joshi A, Harari S, Willoughby I, Treichel C, Leaf EM, Bloom JD, King NP, Tait-Burkard C, Whittaker GR, Veesler D | Nature | 40634609 | Nature | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40634609 |
| Phylogeny-driven design of broadly protective sarbecovirus receptor-binding domain nanoparticle vaccines. | Addetia A, Schäfer A, Sprouse K, Valdez A, Taylor A, Navarro MJ, Brown JT, Leaf EM, Miranda MC, Walls AC, Lee J, Catanzaro NJ, Treichel C, Willoughby I, Powers J, Martinez DR, Vesari B, Ravichandran R, Seo AJ, Stewart C, Merz B, Beirne E, Zepeda S, Cook A, Pessaint L, Sharma A, Edwards D, Lee K, Smith K, Starr T, Baric R, King NP, Veesler D | bioRxiv : the preprint server for biology | 40463102 | bioRxiv | 2025 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/40463102 |
| TMPRSS2 inhibitors with broad-spectrum efficacy against SARS-CoV-2 (JN.1) and influenza A (H1N1) viruses protect mice from influenza A infection. | Presley L, Pérez-Vargas J, Saintigny A, Villanueva I, Ho M, Fone J, Brinsden L, Kaushik N, Olver S, Thompson CAH, Bautista-Sánchez D, Ennis S, Chen M, McCallum M, Brown JT, Ferková S, Hetrick B, Veesler D, Leduc R, Niikura M, Boudreault PL, Warner B, Jean F | Emerging microbes & infections | 41612887 | Emerg Microbes Infect | 2026 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41612887 |
| 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 |
| 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 |
| 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 |
| Potent neutralization of Marburg virus by a vaccine-elicited antibody. | Addetia A, Perruzza L, Sprouse K, Park YJ, McCallum M, Stewart C, Partini B, Brown JT, Donati A, Culap K, Balmelli A, Chawla B, Kar S, Gazi M, Alfson K, Goez-Gazi Y, Carrion R Jr, Corti D, Benigni F, Veesler D | Nature | 41225006 | Nature | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41225006 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Cell | 40132580 | Cell | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40132580 |
| 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 |
| 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 |
| Local structural flexibility drives oligomorphism in computationally designed protein assemblies. | Khmelinskaia A, Bethel NP, Fatehi F, Mallik BB, Antanasijevic A, Borst AJ, Lai SH, Chim HY, Wang JY', Miranda MC, Watkins AM, Ogohara C, Caldwell S, Wu M, Heck AJR, Veesler D, Ward AB, Baker D, Twarock R, King NP | Nature structural & molecular biology | 40011747 | Nat Struct Mol Biol | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40011747 |
| 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 |
| Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. | McCallum M, Park YJ, Stewart C, Sprouse KR, Addetia A, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D | Cell | 38964328 | Cell | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/38964328 |
| 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 |
| 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 |
| HKU25 clade MERS-related coronaviruses use ACE2 as a functional receptor. | Liu C, Park YJ, Ma CB, Gen R, Stewart C, Sun YC, Yang X, Lin MY, Xiong Q, Si JY, Liu P, Veesler D, Yan H | Nature microbiology | 41168429 | Nat Microbiol | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/41168429 |
| A stabilized MERS-CoV spike ferritin nanoparticle vaccine elicits robust and protective neutralizing antibody responses. | Powell AE, Caruso H, Park S, Chen JL, O'Rear J, Ferrer BJ, Stieh DJ, Weiss AM, Belnap DM, Walker A, Bruening A, Hartwig A, Sprouse KR, Addetia A, Alshukairi AN, Ahyong V, Dougherty CS, Veesler D, Bowen R, Ledgerwood JE, Kay MS, Weidenbacher PA, Palanski BA | Nature communications | 41644950 | Nat Commun | 2026 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/41644950 |
| Functional and antigenic constraints on the Nipah virus fusion protein. | Larsen BB, Harari S, Gen R, Stewart C, Veesler D, Bloom JD | Proceedings of the National Academy of Sciences of the United States of America | 41650235 | Proc Natl Acad Sci U S A | 2026 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/41650235 |
| 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 |
| 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 |
| Exceptionally broad HIV-1 neutralization via bispecific antibody-mediated prepositioning. | Kim S, Travisano KA, Wilder B, Palomares M, Cao Z, Seaman MS, Kim PS | Proceedings of the National Academy of Sciences of the United States of America | 41026814 | Proc Natl Acad Sci U S A | 2025 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/41026814 |
| 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 |
| 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 |
| 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 |
| 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 |
| Oriented Multivalent Display Drives Consistent Serum Immunodominance to the Ebola Virus Glycoprotein. | Zheng C, Rubio AA, Vasquez S, Pham D, Pan Z, Barnes CO, Kim PS | ACS central science | 41625225 | ACS Cent Sci | 2026 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/41625225 |
| 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 |
| 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 |
| 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 |
| Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad Repeat. | Filsinger Interrante MV, Tang S, Kim S, Shanker VR, Hie BL, Bruun TUJ, Wu W, Pak JE, Fernandez D, Kim PS | ACS chemical biology | 40540236 | ACS Chem Biol | 2025 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/40540236 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A broad antibody with enhanced HIV-1 neutralization via bispecific antibody-mediated prepositioning. | Kim S, Radford CE, Xu D, Zhong J, Do J, Pham DM, Travisano KA, Filsinger Interrante MV, Bruun TUJ, Rezek V, Wilder B, Palomares M, Seaman MS, Kitchen SG, Bloom JD, Kim PS | Nature communications | 40383778 | Nat Commun | 2025 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/40383778 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| IFIT1 is rapidly evolving and exhibits disparate antiviral activities across 11 mammalian orders. | McDougal MB, Boys IN, De Maria AM, Nakahara E, Schoggins JW | bioRxiv : the preprint server for biology | 38798375 | bioRxiv | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38798375 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| IFIT1 is rapidly evolving and exhibits disparate antiviral activities across 11 mammalian orders. | McDougal MB, Boys IN, De Maria AM, Nakahara E, Schoggins JW | eLife | 41123582 | Elife | 2025 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/41123582 |
| 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 |
| 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 |
| Substrate recognition by TRIM and TRIM-like proteins in innate immunity. | Wang HT, Hur S | Seminars in cell & developmental biology | 33092958 | Semin Cell Dev Biol | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33092958 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| GoldenBraid2.0 E. coli: a comprehensive and characterized toolkit for enterics. | Cooke MB, Welch KT, Ramirez LD, Wen AX, Marciano DC, Herman C | Synthetic biology (Oxford, England) | 40927394 | Synth Biol (Oxf) | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40927394 |
| 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 |
| Transcription-replication collisions trigger high-fidelity replication reset. | Cooke MB, Welch KT, Deus Ramirez L, Hagstrom KM, Wen AX, Halliday JA, Rosenberg SM, Herman C | Nucleic acids research | 41297800 | Nucleic Acids Res | 2025 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/41297800 |
| 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 |
| 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 |
| Endogenous DNA damage at sites of terminated transcripts. | Liu J, Perren JO, Rogers CM, Nimer S, Wen AX, Halliday JA, Fitzgerald DM, Mei Q, Nehring RB, Crum M, Kozmin SG, Xia J, Cooke MB, Zhai Y, Bates D, Li L, Hastings PJ, Artsimovitch I, Herman C, Sung PM, Miller KM, Rosenberg SM | Nature | 39972147 | Nature | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/39972147 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A nanobody that binds to the backside of the ubiquitin conjugating enzyme Ube2G2 differentially affects interactions with its partner E3 Ligases. | Suresh P, Wijne C, Sun ZJ, Becht N, Sahay I, Pishesha N, Ploegh H | Communications biology | 40234692 | Commun Biol | 2025 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/40234692 |
| 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 |
| A modular Uba1-nanobody fusion enables selective ubiquitin transfer to tagged E2 enzymes. | Wijne C, D'Amico F, Pérez Berrocal DA, Mulder MPC, Ploegh HL, Gan J | The Journal of biological chemistry | 41203132 | J Biol Chem | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41203132 |
| 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 |
| 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 |
| Nanobody-based bispecific antibody engagers targeting CTLA-4 or PD-L1 for cancer immunotherapy. | Liu X, Le Gall C, Alexander RK, Borgman E, Balligand T, Ploegh HL | Nature biomedical engineering | 40670719 | Nat Biomed Eng | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/40670719 |
| 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 |
| 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 |
| Growth inhibition of Saccharomyces cerevisiae by SUMO-specific nanobodies. | Suresh P, Jim SZ, Sahay I, Tang AY, Wijne C, Gan J, Pishesha N, Avalos JL, Ploegh H | Scientific reports | 40419540 | Sci Rep | 2025 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/40419540 |
| Identification and characterization of nanobodies specific for the human ubiquitin-like ISG15 protein. | Gan J, Dabhade P, Wijne C, McKibben W, Draganov SD, Alrawili H, Sun ZJ, Houghton JW, Tate EW, Le Gall C, Suresh P, Pishesha N, Pinto-Fernández A, Schwartz TU, Ploegh HL | The Journal of biological chemistry | 40774387 | J Biol Chem | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40774387 |
| 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 |
| 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 |
| 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 |
| A monoclonal anti-hemagglutinin stem antibody modified with zanamivir protects against both influenza A and B viruses. | Liu X, Balligand T, Le Gall C, Ploegh HL | Proceedings of the National Academy of Sciences of the United States of America | 40193611 | Proc Natl Acad Sci U S A | 2025 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/40193611 |
| 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 |
| Immunometabolism of infections. | Ayres JS | Nature reviews. Immunology | 31892735 | Nat Rev Immunol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31892735 |
| 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 |
| 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 |
| 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 |
| Pre-infection cerebral cortex structure predicts murine sepsis outcome. | Gallant RM, Alam S, Venkataraman K, McKenna BS, Khairy K, Ayres JS | PloS one | 40961093 | PLoS One | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40961093 |
| The Biology of Physiological Health. | Ayres JS | Cell | 32302569 | Cell | 2020 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/32302569 |
| 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 |
| 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 |
| Dietary methionine mitigates immune-mediated damage by enhancing renal clearance of cytokines. | Troha K, Kambhampati S, Insenga A, Metallo CM, Ayres JS | Cell metabolism | 41576934 | Cell Metab | 2026 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/41576934 |
| 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 |
| A metabolic handbook for the COVID-19 pandemic. | Ayres JS | Nature metabolism | 32694793 | Nat Metab | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32694793 |
| 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 |
| Surviving COVID-19: A disease tolerance perspective. | Ayres JS | Science advances | 32494691 | Sci Adv | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32494691 |
| 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 |
| 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 |
| 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 |
| 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 |
| Disease tolerance and infection pathogenesis age-related tradeoffs in mice. | Sanchez KK, McCarville JL, Stengel SJ, Snyder JM, Williams AE, Ayres JS | Nature | 41535469 | Nature | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41535469 |
| Proximity-dependent labeling identifies dendritic cells that drive the tumor-specific CD4(+) T cell response. | Chudnovskiy A, Castro TBR, Nakandakari-Higa S, Cui A, Lin CH, Sade-Feldman M, Phillips BK, Pae J, Mesin L, Bortolatto J, Schweitzer LD, Pasqual G, Lu LF, Hacohen N, Victora GD | Science immunology | 39365874 | Sci Immunol | 2024 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/39365874 |
| 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 |
| 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 |
| Identification of antigen-presenting cell-T cell interactions driving immune responses to food. | Campos Canesso MC, de Castro TBR, Nakandakari-Higa S, Lockhart A, Luehr J, Bortolatto J, Parsa R, Esterházy D, Lyu M, Liu TT, Murphy KM, Sonnenberg GF, Reis BS, Victora GD, Mucida D | Science (New York, N.Y.) | 39700315 | Science | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/39700315 |
| 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 |
| 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 |
| Distinct components of mRNA vaccines cooperate to instruct efficient germinal center responses. | Castaño D, Bettini E, Kumar B, Chudnovskiy A, Siv A, Protti G, Nakadakari-Higa S, Ceglia S, De Luna N, Chiu JE, Lederer K, Li SH, Ibrahim H, Muramatsu H, Mdluli T, Abraham E, Sahingur SE, Maillard I, Tam YK, Shin S, Hensley SE, Miner JJ, Lipinszki Z, Reboldi A, Pardi N, Spreafico R, Victora GD, Locci M | Cell | 41406961 | Cell | 2025 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/41406961 |
| Universal recording of cell-cell contacts in vivo for interaction-based transcriptomics. | Nakandakari-Higa S, Canesso MCC, Walker S, Chudnovskiy A, Jacobsen JT, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Pritykin Y, Victora GD | bioRxiv : the preprint server for biology | 36993443 | bioRxiv | 2023 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/36993443 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Tolerance to non-inherited maternal antigen is sustained by LysM(+) CD11c(+) maternal microchimeric cells. | Peng Y, Pham G, Sun J, Adhikari U, Kumar S, Shao TY, Kinder JM, Turner LH, Way SS | Immunity | 40902588 | Immunity | 2025 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/40902588 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Diffuse neuroinflammation and immature neuron loss in fetal Rhesus macaques after short-term intrauterine infection. | Presicce P, Beckman D, Diniz GB, Cappelletti M, Ott S, Bercovici S, Kale S, Babb P, Mohole J, Richardson LS, Kammala AK, Menon R, Miller LA, Crouch EE, Jobe AH, Divanovic S, Chougnet CA, Way SS, Morrison JH, Kallapur SG | Journal of neuroinflammation | 41535926 | J Neuroinflammation | 2026 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/41535926 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Spacing, Stopping, or Postponing? Fertility Desires in a Sub-Saharan Setting. | Hayford SR, Agadjanian V | Demography | 30652298 | Demography | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30652298 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Religious differences in female genital cutting: a case study from Burkina Faso. | Hayford SR, Trinitapoli J | Journal for the scientific study of religion | 21969936 | J Sci Study Relig | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21969936 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Mycobacterium tuberculosis triggers reduced inflammatory cytokine responses and virulence in mice lacking Tax1bp1. | Chin J, Abeydeera N, Repasy T, Rivera-Lugo R, Mitchell G, Nguyen VQ, Zheng W, Richards A, Stevenson E, Swaney DL, Krogan NJ, Ernst JD, Cox JS, Budzik JM | PLoS pathogens | 41171885 | PLoS Pathog | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/41171885 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Clinical and MRI Correlates of β-Amyloid Load Inconsistent With Its Presumed Neurotoxicity in Cognitively Healthy Ageing. | Filip P, McCarten JR, Hemmy L, Crocker J, Wolf M, Thotland J, Cayci Z, Kes T, Michaeli S, Terpstra M, Mangia S | Journal of neurochemistry | 40984796 | J Neurochem | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40984796 |
| 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 |
| Outlook on zero/ultrashort echo time techniques in functional MRI. | Mangia S, Michaeli S, Gröhn O | Magnetic resonance in medicine | 40913418 | Magn Reson Med | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/40913418 |
| R(1ρ) relaxation functions for weak, intermediate and strong collision models, revisited for frequency swept RF pulses. | Sorce DJ, Michaeli S | Journal of magnetic resonance (San Diego, Calif. : 1997) | 41831298 | J Magn Reson | 2026 May | https://www.ncbi.nlm.nih.gov/pubmed/41831298 |
| Simultaneous zero echo time fMRI of rat brain and spinal cord. | Laakso H, Wu L, Ponticorvo S, Salo RA, Paasonen J, Paasonen E, Kettunen M, Lagore RL, DeLabarre L, Polcyn E, Adriany G, Istúriz J, Koski DM, Idiyatullin D, Gröhn O, Mangia S, Michaeli S | Magnetic resonance in medicine | 40674622 | Magn Reson Med | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/40674622 |
| A Bird's-Eye View of Glycolytic Upregulation in Activated Brain: The Major Fate of Lactate Is Release From Activated Tissue, Not Shuttling to Nearby Neurons. | Dienel GA, Rothman DL, Mangia S | Journal of neurochemistry | 40476345 | J Neurochem | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40476345 |
| Diagnostic Performance of Coronary Angiography Derived Computational Fractional Flow Reserve. | Vardhan M, Tanade C, Chen SJ, Mahmood O, Chakravartti J, Jones WS, Kahn AM, Vemulapalli S, Patel M, Leopold JA, Randles A | Journal of the American Heart Association | 38904250 | J Am Heart Assoc | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/38904250 |
| Photon-Counting CT for Evaluation of Coiled Intracranial Aneurysms. | Mac Grory B, Randles A, Urick DM, Schwartz FR, Hasan D, Calabrese ED | AJNR. American journal of neuroradiology | 40973460 | AJNR Am J Neuroradiol | 2026 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/40973460 |
| Systematic characterization and automated alignment of coronary tree geometries. | Ghorbannia A, Randles A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 40040172 | Annu Int Conf IEEE Eng Med Biol Soc | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40040172 |
| 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 | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 40039291 | Annu Int Conf IEEE Eng Med Biol Soc | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40039291 |
| Establishing the longitudinal hemodynamic mapping framework for wearable-driven coronary digital twins. | Tanade C, Khan NS, Rakestraw E, Ladd WD, Draeger EW, Randles A | NPJ digital medicine | 39242829 | NPJ Digit Med | 2024 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/39242829 |
| 3D pore shape is predictable in randomly packed particle systems. | Saxena Y, Riley L, Wu R, Kabir MS, Randles A, Segura T | Matter | 41268054 | Matter | 2025 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/41268054 |
| Real-Time Peripheral Revascularization Planning in Chronic Limb Threatening Ischemia Using HarVI: A Digital Twin Approach. | Tanade C, Jensen CW, Ferreira G, Randles A | Cardiovascular engineering and technology | 41803561 | Cardiovasc Eng Technol | 2026 Jun | https://www.ncbi.nlm.nih.gov/pubmed/41803561 |
| Identifying When Steady-State Flow Simulations In Patient-Specific Coronaries Recapitulate Pulsatile Flow Dynamics. | Huber M, Jiang J, Tanade C, Randles A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 40039843 | Annu Int Conf IEEE Eng Med Biol Soc | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40039843 |
| 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 |
| 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 |
| Optimizing Non-invasive Fractional Flow Reserve Estimation with Machine Learning-Enhanced 1D Hemodynamic Modeling. | Tanade C, Mavi JK, Ferreira G, Schwaller S, Randles A | Cardiovascular engineering and technology | 42053731 | Cardiovasc Eng Technol | 2026 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/42053731 |
| 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 |
| Hemodynamics comparison of an hour-long rest and activity state data in a human coronary digital twin. | Mavi JK, Tanade C, Ladd W, Geddes J, Khan NS, Randles A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 40039549 | Annu Int Conf IEEE Eng Med Biol Soc | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40039549 |
| Surgical Modulation of Pulmonary Artery Shear Stress: A Patient-Specific CFD Analysis of the Norwood Procedure. | Chidyagwai SG, Kaplan MS, Jensen CW, Chen JS, Chamberlain RC, Hill KD, Barker PCA, Slesnick TC, Randles A | Cardiovascular engineering and technology | 38459240 | Cardiovasc Eng Technol | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38459240 |
| Digital twins for noninvasively measuring predictive markers of right heart failure. | Geddes JR, Jensen CW, Tanade C, Ghorbannia A, Fudim M, Patel MR, Randles A | NPJ digital medicine | 40855169 | NPJ Digit Med | 2025 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/40855169 |
| 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 |
| Pseudomonas aeruginosa modulates both Caenorhabditis elegans attraction and pathogenesis by regulating nitrogen assimilation. | Marogi JG, Murphy CT, Myhrvold C, Gitai Z | Nature communications | 39256376 | Nat Commun | 2024 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/39256376 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Life, the genome and everything. | Rosenberg SM | Journal of bacteriology | 38018999 | J Bacteriol | 2023 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/38018999 |
| 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 |
| Cancer drug-tolerant persister cells: from biological questions to clinical opportunities. | Russo M, Chen M, Mariella E, Peng H, Rehman SK, Sancho E, Sogari A, Toh TS, Balaban NQ, Batlle E, Bernards R, Garnett MJ, Hangauer M, Leucci E, Marine JC, O'Brien CA, Oren Y, Patton EE, Robert C, Rosenberg SM, Shen S, Bardelli A | Nature reviews. Cancer | 39223250 | Nat Rev Cancer | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39223250 |
| 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 |
| 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 |
| 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 |
| Antimicrobial peptoids pass rapidly through bacterial membranes and flocculate ribosomes and DNA: A single-cell fluorescence study. | Zhu Y, Nielsen JE, Molchanova N, Mustafi M, Herlan C, Fleck B, Bräse S, Schepers U, Sørensen K, Zielke C, Lin JS, Weisshaar JC, Jenssen H, Barron AE | Proceedings of the National Academy of Sciences of the United States of America | 42372144 | Proc Natl Acad Sci U S A | 2026 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/42372144 |
| The effect of immobilisation strategies on the ability of peptoids to reduce the adhesion of P. aeruginosa strains to contact lenses. | Sara M, Chakraborty S, Chen R, Palms D, Katsifis G, Li Z, Farajikhah S, Massedupally V, Hui A, Wong EHH, Kumar N, Vasilev K, Mackenzie D, Losurdo L, Dehghani F, Jenssen H, Sorensen K, Lin JS, Barron AE, Willcox M | Experimental eye research | 39571778 | Exp Eye Res | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39571778 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The dysregulation of innate immunity by Porphyromonas gingivalis in the etiology of Alzheimer's disease. | Barron AE, Lin JS, Ryder MI, Bergman P | Journal of internal medicine | 41424314 | J Intern Med | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41424314 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Human cathelicidin peptide LL-37 compacts nucleic acids and alters neutrophil extracellular trap structure. | Zielke C, Rad B, Nielsen JE, Li J, Pimcharoen S, Sawant M, Kamayirese S, Lin JS, Thiam HR, Barron AE | Scientific reports | 42156793 | Sci Rep | 2026 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/42156793 |
| Peptoid-based antimicrobial strategies against polymyxin-resistant Gram-negative bacteria. | Mishra SK, Shen J, Akter T, Tigabu A, Urmi UL, Damtie MA, Mekonen ES, Kuppusamy R, Sørensen K, Lin JS, Wong EHH, Hui A, Barron AE, Willcox M | Journal of applied microbiology | 41968108 | J Appl Microbiol | 2026 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/41968108 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The art of observation: bridging science and art to see the unexpected. | Gonzalez LE, Wei H, Greco V, Friedlaender LK | Development (Cambridge, England) | 38477686 | Development | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/38477686 |
| 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 |
| 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 |
| 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 |
| Fibroblast depletion reveals mammalian epithelial resilience across neonatal and adult stages. | Gaeta IM, Du S, Villeneuve C, Gonzalez DG, Matte-Martone C, Ganesan S, Simpson D, Tibebu H, Moore JL, Kam CY, Gallini S, Wei H, Bertillot F, Zeuschner D, Gonzalez LE, Rana U, Sumigray KD, Wickström SA, Greco V | bioRxiv : the preprint server for biology | 40766486 | bioRxiv | 2026 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/40766486 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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(+) 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Simple, Single-Shot Phosphoproteomic Analysis of Heat-Stable Tau Identifies Age-Related Changes in pS235- and pS396-Tau Levels in Non-human Primates. | Leslie SN, Kanyo J, Datta D, Wilson RS, Zeiss C, Duque A, Lam TT, Arnsten AFT, Nairn AC | Frontiers in aging neuroscience | 34867294 | Front Aging Neurosci | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34867294 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The Aging Epigenome. | Booth LN, Brunet A | Molecular cell | 27259204 | Mol Cell | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27259204 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| Slowing Down Aging. | Meyer K, Yankner BA | Cell metabolism | 28978424 | Cell Metab | 2017 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/28978424 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
