NIH Director's Transformative Research Award
NIH Director's Transformative Research Award
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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 |
|---|---|---|---|---|---|---|
| Quantitative Mass Spectrometry Imaging of Intact Proteins in Tissues. | Iqfath M, Swansiger AK, Yang M, Miller L, Moore AM, Hernly E, Bai Y, Zhang ZY, Prell JS, Laskin J | Analytical chemistry | 41538409 | Anal Chem | 2026 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/41538409 |
| Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples. | Pang M, Jones JJ, Wang TY, Quan B, Kubat NJ, Qiu Y, Roukes ML, Chou TF | Journal of proteome research | 38832920 | J Proteome Res | 2025 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/38832920 |
| Molecularly-guided spatial proteomics captures single-cell identity and heterogeneity of the nervous system. | Dutta S, Pang M, Coughlin GM, Gudavalli S, Roukes ML, Chou TF, Gradinaru V | bioRxiv : the preprint server for biology | 39990460 | bioRxiv | 2025 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/39990460 |
| Nanomechanical mass measurements through feature-based time series clustering. | Neumann AP, Gomez A, Nunn AR, Sader JE, Roukes ML | The Review of scientific instruments | 38341716 | Rev Sci Instrum | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/38341716 |
| A Hybrid Orbitrap-Nanoelectromechanical Systems Approach for the Analysis of Individual, Intact Proteins in Real Time. | Neumann AP, Sage E, Boll D, Reinhardt-Szyba M, Fon W, Masselon C, Hentz S, Sader JE, Makarov A, Roukes ML | Angewandte Chemie (International ed. in English) | 38769756 | Angew Chem Int Ed Engl | 2024 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/38769756 |
| Pneumatically Assisted Microfluidic Probe for Enhanced Mass Spectrometry Imaging Performance. | Jiang LX, Laskin J | Journal of the American Society for Mass Spectrometry | 40116008 | J Am Soc Mass Spectrom | 2025 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/40116008 |
| Data-driven fingerprint nanoelectromechanical mass spectrometry. | Sader JE, Gomez A, Neumann AP, Nunn A, Roukes ML | Nature communications | 39438454 | Nat Commun | 2024 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/39438454 |
| Assessing the Validity of the Ask Suicide-Screening Questions in Black Youth. | Horowitz LM, Mournet AM, Sheftall A, He JP, Lowry NJ, Aguinaldo LD, Sullivant SA, Wharff EA, Merikangas KR, Pao M, Bridge JA | Journal of the Academy of Consultation-Liaison Psychiatry | 36273745 | J Acad Consult Liaison Psychiatry | 2023 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/36273745 |
| National Trends in Suicide Among Asian American or Pacific Islander Youth. | Keum BT, Oh S, Sheftall AH | JAMA network open | 39052296 | JAMA Netw Open | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/39052296 |
| Alterations in performance and discriminating power of the death/suicide implicit association test across the lifespan. | Ruch DA, Bridge JA, Tissue J, Madden SP, Galfavy H, Gorlyn M, Sheftall AH, Szanto K, Keilp JG | Psychiatry research | 38492262 | Psychiatry Res | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38492262 |
| Entrapment and social problem-solving in suicidal behavior across the adult lifespan. | Wang C, Keilp JG, Galfalvy H, Bridge JA, Sheftall AH, Szanto K | Journal of affective disorders | 36842650 | J Affect Disord | 2023 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/36842650 |
| Preteen Suicide Risk Screening in the Pediatric Outpatient Setting: A Clinical Pathway. | Hennefield L, Denton EG, Chen PG, Sheftall AH, Ayer L | Journal of the Academy of Consultation-Liaison Psychiatry | 38908827 | J Acad Consult Liaison Psychiatry | 2024 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/38908827 |
| Longitudinal trajectories of suicidal ideation among child welfare-involved 7- to 12-year-old children. | Ayer L, Hassler G, Ohana E, Sheftall AH, Anderson NW, Griffin BA | Journal of child psychology and psychiatry, and allied disciplines | 38659338 | J Child Psychol Psychiatry | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38659338 |
| Understanding of death and related constructs in children with suicidal thoughts and behaviors: A review and future directions. | Ortin-Peralta A, Hennefield L, Eichenbaum M, Espinosa-Polanco M, Sheftall AH | Clinical child psychology and psychiatry | 39825789 | Clin Child Psychol Psychiatry | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/39825789 |
| Anticipated Discrimination and Suicidal Behaviors Among Black Gay and Bisexual Male Adolescents: The Moderating Role of Developmental Assets. | Boyd DT, Sheftall AH | Research square | 41646393 | Res Sq | 2026 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/41646393 |
| Understanding suicidal thoughts and behaviors in Black youth within the child welfare system: An exploration of protective factors. | Sheftall AH, Picou PN, Ohana E, Hassler G, Griffin BA, Ayer L | Child abuse & neglect | 41172767 | Child Abuse Negl | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41172767 |
| School Connectedness and Suicidal Ideation Among Black Youth: A Latent Class Analysis. | Harrell DR, Richardson SC, Sheftall AH | School mental health | 41403887 | School Ment Health | 2025 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/41403887 |
| Neurocognitive and clinical characteristics of elementary school-aged children with a history of suicidal thoughts and behaviors. | Chen Q, Armstrong SE, Vakil F, Bridge JA, Keilp JG, Sheftall AH | Journal of affective disorders | 37442443 | J Affect Disord | 2023 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/37442443 |
| Severity and Transition of Suicidal Behaviors in Childhood: Sex, Racial, and Ethnic Differences in the Adolescent Brain Cognitive Development (ABCD) Study. | Ortin-Peralta A, Sheftall AH, Osborn A, Miranda R | The Journal of adolescent health : official publication of the Society for Adolescent Medicine | 37389520 | J Adolesc Health | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37389520 |
| The valine-arginine dipeptide repeat protein encoded by mammalian telomeric RNA appears highly expressed in mitosis and may repress global translation. | Al-Turki TM, Mantri V, Willcox S, Mills CA, Herring LE, Cho SJ, Lee H, Meyer C, Anton ES, Griffith JD | bioRxiv : the preprint server for biology | 39211251 | bioRxiv | 2024 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/39211251 |
| Ultrastructural reconstruction of the endodermal nerve net of Hydra vulgaris. | Zhang S, Ofer N, Dupre C, Wang X, Schalek R, Wu Y, Lin M, Roth M, Adhinarta J, Gohain A, Fan Y, Yin W, Wei D, Lichtman J, Yuste R | Current biology : CB | 41167196 | Curr Biol | 2025 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/41167196 |
| The telomeric valine-arginine dipeptide repeat protein changes state to diffuse staining in mitosis and represses in vitro translation. | Al-Turki T, Mantri V, Willcox S, Mills CA, Herring LE, Cho SJ, Lee H, Meyer C, Anton ES, Griffith JD | Proceedings of the National Academy of Sciences of the United States of America | 41269794 | Proc Natl Acad Sci U S A | 2025 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/41269794 |
| Radial glia promote microglial development through integrin α(V)β(8) -TGFβ1 signaling. | McKinsey GL, Santander N, Zhang X, Kleemann K, Tran L, Katewa A, Conant K, Barraza M, Waddell K, Lizama C, La Russa M, Koo HJ, Lee H, Mukherjee D, Paidassi H, Anton ES, Atabai K, Sheppard D, Butovsky O, Arnold TD | bioRxiv : the preprint server for biology | 37790363 | bioRxiv | 2023 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/37790363 |
| Mapping of neuronal and glial primary cilia contactome and connectome in the human cerebral cortex. | Wu JY, Cho SJ, Descant K, Li PH, Shapson-Coe A, Januszewski M, Berger DR, Meyer C, Casingal C, Huda A, Liu J, Ghashghaei T, Brenman M, Jiang M, Scarborough J, Pope A, Jain V, Stein JL, Guo J, Yasuda R, Lichtman JW, Anton ES | Neuron | 37898123 | Neuron | 2024 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/37898123 |
| The T Cell Antigen Receptor α Transmembrane Domain Coordinates Triggering through Regulation of Bilayer Immersion and CD3 Subunit Associations. | Brazin KN, Mallis RJ, Boeszoermenyi A, Feng Y, Yoshizawa A, Reche PA, Kaur P, Bi K, Hussey RE, Duke-Cohan JS, Song L, Wagner G, Arthanari H, Lang MJ, Reinherz EL | Immunity | 30389415 | Immunity | 2018 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/30389415 |
| NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology. | Mallis RJ, Brazin KN, Duke-Cohan JS, Hwang W, Wang JH, Wagner G, Arthanari H, Lang MJ, Reinherz EL | Journal of biomolecular NMR | 30815789 | J Biomol NMR | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30815789 |
| TCR-pMHC encounter differentially regulates transcriptomes of tissue-resident CD8 T cells. | Yoshizawa A, Bi K, Keskin DB, Zhang G, Reinhold B, Reinherz EL | European journal of immunology | 28872670 | Eur J Immunol | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28872670 |
| αβ T Cell Receptor Mechanosensing Forces out Serial Engagement. | Feng Y, Reinherz EL, Lang MJ | Trends in immunology | 30060805 | Trends Immunol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30060805 |
| The Gene Conundrum in Alzheimer's Disease. | Chun J | Cerebrum : the Dana forum on brain science | 32206173 | Cerebrum | 2019 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/32206173 |
| Mosaic Somatic Gene Recombination as a Potentially Unifying Hypothesis for Alzheimer's Disease. | Kaeser GE, Chun J | Frontiers in genetics | 32457796 | Front Genet | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32457796 |
| Brain cell somatic gene recombination and its phylogenetic foundations. | Kaeser G, Chun J | The Journal of biological chemistry | 32699111 | J Biol Chem | 2020 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/32699111 |
| Reply to: APP gene copy number changes reflect exogenous contamination. | Lee MH, Liu CS, Zhu Y, Kaeser GE, Rivera R, Romanow WJ, Kihara Y, Chun J | Nature | 32814882 | Nature | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32814882 |
| Cardiac function modulates endocardial cell dynamics to shape the cardiac outflow tract. | Sidhwani P, Leerberg DM, Boezio GLM, Capasso TL, Yang H, Chi NC, Roman BL, Stainier DYR, Yelon D | Development (Cambridge, England) | 32439760 | Development | 2020 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/32439760 |
| The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes. | Boos F, Chen J, Brunet A | Cold Spring Harbor protocols | 37100468 | Cold Spring Harb Protoc | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/37100468 |
| Tutorial: practical considerations for tissue clearing and imaging. | Weiss KR, Voigt FF, Shepherd DP, Huisken J | Nature protocols | 34021294 | Nat Protoc | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34021294 |
| Dermomyotome-derived endothelial cells migrate to the dorsal aorta to support hematopoietic stem cell emergence. | Sahai-Hernandez P, Pouget C, Eyal S, Svoboda O, Chacon J, Grimm L, Gjøen T, Traver D | eLife | 37695317 | Elife | 2023 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/37695317 |
| Drivers of vessel progenitor fate define intermediate mesoderm dimensions by inhibiting kidney progenitor specification. | Perens EA, Yelon D | Developmental biology | 39307382 | Dev Biol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39307382 |
| PIKFYVE inhibition mitigates disease in models of diverse forms of ALS. | Hung ST, Linares GR, Chang WH, Eoh Y, Krishnan G, Mendonca S, Hong S, Shi Y, Santana M, Kueth C, Macklin-Isquierdo S, Perry S, Duhaime S, Maios C, Chang J, Perez J, Couto A, Lai J, Li Y, Alworth SV, Hendricks E, Wang Y, Zlokovic BV, Dickman DK, Parker JA, Zarnescu DC, Gao FB, Ichida JK | Cell | 36754049 | Cell | 2023 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/36754049 |
| SYF2 suppression mitigates neurodegeneration in models of diverse forms of ALS. | Linares GR, Li Y, Chang WH, Rubin-Sigler J, Mendonca S, Hong S, Eoh Y, Guo W, Huang YH, Chang J, Tu S, Dorjsuren N, Santana M, Hung ST, Yu J, Perez J, Chickering M, Cheng TY, Huang CC, Lee SJ, Deng HJ, Bach KT, Gray K, Subramanyam V, Rosenfeld J, Alworth SV, Goodarzi H, Ichida JK | Cell stem cell | 36736291 | Cell Stem Cell | 2023 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/36736291 |
| CLIP-Seq analysis enables the design of protective ribosomal RNA bait oligonucleotides against C9ORF72 ALS/FTD poly-GR pathophysiology. | Ortega JA, Sasselli IR, Boccitto M, Fleming AC, Fortuna TR, Li Y, Sato K, Clemons TD, Mckenna ED, Nguyen TP, Anderson EN, Asin J, Ichida JK, Pandey UB, Wolin SL, Stupp SI, Kiskinis E | Science advances | 37948524 | Sci Adv | 2023 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/37948524 |
| Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. | Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker JR, Ichida JK, Shen Y, Zeng J, Tsao PS, Snyder MP | bioRxiv : the preprint server for biology | 38798507 | bioRxiv | 2024 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/38798507 |
| Antisense oligonucleotide depletion of CCDC146 is a broad-spectrum therapeutic strategy for ALS. | Zhang S, Moll T, Rubin-Sigler J, Tu S, Li S, Yuan E, Liu M, King M, Alhathli E, Treanor C, Twelvetrees A, Weinreich M, Bonsall S, Harvey C, Gornall S, Shaw A, Ganssauge J, Bhinge A, Souza CDS, Ferraiuolo L, Hornstein E, Shalem O, Avila A, Shelkovnikova T, van Dijk CH, Timpanaro IS, Kenna KP, Zeng J, van Damme P, Tsao PS, Shaw PJ, Ichida JK, Cooper-Knock J, Snyder MP | medRxiv : the preprint server for health sciences | 38633814 | medRxiv | 2025 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/38633814 |
| Stem cell therapy for central nervous system disorders: Metabolic interactions between transplanted cells and local microenvironments. | Sakowski SA, Chen KS | Neurobiology of disease | 35988874 | Neurobiol Dis | 2022 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/35988874 |
| Occupational history associates with ALS survival and onset segment. | Goutman SA, Boss J, Godwin C, Mukherjee B, Feldman EL, Batterman SA | Amyotrophic lateral sclerosis & frontotemporal degeneration | 36193557 | Amyotroph Lateral Scler Frontotemporal Degener | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36193557 |
| Emerging insights into the complex genetics and pathophysiology of amyotrophic lateral sclerosis. | Goutman SA, Hardiman O, Al-Chalabi A, Chió A, Savelieff MG, Kiernan MC, Feldman EL | The Lancet. Neurology | 35334234 | Lancet Neurol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35334234 |
| Avocational exposure associations with ALS risk, survival, and phenotype: A Michigan-based case-control study. | Goutman SA, Boss J, Jang DG, Piecuch C, Farid H, Batra M, Mukherjee B, Feldman EL, Batterman SA | Journal of the neurological sciences | 38278093 | J Neurol Sci | 2024 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/38278093 |
| Role of the Exposome in Neurodegenerative Disease: Recent Insights and Future Directions. | Sakowski SA, Koubek EJ, Chen KS, Goutman SA, Feldman EL | Annals of neurology | 38411261 | Ann Neurol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38411261 |
| Residential exposure associations with ALS risk, survival, and phenotype: a Michigan-based case-control study. | Goutman SA, Boss J, Jang DG, Piecuch C, Farid H, Batra M, Mukherjee B, Feldman EL, Batterman SA | Amyotrophic lateral sclerosis & frontotemporal degeneration | 38557405 | Amyotroph Lateral Scler Frontotemporal Degener | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38557405 |
| Multiple metal exposures associate with higher amyotrophic lateral sclerosis risk and mortality independent of genetic risk and correlate to self-reported exposures: a case-control study. | Jang DG, Dou JF, Koubek EJ, Teener S, Zhou L, Bakulski KM, Mukherjee B, Batterman SA, Feldman EL, Goutman SA | Journal of neurology, neurosurgery, and psychiatry | 39107037 | J Neurol Neurosurg Psychiatry | 2025 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/39107037 |
| Improving prediction models of amyotrophic lateral sclerosis (ALS) using polygenic, pre-existing conditions, and survey-based risk scores in the UK Biobank. | Jin W, Boss J, Bakulski KM, Goutman SA, Feldman EL, Fritsche LG, Mukherjee B | Journal of neurology | 39249108 | J Neurol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39249108 |
| Gene expression signatures from whole blood predict amyotrophic lateral sclerosis case status and survival. | Zhao Y, Savelieff MG, Li X, Guo K, Wang K, Li M, Li B, Iyer G, Sakowski SA, Zhao L, Teener SJ, Bakulski KM, Dou JF, Traynor BJ, Karnovsky A, Batterman SA, Hur J, Goutman SA, Sartor MA, Feldman EL | Nature communications | 41173979 | Nat Commun | 2025 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/41173979 |
| The amyotrophic lateral sclerosis exposome: recent advances and future directions. | Goutman SA, Savelieff MG, Jang DG, Hur J, Feldman EL | Nature reviews. Neurology | 37709948 | Nat Rev Neurol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37709948 |
| Environmental risk scores of persistent organic pollutants associate with higher ALS risk and shorter survival in a new Michigan case/control cohort. | Goutman SA, Boss J, Jang DG, Mukherjee B, Richardson RJ, Batterman S, Feldman EL | Journal of neurology, neurosurgery, and psychiatry | 37758454 | J Neurol Neurosurg Psychiatry | 2024 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/37758454 |
| Nanoplastics and Neurodegeneration in ALS. | Eisen A, Pioro EP, Goutman SA, Kiernan MC | Brain sciences | 38790450 | Brain Sci | 2024 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/38790450 |
| Cumulative Genetic Score and C9orf72 Repeat Status Independently Contribute to Amyotrophic Lateral Sclerosis Risk in 2 Case-Control Studies. | Dou J, Bakulski K, Guo K, Hur J, Zhao L, Saez-Atienzar S, Stark A, Chia R, García-Redondo A, Rojas-Garcia R, Vázquez Costa JF, Fernandez Santiago R, Bandres-Ciga S, Gómez-Garre P, Periñán MT, Mir P, Pérez-Tur J, Cardona F, Menendez-Gonzalez M, Riancho J, Borrego-Hernández D, Galán-Dávila L, Infante Ceberio J, Pastor P, Paradas C, Dols-Icardo O, Traynor BJ, Feldman EL, Goutman SA, Spanish Neurological Consortium | Neurology. Genetics | 37293291 | Neurol Genet | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37293291 |
| miRNA analysis reveals novel dysregulated pathways in amyotrophic lateral sclerosis. | Hur J, Paez-Colasante X, Figueroa-Romero C, Lo TW, Barmada SJ, Paulsen MT, Ljungman M, Alakwaa FM, Savelieff MG, Goutman SA, Feldman EL | Human molecular genetics | 36219176 | Hum Mol Genet | 2023 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/36219176 |
| Body mass index associates with amyotrophic lateral sclerosis survival and metabolomic profiles. | Goutman SA, Boss J, Iyer G, Habra H, Savelieff MG, Karnovsky A, Mukherjee B, Feldman EL | Muscle & nerve | 36321729 | Muscle Nerve | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36321729 |
| Recent advances in the diagnosis and prognosis of amyotrophic lateral sclerosis. | Goutman SA, Hardiman O, Al-Chalabi A, Chió A, Savelieff MG, Kiernan MC, Feldman EL | The Lancet. Neurology | 35334233 | Lancet Neurol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35334233 |
| Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods. | Du J, Boss J, Han P, Beesley LJ, Kleinsasser M, Goutman SA, Batterman S, Feldman EL, Mukherjee B | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 36644406 | J Comput Graph Stat | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36644406 |
| Peripheral Immune Profiles Predict ALS Progression in an Age- and Sex-Dependent Manner. | Murdock BJ, Zhao B, Pawlowski KD, Famie JP, Piecuch CE, Webber-Davis IF, Teener SJ, Feldman EL, Zhao L, Goutman SA | Neurology(R) neuroimmunology & neuroinflammation | 38626361 | Neurol Neuroimmunol Neuroinflamm | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38626361 |
| Life Course Exposure to Cyanobacteria and Amyotrophic Lateral Sclerosis Survival. | Batterman SA, Islam MK, Jang DG, Feldman EL, Goutman SA | International journal of environmental research and public health | 40427878 | Int J Environ Res Public Health | 2025 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/40427878 |
| In Vitro Modeling of Natural Killer Cell Cytotoxicity to Inform Personalized ALS Therapeutics. | Murdock BJ, Park J, Jang DG, Zhao B, Teener SJ, Webber-Davis IF, Zhao L, Feldman EL, Goutman SA | Annals of clinical and translational neurology | 40629698 | Ann Clin Transl Neurol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40629698 |
| Awareness and care practices for rare neurologic diseases among senior neurologists: A global survey. | Jang DG, Federico A, Savelieff MG, Grisold W, Mancuso M, Molnar MJ, Feldman EL, Reynolds EL, World Federation of Neurology Subspecialist Group on Rare Neurologic Diseases | Journal of the neurological sciences | 39855013 | J Neurol Sci | 2025 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/39855013 |
| Natural Killer Cell Dysregulation During ALS Disease Progression: A Gene Expression Analysis. | Goutman SA, Guo K, Park J, Jang DG, Teener SJ, Webber-Davis IF, Famie JP, Piecuch CE, Hur J, Murdock BJ | Neurology open access | 41684905 | Neurol Open Access | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41684905 |
| Development of Life Course Exposure Estimates Using Geospatial Data and Residence History. | Batterman S, Islam MK, Goutman S | International journal of environmental research and public health | 41302575 | Int J Environ Res Public Health | 2025 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/41302575 |
| Metal mixtures associate with higher amyotrophic lateral sclerosis risk and mortality independent of genetic risk and correlate to self-reported exposures: a case-control study. | Jang DG, Dou J, Koubek EJ, Teener S, Zhao L, Bakulski KM, Mukherjee B, Batterman SA, Feldman EL, Goutman SA | medRxiv : the preprint server for health sciences | 38464233 | medRxiv | 2024 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/38464233 |
| Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis. | Guo K, Figueroa-Romero C, Noureldein MH, Murdock BJ, Savelieff MG, Hur J, Goutman SA, Feldman EL | Brain : a journal of neurology | 37721161 | Brain | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/37721161 |
| Improving prediction models of amyotrophic lateral sclerosis (ALS) using polygenic, pre-existing conditions, and survey-based risk scores in the UK Biobank. | Jin W, Boss J, Bakulski KM, Goutman SA, Feldman EL, Fritsche LG, Mukherjee B | medRxiv : the preprint server for health sciences | 38585910 | medRxiv | 2024 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/38585910 |
| Genetic and Mechanistic Insights Inform Amyotrophic Lateral Sclerosis Treatment and Symptomatic Management: Current and Emerging Therapeutics and Clinical Trial Design Considerations. | Quigley SE, Quigg KH, Goutman SA | CNS drugs | 40897992 | CNS Drugs | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40897992 |
| Impact of the Adverse Social Exposome on Survival in Individuals With Amyotrophic Lateral Sclerosis. | Jang DG, Kind AJ, Patterson A, Pedde M, Powell WR, Feldman EL, Goutman SA | Neurology | 39879575 | Neurology | 2025 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/39879575 |
| Epigenetic age acceleration is associated with occupational exposures, sex, and survival in amyotrophic lateral sclerosis. | Zhao Y, Li X, Wang K, Iyer G, Sakowski SA, Zhao L, Teener S, Bakulski KM, Dou JF, Traynor BJ, Karnovsky A, Batterman SA, Feldman EL, Sartor MA, Goutman SA | EBioMedicine | 39369616 | EBioMedicine | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39369616 |
| Sex Hormones Associate With Amyotrophic Lateral Sclerosis Risk and Survival. | Goutman SA, Stouffer DG, Jang DG, Park J, Murdock BJ, Auchus RJ | Annals of clinical and translational neurology | 41412960 | Ann Clin Transl Neurol | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41412960 |
| Amyotrophic lateral sclerosis. | Feldman EL, Goutman SA, Petri S, Mazzini L, Savelieff MG, Shaw PJ, Sobue G | Lancet (London, England) | 36116464 | Lancet | 2022 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/36116464 |
| Priorities and Recommendations to Make ALS a Livable Disease Emanating from the 2024 National Academies of Sciences, Engineering, and Medicine Report Living with ALS. | Howard IM, Babu S, Carter C, Sakowski SA, Kurent JE, Cudkowicz ME, Feldman EL | Annals of neurology | 39390661 | Ann Neurol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39390661 |
| Longitudinal Metabolomics in Amyotrophic Lateral Sclerosis Implicates Impaired Lipid Metabolism. | Guo K, Savelieff MG, Jang DG, Teener SJ, Zhao L, Hur J, Goutman SA, Feldman EL | Annals of neurology | 39976286 | Ann Neurol | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39976286 |
| Human microglial state dynamics in Alzheimer's disease progression. | Sun N, Victor MB, Park YP, Xiong X, Scannail AN, Leary N, Prosper S, Viswanathan S, Luna X, Boix CA, James BT, Tanigawa Y, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M | Cell | 37774678 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37774678 |
| Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion. | Xiong X, James BT, Boix CA, Park YP, Galani K, Victor MB, Sun N, Hou L, Ho LL, Mantero J, Scannail AN, Dileep V, Dong W, Mathys H, Bennett DA, Tsai LH, Kellis M | Cell | 37774680 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37774680 |
| Single-cell multiregion dissection of Alzheimer's disease. | Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, Prokopenko D, Tanzi RE, Bennett DA, Tsai LH, Kellis M | Nature | 39048816 | Nature | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/39048816 |
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| Multifaceted impact of specialized neuropeptide-intensive neurons on the selective vulnerability in Alzheimer's disease. | Li M, Flack N, Larsen PA | bioRxiv : the preprint server for biology | 38014130 | bioRxiv | 2024 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/38014130 |
| Opposing roles of p38α-mediated phosphorylation and PRMT1-mediated arginine methylation in driving TDP-43 proteinopathy. | Aikio M, Odeh HM, Wobst HJ, Lee BL, Chan Ú, Mauna JC, Mack KL, Class B, Ollerhead TA, Ford AF, Barbieri EM, Cupo RR, Drake LE, Smalley JL, Lin YT, Lam S, Thomas R, Castello N, Baral A, Beyer JN, Najar MA, Dunlop J, Gitler AD, Javaherian A, Kaye JA, Burslem GM, Brown DG, Donnelly CJ, Finkbeiner S, Moss SJ, Brandon NJ, Shorter J | Cell reports | 39817908 | Cell Rep | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39817908 |
| Integrating single-cell RNA-seq datasets with substantial batch effects. | Hrovatin K, Moinfar AA, Zappia L, Lapuerta AT, Lengerich B, Kellis M, Theis FJ | bioRxiv : the preprint server for biology | 37961672 | bioRxiv | 2024 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/37961672 |
| Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology. | Mathys H, Peng Z, Boix CA, Victor MB, Leary N, Babu S, Abdelhady G, Jiang X, Ng AP, Ghafari K, Kunisky AK, Mantero J, Galani K, Lohia VN, Fortier GE, Lotfi Y, Ivey J, Brown HP, Patel PR, Chakraborty N, Beaudway JI, Imhoff EJ, Keeler CF, McChesney MM, Patel HH, Patel SP, Thai MT, Bennett DA, Kellis M, Tsai LH | Cell | 37774677 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37774677 |
| Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer's disease. | Sun N, Akay LA, Murdock MH, Park Y, Galiana-Melendez F, Bubnys A, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M | Nature neuroscience | 37264161 | Nat Neurosci | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37264161 |
| CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function. | Xie L, Merjane J, Bergmann CA, Xu J, Hurtle B, Donnelly CJ | bioRxiv : the preprint server for biology | 39026766 | bioRxiv | 2024 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/39026766 |
| Single-cell multiregion epigenomic rewiring in Alzheimer's disease progression and cognitive resilience. | Liu Z, Zhang S, James BT, Galani K, Mangan RJ, Fass SB, Liang C, Wagle MM, Boix CA, Tanigawa Y, Yun S, Sung Y, Xiong X, Sun N, Hou L, Wohlwend M, Qiu M, Han X, Xiong L, Preka E, Huang L, Li WF, Ho LL, Grayson A, Mantero J, Kozlenkov A, Mathys H, Chen T, Dracheva S, Bennett DA, Tsai LH, Kellis M | Cell | 40752494 | Cell | 2025 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/40752494 |
| Hypometric genetics: Improved power in genetic discovery by incorporating quality control flags. | Tanigawa Y, Kellis M | American journal of human genetics | 39442521 | Am J Hum Genet | 2024 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/39442521 |
| High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood. | Vochteloo M, Kooijmans A, Bakker J, Oelen R, Niewold J, Kaptijn D, Bonder MJ, van der Wijst M, Huang Y, Bryois J, Tsai EA, Franke L, Westra HJ | bioRxiv : the preprint server for biology | 41394650 | bioRxiv | 2025 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/41394650 |
| Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD. | Pineda SS, Lee H, Ulloa-Navas MJ, Linville RM, Garcia FJ, Galani K, Engelberg-Cook E, Castanedes MC, Fitzwalter BE, Pregent LJ, Gardashli ME, DeTure M, Vera-Garcia DV, Hucke ATS, Oskarsson BE, Murray ME, Dickson DW, Heiman M, Belzil VV, Kellis M | Cell | 38521060 | Cell | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38521060 |
| TurboID-Mediated Profiling of Glioblastoma-Derived Extracellular Vesicle Cargo Proteins. | Russo MN, Norton ES, Ulloa-Navas MJ, Zarco N, Wang W, Lam TT, Quiñones-Hinojosa A, Belzil VV, Guerrero-Cázares H | Journal of extracellular vesicles | 40985879 | J Extracell Vesicles | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40985879 |
| Context-dependent Interactors Regulate TDP-43 Dysfunction in ALS/FTLD. | Xie L, Zhu Y, Hurtle BT, Wright M, Robinson JL, Mauna JC, Brown EE, Ngo M, Bergmann CA, Xu J, Merjane J, Gleixner AM, Grigorean G, Liu F, Rossoll W, Lee EB, Kiskinis E, Chikina M, Donnelly CJ | bioRxiv : the preprint server for biology | 40291645 | bioRxiv | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/40291645 |
| A polygenic score method boosted by non-additive models. | Ohta R, Tanigawa Y, Suzuki Y, Kellis M, Morishita S | Nature communications | 38811555 | Nat Commun | 2024 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/38811555 |
| Defining RNA oligonucleotides that reverse deleterious phase transitions of RNA-binding proteins with prion-like domains. | Guo L, Mann JR, Mauna JC, Copley KE, Wang H, Rubien JD, Bergmann CA, Carey JL, Merjane J, Ngo M, Xu J, Odeh HM, Lin J, Lee BL, Ganser L, Robinson E, Kim KM, Murthy AC, Paul T, Portz B, Gleixner AM, Diaz Z, Smirnov A, Padilla G, Lavorando E, Espy C, Shang Y, Huang EJ, Chesi A, Fawzi NL, Myong S, Donnelly CJ, Shorter J | Molecular cell | 41512823 | Mol Cell | 2026 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/41512823 |
| Local translation in primary afferents and its contribution to pain. | Gale JR, Gedeon JY, Donnelly CJ, Gold MS | Pain | 35438669 | Pain | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/35438669 |
| Microglial States Are Susceptible to Senescence and Cholesterol Dysregulation in Alzheimer's Disease. | Li B, Wang S, Kerman B, Hugo C, Shwab EK, Shu C, Chiba-Falek O, Arvanitakis Z, N Yassine H | Aging cell | 40790613 | Aging Cell | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40790613 |
| Novel Kinesin Family Member 1A Variants Linked to Atypical Parkinsonism Elicit Altered Neuronal Transactive Response DNA Binding Protein 43 kDa Interactions and Dendritic Atrophy. | Homayoun H, DeChellis-Marks MR, Kofler J, Fricklas G, Gleixner AM, Yeh FC, Lacomis D, Chu CT, Donnelly CJ | The American journal of pathology | 40543705 | Am J Pathol | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40543705 |
| Assays to measure small molecule Hsp70 agonist activity in vitro and in vivo. | Shapiro O, Woods C, Gleixner AM, Sannino S, Ngo M, McDaniels MD, Wipf P, Hukriede NA, Donnelly CJ, Brodsky JL | Analytical biochemistry | 39522672 | Anal Biochem | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39522672 |
| Multifaceted Role of Specialized Neuropeptide-Intensive Neurons on the Selective Vulnerability to Alzheimer's Disease in the Human Brain. | Li M, Flack N, Larsen PA | Biomolecules | 39766225 | Biomolecules | 2024 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/39766225 |
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| Power of inclusion: Enhancing polygenic prediction with admixed individuals. | Tanigawa Y, Kellis M | American journal of human genetics | 37890495 | Am J Hum Genet | 2023 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/37890495 |
| Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease. | Linna-Kuosmanen S, Schmauch E, Galani K, Ojanen J, Boix CA, Örd T, Toropainen A, Singha PK, Moreau PR, Harju K, Blazeski A, Segerstolpe Å, Lahtinen V, Hou L, Kang K, Meibalan E, Agudelo LZ, Kokki H, Halonen J, Jalkanen J, Gunn J, MacRae CA, Hollmén M, Hartikainen JEK, Kaikkonen MU, García-Cardeña G, Tavi P, Kiviniemi T, Kellis M | Cell reports. Medicine | 38776872 | Cell Rep Med | 2024 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/38776872 |
| TDP-43 dysfunction compromises UPF1-dependent mRNA metabolism in ALS. | Alessandrini F, Wright M, Kurosaki T, Perloff OS, Ngo M, Kofler JK, Donnelly CJ, Maquat LE, Kiskinis E | Neuron | 41389796 | Neuron | 2026 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/41389796 |
| PRISM: ancestry-aware integration of tissue-specific genomic annotations enhances the transferability of polygenic scores. | Tian X, Fabiha T, Li WF, Dey KK, Kellis M, Tanigawa Y | bioRxiv : the preprint server for biology | 41292742 | bioRxiv | 2025 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/41292742 |
| sc4D: spatio-temporal single-cell transcriptomics analysis through embedded optimal transport identifies joint glial response to Alzheimer's disease pathology. | Rao I, Kellis M, Tanigawa Y | bioRxiv : the preprint server for biology | 41332677 | bioRxiv | 2025 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/41332677 |
| Autophagy at the synapse, an early site of dysfunction in neurodegeneration. | Jasutkar HG, Yamamoto A | Current opinion in physiology | 36968133 | Curr Opin Physiol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36968133 |
| Phase Separation in Biology and Disease; Current Perspectives and Open Questions. | Boeynaems S, Chong S, Gsponer J, Holt L, Milovanovic D, Mitrea DM, Mueller-Cajar O, Portz B, Reilly JF, Reinkemeier CD, Sabari BR, Sanulli S, Shorter J, Sontag E, Strader L, Stachowiak J, Weber SC, White M, Zhang H, Zweckstetter M, Elbaum-Garfinkle S, Kriwacki R | Journal of molecular biology | 36690068 | J Mol Biol | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36690068 |
| The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae. | Terhorst A, Sandikci A, Whittaker CA, Szórádi T, Holt LJ, Neurohr GE, Amon A | Frontiers in cell and developmental biology | 37123399 | Front Cell Dev Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37123399 |
| Condensation of LINE-1 is critical for retrotransposition. | Sil S, Keegan S, Ettefa F, Denes LT, Boeke JD, Holt LJ | eLife | 37114770 | Elife | 2023 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/37114770 |
| Brain Iron as a Surrogate Biomarker of Pathological TDP-43 Identifies Brain Region-Specific Signatures in Ageing, Alzheimer's Disease and Amyotrophic Lateral Sclerosis. | Waldron FM, Spence H, Taso OS, Read FL, Sinha IR, Irwin KE, Wong PC, Ling JP, Gregory JM | bioRxiv : the preprint server for biology | 41256466 | bioRxiv | 2025 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/41256466 |
| Skin TDP-43 pathology as a candidate biomarker for predicting amyotrophic lateral sclerosis decades prior to motor symptom onset. | Waldron FM, Langerová T, Rahmanova A, Read FL, Spence H, Roberts K, Macleod AD, Pattle SB, Hanna K, Gregory JM | bioRxiv : the preprint server for biology | 41256495 | bioRxiv | 2025 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/41256495 |
| Single-molecule validation and optimised protocols for the use of secondary nanobodies in multiplexed immunoassays. | Saleeb R, O'Shaughnessy J, Ferguson R, Adams CT, Horrocks MH | Journal of microscopy | 41563121 | J Microsc | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41563121 |
| Polysome collapse and RNA condensation fluidize the cytoplasm. | Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ | Molecular cell | 39059370 | Mol Cell | 2024 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/39059370 |
| The broken Alzheimer's disease genome. | Gouveia Roque C, Phatnani H, Hengst U | Cell genomics | 38697121 | Cell Genom | 2024 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/38697121 |
| Macromolecular crowding: Sensing without a sensor. | Holt LJ, Delarue M | Current opinion in cell biology | 37897928 | Curr Opin Cell Biol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37897928 |
| Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons. | Sinha IR, Sandal PS, Spence H, Burns GD, Mallika AP, Abbasinejad F, Irwin KE, Cruz ALF, Wang V, Marx SR, Rodríguez JL, Langmead B, Gregory JM, Wong PC, Ling JP | Nature communications | 40715064 | Nat Commun | 2025 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/40715064 |
| Epithelial tissue confinement inhibits cell growth and leads to volume-reducing divisions. | Devany J, Falk MJ, Holt LJ, Murugan A, Gardel ML | Developmental cell | 37339629 | Dev Cell | 2023 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/37339629 |
| A genome-wide CRISPR screen identifies WDFY3 as a regulator of macrophage efferocytosis. | Shi J, Wu X, Wang Z, Li F, Meng Y, Moore RM, Cui J, Xue C, Croce KR, Yurdagul A Jr, Doench JG, Li W, Zarbalis KS, Tabas I, Yamamoto A, Zhang H | Nature communications | 36566259 | Nat Commun | 2022 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/36566259 |
| RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS. | Spence H, Waldron FM, Saleeb RS, Brown AL, Rifai OM, Gilodi M, Read F, Roberts K, Milne G, Wilkinson D, O'Shaughnessy J, Pastore A, Fratta P, Shneider N, Tartaglia GG, Zacco E, Horrocks MH, Gregory JM | Acta neuropathologica | 38443601 | Acta Neuropathol | 2024 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/38443601 |
| Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. | Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN | Proceedings of the National Academy of Sciences of the United States of America | 39854229 | Proc Natl Acad Sci U S A | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39854229 |
| mRNA condensation fluidizes the cytoplasm. | Xie Y, Liu T, Gresham D, Holt LJ | bioRxiv : the preprint server for biology | 37398029 | bioRxiv | 2023 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/37398029 |
| Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts. | Rifai OM, O'Shaughnessy J, Dando OR, Munro AF, Sewell MDE, Abrahams S, Waldron FM, Sibley CR, Gregory JM | Brain : a journal of neurology | 37450566 | Brain | 2023 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/37450566 |
| Macromolecular crowding limits growth under pressure. | Alric B, Formosa-Dague C, Dague E, Holt LJ, Delarue M | Nature physics | 37152719 | Nat Phys | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37152719 |
| Two-color coincidence single-molecule pulldown for the specific detection of disease-associated protein aggregates. | Saleeb RS, Leighton C, Lee JE, O'Shaughnessy J, Jeacock K, Chappard A, Cumberland R, Zhao T, Ball SR, Sunde M, Clarke DJ, Piché K, McPhail JA, Louwrier A, Angers R, Gandhi S, Downey P, Kunath T, Horrocks MH | Science advances | 37967183 | Sci Adv | 2023 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/37967183 |
| Condensed-phase signaling can expand kinase specificity and respond to macromolecular crowding. | Sang D, Shu T, Pantoja CF, Ibáñez de Opakua A, Zweckstetter M, Holt LJ | Molecular cell | 36108633 | Mol Cell | 2022 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/36108633 |
| Increased mesoscale diffusivity in response to acute glucose starvation. | Xie Y, Gresham D, Holt L | bioRxiv : the preprint server for biology | 36711511 | bioRxiv | 2023 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/36711511 |
| How it feels in a cell. | Bonucci M, Shu T, Holt LJ | Trends in cell biology | 37286396 | Trends Cell Biol | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37286396 |
| Mesoscale molecular assembly is favored by the active, crowded cytoplasm. | Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ | bioRxiv : the preprint server for biology | 37781612 | bioRxiv | 2023 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/37781612 |
| Oligodendroglial macroautophagy is essential for myelin sheath turnover to prevent neurodegeneration and death. | Aber ER, Griffey CJ, Davies T, Li AM, Yang YJ, Croce KR, Goldman JE, Grutzendler J, Canman JC, Yamamoto A | Cell reports | 36261002 | Cell Rep | 2022 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/36261002 |
| Clinicopathological analysis of NEK1 variants in amyotrophic lateral sclerosis. | Rifai OM, Waldron FM, Sleibi D, O'Shaughnessy J, Leighton DJ, Gregory JM | Brain pathology (Zurich, Switzerland) | 38986433 | Brain Pathol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38986433 |
| Amygdala TDP-43 pathology is associated with behavioural dysfunction and ferritin accumulation in amyotrophic lateral sclerosis. | Rifai OM, Waldron FM, O'Shaughnessy J, Read FL, Gilodi M, Pastore A, Shneider N, Tartaglia GG, Zacco E, Spence H, Gregory JM | bioRxiv : the preprint server for biology | 38854008 | bioRxiv | 2024 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/38854008 |
| Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. | Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN | bioRxiv : the preprint server for biology | 38585850 | bioRxiv | 2024 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/38585850 |
| A rare genetic variant confers resistance to neurodegeneration across multiple neurological disorders by augmenting selective autophagy. | Croce KR, Ng C, Pankiv S, Albarran E, Langfelder P, Ramos de Jesus A, Duncan GM, Wang N, Basile A, McHugh C, Litt NA, Li A, Friedman S, Cortes EP, Zody MC, Yang XW, Ding JB, Vonsattel JPG, Simonsen A, Housman DE, Wexler NS, Yamamoto A | Neuron | 40945514 | Neuron | 2025 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/40945514 |
| Mesoscale molecular assembly is favored by the active, crowded cytoplasm. | Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ | PRX life | 40162127 | PRX Life | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40162127 |
| Amyotrophic lateral sclerosis caused by TARDBP mutations: from genetics to TDP-43 proteinopathy. | Balendra R, Sreedharan J, Hallegger M, Luisier R, Lashuel HA, Gregory JM, Patani R | The Lancet. Neurology | 40252666 | Lancet Neurol | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40252666 |
| Autophagy Dysfunction and Neurodegeneration: Where Does It Go Wrong? | Oettinger D, Yamamoto A | Journal of molecular biology | 40383464 | J Mol Biol | 2025 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/40383464 |
| Exenatide Once Weekly in the Treatment of Patients with Multiple System Atrophy. | Vijiaratnam N, Girges C, Wiegand M, Ismail C, Lameirinhas A, Yarnall A, Kirk C, Del-Din S, Rochester L, Kobylecki C, Ambler G, Skene S, Houlden H, Chelban V, Heslegrave A, Phillips W, Whone A, Quinn N, Lambert C, Dore C, Morris HR, Horrocks MH, Lee JE, O'Shaughnessy J, Li Y, Greig NH, Gandhi S, Libri V, Athauda D, Foltynie T | Annals of neurology | 40727970 | Ann Neurol | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40727970 |
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| Controlling the crowd with a WNK. | Holt LJ, Denes LT | Cell | 36423576 | Cell | 2022 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/36423576 |
| Machine learning identifies routine blood tests as accurate predictive measures of pollution-dependent poor cognitive function. | Johnson H, Longden J, Cameron G, Waiter GD, Waldron FM, Gregory JM, Spence H | bioRxiv : the preprint server for biology | 39868217 | bioRxiv | 2025 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/39868217 |
| Increased mesoscale diffusivity in response to acute glucose starvation. | Xie Y, Gresham D, Holt LJ | microPublication biology | 36908311 | MicroPubl Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36908311 |
| Adult-onset deactivation of autophagy leads to loss of synapse homeostasis and cognitive impairment, with implications for alzheimer disease. | Grosso Jasutkar H, Wasserlein EM, Ishola A, Litt N, Staniszewski A, Arancio O, Yamamoto A | Autophagy | 38949671 | Autophagy | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38949671 |
| SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain. | Mali SS, Silva R, Gong Z, Cronce M, Vo U, Vuong C, Moayedi Y, Cox JS, Bautista DM | bioRxiv : the preprint server for biology | 38260476 | bioRxiv | 2024 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/38260476 |
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| Spatiotemporal control of opioid signaling and behavior. | Siuda ER, Copits BA, Schmidt MJ, Baird MA, Al-Hasani R, Planer WJ, Funderburk SC, McCall JG, Gereau RW 4th, Bruchas MR | Neuron | 25937173 | Neuron | 2015 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/25937173 |
| A bright future? Optogenetics in the periphery for pain research and therapy. | Mickle AD, Gereau RW 4th | Pain | 30113949 | Pain | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30113949 |
| A wireless closed-loop system for optogenetic peripheral neuromodulation. | Mickle AD, Won SM, Noh KN, Yoon J, Meacham KW, Xue Y, McIlvried LA, Copits BA, Samineni VK, Crawford KE, Kim DH, Srivastava P, Kim BH, Min S, Shiuan Y, Yun Y, Payne MA, Zhang J, Jang H, Li Y, Lai HH, Huang Y, Park SI, Gereau RW 4th, Rogers JA | Nature | 30602791 | Nature | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30602791 |
| Optogenetic silencing of nociceptive primary afferents reduces evoked and ongoing bladder pain. | Samineni VK, Mickle AD, Yoon J, Grajales-Reyes JG, Pullen MY, Crawford KE, Noh KN, Gereau GB, Vogt SK, Lai HH, Rogers JA, Gereau RW 4th | Scientific reports | 29158567 | Sci Rep | 2017 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/29158567 |
| Stretchable multichannel antennas in soft wireless optoelectronic implants for optogenetics. | Park SI, Shin G, McCall JG, Al-Hasani R, Norris A, Xia L, Brenner DS, Noh KN, Bang SY, Bhatti DL, Jang KI, Kang SK, Mickle AD, Dussor G, Price TJ, Gereau RW 4th, Bruchas MR, Rogers JA | Proceedings of the National Academy of Sciences of the United States of America | 27911798 | Proc Natl Acad Sci U S A | 2016 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/27911798 |
| Optodynamic simulation of β-adrenergic receptor signalling. | Siuda ER, McCall JG, Al-Hasani R, Shin G, Il Park S, Schmidt MJ, Anderson SL, Planer WJ, Rogers JA, Bruchas MR | Nature communications | 26412387 | Nat Commun | 2015 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/26412387 |
| Divergent Modulation of Nociception by Glutamatergic and GABAergic Neuronal Subpopulations in the Periaqueductal Gray. | Samineni VK, Grajales-Reyes JG, Copits BA, O'Brien DE, Trigg SL, Gomez AM, Bruchas MR, Gereau RW 4th | eNeuro | 28374016 | eNeuro | 2017 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/28374016 |
| Ultraminiaturized photovoltaic and radio frequency powered optoelectronic systems for wireless optogenetics. | Park SI, Shin G, Banks A, McCall JG, Siuda ER, Schmidt MJ, Chung HU, Noh KN, Mun JG, Rhodes J, Bruchas MR, Rogers JA | Journal of neural engineering | 26193450 | J Neural Eng | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26193450 |
| Soft, stretchable, fully implantable miniaturized optoelectronic systems for wireless optogenetics. | Park SI, Brenner DS, Shin G, Morgan CD, Copits BA, Chung HU, Pullen MY, Noh KN, Davidson S, Oh SJ, Yoon J, Jang KI, Samineni VK, Norman M, Grajales-Reyes JG, Vogt SK, Sundaram SS, Wilson KM, Ha JS, Xu R, Pan T, Kim TI, Huang Y, Montana MC, Golden JP, Bruchas MR, Gereau RW 4th, Rogers JA | Nature biotechnology | 26551059 | Nat Biotechnol | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26551059 |
| Battery-free, fully implantable optofluidic cuff system for wireless optogenetic and pharmacological neuromodulation of peripheral nerves. | Zhang Y, Mickle AD, Gutruf P, McIlvried LA, Guo H, Wu Y, Golden JP, Xue Y, Grajales-Reyes JG, Wang X, Krishnan S, Xie Y, Peng D, Su CJ, Zhang F, Reeder JT, Vogt SK, Huang Y, Rogers JA, Gereau RW 4th | Science advances | 31281895 | Sci Adv | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31281895 |
| Intraoperative monitoring of neuromuscular function with soft, skin-mounted wireless devices. | Liu Y, Tian L, Raj MS, Cotton M, Ma Y, Ma S, McGrane B, Pendharkar AV, Dahaleh N, Olson L, Luan H, Block O, Suleski B, Zhou Y, Jayaraman C, Koski T, Aranyosi AJ, Wright JA, Jayaraman A, Huang Y, Ghaffari R, Kliot M, Rogers JA | NPJ digital medicine | 30882044 | NPJ Digit Med | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30882044 |
| Injectable, cellular-scale optoelectronics with applications for wireless optogenetics. | Kim TI, McCall JG, Jung YH, Huang X, Siuda ER, Li Y, Song J, Song YM, Pao HA, Kim RH, Lu C, Lee SD, Song IS, Shin G, Al-Hasani R, Kim S, Tan MP, Huang Y, Omenetto FG, Rogers JA, Bruchas MR | Science (New York, N.Y.) | 23580530 | Science | 2013 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/23580530 |
| Spotlight on pain: optogenetic approaches for interrogating somatosensory circuits. | Copits BA, Pullen MY, Gereau RW 4th | Pain | 27340912 | Pain | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27340912 |
| Optogenetic Induction of Colonic Motility in Mice. | Hibberd TJ, Feng J, Luo J, Yang P, Samineni VK, Gereau RW 4th, Kelley N, Hu H, Spencer NJ | Gastroenterology | 29782847 | Gastroenterology | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29782847 |
| Differential Regulation of Bladder Pain and Voiding Function by Sensory Afferent Populations Revealed by Selective Optogenetic Activation. | DeBerry JJ, Samineni VK, Copits BA, Sullivan CJ, Vogt SK, Albers KM, Davis BM, Gereau RW IV | Frontiers in integrative neuroscience | 29483864 | Front Integr Neurosci | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29483864 |
| Miniaturized, Battery-Free Optofluidic Systems with Potential for Wireless Pharmacology and Optogenetics. | Noh KN, Park SI, Qazi R, Zou Z, Mickle AD, Grajales-Reyes JG, Jang KI, Gereau RW 4th, Xiao J, Rogers JA, Jeong JW | Small (Weinheim an der Bergstrasse, Germany) | 29215787 | Small | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29215787 |
| Fully implantable, battery-free wireless optoelectronic devices for spinal optogenetics. | Samineni VK, Yoon J, Crawford KE, Jeong YR, McKenzie KC, Shin G, Xie Z, Sundaram SS, Li Y, Yang MY, Kim J, Wu D, Xue Y, Feng X, Huang Y, Mickle AD, Banks A, Ha JS, Golden JP, Rogers JA, Gereau RW 4th | Pain | 28700536 | Pain | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28700536 |
| A dynamic set point for thermal adaptation requires phospholipase C-mediated regulation of TRPM8 in vivo. | Brenner DS, Golden JP, Vogt SK, Dhaka A, Story GM, Gereau RW IV | Pain | 25109670 | Pain | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25109670 |
| Wireless Optofluidic Systems for Programmable In Vivo Pharmacology and Optogenetics. | Jeong JW, McCall JG, Shin G, Zhang Y, Al-Hasani R, Kim M, Li S, Sim JY, Jang KI, Shi Y, Hong DY, Liu Y, Schmitz GP, Xia L, He Z, Gamble P, Ray WZ, Huang Y, Bruchas MR, Rogers JA | Cell | 26189679 | Cell | 2015 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/26189679 |
| Distinct Subpopulations of Nucleus Accumbens Dynorphin Neurons Drive Aversion and Reward. | Al-Hasani R, McCall JG, Shin G, Gomez AM, Schmitz GP, Bernardi JM, Pyo CO, Park SI, Marcinkiewcz CM, Crowley NA, Krashes MJ, Lowell BB, Kash TL, Rogers JA, Bruchas MR | Neuron | 26335648 | Neuron | 2015 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/26335648 |
| Erratum: Thermal analysis of injectable, cellular-scale optoelectronics with pulsed power. | Li Y, Shi X, Song J, Lü C, Kim TI, McCall JG, Bruchas MR, Rogers JA, Huang Y | Proceedings. Mathematical, physical, and engineering sciences | 24062627 | Proc Math Phys Eng Sci | 2013 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/24062627 |
| A technique to measure cold adaptation in freely behaving mice. | Brenner DS, Vogt SK, Gereau RW 4th | Journal of neuroscience methods | 25128723 | J Neurosci Methods | 2014 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/25128723 |
| Flexible Near-Field Wireless Optoelectronics as Subdermal Implants for Broad Applications in Optogenetics. | Shin G, Gomez AM, Al-Hasani R, Jeong YR, Kim J, Xie Z, Banks A, Lee SM, Han SY, Yoo CJ, Lee JL, Lee SH, Kurniawan J, Tureb J, Guo Z, Yoon J, Park SI, Bang SY, Nam Y, Walicki MC, Samineni VK, Mickle AD, Lee K, Heo SY, McCall JG, Pan T, Wang L, Feng X, Kim TI, Kim JK, Li Y, Huang Y, Gereau RW 4th, Ha JS, Bruchas MR, Rogers JA | Neuron | 28132830 | Neuron | 2017 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/28132830 |
| Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer. | Vanharanta S, Marney CB, Shu W, Valiente M, Zou Y, Mele A, Darnell RB, Massagué J | eLife | 24898756 | Elife | 2014 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/24898756 |
| RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. | Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB | The New England journal of medicine | 32668112 | N Engl J Med | 2020 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/32668112 |
| PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage. | Hwang HW, Park CY, Goodarzi H, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB | Cell reports | 27050522 | Cell Rep | 2016 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/27050522 |
| Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. | Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma'ayan A, Buxbaum JD, Darnell RB | eLife | 26894958 | Elife | 2016 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/26894958 |
| ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity. | Moore MJ, Blachere NE, Fak JJ, Park CY, Sawicka K, Parveen S, Zucker-Scharff I, Moltedo B, Rudensky AY, Darnell RB | eLife | 29848443 | Elife | 2018 May 31 | https://www.ncbi.nlm.nih.gov/pubmed/29848443 |
| FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons. | Hale CR, Sawicka K, Mora K, Fak JJ, Kang JJ, Cutrim P, Cialowicz K, Carroll TS, Darnell RB | eLife | 34939924 | Elife | 2021 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/34939924 |
| NOVA2-mediated RNA regulation is required for axonal pathfinding during development. | Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB | eLife | 27223325 | Elife | 2016 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/27223325 |
| Excess Translation of Epigenetic Regulators Contributes to Fragile X Syndrome and Is Alleviated by Brd4 Inhibition. | Korb E, Herre M, Zucker-Scharff I, Gresack J, Allis CD, Darnell RB | Cell | 28823556 | Cell | 2017 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/28823556 |
| Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding. | Hacisuleyman E, Hale CR, Noble N, Luo JD, Fak JJ, Saito M, Chen J, Weissman JS, Darnell RB | Nature neuroscience | 38589584 | Nat Neurosci | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38589584 |
| Prediction of clustered RNA-binding protein motif sites in the mammalian genome. | Zhang C, Lee KY, Swanson MS, Darnell RB | Nucleic acids research | 23685613 | Nucleic Acids Res | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23685613 |
| Progressive impairment of muscle regeneration in muscleblind-like 3 isoform knockout mice. | Poulos MG, Batra R, Li M, Yuan Y, Zhang C, Darnell RB, Swanson MS | Human molecular genetics | 23660517 | Hum Mol Genet | 2013 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/23660517 |
| NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. | Eom T, Zhang C, Wang H, Lay K, Fak J, Noebels JL, Darnell RB | eLife | 23359859 | Elife | 2013 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/23359859 |
| HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. | Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C | Cell reports | 24613350 | Cell Rep | 2014 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/24613350 |
| T cells targeting a neuronal paraneoplastic antigen mediate tumor rejection and trigger CNS autoimmunity with humoral activation. | Blachère NE, Orange DE, Santomasso BD, Doerner J, Foo PK, Herre M, Fak J, Monette S, Gantman EC, Frank MO, Darnell RB | European journal of immunology | 25103845 | Eur J Immunol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25103845 |
| BET protein Brd4 activates transcription in neurons and BET inhibitor Jq1 blocks memory in mice. | Korb E, Herre M, Zucker-Scharff I, Darnell RB, Allis CD | Nature neuroscience | 26301327 | Nat Neurosci | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26301327 |
| Microexons--tiny but mighty. | Scheckel C, Darnell RB | The EMBO journal | 25535247 | EMBO J | 2015 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/25535247 |
| cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation. | Hwang HW, Saito Y, Park CY, Blachère NE, Tajima Y, Fak JJ, Zucker-Scharff I, Darnell RB | Neuron | 28910620 | Neuron | 2017 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/28910620 |
| Comprehensive Identification of mRNA Polyadenylation Sites by PAPERCLIP. | Hwang HW, Darnell RB | Methods in molecular biology (Clifton, N.J.) | 28766291 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28766291 |
| NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cells. | Saito Y, Yang Y, Saito M, Park CY, Funato K, Tabar V, Darnell RB | Proceedings of the National Academy of Sciences of the United States of America | 38416679 | Proc Natl Acad Sci U S A | 2024 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/38416679 |
| Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability. | Ince-Dunn G, Okano HJ, Jensen KB, Park WY, Zhong R, Ule J, Mele A, Fak JJ, Yang C, Zhang C, Yoo J, Herre M, Okano H, Noebels JL, Darnell RB | Neuron | 22998874 | Neuron | 2012 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/22998874 |
| RNA protein interaction in neurons. | Darnell RB | Annual review of neuroscience | 23701460 | Annu Rev Neurosci | 2013 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/23701460 |
| A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation. | Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, Haripal B, Zucker-Scharff I, Moore MJ, Park CY, Vågbø CB, Kusśnierczyk A, Klungland A, Darnell JE Jr, Darnell RB | Genes & development | 26404942 | Genes Dev | 2015 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/26404942 |
| A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration. | Scheel TK, Luna JM, Liniger M, Nishiuchi E, Rozen-Gagnon K, Shlomai A, Auray G, Gerber M, Fak J, Keller I, Bruggmann R, Darnell RB, Ruggli N, Rice CM | Cell host & microbe | 26962949 | Cell Host Microbe | 2016 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/26962949 |
| miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity. | Moore MJ, Scheel TK, Luna JM, Park CY, Fak JJ, Nishiuchi E, Rice CM, Darnell RB | Nature communications | 26602609 | Nat Commun | 2015 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/26602609 |
| FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory. | Sawicka K, Hale CR, Park CY, Fak JJ, Gresack JE, Van Driesche SJ, Kang JJ, Darnell JC, Darnell RB | eLife | 31860442 | Elife | 2019 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/31860442 |
| Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. | Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG | Nature genetics | 31133750 | Nat Genet | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31133750 |
| Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer. | Luna JM, Barajas JM, Teng KY, Sun HL, Moore MJ, Rice CM, Darnell RB, Ghoshal K | Molecular cell | 28735896 | Mol Cell | 2017 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/28735896 |
| Hepatitis C virus RNA functionally sequesters miR-122. | Luna JM, Scheel TK, Danino T, Shaw KS, Mele A, Fak JJ, Nishiuchi E, Takacs CN, Catanese MT, de Jong YP, Jacobson IM, Rice CM, Darnell RB | Cell | 25768906 | Cell | 2015 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/25768906 |
| The Genetic Control of Stoichiometry Underlying Autism. | Darnell RB | Annual review of neuroscience | 32640929 | Annu Rev Neurosci | 2020 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/32640929 |
| PRIME Cells Predicting Rheumatoid Arthritis Flares. Reply. | Orange DE, Darnell RB | The New England journal of medicine | 33053295 | N Engl J Med | 2020 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/33053295 |
| Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. | Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY | Molecular cell | 23142080 | Mol Cell | 2012 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/23142080 |
| m(6)A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. | Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE Jr, Darnell RB | Genes & development | 28637692 | Genes Dev | 2017 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/28637692 |
| NOVA regulates Dcc alternative splicing during neuronal migration and axon guidance in the spinal cord. | Leggere JC, Saito Y, Darnell RB, Tessier-Lavigne M, Junge HJ, Chen Z | eLife | 27223328 | Elife | 2016 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/27223328 |
| Immune Escape via a Transient Gene Expression Program Enables Productive Replication of a Latent Pathogen. | Linderman JA, Kobayashi M, Rayannavar V, Fak JJ, Darnell RB, Chao MV, Wilson AC, Mohr I | Cell reports | 28147283 | Cell Rep | 2017 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/28147283 |
| Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. | Jereb S, Hwang HW, Van Otterloo E, Govek EE, Fak JJ, Yuan Y, Hatten ME, Darnell RB | eLife | 29578408 | Elife | 2018 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/29578408 |
| Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. | Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB | Nature protocols | 24407355 | Nat Protoc | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24407355 |
| AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke. | Kobayashi M, Benakis C, Anderson C, Moore MJ, Poon C, Uekawa K, Dyke JP, Fak JJ, Mele A, Park CY, Zhou P, Anrather J, Iadecola C, Darnell RB | Cell reports | 31340158 | Cell Rep | 2019 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/31340158 |
| Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function. | Saito Y, Yuan Y, Zucker-Scharff I, Fak JJ, Jereb S, Tajima Y, Licatalosi DD, Darnell RB | Neuron | 30638744 | Neuron | 2019 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/30638744 |
| NOVA1 acts on Impact to regulate hypothalamic function and translation in inhibitory neurons. | Tajima Y, Ito K, Yuan Y, Frank MO, Saito Y, Darnell RB | Cell reports | 36716149 | Cell Rep | 2023 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/36716149 |
| Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson's disease. | Irmady K, Hale CR, Qadri R, Fak J, Simelane S, Carroll T, Przedborski S, Darnell RB | Nature communications | 37407548 | Nat Commun | 2023 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/37407548 |
| A survey of human brain transcriptome diversity at the single cell level. | Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR | Proceedings of the National Academy of Sciences of the United States of America | 26060301 | Proc Natl Acad Sci U S A | 2015 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/26060301 |
| Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells. | Sloan SA, Darmanis S, Huber N, Khan TA, Birey F, Caneda C, Reimer R, Quake SR, Barres BA, Paşca SP | Neuron | 28817799 | Neuron | 2017 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/28817799 |
| Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. | Dong X, Chen K, Cuevas-Diaz Duran R, You Y, Sloan SA, Zhang Y, Zong S, Cao Q, Barres BA, Wu JQ | PLoS genetics | 26683846 | PLoS Genet | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26683846 |
| Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma. | Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, Zhang Y, Neff N, Kowarsky M, Caneda C, Li G, Chang SD, Connolly ID, Li Y, Barres BA, Gephart MH, Quake SR | Cell reports | 29091775 | Cell Rep | 2017 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/29091775 |
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| Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits. | Hayworth KJ, Morgan JL, Schalek R, Berger DR, Hildebrand DG, Lichtman JW | Frontiers in neural circuits | 25018701 | Front Neural Circuits | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25018701 |
| Saturated Reconstruction of a Volume of Neocortex. | Kasthuri N, Hayworth KJ, Berger DR, Schalek RL, Conchello JA, Knowles-Barley S, Lee D, Vázquez-Reina A, Kaynig V, Jones TR, Roberts M, Morgan JL, Tapia JC, Seung HS, Roncal WG, Vogelstein JT, Burns R, Sussman DL, Priebe CE, Pfister H, Lichtman JW | Cell | 26232230 | Cell | 2015 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/26232230 |
| Reconstruction of genetically identified neurons imaged by serial-section electron microscopy. | Joesch M, Mankus D, Yamagata M, Shahbazi A, Schalek R, Suissa-Peleg A, Meister M, Lichtman JW, Scheirer WJ, Sanes JR | eLife | 27383271 | Elife | 2016 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/27383271 |
| Multispectral tracing in densely labeled mouse brain with nTracer. | Roossien DH, Sadis BV, Yan Y, Webb JM, Min LY, Dizaji AS, Bogart LJ, Mazuski C, Huth RS, Stecher JS, Akula S, Shen F, Li Y, Xiao T, Vandenbrink M, Lichtman JW, Hensch TK, Herzog ED, Cai D | Bioinformatics (Oxford, England) | 30715234 | Bioinformatics | 2019 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/30715234 |
| Why not connectomics? | Morgan JL, Lichtman JW | Nature methods | 23722208 | Nat Methods | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23722208 |
| Methods for Mapping Neuronal Activity to Synaptic Connectivity: Lessons From Larval Zebrafish. | Wanner AA, Vishwanathan A | Frontiers in neural circuits | 30410437 | Front Neural Circuits | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30410437 |
| The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus. | Morgan JL, Berger DR, Wetzel AW, Lichtman JW | Cell | 27015312 | Cell | 2016 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/27015312 |
| The big data challenges of connectomics. | Lichtman JW, Pfister H, Shavit N | Nature neuroscience | 25349911 | Nat Neurosci | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25349911 |
| Neural Circuit Inference from Function to Structure. | Real E, Asari H, Gollisch T, Meister M | Current biology : CB | 28065610 | Curr Biol | 2017 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/28065610 |
| Space-time wiring specificity supports direction selectivity in the retina. | Kim JS, Greene MJ, Zlateski A, Lee K, Richardson M, Turaga SC, Purcaro M, Balkam M, Robinson A, Behabadi BF, Campos M, Denk W, Seung HS, EyeWirers | Nature | 24805243 | Nature | 2014 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/24805243 |
| An Individual Interneuron Participates in Many Kinds of Inhibition and Innervates Much of the Mouse Visual Thalamus. | Morgan JL, Lichtman JW | Neuron | 32142646 | Neuron | 2020 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/32142646 |
| Electron Microscopic Reconstruction of Functionally Identified Cells in a Neural Integrator. | Vishwanathan A, Daie K, Ramirez AD, Lichtman JW, Aksay ERF, Seung HS | Current biology : CB | 28712570 | Curr Biol | 2017 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/28712570 |
| Digital Museum of Retinal Ganglion Cells with Dense Anatomy and Physiology. | Bae JA, Mu S, Kim JS, Turner NL, Tartavull I, Kemnitz N, Jordan CS, Norton AD, Silversmith WM, Prentki R, Sorek M, David C, Jones DL, Bland D, Sterling ALR, Park J, Briggman KL, Seung HS, Eyewirers | Cell | 29775596 | Cell | 2018 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/29775596 |
| Large-scale automatic reconstruction of neuronal processes from electron microscopy images. | Kaynig V, Vazquez-Reina A, Knowles-Barley S, Roberts M, Jones TR, Kasthuri N, Miller E, Lichtman J, Pfister H | Medical image analysis | 25791436 | Med Image Anal | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25791436 |
| NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity. | Al-Awami AK, Beyer J, Strobelt H, Kasthuri N, Lichtman JW, Pfister H, Hadwiger M | IEEE transactions on visualization and computer graphics | 26356951 | IEEE Trans Vis Comput Graph | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26356951 |
| Analogous Convergence of Sustained and Transient Inputs in Parallel On and Off Pathways for Retinal Motion Computation. | Greene MJ, Kim JS, Seung HS, EyeWirers | Cell reports | 26904938 | Cell Rep | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26904938 |
| Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers. | Ricarte-Filho JC, Li S, Garcia-Rendueles ME, Montero-Conde C, Voza F, Knauf JA, Heguy A, Viale A, Bogdanova T, Thomas GA, Mason CE, Fagin JA | The Journal of clinical investigation | 24135138 | J Clin Invest | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24135138 |
| Characterizing multi-omic data in systems biology. | Mason CE, Porter SG, Smith TM | Advances in experimental medicine and biology | 24292960 | Adv Exp Med Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24292960 |
| Dynamic evolution of clonal epialleles revealed by methclone. | Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D'Andrea RJ, Ross ME, Levine R, Carroll M, Melnick A, Mason CE | Genome biology | 25260792 | Genome Biol | 2014 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/25260792 |
| Rare LRP6 variants identified in spina bifida patients. | Lei Y, Fathe K, McCartney D, Zhu H, Yang W, Ross ME, Shaw GM, Finnell RH | Human mutation | 25546815 | Hum Mutat | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25546815 |
| An optimized algorithm for detecting and annotating regional differential methylation. | Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, Mason CE | BMC bioinformatics | 23735126 | BMC Bioinformatics | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23735126 |
| The continuing challenge of understanding, preventing, and treating neural tube defects. | Wallingford JB, Niswander LA, Shaw GM, Finnell RH | Science (New York, N.Y.) | 23449594 | Science | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23449594 |
| A GCH1 haplotype and risk of neural tube defects in the National Birth Defects Prevention Study. | Lupo PJ, Chapa C, Nousome D, Duhon C, Canfield MA, Shaw GM, Finnell RH, Zhu H, National Birth Defects Prevention Study | Molecular genetics and metabolism | 23059057 | Mol Genet Metab | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23059057 |
| The birth of the Epitranscriptome: deciphering the function of RNA modifications. | Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE | Genome biology | 23113984 | Genome Biol | 2012 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/23113984 |
| Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. | Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME | PLoS genetics | 22737091 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22737091 |
| Rfx2 is required for spermatogenesis in the mouse. | Shawlot W, Vazquez-Chantada M, Wallingford JB, Finnell RH | Genesis (New York, N.Y. : 2000) | 26248850 | Genesis | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26248850 |
| Genetic and epigenetic heterogeneity in acute myeloid leukemia. | Li S, Mason CE, Melnick A | Current opinion in genetics & development | 27162099 | Curr Opin Genet Dev | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27162099 |
| Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. | Bezdan D, Grigorev K, Meydan C, Pelissier Vatter FA, Cioffi M, Rao V, MacKay M, Nakahira K, Burnham P, Afshinnekoo E, Westover C, Butler D, Mozsary C, Donahoe T, Foox J, Mishra T, Lucotti S, Rana BK, Melnick AM, Zhang H, Matei I, Kelsen D, Yu K, Lyden DC, Taylor L, Bailey SM, Snyder MP, Garrett-Bakelman FE, Ossowski S, De Vlaminck I, Mason CE | iScience | 33376973 | iScience | 2020 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/33376973 |
| A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. | Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY | Science advances | 33536218 | Sci Adv | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33536218 |
| Autism-Like Behavior and Epigenetic Changes Associated with Autism as Consequences of In Utero Exposure to Environmental Pollutants in a Mouse Model. | Hill DS, Cabrera R, Wallis Schultz D, Zhu H, Lu W, Finnell RH, Wlodarczyk BJ | Behavioural neurology | 26586927 | Behav Neurol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26586927 |
| Genomic approaches to the assessment of human spina bifida risk. | Ross ME, Mason CE, Finnell RH | Birth defects research | 27883265 | Birth Defects Res | 2017 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/27883265 |
| Epigenetic therapy in a new era of medicine: creating and integrating molecular profiles of patients. | Afshinnekoo E, Mason CE | Annals of translational medicine | 27942527 | Ann Transl Med | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27942527 |
| The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. | MetaSUB International Consortium | Microbiome | 27255532 | Microbiome | 2016 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/27255532 |
| Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain. | Nandi S, Chandramohan D, Fioriti L, Melnick AM, Hébert JM, Mason CE, Rajasethupathy P, Kandel ER | Proceedings of the National Academy of Sciences of the United States of America | 27791114 | Proc Natl Acad Sci U S A | 2016 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/27791114 |
| Nanopore sequencing in microgravity. | McIntyre ABR, Rizzardi L, Yu AM, Alexander N, Rosen GL, Botkin DJ, Stahl SE, John KK, Castro-Wallace SL, McGrath K, Burton AS, Feinberg AP, Mason CE | NPJ microgravity | 28725742 | NPJ Microgravity | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28725742 |
| Folate-dependent methylation of septins governs ciliogenesis during neural tube closure. | Toriyama M, Toriyama M, Wallingford JB, Finnell RH | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 28432198 | FASEB J | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28432198 |
| Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity. | Goldman SL, Hassan C, Khunte M, Soldatenko A, Jong Y, Afshinnekoo E, Mason CE | Frontiers in genetics | 30881380 | Front Genet | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30881380 |
| Fuz mutant mice reveal shared mechanisms between ciliopathies and FGF-related syndromes. | Tabler JM, Barrell WB, Szabo-Rogers HL, Healy C, Yeung Y, Perdiguero EG, Schulz C, Yannakoudakis BZ, Mesbahi A, Wlodarczyk B, Geissmann F, Finnell RH, Wallingford JB, Liu KJ | Developmental cell | 23806618 | Dev Cell | 2013 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/23806618 |
| Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. | Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR | Nature methods | 26121403 | Nat Methods | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26121403 |
| High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. | Lipovich L, Hou ZC, Jia H, Sinkler C, McGowen M, Sterner KN, Weckle A, Sugalski AB, Pipes L, Gatti DL, Mason CE, Sherwood CC, Hof PR, Kuzawa CW, Grossman LI, Goodman M, Wildman DE | The Journal of comparative neurology | 26132897 | J Comp Neurol | 2016 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26132897 |
| The impact of read length on quantification of differentially expressed genes and splice junction detection. | Chhangawala S, Rudy G, Mason CE, Rosenfeld JA | Genome biology | 26100517 | Genome Biol | 2015 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/26100517 |
| A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. | SEQC/MAQC-III Consortium | Nature biotechnology | 25150838 | Nat Biotechnol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25150838 |
| Enabling large-scale next-generation sequence assembly with Blacklight. | Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD | Concurrency and computation : practice & experience | 25294974 | Concurr Comput | 2014 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/25294974 |
| Mutational cooperativity linked to combinatorial epigenetic gain of function in acute myeloid leukemia. | Shih AH, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer SD, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine RL | Cancer cell | 25873173 | Cancer Cell | 2015 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/25873173 |
| Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. | Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE | Nature biotechnology | 25150835 | Nat Biotechnol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25150835 |
| Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). | Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE | Nucleic acids research | 25392405 | Nucleic Acids Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25392405 |
| Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. | Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM | Journal of visualized experiments : JoVE | 25742437 | J Vis Exp | 2015 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/25742437 |
| Clinical Genomics: Challenges and Opportunities. | Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S | Critical reviews in eukaryotic gene expression | 27480773 | Crit Rev Eukaryot Gene Expr | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27480773 |
| Haplotype diversity and sequence heterogeneity of human telomeres. | Grigorev K, Foox J, Bezdan D, Butler D, Luxton JJ, Reed J, McKenna MJ, Taylor L, George KA, Meydan C, Bailey SM, Mason CE | Genome research | 34162698 | Genome Res | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34162698 |
| Translating current biomedical therapies for long duration, deep space missions. | Iosim S, MacKay M, Westover C, Mason CE | Precision clinical medicine | 31886035 | Precis Clin Med | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31886035 |
| Single-molecule sequencing detection of N6-methyladenine in microbial reference materials. | McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE | Nature communications | 30718479 | Nat Commun | 2019 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/30718479 |
| Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. | Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE | Nature communications | 26836631 | Nat Commun | 2016 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/26836631 |
| The Impact of Heterogeneity on Single-Cell Sequencing. | Goldman SL, MacKay M, Afshinnekoo E, Melnick AM, Wu S, Mason CE | Frontiers in genetics | 30881372 | Front Genet | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30881372 |
| Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance. | Afshinnekoo E, Chou C, Alexander N, Ahsanuddin S, Schuetz AN, Mason CE | Journal of biomolecular techniques : JBT | 28337072 | J Biomol Tech | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28337072 |
| Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia. | Shih AH, Meydan C, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL | Cancer discovery | 28193779 | Cancer Discov | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28193779 |
| Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. | Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D'Andrea RJ, Carroll M, Park CY, Neuberg D, Levine R, Melnick AM, Mason CE | Nature medicine | 27322744 | Nat Med | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27322744 |
| Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments. | Westover C, Rahmatulloev S, Danko D, Afshin EE, O'Hara NB, Ounit R, Bezdan D, Mason CE | Genes | 36672826 | Genes (Basel) | 2022 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/36672826 |
| Two methods for full-length RNA sequencing for low quantities of cells and single cells. | Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, Lamotte RH, Park IH, Snyder MP, Mason CE, Weissman SM | Proceedings of the National Academy of Sciences of the United States of America | 23267071 | Proc Natl Acad Sci U S A | 2013 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/23267071 |
| Antiepileptic drugs and pregnancy outcomes. | Wlodarczyk BJ, Palacios AM, George TM, Finnell RH | American journal of medical genetics. Part A | 22711424 | Am J Med Genet A | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22711424 |
| Neural tube defects, folate, and immune modulation. | Denny KJ, Jeanes A, Fathe K, Finnell RH, Taylor SM, Woodruff TM | Birth defects research. Part A, Clinical and molecular teratology | 24078477 | Birth Defects Res A Clin Mol Teratol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24078477 |
| Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. | Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D | Genome biology | 24020486 | Genome Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24020486 |
| Assessment of pharmacogenomic agreement. | Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B | F1000Research | 27408686 | F1000Res | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27408686 |
| The Power of Engaging Citizen Scientists for Scientific Progress. | Garbarino J, Mason CE | Journal of microbiology & biology education | 27047581 | J Microbiol Biol Educ | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27047581 |
| New Techniques for the Study of Neural Tube Defects. | Lei Y, Finnell RH | Advanced techniques in biology & medicine | 27066597 | Adv Tech Biol Med | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27066597 |
| Autoantibodies against homocysteinylated protein in a mouse model of folate deficiency-induced neural tube defects. | Denny KJ, Kelly CF, Kumar V, Witham KL, Cabrera RM, Finnell RH, Taylor SM, Jeanes A, Woodruff TM | Birth defects research. Part A, Clinical and molecular teratology | 26900104 | Birth Defects Res A Clin Mol Teratol | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26900104 |
| Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability. | Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF | Orphanet journal of rare diseases | 27179618 | Orphanet J Rare Dis | 2016 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/27179618 |
| The Microbe Directory: An annotated, searchable inventory of microbes' characteristics. | Shaaban H, Westfall DA, Mohammad R, Danko D, Bezdan D, Afshinnekoo E, Segata N, Mason CE | Gates open research | 29630066 | Gates Open Res | 2018 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/29630066 |
| Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications. | Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE | Journal of biomolecular techniques : JBT | 28344519 | J Biomol Tech | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28344519 |
| Detecting and correcting systematic variation in large-scale RNA sequencing data. | Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D, Thierry-Mieg J, Kreil DP, Mason CE | Nature biotechnology | 25150837 | Nat Biotechnol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25150837 |
| Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. | Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG | Journal of medical primatology | 24810475 | J Med Primatol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24810475 |
| Identification of novel CELSR1 mutations in spina bifida. | Lei Y, Zhu H, Yang W, Ross ME, Shaw GM, Finnell RH | PloS one | 24632739 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24632739 |
| Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. | Aguiar-Pulido V, Wolujewicz P, Martinez-Fundichely A, Elhaik E, Thareja G, Abdel Aleem A, Chalhoub N, Cuykendall T, Al-Zamer J, Lei Y, El-Bashir H, Musser JM, Al-Kaabi A, Shaw GM, Khurana E, Suhre K, Mason CE, Elemento O, Finnell RH, Ross ME | Proceedings of the National Academy of Sciences of the United States of America | 34916285 | Proc Natl Acad Sci U S A | 2021 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/34916285 |
| Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity. | Gertz ML, Chin CR, Tomoiaga D, MacKay M, Chang C, Butler D, Afshinnekoo E, Bezdan D, Schmidt MA, Mozsary C, Melnick A, Garrett-Bakelman F, Crucian B, Lee SMC, Zwart SR, Smith SM, Meydan C, Mason CE | Cell reports | 33242408 | Cell Rep | 2020 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/33242408 |
| CIC missense variants contribute to susceptibility for spina bifida. | Han X, Cao X, Aguiar-Pulido V, Yang W, Karki M, Ramirez PAP, Cabrera RM, Lin YL, Wlodarczyk BJ, Shaw GM, Ross ME, Zhang C, Finnell RH, Lei Y | Human mutation | 36054333 | Hum Mutat | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36054333 |
| methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. | Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE | Genome biology | 23034086 | Genome Biol | 2012 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/23034086 |
| Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. | Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR | Cell | 22608085 | Cell | 2012 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/22608085 |
| The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. | Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG | Nucleic acids research | 23203872 | Nucleic Acids Res | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23203872 |
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| Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. | Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS | Nature protocols | 26890679 | Nat Protoc | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26890679 |
| Mosaic copy number variation in human neurons. | McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH | Science (New York, N.Y.) | 24179226 | Science | 2013 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/24179226 |
| Conserved expression of transposon-derived non-coding transcripts in primate stem cells. | Ramsay L, Marchetto MC, Caron M, Chen SH, Busche S, Kwan T, Pastinen T, Gage FH, Bourque G | BMC genomics | 28245871 | BMC Genomics | 2017 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/28245871 |
| Adult Hippocampal Neurogenesis: A Coming-of-Age Story. | Kuhn HG, Toda T, Gage FH | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30381404 | J Neurosci | 2018 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/30381404 |
| Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons. | Schafer ST, Paquola ACM, Stern S, Gosselin D, Ku M, Pena M, Kuret TJM, Liyanage M, Mansour AA, Jaeger BN, Marchetto MC, Glass CK, Mertens J, Gage FH | Nature neuroscience | 30617258 | Nat Neurosci | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30617258 |
| To eat, or not to eat, that is the question: Neural stem cells escape phagocytosis in autism with macrocephaly. | Schafer ST, Gage FH | Proceedings of the National Academy of Sciences of the United States of America | 33883269 | Proc Natl Acad Sci U S A | 2021 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/33883269 |
| Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis. | Niemsiri V, Rosenthal SB, Nievergelt CM, Maihofer AX, Marchetto MC, Santos R, Shekhtman T, Alliey-Rodriguez N, Anand A, Balaraman Y, Berrettini WH, Bertram H, Burdick KE, Calabrese JR, Calkin CV, Conroy C, Coryell WH, DeModena A, Eyler LT, Feeder S, Fisher C, Frazier N, Frye MA, Gao K, Garnham J, Gershon ES, Goes FS, Goto T, Harrington GJ, Jakobsen P, Kamali M, Kelly M, Leckband SG, Lohoff FW, McCarthy MJ, McInnis MG, Craig D, Millett CE, Mondimore F, Morken G, Nurnberger JI, Donovan CO, Øedegaard KJ, Ryan K, Schinagle M, Shilling PD, Slaney C, Stapp EK, Stautland A, Tarwater B, Zandi PP, Alda M, Fisch KM, Gage FH, Kelsoe JR | Molecular psychiatry | 36991131 | Mol Psychiatry | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36991131 |
| FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis. | Webb AE, Pollina EA, Vierbuchen T, Urbán N, Ucar D, Leeman DS, Martynoga B, Sewak M, Rando TA, Guillemot F, Wernig M, Brunet A | Cell reports | 23891001 | Cell Rep | 2013 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/23891001 |
| Neurons generated by direct conversion of fibroblasts reproduce synaptic phenotype caused by autism-associated neuroligin-3 mutation. | Chanda S, Marro S, Wernig M, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 24046374 | Proc Natl Acad Sci U S A | 2013 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/24046374 |
| An indirect approach to generating specific human cell types. | Lujan E, Wernig M | Nature methods | 23269377 | Nat Methods | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23269377 |
| Induced neuronal reprogramming. | Ang CE, Wernig M | The Journal of comparative neurology | 24771471 | J Comp Neurol | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/24771471 |
| Comprehensive qPCR profiling of gene expression in single neuronal cells. | Citri A, Pang ZP, Südhof TC, Wernig M, Malenka RC | Nature protocols | 22193304 | Nat Protoc | 2011 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/22193304 |
| Acute reduction in oxygen tension enhances the induction of neurons from human fibroblasts. | Davila J, Chanda S, Ang CE, Südhof TC, Wernig M | Journal of neuroscience methods | 23562599 | J Neurosci Methods | 2013 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/23562599 |
| Generation of oligodendroglial cells by direct lineage conversion. | Yang N, Zuchero JB, Ahlenius H, Marro S, Ng YH, Vierbuchen T, Hawkins JS, Geissler R, Barres BA, Wernig M | Nature biotechnology | 23584610 | Nat Biotechnol | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23584610 |
| Cerebellins are differentially expressed in selective subsets of neurons throughout the brain. | Seigneur E, Südhof TC | The Journal of comparative neurology | 28714144 | J Comp Neurol | 2017 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/28714144 |
| Evolution of the Autism-Associated Neuroligin-4 Gene Reveals Broad Erosion of Pseudoautosomal Regions in Rodents. | Maxeiner S, Benseler F, Krasteva-Christ G, Brose N, Südhof TC | Molecular biology and evolution | 32011705 | Mol Biol Evol | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32011705 |
| Neuromodulator Signaling Bidirectionally Controls Vesicle Numbers in Human Synapses. | Patzke C, Brockmann MM, Dai J, Gan KJ, Grauel MK, Fenske P, Liu Y, Acuna C, Rosenmund C, Südhof TC | Cell | 31585084 | Cell | 2019 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/31585084 |
| Efficient generation of dopaminergic induced neuronal cells with midbrain characteristics. | Ng YH, Chanda S, Janas JA, Yang N, Kokubu Y, Südhof TC, Wernig M | Stem cell reports | 34171286 | Stem Cell Reports | 2021 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/34171286 |
| Neuroligin-3 confines AMPA receptors into nanoclusters, thereby controlling synaptic strength at the calyx of Held synapses. | Han Y, Cao R, Qin L, Chen LY, Tang AH, Südhof TC, Zhang B | Science advances | 35704570 | Sci Adv | 2022 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/35704570 |
| The cell biology of synapse formation. | Südhof TC | The Journal of cell biology | 34086051 | J Cell Biol | 2021 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/34086051 |
| Deletion of Neuroligins from Astrocytes Does Not Detectably Alter Synapse Numbers or Astrocyte Cytoarchitecture by Maturity. | Golf SR, Trotter JH, Wang J, Nakahara G, Han X, Wernig M, Südhof TC | bioRxiv : the preprint server for biology | 37090508 | bioRxiv | 2025 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/37090508 |
| Molecular self-avoidance in synaptic neurexin complexes. | Wang CY, Trotter JH, Liakath-Ali K, Lee SJ, Liu X, Südhof TC | Science advances | 34919427 | Sci Adv | 2021 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/34919427 |
| Defined human tri-lineage brain microtissues. | Uenaka T, Jung S, Kumar I, Vodehnal K, Rastogi M, Yoo Y, Koontz M, Thome C, Li W, Chan T, Green EM, Chesnov K, Sun Z, Zhang S, Wang J, Venida A, Mellier AM, Atkins M, Jackrel M, Skotheim JM, Wyss-Coray T, Abu-Remaileh M, Lashuel HA, Bassik MC, Südhof TC, Del Sol A, Ullian E, Wernig M | bioRxiv : the preprint server for biology | 40799568 | bioRxiv | 2025 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/40799568 |
| Distinct mechanisms control the specific synaptic functions of Neuroligin 1 and Neuroligin 2. | Wang J, Sudhof T, Wernig M | EMBO reports | 39747663 | EMBO Rep | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39747663 |
| Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells. | Lujan E, Chanda S, Ahlenius H, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 22308465 | Proc Natl Acad Sci U S A | 2012 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/22308465 |
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| Cellular reprogramming: recent advances in modeling neurological diseases. | Ming GL, Brüstle O, Muotri A, Studer L, Wernig M, Christian KM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22072658 | J Neurosci | 2011 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/22072658 |
| Generation of induced neuronal cells by the single reprogramming factor ASCL1. | Chanda S, Ang CE, Davila J, Pak C, Mall M, Lee QY, Ahlenius H, Jung SW, Südhof TC, Wernig M | Stem cell reports | 25254342 | Stem Cell Reports | 2014 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/25254342 |
| Conditional deletion of L1CAM in human neurons impairs both axonal and dendritic arborization and action potential generation. | Patzke C, Acuna C, Giam LR, Wernig M, Südhof TC | The Journal of experimental medicine | 27001749 | J Exp Med | 2016 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/27001749 |
| Multiple signaling pathways are essential for synapse formation induced by synaptic adhesion molecules. | Jiang X, Sando R, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 33431662 | Proc Natl Acad Sci U S A | 2021 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/33431662 |
| Neuroligin-4 Regulates Excitatory Synaptic Transmission in Human Neurons. | Marro SG, Chanda S, Yang N, Janas JA, Valperga G, Trotter J, Zhou B, Merrill S, Yousif I, Shelby H, Vogel H, Kalani MYS, Südhof TC, Wernig M | Neuron | 31257103 | Neuron | 2019 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/31257103 |
| Astrocytic Neuroligin-3 influences gene expression and social behavior, but is dispensable for synapse number. | Qin L, Liu Z, Guo S, Han Y, Wang X, Ren W, Chen J, Zhen H, Nie C, Xing KK, Chen T, Südhof TC, Sun Y, Zhang B | Molecular psychiatry | 39003414 | Mol Psychiatry | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39003414 |
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| Retinoic Acid Receptor RARα-Dependent Synaptic Signaling Mediates Homeostatic Synaptic Plasticity at the Inhibitory Synapses of Mouse Visual Cortex. | Zhong LR, Chen X, Park E, Südhof TC, Chen L | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30355624 | J Neurosci | 2018 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/30355624 |
| Human Neuropsychiatric Disease Modeling using Conditional Deletion Reveals Synaptic Transmission Defects Caused by Heterozygous Mutations in NRXN1. | Pak C, Danko T, Zhang Y, Aoto J, Anderson G, Maxeiner S, Yi F, Wernig M, Südhof TC | Cell stem cell | 26279266 | Cell Stem Cell | 2015 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/26279266 |
| Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons. | Yi F, Danko T, Botelho SC, Patzke C, Pak C, Wernig M, Südhof TC | Science (New York, N.Y.) | 26966193 | Science | 2016 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/26966193 |
| Transdifferentiation of human adult peripheral blood T cells into neurons. | Tanabe K, Ang CE, Chanda S, Olmos VH, Haag D, Levinson DF, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 29866841 | Proc Natl Acad Sci U S A | 2018 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/29866841 |
| Direct Reprogramming of Human Neurons Identifies MARCKSL1 as a Pathogenic Mediator of Valproic Acid-Induced Teratogenicity. | Chanda S, Ang CE, Lee QY, Ghebrial M, Haag D, Shibuya Y, Wernig M, Südhof TC | Cell stem cell | 31155484 | Cell Stem Cell | 2019 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/31155484 |
| Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates. | Mall M, Kareta MS, Chanda S, Ahlenius H, Perotti N, Zhou B, Grieder SD, Ge X, Drake S, Euong Ang C, Walker BM, Vierbuchen T, Fuentes DR, Brennecke P, Nitta KR, Jolma A, Steinmetz LM, Taipale J, Südhof TC, Wernig M | Nature | 28379941 | Nature | 2017 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/28379941 |
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| Analyses of the autism-associated neuroligin-3 R451C mutation in human neurons reveal a gain-of-function synaptic mechanism. | Wang L, Mirabella VR, Dai R, Su X, Xu R, Jadali A, Bernabucci M, Singh I, Chen Y, Tian J, Jiang P, Kwan KY, Pak C, Liu C, Comoletti D, Hart RP, Chen C, Südhof TC, Pang ZP | Molecular psychiatry | 36280753 | Mol Psychiatry | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36280753 |
| Induction of human neuronal cells by defined transcription factors. | Pang ZP, Yang N, Vierbuchen T, Ostermeier A, Fuentes DR, Yang TQ, Citri A, Sebastiano V, Marro S, Südhof TC, Wernig M | Nature | 21617644 | Nature | 2011 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/21617644 |
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| Direct lineage conversions: unnatural but useful? | Vierbuchen T, Wernig M | Nature biotechnology | 21997635 | Nat Biotechnol | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21997635 |
| Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. | Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M | Cell stem cell | 21962918 | Cell Stem Cell | 2011 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/21962918 |
| Unique versus Redundant Functions of Neuroligin Genes in Shaping Excitatory and Inhibitory Synapse Properties. | Chanda S, Hale WD, Zhang B, Wernig M, Südhof TC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28607166 | J Neurosci | 2017 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/28607166 |
| Analysis of conditional heterozygous STXBP1 mutations in human neurons. | Patzke C, Han Y, Covy J, Yi F, Maxeiner S, Wernig M, Südhof TC | The Journal of clinical investigation | 26280581 | J Clin Invest | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26280581 |
| FoxO3 regulates neuronal reprogramming of cells from postnatal and aging mice. | Ahlenius H, Chanda S, Webb AE, Yousif I, Karmazin J, Prusiner SB, Brunet A, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 27402759 | Proc Natl Acad Sci U S A | 2016 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/27402759 |
| The fragile X mutation impairs homeostatic plasticity in human neurons by blocking synaptic retinoic acid signaling. | Zhang Z, Marro SG, Zhang Y, Arendt KL, Patzke C, Zhou B, Fair T, Yang N, Südhof TC, Wernig M, Chen L | Science translational medicine | 30068571 | Sci Transl Med | 2018 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/30068571 |
| Autism-associated neuroligin-4 mutation selectively impairs glycinergic synaptic transmission in mouse brainstem synapses. | Zhang B, Gokce O, Hale WD, Brose N, Südhof TC | The Journal of experimental medicine | 29724786 | J Exp Med | 2018 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/29724786 |
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| Rapid single-step induction of functional neurons from human pluripotent stem cells. | Zhang Y, Pak C, Han Y, Ahlenius H, Zhang Z, Chanda S, Marro S, Patzke C, Acuna C, Covy J, Xu W, Yang N, Danko T, Chen L, Wernig M, Südhof TC | Neuron | 23764284 | Neuron | 2013 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/23764284 |
| In Vivo Reprogramming for Brain and Spinal Cord Repair. | Chen G, Wernig M, Berninger B, Nakafuku M, Parmar M, Zhang CL | eNeuro | 26730402 | eNeuro | 2015 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/26730402 |
| Towards an Understanding of Synapse Formation. | Südhof TC | Neuron | 30359597 | Neuron | 2018 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/30359597 |
| Neuroligin-1 Signaling Controls LTP and NMDA Receptors by Distinct Molecular Pathways. | Wu X, Morishita WK, Riley AM, Hale WD, Südhof TC, Malenka RC | Neuron | 30871858 | Neuron | 2019 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/30871858 |
| Specific factors in blood from young but not old mice directly promote synapse formation and NMDA-receptor recruitment. | Gan KJ, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 31160442 | Proc Natl Acad Sci U S A | 2019 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/31160442 |
| Induction of synapse formation by de novo neurotransmitter synthesis. | Burlingham SR, Wong NF, Peterkin L, Lubow L, Dos Santos Passos C, Benner O, Ghebrial M, Cast TP, Xu-Friedman MA, Südhof TC, Chanda S | Nature communications | 35650274 | Nat Commun | 2022 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/35650274 |
| SPARCL1 Promotes Excitatory But Not Inhibitory Synapse Formation and Function Independent of Neurexins and Neuroligins. | Gan KJ, Südhof TC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 32973045 | J Neurosci | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/32973045 |
| Efficient generation of functional neurons from mouse embryonic stem cells via neurogenin-2 expression. | Liu Y, Wang J, Südhof TC, Wernig M | Nature protocols | 37596357 | Nat Protoc | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37596357 |
| High-Throughput Method of Whole-Brain Sectioning, Using the Tape-Transfer Technique. | Pinskiy V, Jones J, Tolpygo AS, Franciotti N, Weber K, Mitra PP | PloS one | 26181725 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26181725 |
| Out-of-focus brain image detection in serial tissue sections. | Pollatou A, Ferrante DD | Journal of neuroscience methods | 32771371 | J Neurosci Methods | 2020 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/32771371 |
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| A low-cost technique to cryo-protect and freeze rodent brains, precisely aligned to stereotaxic coordinates for whole-brain cryosectioning. | Pinskiy V, Tolpygo AS, Jones J, Weber K, Franciotti N, Mitra PP | Journal of neuroscience methods | 23541995 | J Neurosci Methods | 2013 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/23541995 |
| Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. | Majka P, Chaplin TA, Yu HH, Tolpygo A, Mitra PP, Wójcik DK, Rosa MG | The Journal of comparative neurology | 27099164 | J Comp Neurol | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27099164 |
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| Neuroprotective efficacy of a proneurogenic compound after traumatic brain injury. | Blaya MO, Bramlett HM, Naidoo J, Pieper AA, Dietrich WD | Journal of neurotrauma | 24070637 | J Neurotrauma | 2014 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/24070637 |
| Discovery of a neuroprotective chemical, (S)-N-(3-(3,6-dibromo-9H-carbazol-9-yl)-2-fluoropropyl)-6-methoxypyridin-2-amine [(-)-P7C3-S243], with improved druglike properties. | Naidoo J, De Jesus-Cortes H, Huntington P, Estill S, Morlock LK, Starwalt R, Mangano TJ, Williams NS, Pieper AA, Ready JM | Journal of medicinal chemistry | 24697290 | J Med Chem | 2014 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/24697290 |
| P7C3 neuroprotective chemicals block axonal degeneration and preserve function after traumatic brain injury. | Yin TC, Britt JK, De Jesús-Cortés H, Lu Y, Genova RM, Khan MZ, Voorhees JR, Shao J, Katzman AC, Huntington PJ, Wassink C, McDaniel L, Newell EA, Dutca LM, Naidoo J, Cui H, Bassuk AG, Harper MM, McKnight SL, Ready JM, Pieper AA | Cell reports | 25220467 | Cell Rep | 2014 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/25220467 |
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| Reduced GABA neuron density in auditory cerebral cortex of subjects with major depressive disorder. | Smiley JF, Hackett TA, Bleiwas C, Petkova E, Stankov A, Mann JJ, Rosoklija G, Dwork AJ | Journal of chemical neuroanatomy | 26686292 | J Chem Neuroanat | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26686292 |
| Pharmacologic rescue of motor and sensory function by the neuroprotective compound P7C3 following neonatal nerve injury. | Kemp SWP, Szynkaruk M, Stanoulis KN, Wood MD, Liu EH, Willand MP, Morlock L, Naidoo J, Williams NS, Ready JM, Mangano TJ, Beggs S, Salter MW, Gordon T, Pieper AA, Borschel GH | Neuroscience | 25313000 | Neuroscience | 2015 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/25313000 |
| NPAS1 represses the generation of specific subtypes of cortical interneurons. | Stanco A, Pla R, Vogt D, Chen Y, Mandal S, Walker J, Hunt RF, Lindtner S, Erdman CA, Pieper AA, Hamilton SP, Xu D, Baraban SC, Rubenstein JL | Neuron | 25467980 | Neuron | 2014 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/25467980 |
| Neuroprotective efficacy of aminopropyl carbazoles in a mouse model of Parkinson disease. | De Jesús-Cortés H, Xu P, Drawbridge J, Estill SJ, Huntington P, Tran S, Britt J, Tesla R, Morlock L, Naidoo J, Melito LM, Wang G, Williams NS, Ready JM, McKnight SL, Pieper AA | Proceedings of the National Academy of Sciences of the United States of America | 23027934 | Proc Natl Acad Sci U S A | 2012 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/23027934 |
| P7C3 and an unbiased approach to drug discovery for neurodegenerative diseases. | Pieper AA, McKnight SL, Ready JM | Chemical Society reviews | 24514864 | Chem Soc Rev | 2014 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/24514864 |
| P7C3 neuroprotective chemicals function by activating the rate-limiting enzyme in NAD salvage. | Wang G, Han T, Nijhawan D, Theodoropoulos P, Naidoo J, Yadavalli S, Mirzaei H, Pieper AA, Ready JM, McKnight SL | Cell | 25215490 | Cell | 2014 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/25215490 |
| Applying a Gene Reversal Rate Computational Methodology to Identify Drugs for a Rare Cancer: Inflammatory Breast Cancer. | Ji X, Williams KP, Zheng W | Cancer informatics | 37846218 | Cancer Inform | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37846218 |
| Geospatial Associations between Female Breast Cancer Mortality Rates and Environmental Socioeconomic Indicators for North Carolina. | Burwell A, Kimbro S, Mulrooney T | International journal of environmental research and public health | 37510605 | Int J Environ Res Public Health | 2023 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/37510605 |
| The G-Protein-Coupled Estrogen Receptor Selective Agonist G-1 Attenuates Cell Viability and Migration in High-Grade Serous Ovarian Cancer Cell Lines. | Hanafi D, Onyenwoke RU, Kimbro KS | International journal of molecular sciences | 38928205 | Int J Mol Sci | 2024 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/38928205 |
| Identification of Novel GANT61 Analogs with Activity in Hedgehog Functional Assays and GLI1-Dependent Cancer Cells. | Abu Rabe D, Chdid L, Lamson DR, Laudeman CP, Tarpley M, Elsayed N, Smith GR, Zheng W, Dixon MS, Williams KP | Molecules (Basel, Switzerland) | 38999049 | Molecules | 2024 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/38999049 |
| Identification of small molecule antagonists of sonic hedgehog/heparin binding with activity in hedgehog functional assays. | Lamson DR, Tarpley M, Addo K, Ji X, Abu Rabe D, Ehe B, Hughes M, Smith GR, Daye LR, Musso DL, Zheng W, Williams KP | Biochimica et biophysica acta. General subjects | 39151833 | Biochim Biophys Acta Gen Subj | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39151833 |
| Molecular and socioeconomic characteristics of inflammatory breast cancer in the Carolina Breast Cancer Study. | Wang Q, Van Alsten SC, Ji X, Salim E, Salazar N, Scott JE, Yang X, Onyenwoke RU, Troester MA, Williams KP | Breast cancer research and treatment | 41569442 | Breast Cancer Res Treat | 2026 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/41569442 |
| Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. | Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS | Frontiers in endocrinology | 38577257 | Front Endocrinol (Lausanne) | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38577257 |
| From in silico prediction to experimental validation: Identification of drugs and novel synergistic combinations that inhibit growth of inflammatory breast cancer cells. | Salim EA, Ji X, Tarpley M, Dixon MS, Zheng W, Scott JE, Williams KP | bioRxiv : the preprint server for biology | 41427337 | bioRxiv | 2025 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/41427337 |
| Interventions Across the Translational Research Spectrum: Addressing Disparities Among Racial and Ethnic Minoritized Youth with Type 1 Diabetes. | Ellis DA, Naar S | Endocrinology and metabolism clinics of North America | 37865475 | Endocrinol Metab Clin North Am | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37865475 |
| Study protocol for transforming health equity research in integrated primary care: Antiracism as a disruptive innovation. | Naar S, Pettus C, Anderson N, Pooler-Burgess M, Ralston P, Flynn H, Combs T, Baquet C, Schatschneider C, Luke D | PloS one | 38935743 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38935743 |
| An early experience on the effect of solid organ transplant status on hospitalized COVID-19 patients. | Nair V, Jandovitz N, Hirsch JS, Abate M, Satapathy SK, Roth N, Miyara SJ, Guevara S, Kressel AM, Xiang A, Wu G, Butensky SD, Lin D, Williams S, Bhaskaran MC, Majure DT, Grodstein E, Lau L, Nair G, Fahmy AE, Winnick A, Breslin N, Berlinrut I, Molmenti C, Becker LB, Malhotra P, Gautam-Goyal P, Lima B, Maybaum S, Shah SK, Takegawa R, Hayashida K, Shinozaki K, Teperman LW, Molmenti EP, Northwell Health COVID-19 Research Consortium | American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons | 33443778 | Am J Transplant | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33443778 |
| Usefulness of Elevated Troponin to Predict Death in Patients With COVID-19 and Myocardial Injury. | Majure DT, Gruberg L, Saba SG, Kvasnovsky C, Hirsch JS, Jauhar R, Northwell Health COVID-19 Research Consortium | The American journal of cardiology | 33058800 | Am J Cardiol | 2021 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/33058800 |
| Clinical Mortality in a Large COVID-19 Cohort: Observational Study. | Jarrett M, Schultz S, Lyall J, Wang J, Stier L, De Geronimo M, Nelson K | Journal of medical Internet research | 32930099 | J Med Internet Res | 2020 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/32930099 |
| A Machine Learning Prediction Model of Respiratory Failure Within 48 Hours of Patient Admission for COVID-19: Model Development and Validation. | Bolourani S, Brenner M, Wang P, McGinn T, Hirsch JS, Barnaby D, Zanos TP, Northwell COVID-19 Research Consortium | Journal of medical Internet research | 33476281 | J Med Internet Res | 2021 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/33476281 |
| Estimating the predictive value of negative severe acute respiratory coronavirus virus 2 (SARS-CoV-2) results: A prospective study. | Hirschwerk D, Foley M, Lesser M, Farber B, Crawford JM, Davidson KW, Berry GJ, Smith E, Kast C, Volel V, McGinn T | Infection control and hospital epidemiology | 33298203 | Infect Control Hosp Epidemiol | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33298203 |
| Effectiveness of interventions targeting self-regulation to improve adherence to chronic disease medications: a meta-review of meta-analyses. | Wilson TE, Hennessy EA, Falzon L, Boyd R, Kronish IM, Birk JL | Health psychology review | 31856664 | Health Psychol Rev | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31856664 |
| Clinical Usefulness of Bright White Light Therapy for Depressive Symptoms in Cancer Survivors: Results from a Series of Personalized (N-of-1) Trials. | Kronish IM, Cheung YK, Julian J, Parsons F, Lee J, Yoon S, Valdimarsdottir H, Green P, Suls J, Hershman DL, Davidson KW | Healthcare (Basel, Switzerland) | 31905890 | Healthcare (Basel) | 2019 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/31905890 |
| COVID-19 in kidney transplant recipients. | Nair V, Jandovitz N, Hirsch JS, Nair G, Abate M, Bhaskaran M, Grodstein E, Berlinrut I, Hirschwerk D, Cohen SL, Davidson KW, Dominello AJ, Osorio GA, Richardson S, Teperman LW, Molmenti EP | American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons | 32351040 | Am J Transplant | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32351040 |
| Characteristics, Cardiac Involvement, and Outcomes of Multisystem Inflammatory Syndrome of Childhood Associated with severe acute respiratory syndrome coronavirus 2 Infection. | Capone CA, Subramony A, Sweberg T, Schneider J, Shah S, Rubin L, Schleien C, Northwell Health COVID-19 Research Consortium, Epstein S, Johnson JC, Kessel A, Misra N, Mitchell E, Palumbo N, Rajan S, Rocker J, Williamson K, Davidson KW | The Journal of pediatrics | 32553873 | J Pediatr | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32553873 |
| Significance of Multiple Adverse Social Determinants of Health on the Diagnosis, Control, and Management of Diabetes. | Kim EJ, Abrahams S, Marrast L, Martinez J, Hanchate AD, Conigliaro J | Journal of general internal medicine | 32495092 | J Gen Intern Med | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32495092 |
| In-Hospital 30-Day Survival Among Young Adults With Coronavirus Disease 2019: A Cohort Study. | Richardson S, Gitlin J, Kozel Z, Levy S, Rahman H, Hirsch JS, McGinn T, Diefenbach MA | Open forum infectious diseases | 34183983 | Open Forum Infect Dis | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34183983 |
| Expanding Knowledge and Changing Attitudes About Poverty: An Interactive, Interprofessional Approach. | Marrast LM, Chim C, Tocco J, Coletti DJ, Nouryan C, Block L, Martinez J | Journal of primary care & community health | 35225052 | J Prim Care Community Health | 2022 Jan-Dec | https://www.ncbi.nlm.nih.gov/pubmed/35225052 |
| Risk factors and outcomes for acute-on-chronic liver failure in COVID-19: a large multi-center observational cohort study. | Satapathy SK, Roth NC, Kvasnovsky C, Hirsch JS, Trindade AJ, Molmenti E, Barish M, Hirschwerk D, Da BL, Bernstein D, Northwell Health COVID-19 Research Consortium | Hepatology international | 33826042 | Hepatol Int | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33826042 |
| Effectiveness of SARS-CoV-2 Decontamination and Containment in a COVID-19 ICU. | Brune Z, Kuschner CE, Mootz J, Davidson KW, Pena RCF, Ghanem MH, Fischer A, Gitman M, Teperman L, Mason C, Becker LB | International journal of environmental research and public health | 33802332 | Int J Environ Res Public Health | 2021 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/33802332 |
| Randomized Personalized Trial for Stress Management Compared to Standard of Care. | Goodwin AM, Chandereng T, Ahn H, Miller D, Slotnick S, Perrin A, Cheung YK, Davidson KW, Butler MJ | Journal of personalized medicine | 41590516 | J Pers Med | 2026 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/41590516 |
| Protocol for randomized personalized trial for stress management compared to standard of care. | Goodwin AM, Miller D, D'Angelo S, Perrin A, Wiener R, Greene B, Romain AN, Arader L, Chandereng T, Kuen Cheung Y, Davidson KW, Butler M | Frontiers in psychology | 37794909 | Front Psychol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37794909 |
| Why Do I Get Side Effects? Personalized (N-of-1) Trials for Statin Intolerance and the Nocebo Effect. | Howard JP, Wood FA, Francis DP | Harvard data science review | 38344133 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38344133 |
| A Series of Remote Melatonin Supplement Interventions for Poor Sleep: Protocol for a Feasibility Pilot Study for a Series of Personalized (N-of-1) Trials. | Butler M, D'Angelo S, Perrin A, Rodillas J, Miller D, Arader L, Chandereng T, Cheung YK, Shechter A, Davidson KW | JMIR research protocols | 37535419 | JMIR Res Protoc | 2023 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/37535419 |
| Envisioning a future for precision health psychology: innovative applied statistical approaches to N-of-1 studies. | Davidson KW, Cheung YK | Health psychology review | 28651455 | Health Psychol Rev | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28651455 |
| Patient preferences for personalized (N-of-1) trials: a conjoint analysis. | Moise N, Wood D, Cheung YKK, Duan N, Onge TS, Duer-Hefele J, Pu T, Davidson KW, Kronish IM, Members of the “Personalized Trial Collaboratory” | Journal of clinical epidemiology | 29859242 | J Clin Epidemiol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29859242 |
| Are Nomothetic or Ideographic Approaches Superior in Predicting Daily Exercise Behaviors? | Cheung YK, Hsueh PS, Qian M, Yoon S, Meli L, Diaz KM, Schwartz JE, Kronish IM, Davidson KW | Methods of information in medicine | 29582914 | Methods Inf Med | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29582914 |
| Using Behavioral Analytics to Increase Exercise: A Randomized N-of-1 Study. | Yoon S, Schwartz JE, Burg MM, Kronish IM, Alcantara C, Julian J, Parsons F, Davidson KW, Diaz KM | American journal of preventive medicine | 29429607 | Am J Prev Med | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29429607 |
| BMI as a Risk Factor for Clinical Outcomes in Patients Hospitalized with COVID-19 in New York. | Kim TS, Roslin M, Wang JJ, Kane J, Hirsch JS, Kim EJ, Northwell Health COVID-19 Research Consortium | Obesity (Silver Spring, Md.) | 33128848 | Obesity (Silver Spring) | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33128848 |
| Scientific opportunities in resilience research for cardiovascular health and wellness. Report from a National Heart, Lung, and Blood Institute workshop. | Taylor HA, Finkel T, Gao Y, Ballinger SW, Campo R, Chen R, Chen SH, Davidson K, Iruela-Arispe ML, Jaquish C, LeBrasseur NK, Odden MC, Papanicolaou GJ, Picard M, Srinivas P, Tjurmina O, Wolz M, Galis ZS | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 36322029 | FASEB J | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36322029 |
| Early Experience of COVID-19 in a US Children's Hospital. | Kainth MK, Goenka PK, Williamson KA, Fishbein JS, Subramony A, Barone S, Belfer JA, Feld LM, Krief WI, Palumbo N, Rajan S, Rocker J, Scotto T, Sharma S, Sokoloff WC, Schleien C, Rubin LG, NORTHWELL HEALTH COVID-19 RESEARCH CONSORTIUM | Pediatrics | 32680880 | Pediatrics | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32680880 |
| Intersectional Identity and Racial Inequality During the COVID-19 Pandemic: Perspectives of Black Physician Mothers. | Louisias M, Marrast L | Journal of women's health (2002) | 32762601 | J Womens Health (Larchmt) | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32762601 |
| Rapid Emergence of SARS-CoV-2 in the Greater New York Metropolitan Area: Geolocation, Demographics, Positivity Rates, and Hospitalization for 46 793 Persons Tested by Northwell Health. | Reichberg SB, Mitra PP, Haghamad A, Ramrattan G, Crawford JM, Northwell COVID-19 Research Consortium, Berry GJ, Davidson KW, Drach A, Duong S, Juretschko S, Maria NI, Yang Y, Ziemba YC | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 32640030 | Clin Infect Dis | 2020 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/32640030 |
| Machine learning to assist clinical decision-making during the COVID-19 pandemic. | Debnath S, Barnaby DP, Coppa K, Makhnevich A, Kim EJ, Chatterjee S, Tóth V, Levy TJ, Paradis MD, Cohen SL, Hirsch JS, Zanos TP, Northwell COVID-19 Research Consortium | Bioelectronic medicine | 32665967 | Bioelectron Med | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32665967 |
| Selected psychological comorbidities in coronary heart disease: Challenges and grand opportunities. | Davidson KW, Alcántara C, Miller GE | The American psychologist | 30394780 | Am Psychol | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30394780 |
| Intubated COVID-19 predictive (ICOP) score for early mortality after intubation in patients with COVID-19. | Nishikimi M, Rasul R, Sison CP, Jafari D, Shoaib M, Shinozaki K, Li T, Hayashida K, Rolston DM, Hirsch JS, Becker LB, Northwell Health COVID-19 Research Consortium | Scientific reports | 34702896 | Sci Rep | 2021 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/34702896 |
| Now is the time to assess the effects of open science practiceswith randomized control trials. | Suls J, Rothman AJ, Davidson KW | The American psychologist | 34807632 | Am Psychol | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34807632 |
| A look at the increasing demographic representation within behavioral medicine. | Yoon S, Falzon L, Anderson NB, Davidson KW | Journal of behavioral medicine | 30825089 | J Behav Med | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30825089 |
| Racial and ethnic minority patient participation in N-of-1 trials: perspectives of healthcare providers and patients. | Marrast L, Conigliaro J, Chan C, Kim EJ, Duer-Hefele J, Diefenbach MA, Davidson KW | Personalized medicine | 34047197 | Per Med | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34047197 |
| Prevalence and Predictors of Venous Thromboembolism or Mortality in Hospitalized COVID-19 Patients. | Cohen SL, Gianos E, Barish MA, Chatterjee S, Kohn N, Lesser M, Giannis D, Coppa K, Hirsch JS, McGinn TG, Goldin ME, Spyropoulos AC, Northwell Health COVID-19 Research Consortium | Thrombosis and haemostasis | 33472255 | Thromb Haemost | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33472255 |
| Examination of patient characteristics and hydroxychloroquine use based on the US Food and Drug Administration's recommendation: a cross-sectional analysis in New York. | Kim EJ, Coppa K, Hirsch JS, Abrahams S, Johnson J, Lesser M, Davidson KW, Conigliaro J, Northwell Health COVID-19 Research Consortium, Northwell Health COVID-19 Research Consortium | BMJ open | 33558355 | BMJ Open | 2021 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/33558355 |
| An R Shiny App for a Chronic Lower Back Pain Study, Personalized N-of-1 Trial. | Chandereng T | Harvard data science review | 37091071 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37091071 |
| The Family of Single-Case Experimental Designs. | Epstein LH, Dallery J | Harvard data science review | 36926648 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36926648 |
| Increasing the Precision of Hypertension Treatment Through Personalized Trials: a Pilot Study. | Kronish IM, Cheung YK, Shimbo D, Julian J, Gallagher B, Parsons F, Davidson KW | Journal of general internal medicine | 30859504 | J Gen Intern Med | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30859504 |
| Using Metabolic Testing to Personalize Behavioral Obesity Treatment. | Epstein LH, Apolzan JW, Moore M, Neuwald NV, Faith MS | Obesity science & practice | 40070464 | Obes Sci Pract | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40070464 |
| N-of-1 Randomized Intervention Trials in Health Psychology: A Systematic Review and Methodology Critique. | Shaffer JA, Kronish IM, Falzon L, Cheung YK, Davidson KW | Annals of behavioral medicine : a publication of the Society of Behavioral Medicine | 30124759 | Ann Behav Med | 2018 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/30124759 |
| Personalized (N-of-1) Trials for Depression: A Systematic Review. | Kronish IM, Hampsey M, Falzon L, Konrad B, Davidson KW | Journal of clinical psychopharmacology | 29596148 | J Clin Psychopharmacol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29596148 |
| Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area. | Richardson S, Hirsch JS, Narasimhan M, Crawford JM, McGinn T, Davidson KW, the Northwell COVID-19 Research Consortium, Barnaby DP, Becker LB, Chelico JD, Cohen SL, Cookingham J, Coppa K, Diefenbach MA, Dominello AJ, Duer-Hefele J, Falzon L, Gitlin J, Hajizadeh N, Harvin TG, Hirschwerk DA, Kim EJ, Kozel ZM, Marrast LM, Mogavero JN, Osorio GA, Qiu M, Zanos TP | JAMA | 32320003 | JAMA | 2020 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/32320003 |
| N-of-1 Trials, Their Reporting Guidelines, and the Advancement of Open Science Principles. | Porcino A, Vohra S | Harvard data science review | 38031562 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38031562 |
| A Series of Virtual Interventions for Chronic Lower Back Pain: A Feasibility Pilot Study for a Series of Personalized (N-of-1) Trials. | Butler M, D'Angelo S, Kaplan M, Tashnim Z, Miller D, Ahn H, Falzon L, Dominello AJ, Foroughi C, Chandereng T, Cheung K, Davidson K | Harvard data science review | 37609556 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37609556 |
| Let Sleeping Patients Lie, avoiding unnecessary overnight vitals monitoring using a clinically based deep-learning model. | Tóth V, Meytlis M, Barnaby DP, Bock KR, Oppenheim MI, Al-Abed Y, McGinn T, Davidson KW, Becker LB, Hirsch JS, Zanos TP | NPJ digital medicine | 33299116 | NPJ Digit Med | 2020 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/33299116 |
| Sex-Based Differences in COVID-19 Outcomes. | Tejpal A, Gianos E, Cerise J, Hirsch JS, Rosen S, Kohn N, Lesser M, Weinberg C, Majure D, Satapathy SK, Bernstein D, Barish MA, Spyropoulos AC, Brown RM | Journal of women's health (2002) | 33885345 | J Womens Health (Larchmt) | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33885345 |
| Experimental Designs to Optimize Treatments for Individuals: Personalized N-of-1 Trials. | Davidson KW, Silverstein M, Cheung K, Paluch RA, Epstein LH | JAMA pediatrics | 33587109 | JAMA Pediatr | 2021 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/33587109 |
| Single case designs for early phase behavioral translational research in health psychology. | Epstein LH, Bickel WK, Czajkowski SM, Paluch RA, Moeyaert M, Davidson KW | Health psychology : official journal of the Division of Health Psychology, American Psychological Association | 34370494 | Health Psychol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34370494 |
| Barriers to and Facilitators for Acceptance of Comprehensive Clinical Decision Support System-Driven Care Maps for Patients With Thoracic Trauma: Interview Study Among Health Care Providers and Nurses. | Jones EK, Banks A, Melton GB, Porta CM, Tignanelli CJ | JMIR human factors | 35293873 | JMIR Hum Factors | 2022 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/35293873 |
| Mortality of Mechanically Ventilated COVID-19 Patients in Traditional versus Expanded Intensive Care Units in New York. | Nishikimi M, Jafari D, Singh N, Shinozaki K, Sison CP, Shoaib M, Gong J, Rasul R, Li T, Hayashida K, Rolston DM, Miyara SJ, Hirsch JS, Gandomi A, White MT, Jarrett MP, Lesser ML, Becker LB, Northwell Health COVID-19 Research Consortium | Annals of the American Thoracic Society | 35213292 | Ann Am Thorac Soc | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35213292 |
| Accomplishing breakthroughs in behavioural medicine research. | Davidson KW, Bacon SL, Bennett GG, Brondolo E, Czajkowski SM, Diefenbach MA, Epel ES, Matthews K, Revenson TA, Ruiz JM, Segerstrom SC, Behavioral Medicine Research Council | Nature human behaviour | 34127817 | Nat Hum Behav | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34127817 |
| Association of race/ethnicity with mortality in patients hospitalized with COVID-19. | Richardson S, Martinez J, Hirsch JS, Cerise J, Lesser M, Roswell RO, Davidson KW, Northwell Health COVID-19 Research Consortium | PloS one | 35925973 | PLoS One | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35925973 |
| Impact of Timing of Tocilizumab Use in Hospitalized Patients With SARS-CoV-2 Infection. | Singh AK, Oks M, Husk G, Dechario SP, Mina B, Singh K, Kirschenbaum L, Carpati CM, Mahmoud O, Gabra NI, Ishikawa O, Altschultz E, Shah V, Mahajan A, Gautam A, Birnbaum B, Antonacci AC, Raoof S | Respiratory care | 34548407 | Respir Care | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34548407 |
| A Series of Personalized Virtual Light Therapy Interventions for Fatigue: Feasibility Randomized Crossover Trial for N-of-1 Treatment. | Butler M, D'Angelo S, Ahn H, Chandereng T, Miller D, Perrin A, Romain AN, Scatoni A, Friel CP, Cheung YK, Davidson KW | JMIR formative research | 37721795 | JMIR Form Res | 2023 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/37721795 |
| Series of virtual light therapy interventions for fatigue: a feasibility pilot study protocol for a series of personalised (N-of-1) trials. | Butler M, D'Angelo S, Lewis C, Miller D, Perrin A, Suls J, Chandereng T, Cheung YK, Davidson KW | BMJ open | 36283748 | BMJ Open | 2022 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/36283748 |
| Evaluating Personalized (N-of-1) Trials in Rare Diseases: How Much Experimentation Is Enough? | Cheung K, Mitsumoto H | Harvard data science review | 38283317 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38283317 |
| Barriers to the Use of Clinical Decision Support for the Evaluation of Pulmonary Embolism: Qualitative Interview Study. | Richardson S, Dauber-Decker KL, McGinn T, Barnaby DP, Cattamanchi A, Pekmezaris R | JMIR human factors | 34346901 | JMIR Hum Factors | 2021 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/34346901 |
| Prevalence of SARS-CoV-2 Antibodies in Health Care Personnel in the New York City Area. | Moscola J, Sembajwe G, Jarrett M, Farber B, Chang T, McGinn T, Davidson KW, Northwell Health COVID-19 Research Consortium | JAMA | 32780804 | JAMA | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32780804 |
| Patients and primary care providers identify opportunities for personalized (N-of-1) trials in the mobile health era. | Kronish IM, Alcántara C, Duer-Hefele J, St Onge T, Davidson KW, Carter EJ, Medina V, Cohn E, Moise N | Journal of clinical epidemiology | 28648833 | J Clin Epidemiol | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28648833 |
| Accommodating Serial Correlation and Sequential Design Elements in Personalized Studies and Aggregated Personalized Studies. | Schork NJ | Harvard data science review | 37032736 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37032736 |
| Conduct and Implementation of Personalized Trials in Research and Practice. | Kravitz RL, Duan N | Harvard data science review | 38009129 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38009129 |
| Introducing Data Sciences to N-of-1 Designs, Statistics, Use-Cases, the Future, and the Moniker 'N-of-1' Trial. | Davidson KW, Cheung YK, Friel CP, Suls J | Harvard data science review | 38009132 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38009132 |
| Personalized Data Science and Personalized (N-of-1) Trials: Promising Paradigms for Individualized Health Care. | Duan N, Norman D, Schmid C, Sim I, Kravitz RL | Harvard data science review | 38009133 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38009133 |
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| Molecular dissection of the role of ACE2 in glucose homeostasis. | Chhabra KH, Shoemaker R, Herath CB, Thomas MC, Filipeanu CM, Lazartigues E | Physiological reviews | 39918873 | Physiol Rev | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/39918873 |
| Stable, neuron-specific gene expression in the mouse brain. | Ahmed O, Ekumi KM, Nardi FV, Maisumu G, Moussawi K, Lazartigues ED, Liang B, Yakoub AM | Journal of biological engineering | 38229168 | J Biol Eng | 2024 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/38229168 |
| The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. | Hazra T, Tapryal N, Chakraborty A, Rayavara K, Wakamiya M, Islam A, Pan L, Hsu J, Tat V, Maruyama J, Hosoki K, Sayed I, Alcantara J, Castillo V, Tindle C, Sarker A, Cardenas V, Sharma G, Alexander LC, Sur S, Ghosh G, Paessler S, Sahoo D, Ghosh P, Das S, Boldogh I, Tseng CT | Research square | 35665009 | Res Sq | 2022 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/35665009 |
| Brain organoids: building higher-order complexity and neural circuitry models. | Maisumu G, Willerth S, Nestor MW, Waldau B, Schülke S, Nardi FV, Ahmed O, Zhou Y, Durens M, Liang B, Yakoub AM | Trends in biotechnology | 40221251 | Trends Biotechnol | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40221251 |
| Protocol for generation of PD modeling induced neurons and detection of α-synuclein forms. | Nardi FV, Maisumu G, Zhou Y, Liang B, Yakoub AM | STAR protocols | 39549235 | STAR Protoc | 2024 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/39549235 |
| Angiotensin-Converting Enzyme 2 Posttranslational Modifications and Implications for Hypertension and SARS-CoV-2: 2023 Lewis K. Dahl Memorial Lecture. | Elgazzaz M, Filipeanu CM, Lazartigues E | Hypertension (Dallas, Tex. : 1979) | 38567498 | Hypertension | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38567498 |
| Ultrafast microfluidic synthesis of hierarchical triangular silver core-silica shell nanoplatelet toward enhanced cellular internalization. | Hao N, Nie Y, Xu Z, Zhang JXJ | Journal of colloid and interface science | 30771632 | J Colloid Interface Sci | 2019 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/30771632 |
| Microfluidic synthesis and on-chip enrichment application of two-dimensional hollow sandwich-like mesoporous silica nanosheet with water ripple-like surface. | Hao N, Nie Y, Closson AB, Zhang JXJ | Journal of colloid and interface science | 30576991 | J Colloid Interface Sci | 2019 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/30576991 |
| Implantable Cardiac Kirigami-Inspired Lead-Based Energy Harvester Fabricated by Enhanced Piezoelectric Composite Film. | Xu Z, Jin C, Cabe A, Escobedo D, Gruslova A, Jenney S, Closson AB, Dong L, Chen Z, Feldman MD, Zhang JXJ | Advanced healthcare materials | 33434407 | Adv Healthc Mater | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33434407 |
| Microfluidic continuous flow synthesis of functional hollow spherical silica with hierarchical sponge-like large porous shell. | Hao N, Nie Y, Xu Z, Closson AB, Usherwood T, J Zhang JX | Chemical engineering journal (Lausanne, Switzerland : 1996) | 31762686 | Chem Eng J | 2019 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/31762686 |
| Silver nanoparticle on zinc oxide array for label-free detection of opioids through surface-enhanced raman spectroscopy. | Zhang M, Jin C, Nie Y, Ren Y, Hao N, Xu Z, Dong L, Zhang JXJ | RSC advances | 35423637 | RSC Adv | 2021 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/35423637 |
| Edge effect of strained bilayer nanofilms for tunable multistability and actuation. | Hu N, Han X, Huang S, Grover HM, Yu X, Zhang LN, Trase I, Zhang JX, Zhang L, Dong LX, Chen Z | Nanoscale | 28067396 | Nanoscale | 2017 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/28067396 |
| Microfluidics for ZnO micro-/nanomaterials development: rational design, controllable synthesis, and on-chip bioapplications. | Hao N, Zhang M, Zhang JXJ | Biomaterials science | 31965125 | Biomater Sci | 2020 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/31965125 |
| Tunable Buckled Beams with Mesoporous PVDF-TrFE/SWCNT Composite Film for Energy Harvesting. | Xu Z, Liu Y, Dong L, Closson AB, Hao N, Oglesby M, Escobar GP, Fu S, Han X, Wen C, Liu J, Feldman MD, Chen Z, Zhang JXJ | ACS applied materials & interfaces | 30199624 | ACS Appl Mater Interfaces | 2018 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/30199624 |
| Scalable Signature-Based Molecular Diagnostics Through On-chip Biomarker Profiling Coupled with Machine Learning. | Molinski J, Tadimety A, Burklund A, Zhang JXJ | Annals of biomedical engineering | 32816167 | Ann Biomed Eng | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32816167 |
| Microfluidics-enabled rational design of ZnO micro-/nanoparticles with enhanced photocatalysis, cytotoxicity, and piezoelectric properties. | Hao N, Xu Z, Nie Y, Jin C, Closson AB, Zhang M, Zhang JXJ | Chemical engineering journal (Lausanne, Switzerland : 1996) | 32831625 | Chem Eng J | 2019 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/32831625 |
| Microfluidic In Situ Patterning of Silver Nanoparticles for Surface-Enhanced Raman Spectroscopic Sensing of Biomolecules. | Nie Y, Jin C, Zhang JXJ | ACS sensors | 34148342 | ACS Sens | 2021 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/34148342 |
| Combined immunomagnetic capture coupled with ultrasensitive plasmonic detection of circulating tumor cells in blood. | Shen W, Song Y, Burklund A, Le B, Zhang R, Wang L, Xi Y, Qian K, Shen T, Zhang JXJ | Biomedical microdevices | 30417219 | Biomed Microdevices | 2018 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/30417219 |
| Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing. | Tadimety A, Zhang Y, Molinski JH, Palinski TJ, Tsongalis GJ, Zhang JXJ | Methods in molecular biology (Clifton, N.J.) | 34837175 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/34837175 |
| Method for Inkjet-printing PEDOT:PSS polymer electrode arrays on piezoelectric PVDF-TrFE fibers. | Closson A, Richards H, Xu Z, Jin C, Dong L, Zhang JXJ | IEEE sensors journal | 34899077 | IEEE Sens J | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34899077 |
| Microfluidics-mediated self-template synthesis of anisotropic hollow ellipsoidal mesoporous silica nanomaterials. | Hao N, Nie Y, Tadimety A, Closson AB, Zhang JXJ | Materials research letters | 30854261 | Mater Res Lett | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/30854261 |
| Flexible Piezoelectric Nanogenerators Using Metal-doped ZnO-PVDF Films. | Jin C, Hao N, Xu Z, Trase I, Nie Y, Dong L, Closson A, Chen Z, Zhang JXJ | Sensors and actuators. A, Physical | 33380776 | Sens Actuators A Phys | 2020 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/33380776 |
| Patterned Plasmonic Surfaces-Theory, Fabrication, and Applications in Biosensing. | Chorsi HT, Zhu Y, Zhang JXJ | Journal of microelectromechanical systems : a joint IEEE and ASME publication on microstructures, microactuators, microsensors, and microsystems | 29276365 | J Microelectromech Syst | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29276365 |
| Microfluidics-enabled rapid manufacturing of hierarchical silica-magnetic microflower toward enhanced circulating tumor cell screening. | Hao N , Nie Y , Tadimety A , Shen T , Zhang JXJ | Biomaterials science | 30375583 | Biomater Sci | 2018 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/30375583 |
| Advances in liquid biopsy on-chip for cancer management: Technologies, biomarkers, and clinical analysis. | Tadimety A, Closson A, Li C, Yi S, Shen T, Zhang JXJ | Critical reviews in clinical laboratory sciences | 29388456 | Crit Rev Clin Lab Sci | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29388456 |
| Microfluidics-enabled rational design of immunomagnetic nanomaterials and their shape effect on liquid biopsy. | Hao N, Nie Y, Shen T, Zhang JXJ | Lab on a chip | 29923569 | Lab Chip | 2018 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/29923569 |
| Microfluidics-Based Organism Isolation from Whole Blood: An Emerging Tool for Bloodstream Infection Diagnosis. | Burklund A, Zhang JXJ | Annals of biomedical engineering | 30980291 | Ann Biomed Eng | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30980291 |
| Multifunctional Pacemaker Lead for Cardiac Energy Harvesting and Pressure Sensing. | Dong L, Closson AB, Jin C, Nie Y, Cabe A, Escobedo D, Huang S, Trase I, Xu Z, Chen Z, Feldman MD, Zhang JXJ | Advanced healthcare materials | 32347010 | Adv Healthc Mater | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32347010 |
| Microfluidic enrichment of bacteria coupled to contact-free lysis on a magnetic polymer surface for downstream molecular detection. | Burklund A, Petryk JD, Hoopes PJ, Zhang JXJ | Biomicrofluidics | 32642021 | Biomicrofluidics | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32642021 |
| Vibration-Energy-Harvesting System: Transduction Mechanisms, Frequency Tuning Techniques, and Biomechanical Applications. | Dong L, Closson AB, Jin C, Trase I, Chen Z, Zhang JXJ | Advanced materials technologies | 33829079 | Adv Mater Technol | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33829079 |
| Plasmonic nanosensors for point-of-care biomarker detection. | Jin C, Wu Z, Molinski JH, Zhou J, Ren Y, Zhang JXJ | Materials today. Bio | 35514435 | Mater Today Bio | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35514435 |
| Flexible Electrostatic Transducer Array with Displacement Control for Haptic Sensing and Actuation. | Trase I, Tan HZ, Chen Z, Zhang JXJ | Sensors and actuators. A, Physical | 33380777 | Sens Actuators A Phys | 2021 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/33380777 |
| Microfluidics for silica biomaterials synthesis: opportunities and challenges. | Hao N , Nie Y , Zhang JXJ | Biomaterials science | 30919847 | Biomater Sci | 2019 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/30919847 |
| Ultrafast Synthesis of Multifunctional Submicrometer Hollow Silica Spheres in Microfluidic Spiral Channels. | Nie Y, Hao N, Zhang JXJ | Scientific reports | 28974729 | Sci Rep | 2017 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/28974729 |
| Biomimetic hierarchical walnut kernel-like and erythrocyte-like mesoporous silica nanomaterials: controllable synthesis and versatile applications. | Hao N, Nie Y, Zhang JXJ | Microporous and mesoporous materials : the official journal of the International Zeolite Association | 29479288 | Microporous Mesoporous Mater | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29479288 |
| The fibrotic tumor stroma. | Yamauchi M, Barker TH, Gibbons DL, Kurie JM | The Journal of clinical investigation | 29293090 | J Clin Invest | 2018 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/29293090 |
| Detection of an Integrin-Binding Mechanoswitch within Fibronectin during Tissue Formation and Fibrosis. | Cao L, Nicosia J, Larouche J, Zhang Y, Bachman H, Brown AC, Holmgren L, Barker TH | ACS nano | 28699736 | ACS Nano | 2017 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/28699736 |
| Fibroblasts: The arbiters of extracellular matrix remodeling. | DeLeon-Pennell KY, Barker TH, Lindsey ML | Matrix biology : journal of the International Society for Matrix Biology | 32504772 | Matrix Biol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32504772 |
| Strain-dependent glutathionylation of fibronectin fibers impacts mechano-chemical behavior and primes an integrin switch. | Li W, Moretti L, Su X, Yeh CR, Torres MP, Barker TH | Nature communications | 39384749 | Nat Commun | 2024 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/39384749 |
| Feeling Things Out: Bidirectional Signaling of the Cell-ECM Interface, Implications in the Mechanobiology of Cell Spreading, Migration, Proliferation, and Differentiation. | Miller AE, Hu P, Barker TH | Advanced healthcare materials | 32037719 | Adv Healthc Mater | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32037719 |
| Macrophage and Fibroblast Interactions in Biomaterial-Mediated Fibrosis. | Witherel CE, Abebayehu D, Barker TH, Spiller KL | Advanced healthcare materials | 30658015 | Adv Healthc Mater | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30658015 |
| αvβ3 Integrin drives fibroblast contraction and strain stiffening of soft provisional matrix during progressive fibrosis. | Fiore VF, Wong SS, Tran C, Tan C, Xu W, Sulchek T, White ES, Hagood JS, Barker TH | JCI insight | 30333317 | JCI Insight | 2018 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/30333317 |
| Fibroblasts: Diverse Cells Critical to Biomaterials Integration. | Hannan RT, Peirce SM, Barker TH | ACS biomaterials science & engineering | 31440581 | ACS Biomater Sci Eng | 2018 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/31440581 |
| Fibroblast mechanoperception instructs pulmonary developmental and pattern specification gene expression programs. | Miller AE, Hu P, Hannan RT, Bhogaraju R, Abebayehu D, Civelek M, Barker TH | PLoS genetics | 41212903 | PLoS Genet | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/41212903 |
| Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology. | Bingham GC, Lee F, Naba A, Barker TH | Matrix biology : journal of the International Society for Matrix Biology | 32416243 | Matrix Biol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32416243 |
| Multi-scale models of lung fibrosis. | Leonard-Duke J, Evans S, Hannan RT, Barker TH, Bates JHT, Bonham CA, Moore BB, Kirschner DE, Peirce SM | Matrix biology : journal of the International Society for Matrix Biology | 32438056 | Matrix Biol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32438056 |
| LEM domain-containing protein 3 antagonizes TGFβ-SMAD2/3 signaling in a stiffness-dependent manner in both the nucleus and cytosol. | Chambers DM, Moretti L, Zhang JJ, Cooper SW, Chambers DM, Santangelo PJ, Barker TH | The Journal of biological chemistry | 30108174 | J Biol Chem | 2018 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/30108174 |
| Thy-1 in Integrin Mediated Mechanotransduction. | Hu P, Barker TH | Frontiers in cell and developmental biology | 30859101 | Front Cell Dev Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30859101 |
| Citrullination of fibronectin alters integrin clustering and focal adhesion stability promoting stromal cell invasion. | Stefanelli VL, Choudhury S, Hu P, Liu Y, Schwenzer A, Yeh CR, Chambers DM, von Beck K, Li W, Segura T, Midwood KS, Torres M, Barker TH | Matrix biology : journal of the International Society for Matrix Biology | 31004743 | Matrix Biol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31004743 |
| Angiocrine functions of organ-specific endothelial cells. | Rafii S, Butler JM, Ding BS | Nature | 26791722 | Nature | 2016 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/26791722 |
| Open the gates: vascular neurocrine signaling mobilizes hematopoietic stem and progenitor cells. | Itkin T, Gómez-Salinero JM, Rafii S | The Journal of clinical investigation | 29130939 | J Clin Invest | 2017 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/29130939 |
| Platelets prime hematopoietic and vascular niche to drive angiocrine-mediated liver regeneration. | Shido K, Chavez D, Cao Z, Ko J, Rafii S, Ding BS | Signal transduction and targeted therapy | 29201496 | Signal Transduct Target Ther | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29201496 |
| Endothelial jagged-2 sustains hematopoietic stem and progenitor reconstitution after myelosuppression. | Guo P, Poulos MG, Palikuqi B, Badwe CR, Lis R, Kunar B, Ding BS, Rabbany SY, Shido K, Butler JM, Rafii S | The Journal of clinical investigation | 29058691 | J Clin Invest | 2017 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/29058691 |
| Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. | Palikuqi B, Nguyen DT, Li G, Schreiner R, Pellegata AF, Liu Y, Redmond D, Geng F, Lin Y, Gómez-Salinero JM, Yokoyama M, Zumbo P, Zhang T, Kunar B, Witherspoon M, Han T, Tedeschi AM, Scottoni F, Lipkin SM, Dow L, Elemento O, Xiang JZ, Shido K, Spence JR, Zhou QJ, Schwartz RE, De Coppi P, Rabbany SY, Rafii S | Nature | 32908310 | Nature | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32908310 |
| In vitro conversion of adult murine endothelial cells to hematopoietic stem cells. | Barcia Durán JG, Lis R, Lu TM, Rafii S | Nature protocols | 30429596 | Nat Protoc | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30429596 |
| Molecular Checkpoint Decisions Made by Subverted Vascular Niche Transform Indolent Tumor Cells into Chemoresistant Cancer Stem Cells. | Cao Z, Scandura JM, Inghirami GG, Shido K, Ding BS, Rafii S | Cancer cell | 27989801 | Cancer Cell | 2017 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/27989801 |
| Sox17 drives functional engraftment of endothelium converted from non-vascular cells. | Schachterle W, Badwe CR, Palikuqi B, Kunar B, Ginsberg M, Lis R, Yokoyama M, Elemento O, Scandura JM, Rafii S | Nature communications | 28091527 | Nat Commun | 2017 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/28091527 |
| Platelet-derived SDF-1 primes the pulmonary capillary vascular niche to drive lung alveolar regeneration. | Rafii S, Cao Z, Lis R, Siempos II, Chavez D, Shido K, Rabbany SY, Ding BS | Nature cell biology | 25621952 | Nat Cell Biol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25621952 |
| Morphological characterization of Etv2 vascular explants using fractal analysis and atomic force microscopy. | Adelson RP, Palikuqi B, Weiss Z, Checco A, Schreiner R, Rafii S, Rabbany SY | Microvascular research | 34146583 | Microvasc Res | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34146583 |
| Endothelial Jak3 expression enhances pro-hematopoietic angiocrine function in mice. | Barcia Durán JG, Lu T, Houghton S, Geng F, Schreiner R, Xiang J, Rafii S, Redmond D, Lis R | Communications biology | 33767339 | Commun Biol | 2021 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/33767339 |
| Systems Biology Analysis of Temporal Dynamics That Govern Endothelial Response to Cyclic Stretch. | Lai MW, Chow N, Checco A, Kunar B, Redmond D, Rafii S, Rabbany SY | Biomolecules | 36551265 | Biomolecules | 2022 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/36551265 |
| Direct conversion of human amniotic cells into endothelial cells without transitioning through a pluripotent state. | Ginsberg M, Schachterle W, Shido K, Rafii S | Nature protocols | 26540589 | Nat Protoc | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26540589 |
| Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells. | Liu Y, Giannopoulou EG, Wen D, Falciatori I, Elemento O, Allis CD, Rafii S, Seandel M | Nature communications | 27117588 | Nat Commun | 2016 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/27117588 |
| Transplantation of Endothelial Cells to Mitigate Acute and Chronic Radiation Injury to Vital Organs. | Rafii S, Ginsberg M, Scandura J, Butler JM, Ding BS | Radiation research | 27459700 | Radiat Res | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27459700 |
| Molecular determinants of nephron vascular specialization in the kidney. | Barry DM, McMillan EA, Kunar B, Lis R, Zhang T, Lu T, Daniel E, Yokoyama M, Gomez-Salinero JM, Sureshbabu A, Cleaver O, Di Lorenzo A, Choi ME, Xiang J, Redmond D, Rabbany SY, Muthukumar T, Rafii S | Nature communications | 31836710 | Nat Commun | 2019 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/31836710 |
| Generation of BMEC Lines and in vitro BMEC-HSPC Co-culture Assays. | Guo P, Rafii S | Bio-protocol | 34532536 | Bio Protoc | 2018 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/34532536 |
| Conversion of adult endothelium to immunocompetent haematopoietic stem cells. | Lis R, Karrasch CC, Poulos MG, Kunar B, Redmond D, Duran JGB, Badwe CR, Schachterle W, Ginsberg M, Xiang J, Tabrizi AR, Shido K, Rosenwaks Z, Elemento O, Speck NA, Butler JM, Scandura JM, Rafii S | Nature | 28514438 | Nature | 2017 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/28514438 |
| Novelties in pharmacological management of cardiopulmonary resuscitation. | Bartos JA, Yannopoulos D | Current opinion in critical care | 23995130 | Curr Opin Crit Care | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23995130 |
| Sounds Impossible, but It's Knot. | Smith LE, Heath DR, Riess ML | Anesthesiology | 30632983 | Anesthesiology | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30632983 |
| Role of epinephrine and extracorporeal membrane oxygenation in the management of ischemic refractory ventricular fibrillation: a randomized trial in pigs. | Bartos JA, Voicu S, Matsuura TR, Tsangaris A, Sideris G, Oestreich BA, George SA, Olson M, Shekar KC, Rees JN, Carlson K, Sebastian P, McKnite S, Raveendran G, Aufderheide TP, Yannopoulos D | JACC. Basic to translational science | 29152600 | JACC Basic Transl Sci | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29152600 |
| Video laryngoscopic oral intubation in rats: a simple and effective method. | Balzer C, Cleveland WJ, Jinka TR, Riess ML | American journal of physiology. Lung cellular and molecular physiology | 32233786 | Am J Physiol Lung Cell Mol Physiol | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32233786 |
| PPARγ-Independent Side Effects of Thiazolidinediones on Mitochondrial Redox State in Rat Isolated Hearts. | Riess ML, Elorbany R, Weihrauch D, Stowe DF, Camara AKS | Cells | 31968546 | Cells | 2020 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/31968546 |
| Therapeutic Hypothermia in Children. | Riess ML, Aufderheide TP, Yannopoulos D | The New England journal of medicine | 26332560 | N Engl J Med | 2015 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/26332560 |
| Arterial flow waveforms, vascular tone, and chronic fatigue: a case report. | Zundel MT, Pattyn M, Chelimsky TC, Riess ML | Autonomic neuroscience : basic & clinical | 25817901 | Auton Neurosci | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25817901 |
| Venous waveform analysis detects acute right ventricular failure in a rat respiratory arrest model. | Lefevre RJ, Barajas MB, Balzer C, Baudenbacher FJ, Riess ML, Staudt G, Hernandez A, Eagle SS | Pediatric research | 36042330 | Pediatr Res | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36042330 |
| Design and Implementation of a Rat Ex Vivo Lung Perfusion Model. | Cleveland WJ, Hees JE, Balzer C, Douglas HF, Stevens T, Riess ML | Journal of visualized experiments : JoVE | 37306411 | J Vis Exp | 2023 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/37306411 |
| Lipid emulsion enhances cardiac performance after ischemia-reperfusion in isolated hearts from summer-active arctic ground squirrels. | Salzman MM, Cheng Q, Deklotz RJ, Dulai GK, Douglas HF, Dikalova AE, Weihrauch D, Barnes BM, Riess ML | Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology | 28364393 | J Comp Physiol B | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28364393 |
| New Developments in Cardiac Arrest Management. | Riess ML | Advances in anesthesia | 28867873 | Adv Anesth | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28867873 |
| Reperfusion injury protection during Basic Life Support improves circulation and survival outcomes in a porcine model of prolonged cardiac arrest. | Debaty G, Lurie K, Metzger A, Lick M, Bartos JA, Rees JN, McKnite S, Puertas L, Pepe P, Fowler R, Yannopoulos D | Resuscitation | 27211835 | Resuscitation | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27211835 |
| Minnesota Resuscitation Consortium's Advanced Perfusion and Reperfusion Cardiac Life Support Strategy for Out-of-Hospital Refractory Ventricular Fibrillation. | Yannopoulos D, Bartos JA, Martin C, Raveendran G, Missov E, Conterato M, Frascone RJ, Trembley A, Sipprell K, John R, George S, Carlson K, Brunsvold ME, Garcia S, Aufderheide TP | Journal of the American Heart Association | 27412906 | J Am Heart Assoc | 2016 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/27412906 |
| Outcomes of intermediate-risk patients treated with transcatheter and surgical aortic valve replacement in the Veterans Affairs Healthcare System: A single center 20-year experience. | Garcia S, Kelly R, Mbai M, Gurevich S, Oestreich B, Yannopoulos D, Adabag S | Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions | 29316204 | Catheter Cardiovasc Interv | 2018 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/29316204 |
| Opioid-induced cardioprotection. | Tanaka K, Kersten JR, Riess ML | Current pharmaceutical design | 24502571 | Curr Pharm Des | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24502571 |
| Intralipid Increases Nitric Oxide Release from Human Endothelial Cells During Oxidative Stress. | Weihrauch D, Shumpert SD, Larson ME, McVey N, Krolikowski JG, Bamkole O, Riess ML | JPEN. Journal of parenteral and enteral nutrition | 32291784 | JPEN J Parenter Enteral Nutr | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32291784 |
| Poloxamer 188 Exerts Direct Protective Effects on Mouse Brain Microvascular Endothelial Cells in an In Vitro Traumatic Brain Injury Model. | Lotze FP, Riess ML | Biomedicines | 34440247 | Biomedicines | 2021 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/34440247 |
| Venous Waveform Analysis Correlates With Echocardiography in Detecting Hypovolemia in a Rat Hemorrhage Model. | Lefevre RJ, Balzer C, Baudenbacher FJ, Riess ML, Hernandez A, Eagle SS | Seminars in cardiothoracic and vascular anesthesia | 32957831 | Semin Cardiothorac Vasc Anesth | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32957831 |
| Mechanical adjuncts for cardiocerebral resuscitation. | Riess ML, Balzer C | Expert review of medical devices | 31353970 | Expert Rev Med Devices | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31353970 |
| Total intravenous versus inhaled anesthesia in transsphenoidal tumor surgery. | Gollapudy S, Poetker DM, Sidhu J, Riess ML | American journal of otolaryngology | 30017373 | Am J Otolaryngol | 2018 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/30017373 |
| Noninvasively Measured Hemoglobin Concentration Reflects Arterial Hemoglobin Concentration Before but Not After Cardiopulmonary Bypass in Patients Undergoing Coronary Artery or Valve Surgery. | Riess ML, Pagel PS | Journal of cardiothoracic and vascular anesthesia | 27475734 | J Cardiothorac Vasc Anesth | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27475734 |
| Identifying Candidates for Advanced Hemodynamic Support After Cardiac Arrest. | Bartos JA, Doonan AL, Yannopoulos D | Circulation | 29335287 | Circulation | 2018 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/29335287 |
| Early Effects of Prolonged Cardiac Arrest and Ischemic Postconditioning during Cardiopulmonary Resuscitation on Cardiac and Brain Mitochondrial Function in Pigs. | Matsuura TR, Bartos JA, Tsangaris A, Shekar KC, Olson MD, Riess ML, Bienengraeber M, Aufderheide TP, Neumar RW, Rees JN, McKnite SH, Dikalova AE, Dikalov SI, Douglas HF, Yannopoulos D | Resuscitation | 28408349 | Resuscitation | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28408349 |
| Bundled postconditioning therapies improve hemodynamics and neurologic recovery after 17 min of untreated cardiac arrest. | Bartos JA, Matsuura TR, Sarraf M, Youngquist ST, McKnite SH, Rees JN, Sloper DT, Bates FS, Segal N, Debaty G, Lurie KG, Neumar RW, Metzger JM, Riess ML, Yannopoulos D | Resuscitation | 25447036 | Resuscitation | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25447036 |
| Non-invasive cardiac output monitoring during sinus surgery. | Gollapudy S, Riess ML | Journal of anesthesia | 25543335 | J Anesth | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25543335 |
| Surgical Field Visualization during Functional Endoscopic Sinus Surgery: Comparison of Propofol- vs Desflurane-Based Anesthesia. | Gollapudy S, Gashkoff DA, Poetker DM, Loehrl TA, Riess ML | Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery | 32450733 | Otolaryngol Head Neck Surg | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32450733 |
| Simulated traumatic brain injury in in-vitro mouse neuronal and brain endothelial cell culture models. | Meyer LJ, Lotze FP, Riess ML | Journal of pharmacological and toxicological methods | 35149185 | J Pharmacol Toxicol Methods | 2022 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/35149185 |
| Buffer glucose adjustment affects myocardial function after ischemia-reperfusion in long-term diabetic rat isolated hearts. | Balzer C, Cleveland WJ, Li Z, Riess ML | Physiological reports | 36324287 | Physiol Rep | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36324287 |
| A new method to predict return of spontaneous circulation by peripheral intravenous analysis during cardiopulmonary resuscitation: a rat model pilot study. | Balzer C, Eagle SS, Baudenbacher FJ, Riess ML | Intensive care medicine experimental | 39531090 | Intensive Care Med Exp | 2024 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/39531090 |
| Cardioprotection by poloxamer 188 is mediated through increased endothelial nitric oxide production. | Chen G, Douglas HF, Li Z, Cleveland WJ, Balzer C, Yannopoulos D, Chen IY, Obal D, Riess ML | Scientific reports | 40307302 | Sci Rep | 2025 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/40307302 |
| Anaesthetic Postconditioning at the Initiation of CPR Improves Myocardial and Mitochondrial Function in a Pig Model of Prolonged Untreated Ventricular Fibrillation. | Riess ML, Matsuura TR, Bartos JA, Bienengraeber M, Aldakkak M, McKnite SH, Rees JN, Aufderheide TP, Sarraf M, Neumar RW, Yannopoulos D | Resuscitation | 25281906 | Resuscitation | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25281906 |
| MicroRNA-21 Mediates Isoflurane-induced Cardioprotection against Ischemia-Reperfusion Injury via Akt/Nitric Oxide Synthase/Mitochondrial Permeability Transition Pore Pathway. | Qiao S, Olson JM, Paterson M, Yan Y, Zaja I, Liu Y, Riess ML, Kersten JR, Liang M, Warltier DC, Bosnjak ZJ, Ge ZD | Anesthesiology | 26259139 | Anesthesiology | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26259139 |
| Early Access to the Cardiac Catheterization Laboratory for Patients Resuscitated From Cardiac Arrest Due to a Shockable Rhythm: The Minnesota Resuscitation Consortium Twin Cities Unified Protocol. | Garcia S, Drexel T, Bekwelem W, Raveendran G, Caldwell E, Hodgson L, Wang Q, Adabag S, Mahoney B, Frascone R, Helmer G, Lick C, Conterato M, Baran K, Bart B, Bachour F, Roh S, Panetta C, Stark R, Haugland M, Mooney M, Wesley K, Yannopoulos D | Journal of the American Heart Association | 26744380 | J Am Heart Assoc | 2016 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/26744380 |
| Sodium nitroprusside enhanced cardiopulmonary resuscitation improves short term survival in a porcine model of ischemic refractory ventricular fibrillation. | Yannopoulos D, Bartos JA, George SA, Sideris G, Voicu S, Oestreich B, Matsuura T, Shekar K, Rees J, Aufderheide TP | Resuscitation | 27771299 | Resuscitation | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27771299 |
| Increasing body mass index predicts increasing difficulty, failure rate, and time to discovery of failure of epidural anesthesia in laboring patients. | Kula AO, Riess ML, Ellinas EH | Journal of clinical anesthesia | 28235511 | J Clin Anesth | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28235511 |
| Identifying Important Gaps in Randomized Controlled Trials of Adult Cardiac Arrest Treatments: A Systematic Review of the Published Literature. | Sinha SS, Sukul D, Lazarus JJ, Polavarapu V, Chan PS, Neumar RW, Nallamothu BK | Circulation. Cardiovascular quality and outcomes | 27756794 | Circ Cardiovasc Qual Outcomes | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27756794 |
| Potential Effects of Poloxamer 188 on Rat Isolated Brain Mitochondria after Oxidative Stress In Vivo and In Vitro. | Pille JA, Riess ML | Brain sciences | 33477541 | Brain Sci | 2021 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/33477541 |
| Poloxamer 188 Protects Isolated Adult Mouse Cardiomyocytes from Reoxygenation Injury. | Salzman MM, Bartos JA, Yannopoulos D, Riess ML | Pharmacology research & perspectives | 33073927 | Pharmacol Res Perspect | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33073927 |
| High central venous pressure amplitude predicts successful defibrillation in a porcine model of cardiac arrest. | Balzer C, Eagle SS, Yannopoulos D, Aufderheide TP, Riess ML | Resuscitation | 36736947 | Resuscitation | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36736947 |
| The relationship between red blood cell deformability metrics and perfusion of an artificial microvascular network. | Sosa JM, Nielsen ND, Vignes SM, Chen TG, Shevkoplyas SS | Clinical hemorheology and microcirculation | 23603326 | Clin Hemorheol Microcirc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/23603326 |
| Centrifugation-free washing reduces buildup of potassium and free hemoglobin in washed red blood cells after the procedure. | Vörös E, Lu M, Lezzar D, Shevkoplyas SS | American journal of hematology | 30184257 | Am J Hematol | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30184257 |
| Influence of feeding hematocrit and perfusion pressure on hematocrit reduction (Fåhraeus effect) in an artificial microvascular network. | Reinhart WH, Piety NZ, Shevkoplyas SS | Microcirculation (New York, N.Y. : 1994) | 28801994 | Microcirculation | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28801994 |
| Dynamics of shape recovery by stored red blood cells during washing at the single cell level. | Lu M, Shevkoplyas SS | Transfusion | 32748970 | Transfusion | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32748970 |
| Deterioration of red blood cell mechanical properties is reduced in anaerobic storage. | Burns JM, Yoshida T, Dumont LJ, Yang X, Piety NZ, Shevkoplyas SS | Blood transfusion = Trasfusione del sangue | 26674833 | Blood Transfus | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26674833 |
| A high-throughput microfluidic approach for 1000-fold leukocyte reduction of platelet-rich plasma. | Xia H, Strachan BC, Gifford SC, Shevkoplyas SS | Scientific reports | 27775049 | Sci Rep | 2016 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/27775049 |
| Deep ensemble learning enables highly accurate classification of stored red blood cell morphology. | Routt AH, Yang N, Piety NZ, Lu M, Shevkoplyas SS | Scientific reports | 36823298 | Sci Rep | 2023 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/36823298 |
| Controlled incremental filtration: a simplified approach to design and fabrication of high-throughput microfluidic devices for selective enrichment of particles. | Gifford SC, Spillane AM, Vignes SM, Shevkoplyas SS | Lab on a chip | 25254358 | Lab Chip | 2014 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/25254358 |
| A rapid paper-based test for quantifying sickle hemoglobin in blood samples from patients with sickle cell disease. | Piety NZ, Yang X, Lezzar D, George A, Shevkoplyas SS | American journal of hematology | 25689370 | Am J Hematol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25689370 |
| Substituting Sodium Hydrosulfite with Sodium Metabisulfite Improves Long-Term Stability of a Distributable Paper-Based Test Kit for Point-of-Care Screening for Sickle Cell Anemia. | Torabian K, Lezzar D, Piety NZ, George A, Shevkoplyas SS | Biosensors | 28930183 | Biosensors (Basel) | 2017 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/28930183 |
| Washing in hypotonic saline reduces the fraction of irreversibly-damaged cells in stored blood: a proof-of-concept study. | Xia H, Khanal G, Strachan BC, Vörös E, Piety NZ, Gifford SC, Shevkoplyas SS | Blood transfusion = Trasfusione del sangue | 28686152 | Blood Transfus | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28686152 |
| Optimal hematocrit in an artificial microvascular network. | Piety NZ, Reinhart WH, Stutz J, Shevkoplyas SS | Transfusion | 28681482 | Transfusion | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28681482 |
| A Paper-Based Test for Screening Newborns for Sickle Cell Disease. | Piety NZ, George A, Serrano S, Lanzi MR, Patel PR, Noli MP, Kahan S, Nirenberg D, Camanda JF, Airewele G, Shevkoplyas SS | Scientific reports | 28367971 | Sci Rep | 2017 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/28367971 |
| Density-based separation in multiphase systems provides a simple method to identify sickle cell disease. | Kumar AA, Patton MR, Hennek JW, Lee SY, D'Alesio-Spina G, Yang X, Kanter J, Shevkoplyas SS, Brugnara C, Whitesides GM | Proceedings of the National Academy of Sciences of the United States of America | 25197072 | Proc Natl Acad Sci U S A | 2014 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/25197072 |
| Washing stored red blood cells in an albumin solution improves their morphologic and hemorheologic properties. | Reinhart WH, Piety NZ, Deuel JW, Makhro A, Schulzki T, Bogdanov N, Goede JS, Bogdanova A, Abidi R, Shevkoplyas SS | Transfusion | 25752902 | Transfusion | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25752902 |
| Concurrent Assessment of Deformability and Adhesiveness of Sickle Red Blood Cells by Measuring Perfusion of an Adhesive Artificial Microvascular Network. | Lu M, Kanne CK, Reddington RC, Lezzar DL, Sheehan VA, Shevkoplyas SS | Frontiers in physiology | 33995119 | Front Physiol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33995119 |
| Microfluidic capillary networks are more sensitive than ektacytometry to the decline of red blood cell deformability induced by storage. | Piety NZ, Stutz J, Yilmaz N, Xia H, Yoshida T, Shevkoplyas SS | Scientific reports | 33436749 | Sci Rep | 2021 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/33436749 |
| Traditional and emerging technologies for washing and volume reducing blood products. | Lu M, Lezzar DL, Vörös E, Shevkoplyas SS | Journal of blood medicine | 30655711 | J Blood Med | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30655711 |
| Centrifugation-free washing: A novel approach for removing immunoglobulin A from stored red blood cells. | Vörös E, Piety NZ, Strachan BC, Lu M, Shevkoplyas SS | American journal of hematology | 29285804 | Am J Hematol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29285804 |
| pH-Responsive Charge-Conversion Progelator Peptides. | Carlini AS, Choi W, McCallum NC, Gianneschi NC | Advanced functional materials | 36530181 | Adv Funct Mater | 2021 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/36530181 |
| Development of a Synthetic 3-ketosteroid Δ(1)-dehydrogenase for the Generation of a Novel Catabolic Pathway Enabling Cholesterol Degradation in Human Cells. | D'Arcy BM, Swingle MR, Schambeau L, Pannell L, Prakash A, Honkanen RE | Scientific reports | 30979909 | Sci Rep | 2019 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/30979909 |
| Angiophagy prevents early embolus washout but recanalizes microvessels through embolus extravasation. | Grutzendler J, Murikinati S, Hiner B, Ji L, Lam CK, Yoo T, Gupta S, Hafler BP, Adelman RA, Yuan P, Rodriguez G | Science translational medicine | 24598589 | Sci Transl Med | 2014 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/24598589 |
| In vivo imaging of cerebral microvascular plasticity from birth to death. | Harb R, Whiteus C, Freitas C, Grutzendler J | Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism | 23093067 | J Cereb Blood Flow Metab | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23093067 |
| In vivo imaging of oligodendrocytes with sulforhodamine 101. | Hill RA, Grutzendler J | Nature methods | 25357236 | Nat Methods | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25357236 |
| 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 |
| Modulation of oligodendrocyte generation during a critical temporal window after NG2 cell division. | Hill RA, Patel KD, Goncalves CM, Grutzendler J, Nishiyama A | Nature neuroscience | 25262495 | Nat Neurosci | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25262495 |
| Angiophagy: mechanism of microvascular recanalization independent of the fibrinolytic system. | Grutzendler J | Stroke | 23709741 | Stroke | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23709741 |
| Perturbed neural activity disrupts cerebral angiogenesis during a postnatal critical period. | Whiteus C, Freitas C, Grutzendler J | Nature | 24305053 | Nature | 2014 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/24305053 |
| Microglia-Mediated Neuroprotection, TREM2, and Alzheimer's Disease: Evidence From Optical Imaging. | Condello C, Yuan P, Grutzendler J | Biological psychiatry | 29169609 | Biol Psychiatry | 2018 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/29169609 |
| Label-free in vivo imaging of myelinated axons in health and disease with spectral confocal reflectance microscopy. | Schain AJ, Hill RA, Grutzendler J | Nature medicine | 24681598 | Nat Med | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24681598 |
| Regional Blood Flow in the Normal and Ischemic Brain Is Controlled by Arteriolar Smooth Muscle Cell Contractility and Not by Capillary Pericytes. | Hill RA, Tong L, Yuan P, Murikinati S, Gupta S, Grutzendler J | Neuron | 26119027 | Neuron | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/26119027 |
| Microglia constitute a barrier that prevents neurotoxic protofibrillar Aβ42 hotspots around plaques. | Condello C, Yuan P, Schain A, Grutzendler J | Nature communications | 25630253 | Nat Commun | 2015 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/25630253 |
| Attenuation of β-Amyloid Deposition and Neurotoxicity by Chemogenetic Modulation of Neural Activity. | Yuan P, Grutzendler J | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26758850 | J Neurosci | 2016 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/26758850 |
| TREM2 Haplodeficiency in Mice and Humans Impairs the Microglia Barrier Function Leading to Decreased Amyloid Compaction and Severe Axonal Dystrophy. | Yuan P, Condello C, Keene CD, Wang Y, Bird TD, Paul SM, Luo W, Colonna M, Baddeley D, Grutzendler J | Neuron | 27196974 | Neuron | 2016 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/27196974 |
| Imaging and optogenetic modulation of vascular mural cells in the live brain. | Tong L, Hill RA, Damisah EC, Murray KN, Yuan P, Bordey A, Grutzendler J | Nature protocols | 33299155 | Nat Protoc | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33299155 |
| The major transitions of life from a network perspective. | Suki B | Frontiers in physiology | 22514542 | Front Physiol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22514542 |
| A mechanical design principle for tissue structure and function in the airway tree. | LaPrad AS, Lutchen KR, Suki B | PLoS computational biology | 23737742 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23737742 |
| Proteoglycans maintain lung stability in an elastase-treated mouse model of emphysema. | Takahashi A, Majumdar A, Parameswaran H, Bartolák-Suki E, Suki B | American journal of respiratory cell and molecular biology | 24450478 | Am J Respir Cell Mol Biol | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24450478 |
| Tidal stretches differently regulate the contractile and cytoskeletal elements in intact airways. | Bartolák-Suki E, LaPrad AS, Harvey BC, Suki B, Lutchen KR | PloS one | 24740101 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24740101 |
| A computational model of the response of adherent cells to stretch and changes in substrate stiffness. | Parameswaran H, Lutchen KR, Suki B | Journal of applied physiology (Bethesda, Md. : 1985) | 24408996 | J Appl Physiol (1985) | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24408996 |
| Acute mechanical forces cause deterioration in lung structure and function in elastase-induced emphysema. | Szabari MV, Parameswaran H, Sato S, Hantos Z, Bartolák-Suki E, Suki B | American journal of physiology. Lung cellular and molecular physiology | 22865550 | Am J Physiol Lung Cell Mol Physiol | 2012 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/22865550 |
| Microtubule dynamics regulate cyclic stretch-induced cell alignment in human airway smooth muscle cells. | Morioka M, Parameswaran H, Naruse K, Kondo M, Sokabe M, Hasegawa Y, Suki B, Ito S | PloS one | 22022610 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22022610 |
| Fluctuation-driven mechanotransduction regulates mitochondrial-network structure and function. | Bartolák-Suki E, Imsirovic J, Parameswaran H, Wellman TJ, Martinez N, Allen PG, Frey U, Suki B | Nature materials | 26213900 | Nat Mater | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26213900 |
| Homeostatic maintenance via degradation and repair of elastic fibers under tension. | Alves C, Araújo AD, Oliveira CL, Imsirovic J, Bartolák-Suki E, Andrade JS, Suki B | Scientific reports | 27279029 | Sci Rep | 2016 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/27279029 |
| Lung tissue mechanics as an emergent phenomenon. | Suki B, Bates JH | Journal of applied physiology (Bethesda, Md. : 1985) | 21212247 | J Appl Physiol (1985) | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21212247 |
| Variable ventilation improves ventilation and lung compliance in preterm lambs. | Pillow JJ, Musk GC, McLean CM, Polglase GR, Dalton RG, Jobe AH, Suki B | Intensive care medicine | 21567115 | Intensive Care Med | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21567115 |
| Regulatory Roles of Fluctuation-Driven Mechanotransduction in Cell Function. | Suki B, Parameswaran H, Imsirovic J, Bartolák-Suki E | Physiology (Bethesda, Md.) | 27511461 | Physiology (Bethesda) | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27511461 |
| Scale dependence of structure-function relationship in the emphysematous mouse lung. | Sato S, Bartolák-Suki E, Parameswaran H, Hamakawa H, Suki B | Frontiers in physiology | 26029115 | Front Physiol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26029115 |
| A novel device to stretch multiple tissue samples with variable patterns: application for mRNA regulation in tissue-engineered constructs. | Imsirovic J, Derricks K, Buczek-Thomas JA, Rich CB, Nugent MA, Suki B | Biomatter | 23628870 | Biomatter | 2013 Jul-Sep | https://www.ncbi.nlm.nih.gov/pubmed/23628870 |
| Computational modeling helps uncover mechanisms related to the progression of emphysema. | Suki B, Parameswaran H | Drug discovery today. Disease models | 24904681 | Drug Discov Today Dis Models | 2014 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/24904681 |
| Combined effects of ventilation mode and positive end-expiratory pressure on mechanics, gas exchange and the epithelium in mice with acute lung injury. | Thammanomai A, Hamakawa H, Bartolák-Suki E, Suki B | PloS one | 23326543 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23326543 |
| Variable ventilation enhances ventilation without exacerbating injury in preterm lambs with respiratory distress syndrome. | Berry CA, Suki B, Polglase GR, Pillow JJ | Pediatric research | 22805999 | Pediatr Res | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22805999 |
| Design of a Novel Equi-Biaxial Stretcher for Live Cellular and Subcellular Imaging. | Imsirovic J, Wellman TJ, Mondoñedo JR, Bartolák-Suki E, Suki B | PloS one | 26466363 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26466363 |
| Correlated variability in the breathing pattern and end-expiratory lung volumes in conscious humans. | Dellaca RL, Aliverti A, Lo Mauro A, Lutchen KR, Pedotti A, Suki B | PloS one | 25803710 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25803710 |
| Aging impairs smooth muscle-mediated regulation of aortic stiffness: a defect in shock absorption function? | Gao YZ, Saphirstein RJ, Yamin R, Suki B, Morgan KG | American journal of physiology. Heart and circulatory physiology | 25128168 | Am J Physiol Heart Circ Physiol | 2014 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/25128168 |
| Emphysema and mechanical stress-induced lung remodeling. | Suki B, Sato S, Parameswaran H, Szabari MV, Takahashi A, Bartolák-Suki E | Physiology (Bethesda, Md.) | 24186935 | Physiology (Bethesda) | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24186935 |
| Epithelial and endothelial damage induced by mechanical ventilation modes. | Suki B, Hubmayr R | Current opinion in critical care | 24300621 | Curr Opin Crit Care | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24300621 |
| Monitoring the temporal changes of respiratory resistance: a novel test for the management of asthma. | Gulotta C, Suki B, Brusasco V, Pellegrino R, Gobbi A, Pedotti A, Dellacà RL | American journal of respiratory and critical care medicine | 22707741 | Am J Respir Crit Care Med | 2012 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/22707741 |
| Complexity and emergent phenomena. | Suki B, Bates JH, Frey U | Comprehensive Physiology | 23737210 | Compr Physiol | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23737210 |
| A network model of correlated growth of tissue stiffening in pulmonary fibrosis. | Oliveira CL, Bates JH, Suki B | New journal of physics | 25484613 | New J Phys | 2014 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/25484613 |
| Effects of recruitment/derecruitment dynamics on the efficacy of variable ventilation. | Ma B, Suki B, Bates JH | Journal of applied physiology (Bethesda, Md. : 1985) | 21372101 | J Appl Physiol (1985) | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21372101 |
| Regulation of Gastrointestinal Smooth Muscle Function by Interstitial Cells. | Sanders KM, Kito Y, Hwang SJ, Ward SM | Physiology (Bethesda, Md.) | 27488743 | Physiology (Bethesda) | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27488743 |
| Efficient formation of single-copy human artificial chromosomes. | Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE | Science (New York, N.Y.) | 38513017 | Science | 2024 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/38513017 |
| Efficient Formation of Single-copy Human Artificial Chromosomes. | Gambogi CW, Mer E, Brown DM, Yankson G, Gavade JN, Logsdon GA, Heun P, Glass JI, Black BE | bioRxiv : the preprint server for biology | 37546784 | bioRxiv | 2023 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/37546784 |
| Rapid assembly of functional modules for generating human artificial chromosome constructs compatible with epigenetic centromere seeding. | Birchak GJ, Gibson DG, Allu PK, Kashyap P, Glass JI, Black BE | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 41324764 | Chromosome Res | 2025 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/41324764 |
| Protein-only centromeric chromatin assembly streamlines human artificial chromosome formation. | Birchak GJ, Allu PK, Kashyap P, Anbalagan GK, Chuang SC, Logsdon GA, Gibson DG, Glass JI, Black BE | bioRxiv : the preprint server for biology | 41659392 | bioRxiv | 2026 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/41659392 |
| Rapid assembly of functional modules for generating human artificial chromosome constructs compatible with epigenetic centromere seeding. | Birchak GJ, Gibson DG, Allu PK, Kashyap P, Glass JI, Black BE | bioRxiv : the preprint server for biology | 41256567 | bioRxiv | 2025 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/41256567 |
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| Urinary triclosan is associated with elevated body mass index in NHANES. | Lankester J, Patel C, Cullen MR, Ley C, Parsonnet J | PloS one | 24278238 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24278238 |
| Infectious diseases in children and body mass index in young adults. | Suh G, Ley C, Parsonnet J | Emerging infectious diseases | 22932124 | Emerg Infect Dis | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22932124 |
| Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination. | Tan SK, Granados AC, Bouquet J, Hoy-Schulz YE, Green L, Federman S, Stryke D, Haggerty TD, Ley C, Yeh MT, Jannat K, Maldonado YA, Andino R, Parsonnet J, Chiu CY | Scientific reports | 32958861 | Sci Rep | 2020 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/32958861 |
| A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the US. | Walters W, Ley C, Hastie T, Ley R, Parsonnet J | Research square | 36711501 | Res Sq | 2023 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/36711501 |
| Triclosan and triclocarban exposure and thyroid function during pregnancy-A randomized intervention. | Ley C, Pischel L, Parsonnet J | Reproductive toxicology (Elmsford, N.Y.) | 28939492 | Reprod Toxicol | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28939492 |
| Household triclosan and triclocarban effects on the infant and maternal microbiome. | Ribado JV, Ley C, Haggerty TD, Tkachenko E, Bhatt AS, Parsonnet J | EMBO molecular medicine | 29030459 | EMBO Mol Med | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29030459 |
| Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. | Nielsen SCA, Roskin KM, Jackson KJL, Joshi SA, Nejad P, Lee JY, Wagar LE, Pham TD, Hoh RA, Nguyen KD, Tsunemoto HY, Patel SB, Tibshirani R, Ley C, Davis MM, Parsonnet J, Boyd SD | Science translational medicine | 30814336 | Sci Transl Med | 2019 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/30814336 |
| Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis. | Pinto Y, Frishman S, Turjeman S, Eshel A, Nuriel-Ohayon M, Shrossel O, Ziv O, Walters W, Parsonnet J, Ley C, Johnson EL, Kumar K, Schweitzer R, Khatib S, Magzal F, Muller E, Tamir S, Tenenbaum-Gavish K, Rautava S, Salminen S, Isolauri E, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Borenstein E, Ley RE, Schwartz B, Louzoun Y, Hadar E, Koren O | Gut | 36627187 | Gut | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36627187 |
| Increased T Cell Differentiation and Cytolytic Function in Bangladeshi Compared to American Children. | Wagar LE, Bolen CR, Sigal N, Lopez Angel CJ, Guan L, Kirkpatrick BD, Haque R, Tibshirani RJ, Parsonnet J, Petri WA Jr, Davis MM | Frontiers in immunology | 31620139 | Front Immunol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31620139 |
| Recall accuracy of weekly automated surveys of health care utilization and infectious disease symptoms among infants over the first year of life. | Ley C, Willis L, de la Luz Sanchez M, Parsonnet J | PloS one | 31846482 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31846482 |
| Influence of environmental exposures on T follicular helper cell function and implications on immunity: a comparison of Bangladeshi and American children. | Van Fossen DM, Cho H, Wagar LE, Ma JZ, Parsonnet J, Haque R, Davis MM, Petri WA | mBio | 40062864 | mBio | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/40062864 |
| Comparison of two methods - regression predictive model and intake shift model - for adjusting self-reported dietary recall of total energy intake of populations. | Lankester J, Perry S, Parsonnet J | Frontiers in public health | 25506048 | Front Public Health | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25506048 |
| Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues. | Yang F, Nielsen SCA, Hoh RA, Röltgen K, Wirz OF, Haraguchi E, Jean GH, Lee JY, Pham TD, Jackson KJL, Roskin KM, Liu Y, Nguyen K, Ohgami RS, Osborne EM, Nadeau KC, Niemann CU, Parsonnet J, Boyd SD | Science (New York, N.Y.) | 33846272 | Science | 2021 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/33846272 |
| Longitudinal comparison of the developing gut virome in infants and their mothers. | Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J, Chiu CY | Cell host & microbe | 36758519 | Cell Host Microbe | 2023 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/36758519 |
| Effect of long-term antibiotic use on weight in adolescents with acne. | Contopoulos-Ioannidis DG, Ley C, Wang W, Ma T, Olson C, Shi X, Luft HS, Hastie T, Parsonnet J | The Journal of antimicrobial chemotherapy | 26782773 | J Antimicrob Chemother | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26782773 |
| Stanford's Outcomes Research in Kids (STORK): a prospective study of healthy pregnant women and their babies in Northern California. | Ley C, Sanchez Mde L, Mathur A, Yang S, Sundaram V, Parsonnet J | BMJ open | 27075843 | BMJ Open | 2016 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/27075843 |
| Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome. | Poole AC, Pischel L, Ley C, Suh G, Goodrich JK, Haggerty TD, Ley RE, Parsonnet J | mSphere | 27303746 | mSphere | 2016 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/27303746 |
| A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the USA. | Walters WA, Ley C, Hastie T, Ley RE, Parsonnet J | BMC medical research methodology | 38302887 | BMC Med Res Methodol | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/38302887 |
| A multiplex extracellular interactome screening method employing high-avidity nanoparticles. | Anaya MA, Wang ML, Gonzalez E, Lam AW, Vasnarungruengkul P, Vielmetter J, Wojtowicz WM, Zinn K | bioRxiv : the preprint server for biology | 40791403 | bioRxiv | 2025 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/40791403 |
| Rapid discovery of new-to-nature protein domains by novelty-first forcing of language models. | Subramanian A, Thomson M | bioRxiv : the preprint server for biology | 41256714 | bioRxiv | 2025 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/41256714 |
| Receptor Elimination by E3 Ubiquitin Ligase Recruitment (REULR): A Targeted Protein Degradation Toolbox. | Siepe DH, Picton LK, Garcia KC | ACS synthetic biology | 37011906 | ACS Synth Biol | 2023 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/37011906 |
| Benchmarking protein language models for protein crystallization. | Mall R, Kaushik R, Martinez ZA, Thomson MW, Castiglione F | Scientific reports | 39827171 | Sci Rep | 2025 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/39827171 |
| An Automated End-to-End Workflow for Production of Secreted Proteins in Transfected Mammalian Cells. | Vasnarungruengkul P, Anaya MA, Lam AW, Gonzalez E, Zhang A, Wang ML, Wojtowicz WM, Zinn K, Vielmetter J | bioRxiv : the preprint server for biology | 40672302 | bioRxiv | 2025 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/40672302 |
| TRILL: ORCHESTRATING MODULAR DEEP-LEARNING WORKFLOWS FOR DEMOCRATIZED, SCALABLE PROTEIN ANALYSIS AND ENGINEERING. | Martinez ZA, Murray RM, Thomson MW | bioRxiv : the preprint server for biology | 37986952 | bioRxiv | 2023 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/37986952 |
| Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM. | Chen X, Chen S, Thomson M | Nature computational science | 38177588 | Nat Comput Sci | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38177588 |
| Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. | Siepe DH, Henneberg LT, Wilson SC, Hess GT, Bassik MC, Zinn K, Garcia KC | eLife | 36178190 | Elife | 2022 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/36178190 |
| Pretrained protein language models choose between sequence novelty and structural completeness. | Subramanian AM, Martinez ZA, Thomson M | bioRxiv : the preprint server for biology | 41256629 | bioRxiv | 2025 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/41256629 |
| AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors. | Danneskiold-Samsøe NB, Kavi D, Jude KM, Nissen SB, Wat LW, Coassolo L, Zhao M, Santana-Oikawa GA, Broido BB, Garcia KC, Svensson KJ | bioRxiv : the preprint server for biology | 36993313 | bioRxiv | 2023 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/36993313 |
| Protein CREATE enables closed-loop design of de novo synthetic protein binders. | Lourenço A, Subramanian A, Spencer R, Anaya M, Miao J, Fu W, Chow E, Thomson M | bioRxiv : the preprint server for biology | 39803556 | bioRxiv | 2025 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/39803556 |
| AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors. | Banhos Danneskiold-Samsøe N, Kavi D, Jude KM, Nissen SB, Wat LW, Coassolo L, Zhao M, Santana-Oikawa GA, Broido BB, Garcia KC, Svensson KJ | Cell systems | 39541981 | Cell Syst | 2024 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/39541981 |
| Spin glasses, error correcting codes, and synchronization of human stem cell organoids. | Thomson M | Cell | 36736298 | Cell | 2023 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/36736298 |
| D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response. | Jiang J, Chen S, Tsou T, McGinnis CS, Khazaei T, Zhu Q, Park JH, Strazhnik IM, Vielmetter J, Gong Y, Hanna J, Chow ED, Sivak DA, Gartner ZJ, Thomson M | bioRxiv : the preprint server for biology | 37131803 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/37131803 |
| Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models. | Subramanian AM, Martinez ZA, Lourenço AL, Yuan SC, Liu S, Thomson M | bioRxiv : the preprint server for biology | 38187750 | bioRxiv | 2025 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/38187750 |
| Deploying synthetic coevolution and machine learning to engineer protein-protein interactions. | Yang A, Jude KM, Lai B, Minot M, Kocyla AM, Glassman CR, Nishimiya D, Kim YS, Reddy ST, Khan AA, Garcia KC | Science (New York, N.Y.) | 37499032 | Science | 2023 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/37499032 |
| Structural ontogeny of protein-protein interactions. | Yang A, Jiang H, Jude KM, Akpinaroglu D, Allenspach S, Li AJ, Bowden J, Perez CP, Liu L, Huang PS, Kortemme T, Listgarten J, Garcia KC | Science (New York, N.Y.) | 41678610 | Science | 2026 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/41678610 |
| Selective axonal translation of the mRNA isoform encoding prenylated Cdc42 supports axon growth. | Lee SJ, Zdradzinski MD, Sahoo PK, Kar AN, Patel P, Kawaguchi R, Aguilar BJ, Lantz KD, McCain CR, Coppola G, Lu Q, Twiss JL | Journal of cell science | 33674450 | J Cell Sci | 2021 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/33674450 |
| KHSRP-mediated decay of axonally localized prenyl-Cdc42 mRNA slows nerve regeneration. | Zdradzinski MD, Vaughn LS, Matoo S, Trumbull K, Smith TP, Noblitt D, Buchanan CN, Loomis A, Thames E, Lee SJ, Perrone-Bizzozero N, Lu Q, Larsen JM, Twiss JL | PLoS genetics | 41202098 | PLoS Genet | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/41202098 |
| Spatial and planar profiling of Rac1/Cdc42 signaling in Alzheimer's disease brain. | Akhtar SN, Tran TD, Chen YH, Lu Q | Journal of Alzheimer's disease : JAD | 39610278 | J Alzheimers Dis | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39610278 |
| KHSRP-mediated Decay of Axonally Localized Prenyl-Cdc42 mRNA Slows Nerve Regeneration. | Zdradzinski MD, Vaughn LS, Matoo S, Trumbull K, Loomis A, Thames E, Lee SJ, Perrone-Bizzozero N, Lu Q, Larsen JM, Twiss JL | bioRxiv : the preprint server for biology | 39975228 | bioRxiv | 2025 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/39975228 |
| Nanoarchitecture and molecular interactions of epithelial cell junction proteins revealed by super-resolution microscopy. | Naser AN, Guiler W, Lu Q, Chen YH | Annals of the New York Academy of Sciences | 35819053 | Ann N Y Acad Sci | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35819053 |
| RhoA-LIMK Signaling Axis Reveals Rostral-Caudal Plane and Spatial Dysregulation in the Brain of Alzheimer's Disease Mouse Models. | Nik Akhtar S, Lu Q | Journal of Alzheimer's disease : JAD | 37718806 | J Alzheimers Dis | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37718806 |
| Enabling systemic identification and functionality profiling for Cdc42 homeostatic modulators. | Malasala S, Azimian F, Chen YH, Twiss JL, Boykin C, Akhtar SN, Lu Q | Communications chemistry | 39562759 | Commun Chem | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39562759 |
| TRPV4: En RhoA To a Cure? | Lu Q, Chen YH | BioEssays : news and reviews in molecular, cellular and developmental biology | 35441721 | Bioessays | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35441721 |
| Trans-Compartmental Regulation of Tight Junction Barrier Function. | Naser AN, Lu Q, Chen YH | Tissue barriers | 36220768 | Tissue Barriers | 2023 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/36220768 |
| G-Protein Signaling in Alzheimer's Disease: Spatial Expression Validation of Semi-supervised Deep Learning-Based Computational Framework. | Zhang DF, Penwell T, Chen YH, Koehler A, Wu R, Nik Akhtar S, Lu Q | The Journal of neuroscience : the official journal of the Society for Neuroscience | 39327003 | J Neurosci | 2024 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/39327003 |
| Crosstalk between the Rho and Rab family of small GTPases in neurodegenerative disorders. | Nik Akhtar S, Bunner WP, Brennan E, Lu Q, Szatmari EM | Frontiers in cellular neuroscience | 36779014 | Front Cell Neurosci | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36779014 |
| Therapeutic Effect of Y-27632 on Tumorigenesis and Cisplatin-Induced Peripheral Sensory Loss through RhoA-NF-κB. | Zhu Y, Howard GA, Pittman K, Boykin C, Herring LE, Wilkerson EM, Verbanac K, Lu Q | Molecular cancer research : MCR | 31189689 | Mol Cancer Res | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31189689 |
| Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. | Shah PP, Lv W, Rhoades JH, Poleshko A, Abbey D, Caporizzo MA, Linares-Saldana R, Heffler JG, Sayed N, Thomas D, Wang Q, Stanton LJ, Bedi K, Morley MP, Cappola TP, Owens AT, Margulies KB, Frank DB, Wu JC, Rader DJ, Yang W, Prosser BL, Musunuru K, Jain R | Cell stem cell | 33529599 | Cell Stem Cell | 2021 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/33529599 |
| Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. | Jiang CL, Goyal Y, Jain N, Wang Q, Truitt RE, Coté AJ, Emert B, Mellis IA, Kiani K, Yang W, Jain R, Raj A | Genome biology | 35382863 | Genome Biol | 2022 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/35382863 |
| Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids. | Triandafillou CG, Sompalle P, Heyman Y, Raj A | bioRxiv : the preprint server for biology | 40766620 | bioRxiv | 2025 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/40766620 |
| Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A | Cell systems | 38335955 | Cell Syst | 2024 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/38335955 |
| AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance. | Li J, Ravindran PT, O'Farrell A, Busch GT, Boe RH, Niu Z, Woo S, Dunagin MC, Jain N, Goyal Y, Sarma K, Herlyn M, Raj A | bioRxiv : the preprint server for biology | 39091739 | bioRxiv | 2024 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/39091739 |
| Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Raj A | bioRxiv : the preprint server for biology | 36798299 | bioRxiv | 2023 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/36798299 |
| Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states. | Reffsin S, Miller J, Ayyanathan K, Dunagin MC, Jain N, Schultz DC, Cherry S, Raj A | bioRxiv : the preprint server for biology | 37461472 | bioRxiv | 2023 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/37461472 |
| Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance. | Boe RH, Triandafillou CG, Lazcano R, Wargo JA, Raj A | bioRxiv : the preprint server for biology | 39005406 | bioRxiv | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/39005406 |
| ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. | Dardani I, Emert BL, Goyal Y, Jiang CL, Kaur A, Lee J, Rouhanifard SH, Alicea GM, Fane ME, Xiao M, Herlyn M, Weeraratna AT, Raj A | Nature methods | 36280724 | Nat Methods | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36280724 |
| Systematically quantifying morphological features reveals constraints on organoid phenotypes. | Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A | Cell systems | 35705097 | Cell Syst | 2022 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/35705097 |
| Social reprogramming in ants induces longevity-associated glia remodeling. | Sheng L, Shields EJ, Gospocic J, Glastad KM, Ratchasanmuang P, Berger SL, Raj A, Little S, Bonasio R | Science advances | 32875108 | Sci Adv | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32875108 |
| Picking Winners and Losers: Cell Competition in Tissue Development and Homeostasis. | Kim W, Jain R | Trends in genetics : TIG | 32418713 | Trends Genet | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32418713 |
| FZD2 Regulates Murine Hair Follicle Function and Maintenance. | Brennan-Crispi DM, Frankfurter M, Murphy C, Sheng E, Xu M, Morrisey EE, Millar SE, Leung TH | The Journal of investigative dermatology | 35051380 | J Invest Dermatol | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35051380 |
| Lineage memory shapes viral resistance barriers in human skin. | Van Eyndhoven LC, Kinsler G, Zhang J, O'Farrell A, Abderrahim R, Srivastav A, Triandafillou CG, Greco TM, Zaret KS, Cristea IM, Orzalli MH, Drayman N, Singh A, Raj A | bioRxiv : the preprint server for biology | 40666908 | bioRxiv | 2025 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/40666908 |
| Gastruloid patterning reflects division of labor among biased stem cell clones. | Ayyappan V, Triandafillou CG, Sarma K, Raj A | bioRxiv : the preprint server for biology | 40791385 | bioRxiv | 2025 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/40791385 |
| Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells. | Goyal Y, Busch GT, Pillai M, Li J, Boe RH, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, Mellis IA, Kiani K, Alicea GM, Fane ME, Ahmed SS, Li H, Chen Y, Chai C, Kaster J, Witt RG, Lazcano R, Ingram DR, Johnson SB, Wani K, Dunagin MC, Lazar AJ, Weeraratna AT, Wargo JA, Herlyn M, Raj A | Nature | 37468627 | Nature | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37468627 |
| Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. | Sanford EM, Emert BL, Coté A, Raj A | eLife | 33284110 | Elife | 2020 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/33284110 |
| Genetic screening for single-cell variability modulators driving therapy resistance. | Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A | Nature genetics | 33398196 | Nat Genet | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33398196 |
| Variability within rare cell states enables multiple paths toward drug resistance. | Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM, Raj A | Nature biotechnology | 33619394 | Nat Biotechnol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33619394 |
| An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. | Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R | Genome biology | 36691074 | Genome Biol | 2023 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/36691074 |
| Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations. | Kiani K, Sanford EM, Goyal Y, Raj A | Molecular systems biology | 36069349 | Mol Syst Biol | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36069349 |
| Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. | Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A | Cell systems | 34352221 | Cell Syst | 2021 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/34352221 |
| Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. | Schuh L, Saint-Antoine M, Sanford EM, Emert BL, Singh A, Marr C, Raj A, Goyal Y | Cell systems | 32325034 | Cell Syst | 2020 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/32325034 |
| Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. | Shaffer SM, Emert BL, Reyes Hueros RA, Cote C, Harmange G, Schaff DL, Sizemore AE, Gupte R, Torre E, Singh A, Bassett DS, Raj A | Cell | 32735851 | Cell | 2020 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/32735851 |
| Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks. | Boe RH, Ayyappan V, Schuh L, Raj A | Cell systems | 36450286 | Cell Syst | 2022 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/36450286 |
| Post-transcriptional splicing can occur in a slow-moving zone around the gene. | Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A | eLife | 38577979 | Elife | 2024 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/38577979 |
| Innate Immune Memory is Stimulus Specific. | O'Farrell A, Niu Z, Li J, Van Eyndhoven LC, Sarma K, Raj A | bioRxiv : the preprint server for biology | 39896612 | bioRxiv | 2025 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/39896612 |
| Heterogeneous therapy-resistant cancer cells have distinct and exploitable drug sensitivity profiles. | Busch GT, Boe RH, Li J, Gruener RF, Arnett MJ, Ravindran PT, Herlyn M, Huang RS, Raj A | bioRxiv : the preprint server for biology | 40654745 | bioRxiv | 2025 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/40654745 |
| A Nature-Inspired Ion Trap for Parallel Manipulation of Ions on a Massive Scale. | Krutchinsky AN, Chait BT | bioRxiv : the preprint server for biology | 40909697 | bioRxiv | 2025 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/40909697 |
| Structural characterization of a peptoid-inspired conformationally constrained oligomer (PICCO) bound to streptavidin. | McEnaney P , Balzarini M , Park H , Kodadek T | Chemical communications (Cambridge, England) | 32785302 | Chem Commun (Camb) | 2020 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/32785302 |
| Mechanistic Studies of the Multiple Myeloma and Melanoma Cell-Selective Toxicity of the Rpn13-Binding Peptoid KDT-11. | Dickson P, Simanski S, Ngundu JM, Kodadek T | Cell chemical biology | 32857986 | Cell Chem Biol | 2020 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/32857986 |
| Physical and Functional Analysis of the Putative Rpn13 Inhibitor RA190. | Dickson P, Abegg D, Vinogradova E, Takaya J, An H, Simanski S, Cravatt BF, Adibekian A, Kodadek T | Cell chemical biology | 32857985 | Cell Chem Biol | 2020 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/32857985 |
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| Tuning sterol extraction kinetics yields a renal-sparing polyene antifungal. | Maji A, Soutar CP, Zhang J, Lewandowska A, Uno BE, Yan S, Shelke Y, Murhade G, Nimerovsky E, Borcik CG, Arango AS, Lange JD, Marin-Toledo JP, Lyu Y, Bailey KL, Roady PJ, Holler JT, Khandelwal A, SantaMaria AM, Sanchez H, Juvvadi PR, Johns G, Hageman MJ, Krise J, Gebremariam T, Youssef EG, Bartizal K, Marr KA, Steinbach WJ, Ibrahim AS, Patterson TF, Wiederhold NP, Andes DR, Pogorelov TV, Schwieters CD, Fan TM, Rienstra CM, Burke MD | Nature | 37938782 | Nature | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37938782 |
| APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. | Park H, Patel P, Haas R, Huerta EA | Proceedings of the National Academy of Sciences of the United States of America | 38913887 | Proc Natl Acad Sci U S A | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/38913887 |
| Automated fibril structure calculations in Xplor-NIH. | Barclay AM, Milchberg MH, Warmuth OA, Tuttle MD, Dennis CJ, Schwieters CD, Rienstra CM | Structure (London, England : 1993) | 39662464 | Structure | 2025 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/39662464 |
| Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism. | Thangapandian S, Fakharzadeh A, Moradi M, Tajkhorshid E | Proceedings of the National Academy of Sciences of the United States of America | 40042900 | Proc Natl Acad Sci U S A | 2025 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/40042900 |
| Probing Solution Dynamics of Tissue Factor Using Molecular Dynamics Simulations Guided by NMR Chemical Shifts. | Lihan M, Pant S, Ojoawo AM, Rienstra CM, Tajkhorshid E | The journal of physical chemistry. B | 41894586 | J Phys Chem B | 2026 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/41894586 |
| Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. | Ciudad S, Puig E, Botzanowski T, Meigooni M, Arango AS, Do J, Mayzel M, Bayoumi M, Chaignepain S, Maglia G, Cianferani S, Orekhov V, Tajkhorshid E, Bardiaux B, Carulla N | Nature communications | 32541820 | Nat Commun | 2020 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/32541820 |
| Polymer-Peptide Conjugates Convert Amyloid into Protein Nanobundles through Fragmentation and Lateral Association. | Smith JW, Jiang X, An H, Barclay AM, Licari G, Tajkhorshid E, Moore EG, Rienstra CM, Moore JS, Chen Q | ACS applied nano materials | 32149271 | ACS Appl Nano Mater | 2020 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/32149271 |
| Molecular mechanism of prestin electromotive signal amplification. | Ge J, Elferich J, Dehghani-Ghahnaviyeh S, Zhao Z, Meadows M, von Gersdorff H, Tajkhorshid E, Gouaux E | Cell | 34390643 | Cell | 2021 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/34390643 |
| Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. | Pant S, Tajkhorshid E | Journal of computational chemistry | 31762060 | J Comput Chem | 2020 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/31762060 |
| Probing cholesterol binding and translocation in P-glycoprotein. | Thangapandian S, Kapoor K, Tajkhorshid E | Biochimica et biophysica acta. Biomembranes | 31676371 | Biochim Biophys Acta Biomembr | 2020 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/31676371 |
| Structural basis for the reaction cycle of DASS dicarboxylate transporters. | Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN | eLife | 32869741 | Elife | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32869741 |
| Twisting and tilting of a mechanosensitive molecular probe detects order in membranes. | Licari G, Strakova K, Matile S, Tajkhorshid E | Chemical science | 32864081 | Chem Sci | 2020 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/32864081 |
| Probing key elements of teixobactin-lipid II interactions in membranes. | Wen PC, Vanegas JM, Rempe SB, Tajkhorshid E | Chemical science | 30210775 | Chem Sci | 2018 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/30210775 |
| Lipids and ions traverse the membrane by the same physical pathway in the nhTMEM16 scramblase. | Jiang T, Yu K, Hartzell HC, Tajkhorshid E | eLife | 28917060 | Elife | 2017 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/28917060 |
| Lipid specificity of the membrane binding domain of coagulation factor X. | Muller MP, Wang Y, Morrissey JH, Tajkhorshid E | Journal of thrombosis and haemostasis : JTH | 28782177 | J Thromb Haemost | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28782177 |
| (31)P-dephased, (13)C-detected REDOR for NMR crystallography at natural isotopic abundance. | Greenwood AI, Clay MC, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 28319851 | J Magn Reson | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28319851 |
| PIP(2)-dependent coupling of voltage sensor and pore domains in K(v)7.2 channel. | Pant S, Zhang J, Kim EC, Lam K, Chung HJ, Tajkhorshid E | Communications biology | 34650221 | Commun Biol | 2021 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/34650221 |
| Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. | Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW | The Journal of biological chemistry | 35122790 | J Biol Chem | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35122790 |
| Targeting lipid-protein interaction to treat Syk-mediated acute myeloid leukemia. | Singaram I, Sharma A, Pant S, Lihan M, Park MJ, Pergande M, Buwaneka P, Hu Y, Mahmud N, Kim YM, Cologna S, Gevorgyan V, Khan I, Tajkhorshid E, Cho W | Nature chemical biology | 36229686 | Nat Chem Biol | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36229686 |
| Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. | Zhang Y, Soubias O, Pant S, Heinrich F, Vogel A, Li J, Li Y, Clifton LA, Daum S, Bacia K, Huster D, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA | Nature communications | 37989735 | Nat Commun | 2023 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/37989735 |
| Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. | Tang Q, Sinclair M, Hasdemir HS, Stein RA, Karakas E, Tajkhorshid E, Mchaourab HS | Nature communications | 37938578 | Nat Commun | 2023 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/37938578 |
| Topological Learning Approach to Characterizing Biological Membranes. | Arango AS, Park H, Tajkhorshid E | bioRxiv : the preprint server for biology | 38076911 | bioRxiv | 2023 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/38076911 |
| Enhancing Spectrometer Performance with Unsupervised Machine Learning. | Harding BD, Hu Z, Hiett A, Delaglio F, Henzler-Wildman KA, Rienstra CM | The journal of physical chemistry. B | 39395040 | J Phys Chem B | 2024 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/39395040 |
| Top-Down Scoring of Spectral Fitness by Image Analysis for Protein Structure Validation. | Harding BD, DeZonia B, Garg R, Hu Z, Delaglio F, Grant T, Rienstra CM | Journal of chemical information and modeling | 41417269 | J Chem Inf Model | 2026 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/41417269 |
| An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells. | Yadav AK, Reinhardt CJ, Arango AS, Huff HC, Dong L, Malkowski MG, Das A, Tajkhorshid E, Chan J | Angewandte Chemie (International ed. in English) | 31854058 | Angew Chem Int Ed Engl | 2020 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/31854058 |
| Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. | Coleman JA, Yang D, Zhao Z, Wen PC, Yoshioka C, Tajkhorshid E, Gouaux E | Nature | 31019304 | Nature | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31019304 |
| Structural Insights into the Lipid A Transport Pathway in MsbA. | Padayatti PS, Lee SC, Stanfield RL, Wen PC, Tajkhorshid E, Wilson IA, Zhang Q | Structure (London, England : 1993) | 31130486 | Structure | 2019 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/31130486 |
| (1)H-Detected REDOR with Fast Magic-Angle Spinning of a Deuterated Protein. | Ghosh M, Rienstra CM | The journal of physical chemistry. B | 28816462 | J Phys Chem B | 2017 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/28816462 |
| A modification of γ-encoded RN symmetry pulses for increasing the scaling factor and more accurate measurements of the strong heteronuclear dipolar couplings. | Nimerovsky E, Soutar CP | Journal of magnetic resonance (San Diego, Calif. : 1997) | 32950918 | J Magn Reson | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32950918 |
| The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. | Radka CD, Grace CR, Hasdemir HS, Li Y, Rodriguez CC, Rodrigues P, Oldham ML, Qayyum MZ, Pitre A, MacCain WJ, Kalathur RC, Tajkhorshid E, Rock CO | The Journal of biological chemistry | 38211817 | J Biol Chem | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38211817 |
| A serine loop in tissue factor mediates substrate selectivity by the tissue factor-factor VIIa complex. | Birkle F, Morrissey JH | Journal of thrombosis and haemostasis : JTH | 32885882 | J Thromb Haemost | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32885882 |
| Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane. | Gorgun D, Lihan M, Kapoor K, Tajkhorshid E | Biophysical journal | 33675757 | Biophys J | 2021 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/33675757 |
| Stoichiometric analysis reveals a unique phosphatidylserine binding site in coagulation factor X. | Paul D, Morrissey JH | Journal of thrombosis and haemostasis : JTH | 34894064 | J Thromb Haemost | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34894064 |
| Molecular View into Preferential Binding of the Factor VII Gla Domain to Phosphatidic Acid. | Muller MP, Morrissey JH, Tajkhorshid E | Biochemistry | 35853076 | Biochemistry | 2022 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/35853076 |
| Fungicidal amphotericin B sponges are assemblies of staggered asymmetric homodimers encasing large void volumes. | Lewandowska A, Soutar CP, Greenwood AI, Nimerovsky E, De Lio AM, Holler JT, Hisao GS, Khandelwal A, Zhang J, SantaMaria AM, Schwieters CD, Pogorelov TV, Burke MD, Rienstra CM | Nature structural & molecular biology | 34887566 | Nat Struct Mol Biol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34887566 |
| Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. | Galles GD, Infield DT, Clark CJ, Hemshorn ML, Manikandan S, Fazan F, Rasouli A, Tajkhorshid E, Galpin JD, Cooley RB, Mehl RA, Ahern CA | Nature communications | 36599844 | Nat Commun | 2023 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/36599844 |
| Structures of the TMC-1 complex illuminate mechanosensory transduction. | Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, Gouaux E | Nature | 36224384 | Nature | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36224384 |
| Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. | Le LTM, Thompson JR, Dehghani-Ghahnaviyeh S, Pant S, Dang PX, French JB, Kanikeyo T, Tajkhorshid E, Alam A | The EMBO journal | 36484366 | EMBO J | 2023 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/36484366 |
| Cross polarization stability in multidimensional NMR spectroscopy of biological solids. | Harding BD, Barclay AM, Piehl DW, Hiett A, Warmuth OA, Han R, Henzler-Wildman K, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 38991266 | J Magn Reson | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38991266 |
| Charge, Hydrophobicity, and Lipid Type Drive Antimicrobial Peptides' Unique Perturbation Ensembles. | Cheng KJ, Shastry S, Campolargo JD, Hallock MJ, Pogorelov TV | Biochemistry | 40105792 | Biochemistry | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40105792 |
| Direct protein-lipid interactions shape the conformational landscape of secondary transporters. | Martens C, Shekhar M, Borysik AJ, Lau AM, Reading E, Tajkhorshid E, Booth PJ, Politis A | Nature communications | 30297844 | Nat Commun | 2018 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/30297844 |
| Structure of the alternative complex III in a supercomplex with cytochrome oxidase. | Sun C, Benlekbir S, Venkatakrishnan P, Wang Y, Hong S, Hosler J, Tajkhorshid E, Rubinstein JL, Gennis RB | Nature | 29695868 | Nature | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29695868 |
| Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane. | Hallock MJ, Greenwood AI, Wang Y, Morrissey JH, Tajkhorshid E, Rienstra CM, Pogorelov TV | Biochemistry | 30456950 | Biochemistry | 2018 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/30456950 |
| Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. | Kumar P, Wang Y, Zhang Z, Zhao Z, Cymes GD, Tajkhorshid E, Grosman C | Proceedings of the National Academy of Sciences of the United States of America | 31911476 | Proc Natl Acad Sci U S A | 2020 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/31911476 |
| Peridinin Is an Exceptionally Potent and Membrane-Embedded Inhibitor of Bilayer Lipid Peroxidation. | Haley HMS, Hill AG, Greenwood AI, Woerly EM, Rienstra CM, Burke MD | Journal of the American Chemical Society | 30388000 | J Am Chem Soc | 2018 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/30388000 |
| A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca(2+)-activated Cl(-) channel ANO1 (TMEM16A). | Yu K, Jiang T, Cui Y, Tajkhorshid E, Hartzell HC | Proceedings of the National Academy of Sciences of the United States of America | 31515451 | Proc Natl Acad Sci U S A | 2019 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/31515451 |
| Relationship among egg quality traits in Japanese quails and prediction of egg weight and color using data mining algorithms. | Çelik Ş, Eyduran E, Şengül AY, Şengül T | Tropical animal health and production | 34195902 | Trop Anim Health Prod | 2021 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/34195902 |
| Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. | Wu Q, Akhter A, Pant S, Cho E, Zhu JX, Garner A, Ohyama T, Tajkhorshid E, van Meyel DJ, Ryan RM | The Journal of clinical investigation | 35167492 | J Clin Invest | 2022 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/35167492 |
| Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1. | Soubias O, Pant S, Heinrich F, Zhang Y, Roy NS, Li J, Jian X, Yohe ME, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA | Science advances | 32998886 | Sci Adv | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32998886 |
| Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter. | Jia R, Martens C, Shekhar M, Pant S, Pellowe GA, Lau AM, Findlay HE, Harris NJ, Tajkhorshid E, Booth PJ, Politis A | Nature communications | 33268777 | Nat Commun | 2020 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/33268777 |
| Conformational changes in the nucleotide-binding domains of P-glycoprotein induced by ATP hydrolysis. | Dehghani-Ghahnaviyeh S, Kapoor K, Tajkhorshid E | FEBS letters | 33159693 | FEBS Lett | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33159693 |
| A cancer mutation promotes EphA4 oligomerization and signaling by altering the conformation of the SAM domain. | Light TP, Gomez-Soler M, Wang Z, Karl K, Zapata-Mercado E, Gehring MP, Lechtenberg BC, Pogorelov TV, Hristova K, Pasquale EB | The Journal of biological chemistry | 34139238 | J Biol Chem | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34139238 |
| Membrane-bound model of the ternary complex between factor VIIa/tissue factor and factor X. | Muller MP, Mortenson A, Sedzro JC, Wen PC, Morrissey JH, Tajkhorshid E | Blood advances | 39671302 | Blood Adv | 2025 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/39671302 |
| Atomistic characterization of β2-glycoprotein I domain V interaction with anionic membranes. | Hasdemir HS, Pozzi N, Tajkhorshid E | Journal of thrombosis and haemostasis : JTH | 39047943 | J Thromb Haemost | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39047943 |
| Cholesterol-targeting Wnt-β-catenin signaling inhibitors for colorectal cancer. | Sharma A, Zalejski J, Bendre SV, Kavrokova S, Hasdemir HS, Ozgulbas DG, Sun J, Pathmasiri KC, Shi R, Aloulou A, Berkley K, Delisle CF, Wang Y, Weisser E, Buweneka P, Pierre-Jacques D, Mukherjee S, Abbasi DA, Lee D, Wang B, Gevorgyan V, Cologna SM, Tajkhorshid E, Nelson ER, Cho W | Nature chemical biology | 40240631 | Nat Chem Biol | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40240631 |
| Topological Learning Approach to Characterizing Biological Membranes. | Arango AS, Park H, Tajkhorshid E | Journal of chemical information and modeling | 38912752 | J Chem Inf Model | 2024 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/38912752 |
| Solid-State NMR (13)C sensitivity at high magnetic field. | Han R, Borcik CG, Wang S, Warmuth OA, Geohring K, Mullen C, Incitti M, Stringer JA, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 38991265 | J Magn Reson | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38991265 |
| Phosphatidylthreonine is a procoagulant lipid detected in human blood and elevated in coronary artery disease. | Hajeyah AA, Protty MB, Paul D, Costa D, Omidvar N, Morgan B, Iwasaki Y, McGill B, Jenkins PV, Yousef Z, Allen-Redpath K, Soyama S, Choudhury A, Mitra R, Yaqoob P, Morrissey JH, Collins PW, O'Donnell VB | Journal of lipid research | 38103786 | J Lipid Res | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38103786 |
| Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. | Lihan M, Tajkhorshid E | Journal of chemical information and modeling | 38844760 | J Chem Inf Model | 2024 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/38844760 |
| Probing the role of membrane in neutralizing activity of antibodies against influenza virus. | Ozgulbas DG, Tan TJC, Wen PC, Teo QW, Lv H, Ghaemi Z, Frank M, Wu NC, Tajkhorshid E | Structure (London, England : 1993) | 41421345 | Structure | 2026 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/41421345 |
| High prevalence of clonal monoallelic expression. | Vigneau S, Vinogradova S, Savova V, Gimelbrant A | Nature genetics | 30082785 | Nat Genet | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30082785 |
| Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene. | Liu XS, Wu H, Krzisch M, Wu X, Graef J, Muffat J, Hnisz D, Li CH, Yuan B, Xu C, Li Y, Vershkov D, Cacace A, Young RA, Jaenisch R | Cell | 29456084 | Cell | 2018 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/29456084 |
| Establishment of human pluripotent stem cell-derived pancreatic β-like cells in the mouse pancreas. | Ma H, Wert KJ, Shvartsman D, Melton DA, Jaenisch R | Proceedings of the National Academy of Sciences of the United States of America | 29599125 | Proc Natl Acad Sci U S A | 2018 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/29599125 |
| RNA sequencing-based screen for reactivation of silenced alleles of autosomal genes. | Gupta S, Lafontaine DL, Vigneau S, Mendelevich A, Vinogradova S, Igarashi KJ, Bortvin A, Alves-Pereira CF, Nag A, Gimelbrant AA | G3 (Bethesda, Md.) | 35100361 | G3 (Bethesda) | 2022 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/35100361 |
| Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. | Mendelevich A, Gupta S, Pakharev A, Teodosiadis A, Mironov AA, Gimelbrant AA | bioRxiv : the preprint server for biology | 36798258 | bioRxiv | 2023 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/36798258 |
| Lipid peroxidation and type I interferon coupling fuels pathogenic macrophage activation causing tuberculosis susceptibility. | Yabaji SM, Zhernovkov V, Araveti PB, Lata S, Rukhlenko OS, Abdullatif SA, Vanvalkenburg A, Alekseyev YO, Ma Q, Dayama G, Lau NC, Johnson WE, Bishai WR, Crossland NA, Campbell JD, Kholodenko BN, Gimelbrant AA, Kobzik L, Kramnik I | eLife | 41037321 | Elife | 2025 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/41037321 |
| Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias. | Dunford A, Weinstock DM, Savova V, Schumacher SE, Cleary JP, Yoda A, Sullivan TJ, Hess JM, Gimelbrant AA, Beroukhim R, Lawrence MS, Getz G, Lane AA | Nature genetics | 27869828 | Nat Genet | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27869828 |
| Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders. | Savova V, Vinogradova S, Pruss D, Gimelbrant AA, Weiss LA | Molecular psychiatry | 28265118 | Mol Psychiatry | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28265118 |
| Editing DNA Methylation in the Mammalian Genome. | Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Dadon D, Young RA, Jaenisch R | Cell | 27662091 | Cell | 2016 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/27662091 |
| Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. | Mendelevich A, Gupta S, Pakharev A, Teodosiadis A, Mironov AA, Gimelbrant AA | Bioinformatics (Oxford, England) | 37387154 | Bioinformatics | 2023 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/37387154 |
| Replicate sequencing libraries are important for quantification of allelic imbalance. | Mendelevich A, Vinogradova S, Gupta S, Mironov AA, Sunyaev SR, Gimelbrant AA | Nature communications | 34099647 | Nat Commun | 2021 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/34099647 |
| dbMAE: the database of autosomal monoallelic expression. | Savova V, Patsenker J, Vigneau S, Gimelbrant AA | Nucleic acids research | 26503248 | Nucleic Acids Res | 2016 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/26503248 |
| 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 |
| Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs. | Song Y, van den Berg PR, Markoulaki S, Soldner F, Dall'Agnese A, Henninger JE, Drotar J, Rosenau N, Cohen MA, Young RA, Semrau S, Stelzer Y, Jaenisch R | Molecular cell | 31422875 | Mol Cell | 2019 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/31422875 |
| Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility. | Yabaji SM, Zhernovkov V, Araveti PB, Lata S, Rukhlenko OS, Abdullatif SA, Vanvalkenburg A, Alekseev Y, Ma Q, Dayama G, Lau NC, Johnson WE, Bishai WR, Crossland NA, Campbell JD, Kholodenko BN, Gimelbrant AA, Kobzik L, Kramnik I | bioRxiv : the preprint server for biology | 38496444 | bioRxiv | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/38496444 |
| Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages. | Yabaji SM, Rukhlenko OS, Chatterjee S, Bhattacharya B, Wood E, Kasaikina M, Kholodenko BN, Gimelbrant AA, Kramnik I | Science advances | 37756395 | Sci Adv | 2023 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/37756395 |
| Value-Based Standards Guide Sexism Inferences for Self and Others. | Mitamura C, Erickson L, Devine PG | Journal of experimental social psychology | 29230069 | J Exp Soc Psychol | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29230069 |
| Laughter and the Management of Divergent Positions in Peer Review Interactions. | Raclaw J, Ford CE | Journal of pragmatics | 29170594 | J Pragmat | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/29170594 |
| Women Are Less Likely Than Men to Be Full Professors in Cardiology: Why Does This Happen and How Can We Fix It? | Carnes M, Bairey Merz CN | Circulation | 28153988 | Circulation | 2017 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/28153988 |
| Inferences About Sexual Orientation: The Roles of Stereotypes, Faces, and The Gaydar Myth. | Cox WT, Devine PG, Bischmann AA, Hyde JS | Journal of sex research | 26219212 | J Sex Res | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26219212 |
| The motivation to express prejudice. | Forscher PS, Cox WT, Graetz N, Devine PG | Journal of personality and social psychology | 26479365 | J Pers Soc Psychol | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26479365 |
| Stereotypes possess heterogeneous directionality: a theoretical and empirical exploration of stereotype structure and content. | Cox WT, Devine PG | PloS one | 25811181 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25811181 |
| A quantitative linguistic analysis of National Institutes of Health R01 application critiques from investigators at one institution. | Kaatz A, Magua W, Zimmerman DR, Carnes M | Academic medicine : journal of the Association of American Medical Colleges | 25140529 | Acad Med | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25140529 |
| A Psychological Profile of the Alt-Right. | Forscher PS, Kteily NS | Perspectives on psychological science : a journal of the Association for Psychological Science | 31747343 | Perspect Psychol Sci | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31747343 |
| Low agreement among reviewers evaluating the same NIH grant applications. | Pier EL, Brauer M, Filut A, Kaatz A, Raclaw J, Nathan MJ, Ford CE, Carnes M | Proceedings of the National Academy of Sciences of the United States of America | 29507248 | Proc Natl Acad Sci U S A | 2018 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/29507248 |
| Parents' Expectations for and Reactions to Children's Racial Biases. | Scott KE, Shutts K, Devine PG | Child development | 30825398 | Child Dev | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/30825398 |
| Providing Epistemic Support For Assessments Through Mobile-Supported Sharing Activities. | Raclaw J, Robles JS, DiDomenico SM | Research on language and social interaction | 28936031 | Res Lang Soc Interact | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28936031 |
| Are Female Applicants Disadvantaged in National Institutes of Health Peer Review? Combining Algorithmic Text Mining and Qualitative Methods to Detect Evaluative Differences in R01 Reviewers' Critiques. | Magua W, Zhu X, Bhattacharya A, Filut A, Potvien A, Leatherberry R, Lee YG, Jens M, Malikireddy D, Carnes M, Kaatz A | Journal of women's health (2002) | 28281870 | J Womens Health (Larchmt) | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28281870 |
| A Gender Bias Habit-Breaking Intervention Led to Increased Hiring of Female Faculty in STEMM Departments. | Devine PG, Forscher PS, Cox WTL, Kaatz A, Sheridan J, Carnes M | Journal of experimental social psychology | 29249837 | J Exp Soc Psychol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29249837 |
| Laughter and the Chair: Social Pressures Influencing Scoring During Grant Peer Review Meetings. | Pier EL, Raclaw J, Carnes M, Ford CE, Kaatz A | Journal of general internal medicine | 30604119 | J Gen Intern Med | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30604119 |
| Breaking the prejudice habit: Mechanisms, timecourse, and longevity. | Forscher PS, Mitamura C, Dix EL, Cox WTL, Devine PG | Journal of experimental social psychology | 29225371 | J Exp Soc Psychol | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29225371 |
| Fair Play: A Study of Scientific Workforce Trainers' Experience Playing an Educational Video Game about Racial Bias. | Kaatz A, Carnes M, Gutierrez B, Savoy J, Samuel C, Filut A, Pribbenow CM | CBE life sciences education | 28450447 | CBE Life Sci Educ | 2017 Summer | https://www.ncbi.nlm.nih.gov/pubmed/28450447 |
| Write More Articles, Get More Grants: The Impact of Department Climate on Faculty Research Productivity. | Sheridan J, Savoy JN, Kaatz A, Lee YG, Filut A, Carnes M | Journal of women's health (2002) | 28375751 | J Womens Health (Larchmt) | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28375751 |
| 'Your comments are meaner than your score': score calibration talk influences intra- and inter-panel variability during scientific grant peer review. | Pier EL, Raclaw J, Kaatz A, Brauer M, Carnes M, Nathan MJ, Ford CE | Research Evaluation | 28458466 | Res Eval | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28458466 |
| Analysis of National Institutes of Health R01 Application Critiques, Impact, and Criteria Scores: Does the Sex of the Principal Investigator Make a Difference? | Kaatz A, Lee YG, Potvien A, Magua W, Filut A, Bhattacharya A, Leatherberry R, Zhu X, Carnes M | Academic medicine : journal of the Association of American Medical Colleges | 27276003 | Acad Med | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27276003 |
| Advancing Women's Health and Women's Leadership With Endowed Chairs in Women's Health. | Carnes M, Johnson P, Klein W, Jenkins M, Bairey Merz CN | Academic medicine : journal of the Association of American Medical Colleges | 27759706 | Acad Med | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27759706 |
| Who Resembles a Scientific Leader-Jack or Jill? How Implicit Bias Could Influence Research Grant Funding. | Kolehmainen C, Carnes M | Circulation | 29459461 | Circulation | 2018 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/29459461 |
| Patterns of Feedback on the Bridge to Independence: A Qualitative Thematic Analysis of NIH Mentored Career Development Award Application Critiques. | Kaatz A, Dattalo M, Regner C, Filut A, Carnes M | Journal of women's health (2002) | 26418619 | J Womens Health (Larchmt) | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26418619 |
| Stuck in the out-group: Jennifer can't grow up, Jane's invisible, and Janet's over the hill. | Kaatz A, Carnes M | Journal of women's health (2002) | 24844292 | J Womens Health (Larchmt) | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24844292 |
| Threats to objectivity in peer review: the case of gender. | Kaatz A, Gutierrez B, Carnes M | Trends in pharmacological sciences | 25086743 | Trends Pharmacol Sci | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25086743 |
| Little race or gender bias in an experiment of initial review of NIH R01 grant proposals. | Forscher PS, Cox WTL, Brauer M, Devine PG | Nature human behaviour | 30953009 | Nat Hum Behav | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30953009 |
| A meta-analysis of procedures to change implicit measures. | Forscher PS, Lai CK, Axt JR, Ebersole CR, Herman M, Devine PG, Nosek BA | Journal of personality and social psychology | 31192631 | J Pers Soc Psychol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31192631 |
| Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets. | Farazi TA, Ten Hoeve JJ, Brown M, Mihailovic A, Horlings HM, van de Vijver MJ, Tuschl T, Wessels LF | Genome biology | 24398324 | Genome Biol | 2014 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/24398324 |
| A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer. | Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ | Molecular cell | 24486018 | Mol Cell | 2014 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/24486018 |
| Structural basis for molecular discrimination by a 3',3'-cGAMP sensing riboswitch. | Ren A, Wang XC, Kellenberger CA, Rajashankar KR, Jones RA, Hammond MC, Patel DJ | Cell reports | 25818298 | Cell Rep | 2015 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/25818298 |
| omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data. | Drewe-Boss P, Wessels HH, Ohler U | Genome biology | 30384847 | Genome Biol | 2018 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/30384847 |
| 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 |
| Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. | Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S | Cell | 28985564 | Cell | 2017 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/28985564 |
| The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. | Garzia A, Jafarnejad SM, Meyer C, Chapat C, Gogakos T, Morozov P, Amiri M, Shapiro M, Molina H, Tuschl T, Sonenberg N | Nature communications | 28685749 | Nat Commun | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28685749 |
| Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. | Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM | Nature communications | 30824702 | Nat Commun | 2019 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/30824702 |
| Multicolor microRNA FISH effectively differentiates tumor types. | Renwick N, Cekan P, Masry PA, McGeary SE, Miller JB, Hafner M, Li Z, Mihailovic A, Morozov P, Brown M, Gogakos T, Mobin MB, Snorrason EL, Feilotter HE, Zhang X, Perlis CS, Wu H, Suárez-Fariñas M, Feng H, Shuda M, Moore PS, Tron VA, Chang Y, Tuschl T | The Journal of clinical investigation | 23728175 | J Clin Invest | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23728175 |
| Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice. | Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y, Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T, Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ, Glickman JF, Ascano M | Nature communications | 28963528 | Nat Commun | 2017 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/28963528 |
| The G3BP1-Family-USP10 Deubiquitinase Complex Rescues Ubiquitinated 40S Subunits of Ribosomes Stalled in Translation from Lysosomal Degradation. | Meyer C, Garzia A, Morozov P, Molina H, Tuschl T | Molecular cell | 31981475 | Mol Cell | 2020 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/31981475 |
| Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. | Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ | Cell reports | 29996105 | Cell Rep | 2018 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/29996105 |
| Deciphering human ribonucleoprotein regulatory networks. | Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U | Nucleic acids research | 30517751 | Nucleic Acids Res | 2019 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/30517751 |
| Global identification of functional microRNA-mRNA interactions in Drosophila. | Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U | Nature communications | 30967537 | Nat Commun | 2019 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/30967537 |
| PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease. | Yang H, Gao P, Rajashankar KR, Patel DJ | Cell | 27984729 | Cell | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27984729 |
| Simultaneous detection of the subcellular localization of RNAs and proteins in cultured cells by combined multicolor RNA-FISH and IF. | Meyer C, Garzia A, Tuschl T | Methods (San Diego, Calif.) | 27664292 | Methods | 2017 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/27664292 |
| The mRNA-bound proteome of the early fly embryo. | Wessels HH, Imami K, Baltz AG, Kolinski M, Beldovskaya A, Selbach M, Small S, Ohler U, Landthaler M | Genome research | 27197210 | Genome Res | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27197210 |
| Multi-disciplinary methods to define RNA-protein interactions and regulatory networks. | Ascano M, Gerstberger S, Tuschl T | Current opinion in genetics & development | 23453689 | Curr Opin Genet Dev | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23453689 |
| Structure and function of the bacterial decapping enzyme NudC. | Höfer K, Li S, Abele F, Frindert J, Schlotthauer J, Grawenhoff J, Du J, Patel DJ, Jäschke A | Nature chemical biology | 27428510 | Nat Chem Biol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27428510 |
| Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS. | Teplova M, Farazi TA, Tuschl T, Patel DJ | Quarterly reviews of biophysics | 26347403 | Q Rev Biophys | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26347403 |
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| Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9. | Yang H, Patel DJ | Molecular cell | 28602637 | Mol Cell | 2017 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/28602637 |
| The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression. | Meyer C, Garzia A, Mazzola M, Gerstberger S, Molina H, Tuschl T | Molecular cell | 29429924 | Mol Cell | 2018 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/29429924 |
| SSMART: sequence-structure motif identification for RNA-binding proteins. | Munteanu A, Mukherjee N, Ohler U | Bioinformatics (Oxford, England) | 29893814 | Bioinformatics | 2018 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/29893814 |
| Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation. | Xie W, Lama L, Adura C, Tomita D, Glickman JF, Tuschl T, Patel DJ | Proceedings of the National Academy of Sciences of the United States of America | 31142647 | Proc Natl Acad Sci U S A | 2019 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/31142647 |
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| Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. | Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T | RNA (New York, N.Y.) | 24860013 | RNA | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24860013 |
| DNA-guided DNA interference by a prokaryotic Argonaute. | Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, van der Oost J | Nature | 24531762 | Nature | 2014 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24531762 |
| Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. | Teplova M, Hafner M, Teplov D, Essig K, Tuschl T, Patel DJ | Genes & development | 23630077 | Genes Dev | 2013 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/23630077 |
| FMRP targets distinct mRNA sequence elements to regulate protein expression. | Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U, Tuschl T | Nature | 23235829 | Nature | 2012 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/23235829 |
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| The RNA-binding protein vigilin regulates VLDL secretion through modulation of Apob mRNA translation. | Mobin MB, Gerstberger S, Teupser D, Campana B, Charisse K, Heim MH, Manoharan M, Tuschl T, Stoffel M | Nature communications | 27665711 | Nat Commun | 2016 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/27665711 |
| Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. | Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A | Proceedings of the National Academy of Sciences of the United States of America | 26374839 | Proc Natl Acad Sci U S A | 2015 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/26374839 |
| Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. | Murn J, Teplova M, Zarnack K, Shi Y, Patel DJ | Nature structural & molecular biology | 26641712 | Nat Struct Mol Biol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26641712 |
| Global target mRNA specification and regulation by the RNA-binding protein ZFP36. | Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U | Genome biology | 24401661 | Genome Biol | 2014 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/24401661 |
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| The evolutionary journey of Argonaute proteins. | Swarts DC, Makarova K, Wang Y, Nakanishi K, Ketting RF, Koonin EV, Patel DJ, van der Oost J | Nature structural & molecular biology | 25192263 | Nat Struct Mol Biol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25192263 |
| DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs. | Yamaji M, Jishage M, Meyer C, Suryawanshi H, Der E, Yamaji M, Garzia A, Morozov P, Manickavel S, McFarland HL, Roeder RG, Hafner M, Tuschl T | Nature | 28297718 | Nature | 2017 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/28297718 |
| A Three-Enzyme Pathway with an Optimised Geometric Arrangement to Facilitate Substrate Transfer. | Liu M, Fu J, Qi X, Wootten S, Woodbury NW, Liu Y, Yan H | Chembiochem : a European journal of chemical biology | 26995014 | Chembiochem | 2016 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/26995014 |
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| Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing. | Nakatsuka N, Yang KA, Abendroth JM, Cheung KM, Xu X, Yang H, Zhao C, Zhu B, Rim YS, Yang Y, Weiss PS, Stojanović MN, Andrews AM | Science (New York, N.Y.) | 30190311 | Science | 2018 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/30190311 |
| DNA origami nanostructures can exhibit preferential renal uptake and alleviate acute kidney injury. | Jiang D, Ge Z, Im HJ, England CG, Ni D, Hou J, Zhang L, Kutyreff CJ, Yan Y, Liu Y, Cho SY, Engle JW, Shi J, Huang P, Fan C, Yan H, Cai W | Nature biomedical engineering | 30505626 | Nat Biomed Eng | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30505626 |
| INTEGRATED MICROFLUIDIC SELEX USING FREE SOLUTION ELECTROKINETICS. | Olsen TR, Tapia-Alveal C, Yang KA, Zhang X, Pereira LJ, Farmakidis N, Pei R, Stojanovic MN, Lin Q | Journal of the Electrochemical Society | 29170564 | J Electrochem Soc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29170564 |
| A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. | Li S, Jiang Q, Liu S, Zhang Y, Tian Y, Song C, Wang J, Zou Y, Anderson GJ, Han JY, Chang Y, Liu Y, Zhang C, Chen L, Zhou G, Nie G, Yan H, Ding B, Zhao Y | Nature biotechnology | 29431737 | Nat Biotechnol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29431737 |
| Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. | Simmons CR, Zhang F, MacCulloch T, Fahmi N, Stephanopoulos N, Liu Y, Seeman NC, Yan H | Journal of the American Chemical Society | 28731332 | J Am Chem Soc | 2017 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/28731332 |
| Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors. | Yang KA, Barbu M, Halim M, Pallavi P, Kim B, Kolpashchikov DM, Pecic S, Taylor S, Worgall TS, Stojanovic MN | Nature chemistry | 25343606 | Nat Chem | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25343606 |
| High-Affinity Nucleic-Acid-Based Receptors for Steroids. | Yang KA, Chun H, Zhang Y, Pecic S, Nakatsuka N, Andrews AM, Worgall TS, Stojanovic MN | ACS chemical biology | 29083858 | ACS Chem Biol | 2017 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/29083858 |
| Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation. | Li J, Green AA, Yan H, Fan C | Nature chemistry | 29064489 | Nat Chem | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29064489 |
| Autonomous molecular cascades for evaluation of cell surfaces. | Rudchenko M, Taylor S, Pallavi P, Dechkovskaia A, Khan S, Butler VP Jr, Rudchenko S, Stojanovic MN | Nature nanotechnology | 23892986 | Nat Nanotechnol | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23892986 |
| Self-Assembly of Complex DNA Tessellations by Using Low-Symmetry Multi-arm DNA Tiles. | Zhang F, Jiang S, Li W, Hunt A, Liu Y, Yan H | Angewandte Chemie (International ed. in English) | 27276237 | Angew Chem Int Ed Engl | 2016 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/27276237 |
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| Insulin Hexamer-Caged Gadolinium Ion as MRI Contrast-o-phore. | Taylor SK, Tran TH, Liu MZ, Harris PE, Sun Y, Jambawalikar SR, Tong L, Stojanovic MN | Chemistry (Weinheim an der Bergstrasse, Germany) | 29873848 | Chemistry | 2018 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/29873848 |
| Integrated Microfluidic Aptasensor for Mass Spectrometric Detection of Vasopressin in Human Plasma Ultrafiltrate. | Yang J, Zhu J, Pei R, Oliver JA, Landry DW, Stojanovic MN, Lin Q | Analytical methods : advancing methods and applications | 28090219 | Anal Methods | 2016 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/28090219 |
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| Amplification of Signal on Cell Surfaces in Molecular Cascades. | Rudchenko S, Taylor S, Milosavic N, Rudchenko M, Wedderhoff Tissi B, Mapara MY, Stojanovic MN | Cells | 38132177 | Cells | 2023 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/38132177 |
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| Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies. | Torres Cabán CC, Yang M, Lai C, Yang L, Subach FV, Smith BO, Piatkevich KD, Boyden ES | ACS sensors | 35427452 | ACS Sens | 2022 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/35427452 |
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| Impact of Hydrophilic Surfaces on Interfacial Water Dynamics Probed with NMR Spectroscopy. | Yoo H, Paranji R, Pollack GH | The journal of physical chemistry letters | 22003430 | J Phys Chem Lett | 2011 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/22003430 |
| Effect of Local and General Anesthetics on Interfacial Water. | Kundacina N, Shi M, Pollack GH | PloS one | 27054588 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27054588 |
| Particle Displacement in Aqueous Suspension Arising from Incident Radiant Energy. | Kimura KW, Pollack GH | Langmuir : the ACS journal of surfaces and colloids | 26335979 | Langmuir | 2015 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/26335979 |
| A peptide tag system for facile purification and single-molecule immobilization. | Huang J, Nagy SS, Koide A, Rock RS, Koide S | Biochemistry | 19928925 | Biochemistry | 2009 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/19928925 |
| Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design. | Gilbreth RN, Truong K, Madu I, Koide A, Wojcik JB, Li NS, Piccirilli JA, Chen Y, Koide S | Proceedings of the National Academy of Sciences of the United States of America | 21518904 | Proc Natl Acad Sci U S A | 2011 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/21518904 |
| Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. | Huang J, Makabe K, Biancalana M, Koide A, Koide S | Journal of molecular biology | 19646997 | J Mol Biol | 2009 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/19646997 |
| Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. | Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nie R, Koide S | Proceedings of the National Academy of Sciences of the United States of America | 23341609 | Proc Natl Acad Sci U S A | 2013 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/23341609 |
| Affinity maturation of single-domain antibodies by yeast surface display. | Koide A, Koide S | Methods in molecular biology (Clifton, N.J.) | 22886267 | Methods Mol Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22886267 |
| Structural insights for engineering binding proteins based on non-antibody scaffolds. | Gilbreth RN, Koide S | Current opinion in structural biology | 22749196 | Curr Opin Struct Biol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22749196 |
| Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation. | Yasui N, Findlay GM, Gish GD, Hsiung MS, Huang J, Tucholska M, Taylor L, Smith L, Boldridge WC, Koide A, Pawson T, Koide S | Molecular cell | 24910098 | Mol Cell | 2014 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/24910098 |
| Architecture of the fungal nuclear pore inner ring complex. | Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A | Science (New York, N.Y.) | 26316600 | Science | 2015 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/26316600 |
| Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface. | Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, Hantschel O, Koide S | The Journal of biological chemistry | 26912659 | J Biol Chem | 2016 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/26912659 |
| Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. | Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, Seeliger M, Koide S, Hantschel O | Journal of molecular biology | 28347651 | J Mol Biol | 2017 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/28347651 |
| Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. | Koide S | Current opinion in biotechnology | 19700302 | Curr Opin Biotechnol | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19700302 |
| Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3). | Koide S, Koide A, Lipovšek D | Methods in enzymology | 22230568 | Methods Enzymol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22230568 |
| Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. | Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S | Journal of molecular biology | 22198408 | J Mol Biol | 2012 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/22198408 |
| ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. | Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J | eLife | 26523391 | Elife | 2015 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/26523391 |
| Inhibition of RAS function through targeting an allosteric regulatory site. | Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, Santana D, Gupta A, Jacobs M, Herrero-Garcia E, Cobbert J, Lavoie H, Smith M, Rajakulendran T, Dowdell E, Okur MN, Dementieva I, Sicheri F, Therrien M, Hancock JF, Ikura M, Koide S, O'Bryan JP | Nature chemical biology | 27820802 | Nat Chem Biol | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27820802 |
| Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase. | Reckel S, Gehin C, Tardivon D, Georgeon S, Kükenshöner T, Löhr F, Koide A, Buchner L, Panjkovich A, Reynaud A, Pinho S, Gerig B, Svergun D, Pojer F, Güntert P, Dötsch V, Koide S, Gavin AC, Hantschel O | Nature communications | 29235475 | Nat Commun | 2017 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/29235475 |
| Targeting the α4-α5 interface of RAS results in multiple levels of inhibition. | Spencer-Smith R, Li L, Prasad S, Koide A, Koide S, O'Bryan JP | Small GTPases | 28692342 | Small GTPases | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28692342 |
| Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery. | Huang J, Koide S | ACS chemical biology | 20143785 | ACS Chem Biol | 2010 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/20143785 |
| Generation of high-performance binding proteins for peptide motifs by affinity clamping. | Koide S, Huang J | Methods in enzymology | 23422435 | Methods Enzymol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23422435 |
| Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. | Sha F, Gencer EB, Georgeon S, Koide A, Yasui N, Koide S, Hantschel O | Proceedings of the National Academy of Sciences of the United States of America | 23980151 | Proc Natl Acad Sci U S A | 2013 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/23980151 |
| Allosteric modulation of a human protein kinase with monobodies. | Zorba A, Nguyen V, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S, Kern D | Proceedings of the National Academy of Sciences of the United States of America | 31239342 | Proc Natl Acad Sci U S A | 2019 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/31239342 |
| Backbone dynamics of cyclotide MCoTI-I free and complexed with trypsin. | Puttamadappa SS, Jagadish K, Shekhtman A, Camarero JA | Angewandte Chemie (International ed. in English) | 20715250 | Angew Chem Int Ed Engl | 2010 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/20715250 |
| Photomodulation of protein trans-splicing through backbone photocaging of the DnaE split intein. | Berrade L, Kwon Y, Camarero JA | Chembiochem : a European journal of chemical biology | 20512791 | Chembiochem | 2010 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/20512791 |
| Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery. | Gould A, Ji Y, Aboye TL, Camarero JA | Current pharmaceutical design | 22204428 | Curr Pharm Des | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22204428 |
| Recombinant production of rhesus θ-defensin-1 (RTD-1) using a bacterial expression system. | Gould A, Li Y, Majumder S, Garcia AE, Carlsson P, Shekhtman A, Camarero JA | Molecular bioSystems | 22327102 | Mol Biosyst | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22327102 |
| Design of a novel cyclotide-based CXCR4 antagonist with anti-human immunodeficiency virus (HIV)-1 activity. | Aboye TL, Ha H, Majumder S, Christ F, Debyser Z, Shekhtman A, Neamati N, Camarero JA | Journal of medicinal chemistry | 23151033 | J Med Chem | 2012 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/23151033 |
| Rapid parallel synthesis of bioactive folded cyclotides by using a tea-bag approach. | Aboye T, Kuang Y, Neamati N, Camarero JA | Chembiochem : a European journal of chemical biology | 25663016 | Chembiochem | 2015 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/25663016 |
| Expression of fluorescent cyclotides using protein trans-splicing for easy monitoring of cyclotide-protein interactions. | Jagadish K, Borra R, Lacey V, Majumder S, Shekhtman A, Wang L, Camarero JA | Angewandte Chemie (International ed. in English) | 23322720 | Angew Chem Int Ed Engl | 2013 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/23322720 |
| Chemical and biological production of cyclotides. | Li Y, Bi T, Camarero JA | Advances in botanical research | 27064329 | Adv Bot Res | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/27064329 |
| Cyclotides, a versatile ultrastable micro-protein scaffold for biotechnological applications. | Camarero JA | Bioorganic & medicinal chemistry letters | 29110985 | Bioorg Med Chem Lett | 2017 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/29110985 |
| In-cell production of a genetically-encoded library based on the θ-defensin RTD-1 using a bacterial expression system. | Bi T, Li Y, Shekhtman A, Camarero JA | Bioorganic & medicinal chemistry | 28927803 | Bioorg Med Chem | 2018 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/28927803 |
| In vivo activation of the p53 tumor suppressor pathway by an engineered cyclotide. | Ji Y, Majumder S, Millard M, Borra R, Bi T, Elnagar AY, Neamati N, Shekhtman A, Camarero JA | Journal of the American Chemical Society | 23848581 | J Am Chem Soc | 2013 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/23848581 |
| In-cell fluorescence activation and labeling of proteins mediated by FRET-quenched split inteins. | Borra R, Dong D, Elnagar AY, Woldemariam GA, Camarero JA | Journal of the American Chemical Society | 22404648 | J Am Chem Soc | 2012 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/22404648 |
| Efficient one-pot cyclization/folding of Rhesus θ-defensin-1 (RTD-1). | Aboye TL, Li Y, Majumder S, Hao J, Shekhtman A, Camarero JA | Bioorganic & medicinal chemistry letters | 22425570 | Bioorg Med Chem Lett | 2012 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/22425570 |
| Expressed protein ligation: a resourceful tool to study protein structure and function. | Berrade L, Camarero JA | Cellular and molecular life sciences : CMLS | 19685006 | Cell Mol Life Sci | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19685006 |
| Biological activities of natural and engineered cyclotides, a novel molecular scaffold for peptide-based therapeutics. | Garcia AE, Camarero JA | Current molecular pharmacology | 20858197 | Curr Mol Pharmacol | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20858197 |
| Legume cyclotides shed light on the genetic origin of knotted circular proteins. | Camarero JA | Proceedings of the National Academy of Sciences of the United States of America | 21653883 | Proc Natl Acad Sci U S A | 2011 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/21653883 |
| Efficient recombinant expression of SFTI-1 in bacterial cells using intein-mediated protein trans-splicing. | Li Y, Aboye T, Breindel L, Shekhtman A, Camarero JA | Biopolymers | 27178003 | Biopolymers | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27178003 |
| Design of a MCoTI-Based Cyclotide with Angiotensin (1-7)-Like Activity. | Aboye T, Meeks CJ, Majumder S, Shekhtman A, Rodgers K, Camarero JA | Molecules (Basel, Switzerland) | 26821010 | Molecules | 2016 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/26821010 |
| Recombinant Expression of Cyclotides Using Split Inteins. | Jagadish K, Camarero JA | Methods in molecular biology (Clifton, N.J.) | 27714609 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/27714609 |
| Protein Chemical Modification Inside Living Cells Using Split Inteins. | Borra R, Camarero JA | Methods in molecular biology (Clifton, N.J.) | 27714613 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/27714613 |
| In vivo Evaluation of an Engineered Cyclotide as Specific CXCR4 Imaging Reagent. | Lesniak WG, Aboye T, Chatterjee S, Camarero JA, Nimmagadda S | Chemistry (Weinheim an der Bergstrasse, Germany) | 28771849 | Chemistry | 2017 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/28771849 |
| In vivo biosynthesis of an Ala-scan library based on the cyclic peptide SFTI-1. | Austin J, Kimura RH, Woo YH, Camarero JA | Amino acids | 19685144 | Amino Acids | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/19685144 |
| Optimizing the future for biotechnology therapies, the key role of protein engineering. | Camarero JA | Advanced drug delivery reviews | 19735684 | Adv Drug Deliv Rev | 2009 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/19735684 |
| "Splicing up" drug discovery. Cell-based expression and screening of genetically-encoded libraries of backbone-cyclized polypeptides. | Sancheti H, Camarero JA | Advanced drug delivery reviews | 19628015 | Adv Drug Deliv Rev | 2009 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/19628015 |
| Cyclotides, a promising molecular scaffold for peptide-based therapeutics. | Jagadish K, Camarero JA | Biopolymers | 20564025 | Biopolymers | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20564025 |
| Recombinant expression of backbone-cyclized polypeptides. | Borra R, Camarero JA | Biopolymers | 23893781 | Biopolymers | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23893781 |
| Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. | Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D | Frontiers in chemistry | 25905098 | Front Chem | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25905098 |
| Recombinant Expression and Phenotypic Screening of a Bioactive Cyclotide Against α-Synuclein-Induced Cytotoxicity in Baker's Yeast. | Jagadish K, Gould A, Borra R, Majumder S, Mushtaq Z, Shekhtman A, Camarero JA | Angewandte Chemie (International ed. in English) | 26096948 | Angew Chem Int Ed Engl | 2015 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/26096948 |
| Biosynthesis and biological screening of a genetically encoded library based on the cyclotide MCoTI-I. | Austin J, Wang W, Puttamadappa S, Shekhtman A, Camarero JA | Chembiochem : a European journal of chemical biology | 19780078 | Chembiochem | 2009 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/19780078 |
| Protein microarrays: novel developments and applications. | Berrade L, Garcia AE, Camarero JA | Pharmaceutical research | 21116694 | Pharm Res | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21116694 |
| Biological synthesis of circular polypeptides. | Aboye TL, Camarero JA | The Journal of biological chemistry | 22707722 | J Biol Chem | 2012 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/22707722 |
| Biosynthesis and antimicrobial evaluation of backbone-cyclized α-defensins. | Garcia AE, Tai KP, Puttamadappa SS, Shekhtman A, Ouellette AJ, Camarero JA | Biochemistry | 22040603 | Biochemistry | 2011 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/22040603 |
| Cellular uptake of cyclotide MCoTI-I follows multiple endocytic pathways. | Contreras J, Elnagar AY, Hamm-Alvarez SF, Camarero JA | Journal of controlled release : official journal of the Controlled Release Society | 21906641 | J Control Release | 2011 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/21906641 |
| Cyclotides: Overview and Biotechnological Applications. | Gould A, Camarero JA | Chembiochem : a European journal of chemical biology | 28544675 | Chembiochem | 2017 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/28544675 |
| Full Sequence Amino Acid Scanning of θ-Defensin RTD-1 Yields a Potent Anthrax Lethal Factor Protease Inhibitor. | Li Y, Gould A, Aboye T, Bi T, Breindel L, Shekhtman A, Camarero JA | Journal of medicinal chemistry | 28151653 | J Med Chem | 2017 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/28151653 |
| Intein applications: from protein purification and labeling to metabolic control methods. | Wood DW, Camarero JA | The Journal of biological chemistry | 24700459 | J Biol Chem | 2014 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/24700459 |
| Insights into the molecular flexibility of θ-defensins by NMR relaxation analysis. | Conibear AC, Wang CK, Bi T, Rosengren KJ, Camarero JA, Craik DJ | The journal of physical chemistry. B | 25375365 | J Phys Chem B | 2014 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/25375365 |
| Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions. | Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT | PLoS genetics | 24453987 | PLoS Genet | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24453987 |
| High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. | Szeto K, Reinholt SJ, Duarte FM, Pagano JM, Ozer A, Yao L, Lis JT, Craighead HG | Analytical and bioanalytical chemistry | 24553662 | Anal Bioanal Chem | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24553662 |
| RAPID-SELEX for RNA aptamers. | Szeto K, Latulippe DR, Ozer A, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG | PloS one | 24376564 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24376564 |
| New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. | Ozer A, Pagano JM, Lis JT | Molecular therapy. Nucleic acids | 25093707 | Mol Ther Nucleic Acids | 2014 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/25093707 |
| Novel strategy for selection of monoclonal antibodies against highly conserved antigens: phage library panning against ephrin-B2 displayed on yeast. | Gu X, Vedvyas Y, Chen X, Kaushik T, Hwang CI, Hu X, Nikitin AY, Jin MM | PloS one | 22292016 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22292016 |
| Self-assembled nanoplatform for targeted delivery of chemotherapy agents via affinity-regulated molecular interactions. | Park S, Kang S, Veach AJ, Vedvyas Y, Zarnegar R, Kim JY, Jin MM | Biomaterials | 20667589 | Biomaterials | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20667589 |
| Cell surface assembly of HIV gp41 six-helix bundles for facile, quantitative measurements of hetero-oligomeric interactions. | Hu X, Saha P, Chen X, Kim D, Devarasetty M, Varadarajan R, Jin MM | Journal of the American Chemical Society | 22888993 | J Am Chem Soc | 2012 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/22888993 |
| Structural basis for conformational switching and GTP loading of the large G protein atlastin. | Byrnes LJ, Singh A, Szeto K, Benvin NM, O'Donnell JP, Zipfel WR, Sondermann H | The EMBO journal | 23334294 | EMBO J | 2013 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/23334294 |
| Multiplexed microcolumn-based process for efficient selection of RNA aptamers. | Latulippe DR, Szeto K, Ozer A, Duarte FM, Kelly CV, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG | Analytical chemistry | 23398198 | Anal Chem | 2013 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/23398198 |
| Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection. | Ozer A, White BS, Lis JT, Shalloway D | Nucleic acids research | 23737446 | Nucleic Acids Res | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23737446 |
| Discovering aptamers by cell-SELEX against human soluble growth factors ectopically expressed on yeast cell surface. | Meng HW, Pagano JM, White BS, Toyoda Y, Min IM, Craighead HG, Shalloway D, Lis JT, Xiao K, Jin MM | PloS one | 24675636 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24675636 |
| Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling. | Ozer A, Tome JM, Friedman RC, Gheba D, Schroth GP, Lis JT | Nature protocols | 26182240 | Nat Protoc | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26182240 |
| Inflamed leukocyte-mimetic nanoparticles for molecular imaging of inflammation. | Chen X, Wong R, Khalidov I, Wang AY, Leelawattanachai J, Wang Y, Jin MM | Biomaterials | 21783245 | Biomaterials | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21783245 |
| Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device. | Reinholt SJ, Ozer A, Lis JT, Craighead HG | Scientific reports | 27432610 | Sci Rep | 2016 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/27432610 |
| Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. | Tome JM, Ozer A, Pagano JM, Gheba D, Schroth GP, Lis JT | Nature methods | 24809628 | Nat Methods | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24809628 |
| What's wrong with correlative experiments? | Vilela M, Danuser G | Nature cell biology | 21892139 | Nat Cell Biol | 2011 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/21892139 |
| Myosin II controls cellular branching morphogenesis and migration in three dimensions by minimizing cell-surface curvature. | Elliott H, Fischer RS, Myers KA, Desai RA, Gao L, Chen CS, Adelstein RS, Waterman CM, Danuser G | Nature cell biology | 25621949 | Nat Cell Biol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25621949 |
| Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM. | Hinde E, Digman MA, Hahn KM, Gratton E | Proceedings of the National Academy of Sciences of the United States of America | 23248275 | Proc Natl Acad Sci U S A | 2013 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/23248275 |
| Imaging the coordination of multiple signalling activities in living cells. | Welch CM, Elliott H, Danuser G, Hahn KM | Nature reviews. Molecular cell biology | 22016058 | Nat Rev Mol Cell Biol | 2011 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/22016058 |
| Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. | Kummer L, Hsu CW, Dagliyan O, MacNevin C, Kaufholz M, Zimmermann B, Dokholyan NV, Hahn KM, Plückthun A | Chemistry & biology | 23790495 | Chem Biol | 2013 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/23790495 |
| A RhoC biosensor reveals differences in the activation kinetics of RhoA and RhoC in migrating cells. | Zawistowski JS, Sabouri-Ghomi M, Danuser G, Hahn KM, Hodgson L | PloS one | 24224016 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24224016 |
| LOVTRAP: an optogenetic system for photoinduced protein dissociation. | Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I, Yumerefendi H, Kuhlman B, Liu R, Danuser G, Hahn KM | Nature methods | 27427858 | Nat Methods | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27427858 |
| Delivery of membrane impermeable cargo into CHO cells by peptide nanoparticles targeted by a protein corona. | Dittrich C, Burckhardt CJ, Danuser G | Biomaterials | 22226586 | Biomaterials | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22226586 |
| Fluctuation analysis of activity biosensor images for the study of information flow in signaling pathways. | Vilela M, Halidi N, Besson S, Elliott H, Hahn K, Tytell J, Danuser G | Methods in enzymology | 23280114 | Methods Enzymol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23280114 |
| FRET binding antenna reports spatiotemporal dynamics of GDI-Cdc42 GTPase interactions. | Hodgson L, Spiering D, Sabouri-Ghomi M, Dagliyan O, DerMardirossian C, Danuser G, Hahn KM | Nature chemical biology | 27501396 | Nat Chem Biol | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27501396 |
| Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation. | Hinde E, Yokomori K, Gaus K, Hahn KM, Gratton E | Scientific reports | 24573109 | Sci Rep | 2014 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/24573109 |
| Manipulation of endogenous kinase activity in living cells using photoswitchable inhibitory peptides. | Yi JJ, Wang H, Vilela M, Danuser G, Hahn KM | ACS synthetic biology | 24905630 | ACS Synth Biol | 2014 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/24905630 |
| Humanin: a harbinger of mitochondrial-derived peptides? | Lee C, Yen K, Cohen P | Trends in endocrinology and metabolism: TEM | 23402768 | Trends Endocrinol Metab | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23402768 |
| IGF-I regulates the age-dependent signaling peptide humanin. | Lee C, Wan J, Miyazaki B, Fang Y, Guevara-Aguirre J, Yen K, Longo V, Bartke A, Cohen P | Aging cell | 25040290 | Aging Cell | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25040290 |
| The effects of humanin and its analogues on male germ cell apoptosis induced by chemotherapeutic drugs. | Jia Y, Ohanyan A, Lue YH, Swerdloff RS, Liu PY, Cohen P, Wang C | Apoptosis : an international journal on programmed cell death | 25666707 | Apoptosis | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25666707 |
| Rat Humanin is encoded and translated in mitochondria and is localized to the mitochondrial compartment where it regulates ROS production. | Paharkova V, Alvarez G, Nakamura H, Cohen P, Lee KW | Molecular and cellular endocrinology | 26116236 | Mol Cell Endocrinol | 2015 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/26116236 |
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| 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 |
| 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 |
| Adrenergic Signaling in Muscularis Macrophages Limits Infection-Induced Neuronal Loss. | Matheis F, Muller PA, Graves CL, Gabanyi I, Kerner ZJ, Costa-Borges D, Ahrends T, Rosenstiel P, Mucida D | Cell | 31923400 | Cell | 2020 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/31923400 |
| Enteric pathogens induce tissue tolerance and prevent neuronal loss from subsequent infections. | Ahrends T, Aydin B, Matheis F, Classon CH, Marchildon F, Furtado GC, Lira SA, Mucida D | Cell | 34717799 | Cell | 2021 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/34717799 |
| Microbiota-modulated CART(+) enteric neurons autonomously regulate blood glucose. | Muller PA, Matheis F, Schneeberger M, Kerner Z, Jové V, Mucida D | Science (New York, N.Y.) | 32855216 | Science | 2020 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/32855216 |
| Microbiota modulate sympathetic neurons via a gut-brain circuit. | Muller PA, Schneeberger M, Matheis F, Wang P, Kerner Z, Ilanges A, Pellegrino K, Del Mármol J, Castro TBR, Furuichi M, Perkins M, Han W, Rao A, Pickard AJ, Cross JR, Honda K, de Araujo I, Mucida D | Nature | 32641826 | Nature | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32641826 |
| Rationale redesign of type III secretion systems: toward the development of non-pathogenic E. coli for in vivo delivery of therapeutic payloads. | González-Prieto C, Lesser CF | Current opinion in microbiology | 29141238 | Curr Opin Microbiol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29141238 |
| Citrobacter rodentium(ϕStx2dact), a murine infection model for enterohemorrhagic Escherichia coli. | Thorpe CM, Pulsifer AR, Osburne MS, Vanaja SK, Leong JM | Current opinion in microbiology | 34929548 | Curr Opin Microbiol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34929548 |
| Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917. | Gelfat I, Aqeel Y, Tremblay JM, Jaskiewicz JJ, Shrestha A, Lee JN, Hu S, Qian X, Magoun L, Sheoran A, Bedenice D, Giem C, Manjula-Basavanna A, Pulsifer AR, Tu HX, Li X, Minus ML, Osburne MS, Tzipori S, Shoemaker CB, Leong JM, Joshi NS | PLoS pathogens | 36107831 | PLoS Pathog | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36107831 |
| In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. | Srivastava R, González-Prieto C, Lynch JP, Muscolo M, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF | bioRxiv : the preprint server for biology | 39131305 | bioRxiv | 2024 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/39131305 |
| Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut. | Lynch JP, González-Prieto C, Reeves AZ, Bae S, Powale U, Godbole NP, Tremblay JM, Schmidt FI, Ploegh HL, Kansra V, Glickman JN, Leong JM, Shoemaker CB, Garrett WS, Lesser CF | Cell host & microbe | 37003258 | Cell Host Microbe | 2023 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/37003258 |
| In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. | Srivastava R, González-Prieto C, Lynch JP, Muscolo ME, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF | PNAS nexus | 39262854 | PNAS Nexus | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39262854 |
| Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics. | Lynch JP, Goers L, Lesser CF | Trends in pharmacological sciences | 35232591 | Trends Pharmacol Sci | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35232591 |
| A host metabolite promotes Salmonella survival. | Lynch JP, Lesser CF | Science (New York, N.Y.) | 33479138 | Science | 2021 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/33479138 |
| Living Engineered Bacterial Therapeutics: Emerging Affordable Precision Interventions. | Srivastava R, Lesser CF | Microbial biotechnology | 39579048 | Microb Biotechnol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39579048 |
| PROT(3)EcT, engineered Escherichia coli for the targeted delivery of therapeutics. | González-Prieto C, Lynch JP, Lesser CF | Trends in molecular medicine | 37574350 | Trends Mol Med | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37574350 |
| Excess pancreatic elastase alters acinar-β cell communication by impairing the mechano-signaling and the PAR2 pathways. | Basile G, Vetere A, Hu J, Ijaduola O, Zhang Y, Liu KC, Eltony AM, De Jesus DF, Fukuda K, Doherty G, Leech CA, Chepurny OG, Holz GG, Yun SH, Andersson O, Choudhary A, Wagner BK, Kulkarni RN | Cell metabolism | 37339634 | Cell Metab | 2023 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/37339634 |
| Native Zinc Catalyzes Selective and Traceless Release of Small Molecules in β-Cells. | Lee M, Maji B, Manna D, Kahraman S, Elgamal RM, Small J, Kokkonda P, Vetere A, Goldberg JM, Lippard SJ, Kulkarni RN, Wagner BK, Choudhary A | Journal of the American Chemical Society | 32175731 | J Am Chem Soc | 2020 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/32175731 |
| Engineering designer beta cells with a CRISPR-Cas9 conjugation platform. | Lim D, Sreekanth V, Cox KJ, Law BK, Wagner BK, Karp JM, Choudhary A | Nature communications | 32792475 | Nat Commun | 2020 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/32792475 |
| Rational Design of Silicon-Based Zinc Ionophores. | Yamada K, Deb A, Shoba VM, Lim D, Maji B, Modell AE, Choudhary A | Angewandte Chemie (International ed. in English) | 35385189 | Angew Chem Int Ed Engl | 2022 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/35385189 |
| Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. | Andrew AL, Perry BW, Card DC, Schield DR, Ruggiero RP, McGaugh SE, Choudhary A, Secor SM, Castoe TA | BMC genomics | 28464824 | BMC Genomics | 2017 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/28464824 |
| A 3D culture platform enables development of zinc-binding prodrugs for targeted proliferation of β cells. | Yang K, Lee M, Jones PA, Liu SS, Zhou A, Xu J, Sreekanth V, Wu JLY, Vo L, Lee EA, Pop R, Lee Y, Wagner BK, Melton DA, Choudhary A, Karp JM | Science advances | 33208361 | Sci Adv | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33208361 |
| Molecular transport through primary human small intestinal monolayers by culture on a collagen scaffold with a gradient of chemical cross-linking. | Speer JE, Gunasekara DB, Wang Y, Fallon JK, Attayek PJ, Smith PC, Sims CE, Allbritton NL | Journal of biological engineering | 31061676 | J Biol Eng | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31061676 |
| Reserve Stem Cells in Intestinal Homeostasis and Injury. | Bankaitis ED, Ha A, Kuo CJ, Magness ST | Gastroenterology | 30118745 | Gastroenterology | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30118745 |
| Bioengineered Systems and Designer Matrices That Recapitulate the Intestinal Stem Cell Niche. | Wang Y, Kim R, Hinman SS, Zwarycz B, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29675459 | Cell Mol Gastroenterol Hepatol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29675459 |
| In vitro generation of self-renewing human intestinal epithelia over planar and shaped collagen hydrogels. | Hinman SS, Wang Y, Kim R, Allbritton NL | Nature protocols | 33299154 | Nat Protoc | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33299154 |
| Magnetically-propelled fecal surrogates for modeling the impact of solid-induced shear forces on primary colonic epithelial cells. | Hinman SS, Huling J, Wang Y, Wang H, Bretherton RC, DeForest CA, Allbritton NL | Biomaterials | 34412014 | Biomaterials | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34412014 |
| Design of 8-mer Peptides that Block Clostridioides difficile Toxin A in Intestinal Cells. | Sarma S, Catella CM, Pedro ETS, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK | bioRxiv : the preprint server for biology | 36711911 | bioRxiv | 2023 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/36711911 |
| "Fix and Click" for Assay of Sphingolipid Signaling in Single Primary Human Intestinal Epithelial Cells. | Gallion LA, Wang Y, Massaro A, Yao M, Petersen BV, Zhang Q, Huang W, Carr AJ, Zhang Q, Allbritton NL | Analytical chemistry | 35020354 | Anal Chem | 2022 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/35020354 |
| Efficient transgenesis and homology-directed gene targeting in monolayers of primary human small intestinal and colonic epithelial stem cells. | Breau KA, Ok MT, Gomez-Martinez I, Burclaff J, Kohn NP, Magness ST | Stem cell reports | 35523179 | Stem Cell Reports | 2022 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/35523179 |
| Preparing Chamber Slides With Pressed Collagen for Live Imaging Monolayers of Primary Human Intestinal Stem Cells. | Burclaff J, Magness ST | Bio-protocol | 39600970 | Bio Protoc | 2024 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/39600970 |
| TGFB1 induces fetal reprogramming and enhances intestinal regeneration. | Chen L, Qiu X, Dupre A, Pellon-Cardenas O, Fan X, Xu X, Rout P, Walton KD, Burclaff J, Zhang R, Fang W, Ofer R, Logerfo A, Vemuri K, Bandyopadhyay S, Wang J, Barbet G, Wang Y, Gao N, Perekatt AO, Hu W, Magness ST, Spence JR, Verzi MP | Cell stem cell | 37865088 | Cell Stem Cell | 2023 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/37865088 |
| Integrative microphysiological tissue systems of cancer metastasis to the liver. | Clark AM, Allbritton NL, Wells A | Seminars in cancer biology | 32580025 | Semin Cancer Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32580025 |
| A Monolayer of Primary Colonic Epithelium Generated on a Scaffold with a Gradient of Stiffness for Drug Transport Studies. | Gunasekara DB, Speer J, Wang Y, Nguyen DL, Reed MI, Smiddy NM, Parker JS, Fallon JK, Smith PC, Sims CE, Magness ST, Allbritton NL | Analytical chemistry | 30350627 | Anal Chem | 2018 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/30350627 |
| Butyrate consumption of differentiated colonocytes in the upper crypt promotes homeostatic proliferation of stem and progenitor cells near the crypt base. | Bultman SJ | Translational cancer research | 30568890 | Transl Cancer Res | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30568890 |
| In Vitro Generation of Mouse Colon Crypts. | Wang Y, Gunasekara DB, Attayek PJ, Reed MI, DiSalvo M, Nguyen DL, Dutton JS, Lebhar MS, Bultman SJ, Sims CE, Magness ST, Allbritton NL | ACS biomaterials science & engineering | 30854421 | ACS Biomater Sci Eng | 2017 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/30854421 |
| Recombination drives the evolution of mutational robustness. | Singhal S, Gomez SM, Burch CL | Current opinion in systems biology | 31572829 | Curr Opin Syst Biol | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31572829 |
| Building a Thick Mucus Hydrogel Layer to Improve the Physiological Relevance of In Vitro Primary Colonic Epithelial Models. | Wang Y, Kim R, Sims CE, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 31356887 | Cell Mol Gastroenterol Hepatol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31356887 |
| An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface. | Kim R, Attayek PJ, Wang Y, Furtado KL, Tamayo R, Sims CE, Allbritton NL | Biofabrication | 31519008 | Biofabrication | 2019 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/31519008 |
| Self-renewing Monolayer of Primary Colonic or Rectal Epithelial Cells. | Wang Y, DiSalvo M, Gunasekara DB, Dutton J, Proctor A, Lebhar MS, Williamson IA, Speer J, Howard RL, Smiddy NM, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29204504 | Cell Mol Gastroenterol Hepatol | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29204504 |
| Development of Arrayed Colonic Organoids for Screening of Secretagogues Associated with Enterotoxins. | Gunasekara DB, DiSalvo M, Wang Y, Nguyen DL, Reed MI, Speer J, Sims CE, Magness ST, Allbritton NL | Analytical chemistry | 29281259 | Anal Chem | 2018 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/29281259 |
| A leaky human colon model reveals uncoupled apical/basal cytotoxicity in early Clostridioides difficile toxin exposure. | Ok MT, Liu J, Bliton RJ, Hinesley CM, San Pedro EET, Breau KA, Gomez-Martinez I, Burclaff J, Magness ST | American journal of physiology. Gastrointestinal and liver physiology | 36749911 | Am J Physiol Gastrointest Liver Physiol | 2023 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/36749911 |
| In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A. | Xiao X, Sarma S, Menegatti S, Crook N, Magness ST, Hall CK | ACS chemical biology | 34965093 | ACS Chem Biol | 2022 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/34965093 |
| Chromatin profiling to identify biomarkers in inflammatory bowel diseases. | Awad A, Alcala AJ, Cowles MW, Sheikh SZ | Current opinion in gastroenterology | 40304726 | Curr Opin Gastroenterol | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40304726 |
| Myeloid Cell Adhesion Molecule 1 (CADM1) Promotes Proinflammatory Signaling in Human Inflammatory Bowel Diseases. | Darlington KC, Shumway AJ, Sona C, Khaled Z, Steinbach EC, Kikuchi Y, Fan S, Gartner V, Clough KM, Nishiyama NC, Ng MK, VanLandingham N, Schaner MR, Silverstein S, Lau G, Lian G, Huan B, Zhu LC, Bantumilli S, Furey B, Chaudhry EA, Kapadia MR, Sadiq TS, Barnes EL, Shanahan MT, Rahbar R, Vilen BJ, Bi X, Chen H, Jain D, Akram M, Wong J, Mangada M, Bain G, Nagy ML, Hav M, Ito A, Yan X, Komatsu M, Awad A, Furey TS, Sethupathy P, Poy MN, Sheikh SZ | Cellular and molecular gastroenterology and hepatology | 40882838 | Cell Mol Gastroenterol Hepatol | 2026 | https://www.ncbi.nlm.nih.gov/pubmed/40882838 |
| Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer. | Bultman SJ | Molecular nutrition & food research | 27138454 | Mol Nutr Food Res | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27138454 |
| A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. | Wang Y, Gunasekara DB, Reed MI, DiSalvo M, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Biomaterials | 28288348 | Biomaterials | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28288348 |
| The role of the microbiome in cancer development and therapy. | Bhatt AP, Redinbo MR, Bultman SJ | CA: a cancer journal for clinicians | 28481406 | CA Cancer J Clin | 2017 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/28481406 |
| Genomewide CRISPR knockout screen identified PLAC8 as an essential factor for SADS-CoVs infection. | Tse LV, Meganck RM, Araba KC, Yount BL, Shaffer KM, Hou YJ, Munt JE, Adams LE, Wykoff JA, Morowitz JM, Dong S, Magness ST, Marzluff WF, Gonzalez LM, Ehre C, Baric RS | Proceedings of the National Academy of Sciences of the United States of America | 35476513 | Proc Natl Acad Sci U S A | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/35476513 |
| Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn's Disease. | Toyonaga T, Steinbach EC, Keith BP, Barrow JB, Schaner MR, Wolber EA, Beasley C, Huling J, Wang Y, Allbritton NL, Chaumont N, Sadiq TS, Koruda MJ, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Shanahan MT, Rahbar R, Furey TS, Sethupathy P, Sheikh SZ | Cellular and molecular gastroenterology and hepatology | 32561494 | Cell Mol Gastroenterol Hepatol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32561494 |
| Enterochromaffin Cell-Enriched Monolayer Platform for Assaying Serotonin Release from Human Primary Intestinal Cells. | Wang Y, Sims CE, Allbritton NL | Analytical chemistry | 32819098 | Anal Chem | 2020 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/32819098 |
| Microphysiological System Design: Simplicity Is Elegance. | Hinman SS, Kim R, Wang Y, Phillips KS, Attayek PJ, Allbritton NL | Current opinion in biomedical engineering | 32095672 | Curr Opin Biomed Eng | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32095672 |
| Photopatterned Membranes and Chemical Gradients Enable Scalable Phenotypic Organization of Primary Human Colon Epithelial Models. | Hinman SS, Wang Y, Allbritton NL | Analytical chemistry | 31692334 | Anal Chem | 2019 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/31692334 |
| Evaluation of human primary intestinal monolayers for drug metabolizing capabilities. | Speer JE, Wang Y, Fallon JK, Smith PC, Allbritton NL | Journal of biological engineering | 31709009 | J Biol Eng | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31709009 |
| Primary Cell-Derived Intestinal Models: Recapitulating Physiology. | Dutton JS, Hinman SS, Kim R, Wang Y, Allbritton NL | Trends in biotechnology | 30591184 | Trends Biotechnol | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30591184 |
| Formation of Human Colonic Crypt Array by Application of Chemical Gradients Across a Shaped Epithelial Monolayer. | Wang Y, Kim R, Gunasekara DB, Reed MI, DiSalvo M, Nguyen DL, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29693040 | Cell Mol Gastroenterol Hepatol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29693040 |
| Nonsteroidal Anti-Inflammatory Drug-Induced Leaky Gut Modeled Using Polarized Monolayers of Primary Human Intestinal Epithelial Cells. | Bhatt AP, Gunasekara DB, Speer J, Reed MI, Peña AN, Midkiff BR, Magness ST, Bultman SJ, Allbritton NL, Redinbo MR | ACS infectious diseases | 29094594 | ACS Infect Dis | 2018 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/29094594 |
| A new microphysiological system shows hypoxia primes human ISCs for interleukin-dependent rescue of stem cell activity. | Rivera KR, Bliton RJ, Burclaff J, Czerwinski MJ, Liu J, Trueblood JM, Hinesley CM, Breau KA, Joshi S, Pozdin VA, Yao M, Ziegler AL, Blikslager AT, Daniele MA, Magness ST | bioRxiv : the preprint server for biology | 36778265 | bioRxiv | 2023 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/36778265 |
| Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells. | Sarma S, Catella CM, San Pedro ET, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK | Communications biology | 37634026 | Commun Biol | 2023 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/37634026 |
| An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal stem cells. | Cotton MJ, Ariel P, Chen K, Walcott VA, Dixit M, Breau KA, Hinesley CM, Kedziora K, Tang CY, Zheng A, Magness ST, Burclaff J | bioRxiv : the preprint server for biology | 37873351 | bioRxiv | 2023 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/37873351 |
| Replicating Host-Microbiome Interactions: Harnessing Organ-on-a-Chip and Organoid Technologies to Model Vaginal and Lung Physiology. | Coxon J, Linder E, Sweet C, Magness S, Green L | Annual review of biomedical engineering | 39971348 | Annu Rev Biomed Eng | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39971348 |
| Coupling mathematical modeling with a novel human intestinal stem cell system to understand feedback regulation during planar cell polarity. | Breau KA, Dunahey EG, Fosnocht HV, Magness ST, Elston TC | bioRxiv : the preprint server for biology | 41279301 | bioRxiv | 2025 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/41279301 |
| The microbiome and its potential as a cancer preventive intervention. | Bultman SJ | Seminars in oncology | 26970128 | Semin Oncol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26970128 |
| Formation of arrays of planar, murine, intestinal crypts possessing a stem/proliferative cell compartment and differentiated cell zone. | Kim R, Wang Y, Hwang SJ, Attayek PJ, Smiddy NM, Reed MI, Sims CE, Allbritton NL | Lab on a chip | 29944153 | Lab Chip | 2018 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/29944153 |
| "Fix and assay": separating in-cellulo sphingolipid reactions from analytical assay in time and space using an aldehyde-based fixative. | Proctor A , Allbritton NL | The Analyst | 30207332 | Analyst | 2019 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/30207332 |
| Analysis of Interleukin 8 Secretion by a Stem-Cell-Derived Human-Intestinal-Epithelial-Monolayer Platform. | Wang Y, Kim R, Hwang SJ, Dutton J, Sims CE, Allbritton NL | Analytical chemistry | 30199234 | Anal Chem | 2018 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/30199234 |
| A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. | Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST | Cellular and molecular gastroenterology and hepatology | 30123820 | Cell Mol Gastroenterol Hepatol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30123820 |
| A Planar Culture Model of Human Absorptive Enterocytes Reveals Metformin Increases Fatty Acid Oxidation and Export. | Gomez-Martinez I, Bliton RJ, Breau KA, Czerwinski MJ, Williamson IA, Wen J, Rawls JF, Magness ST | Cellular and molecular gastroenterology and hepatology | 35489715 | Cell Mol Gastroenterol Hepatol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35489715 |
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| The Jeremiah Metzger Lecture: Global warming redux: the disappearing microbiota and epidemic obesity. | Blaser MJ | Transactions of the American Clinical and Climatological Association | 23303990 | Trans Am Clin Climatol Assoc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23303990 |
| The human microbiome: at the interface of health and disease. | Cho I, Blaser MJ | Nature reviews. Genetics | 22411464 | Nat Rev Genet | 2012 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/22411464 |
| Microbiome and malignancy. | Plottel CS, Blaser MJ | Cell host & microbe | 22018233 | Cell Host Microbe | 2011 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/22018233 |
| Pathways in microbe-induced obesity. | Cox LM, Blaser MJ | Cell metabolism | 23747247 | Cell Metab | 2013 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/23747247 |
| A brave new world: the lung microbiota in an era of change. | Segal LN, Blaser MJ | Annals of the American Thoracic Society | 24437400 | Ann Am Thorac Soc | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24437400 |
| Helicobacter pylori and esophageal disease: wake-up call? | Blaser MJ | Gastroenterology | 21029801 | Gastroenterology | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21029801 |
| Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. | Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R | Gastroenterology | 21530737 | Gastroenterology | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21530737 |
| The effect of H. pylori eradication on meal-associated changes in plasma ghrelin and leptin. | Francois F, Roper J, Joseph N, Pei Z, Chhada A, Shak JR, de Perez AZ, Perez-Perez GI, Blaser MJ | BMC gastroenterology | 21489301 | BMC Gastroenterol | 2011 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/21489301 |
| Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. | Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ | Nature communications | 26123276 | Nat Commun | 2015 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/26123276 |
| Risks of Antibiotic Exposures Early in Life on the Developing Microbiome. | Schulfer A, Blaser MJ | PLoS pathogens | 26135581 | PLoS Pathog | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26135581 |
| Antibiotics in early life and obesity. | Cox LM, Blaser MJ | Nature reviews. Endocrinology | 25488483 | Nat Rev Endocrinol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25488483 |
| Sparse and compositionally robust inference of microbial ecological networks. | Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA | PLoS computational biology | 25950956 | PLoS Comput Biol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25950956 |
| Antibiotic use and its consequences for the normal microbiome. | Blaser MJ | Science (New York, N.Y.) | 27126037 | Science | 2016 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/27126037 |
| The Intestinal Microbiome and Estrogen Receptor-Positive Female Breast Cancer. | Kwa M, Plottel CS, Blaser MJ, Adams S | Journal of the National Cancer Institute | 27107051 | J Natl Cancer Inst | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27107051 |
| Predominance of Lactobacillus spp. Among Patients Who Do Not Acquire Multidrug-Resistant Organisms. | Araos R, Tai AK, Snyder GM, Blaser MJ, D'Agata EMC | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 27358350 | Clin Infect Dis | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27358350 |
| Loss of HDAC6 alters gut microbiota and worsens obesity. | Lieber AD, Beier UH, Xiao H, Wilkins BJ, Jiao J, Li XS, Schugar RC, Strauch CM, Wang Z, Brown JM, Hazen SL, Bokulich NA, Ruggles KV, Akimova T, Hancock WW, Blaser MJ | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 30102568 | FASEB J | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30102568 |
| Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. | Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC | Nature medicine | 26828196 | Nat Med | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26828196 |
| A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping. | Koh H, Blaser MJ, Li H | Microbiome | 28438217 | Microbiome | 2017 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/28438217 |
| Severe lung disease characterized by lymphocytic bronchiolitis, alveolar ductitis, and emphysema (BADE) in industrial machine-manufacturing workers. | Cummings KJ, Stanton ML, Nett RJ, Segal LN, Kreiss K, Abraham JL, Colby TV, Franko AD, Green FHY, Sanyal S, Tallaksen RJ, Wendland D, Bachelder VD, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Crawford JA, Green BJ, LeBouf RF, Blaser MJ, Weissman DN | American journal of industrial medicine | 31461179 | Am J Ind Med | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31461179 |
| Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity. | Shen N, Caixàs A, Ahlers M, Patel K, Gao Z, Dutia R, Blaser MJ, Clemente JC, Laferrère B | Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery | 31296445 | Surg Obes Relat Dis | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31296445 |
| Antibiotics, birth mode, and diet shape microbiome maturation during early life. | Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, D Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ | Science translational medicine | 27306664 | Sci Transl Med | 2016 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/27306664 |
| A multivariate distance-based analytic framework for microbial interdependence association test in longitudinal study. | Zhang Y, Han SW, Cox LM, Li H | Genetic epidemiology | 28872698 | Genet Epidemiol | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28872698 |
| Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. | Segal LN, Clemente JC, Tsay JC, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD | Nature microbiology | 27572644 | Nat Microbiol | 2016 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/27572644 |
| Helminth infection promotes colonization resistance via type 2 immunity. | Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, Gause WC, Blaser MJ, Bonneau RA, Lim YA, Loke P, Cadwell K | Science (New York, N.Y.) | 27080105 | Science | 2016 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/27080105 |
| Helicobacter pylori and the birth cohort effect: evidence for stabilized colonization rates in childhood. | den Hoed CM, Vila AJ, Holster IL, Perez-Perez GI, Blaser MJ, de Jongste JC, Kuipers EJ | Helicobacter | 21923687 | Helicobacter | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21923687 |
| Infant antibiotic exposures and early-life body mass. | Trasande L, Blustein J, Liu M, Corwin E, Cox LM, Blaser MJ | International journal of obesity (2005) | 22907693 | Int J Obes (Lond) | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22907693 |
| Candida krusei colonization in patients with gastrointestinal diseases. | Huong DT, Zhao Y, Nguyet NT, Loan TT, Binh NT, Thinh NV, Hanh NT, Perez-Perez GI, Perlin DS | Medical mycology | 23815437 | Med Mycol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23815437 |
| Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. | Segal LN, Blaser MJ | The Journal of pediatrics | 25934071 | J Pediatr | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25934071 |
| Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. | Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL | mBio | 27178263 | mBio | 2016 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/27178263 |
| Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. | Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ | Genome medicine | 27124954 | Genome Med | 2016 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/27124954 |
| Role of childhood infection in the sequelae of H. pylori disease. | Harris PR, Smythies LE, Smith PD, Perez-Perez GI | Gut microbes | 24275060 | Gut Microbes | 2013 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/24275060 |
| Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. | Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD | Microbiome | 24450871 | Microbiome | 2013 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/24450871 |
| Ethnicity is a strong predictor for Helicobacter pylori infection in young women in a multi-ethnic European city. | den Hollander WJ, Holster IL, den Hoed CM, van Deurzen F, van Vuuren AJ, Jaddoe VW, Hofman A, Perez Perez GI, Blaser MJ, Moll HA, Kuipers EJ | Journal of gastroenterology and hepatology | 23808840 | J Gastroenterol Hepatol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23808840 |
| The Human Microbiome before Birth. | Blaser MJ, Dominguez-Bello MG | Cell host & microbe | 27832586 | Cell Host Microbe | 2016 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/27832586 |
| Helicobacter pylori colonization and pregnancies complicated by preeclampsia, spontaneous prematurity, and small for gestational age birth. | den Hollander WJ, Schalekamp-Timmermans S, Holster IL, Jaddoe VW, Hofman A, Moll HA, Perez-Perez GI, Blaser MJ, Steegers EA, Kuipers EJ | Helicobacter | 27786400 | Helicobacter | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27786400 |
| The theory of disappearing microbiota and the epidemics of chronic diseases. | Blaser MJ | Nature reviews. Immunology | 28749457 | Nat Rev Immunol | 2017 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/28749457 |
| Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice. | Schulfer AF, Battaglia T, Alvarez Y, Bijnens L, Ruiz VE, Ho M, Robinson S, Ward T, Cox LM, Rogers AB, Knights D, Sartor RB, Blaser MJ | Nature microbiology | 29180726 | Nat Microbiol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29180726 |
| A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. | Ruiz VE, Battaglia T, Kurtz ZD, Bijnens L, Ou A, Engstrand I, Zheng X, Iizumi T, Mullins BJ, Müller CL, Cadwell K, Bonneau R, Perez-Perez GI, Blaser MJ | Nature communications | 28894149 | Nat Commun | 2017 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/28894149 |
| Joint modeling of zero-inflated longitudinal proportions and time-to-event data with application to a gut microbiome study. | Hu J, Wang C, Blaser MJ, Li H | Biometrics | 34213763 | Biometrics | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34213763 |
| 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 |
| The impact of early-life sub-therapeutic antibiotic treatment (STAT) on excessive weight is robust despite transfer of intestinal microbes. | Schulfer AF, Schluter J, Zhang Y, Brown Q, Pathmasiri W, McRitchie S, Sumner S, Li H, Xavier JB, Blaser MJ | The ISME journal | 30651608 | ISME J | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30651608 |
| Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota. | den Hartigh LJ, Gao Z, Goodspeed L, Wang S, Das AK, Burant CF, Chait A, Blaser MJ | The Journal of nutrition | 29659960 | J Nutr | 2018 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/29659960 |
| Risk of Clostridium difficile Infection in Patients With Celiac Disease: A Population-Based Study. | Lebwohl B, Nobel YR, Green PHR, Blaser MJ, Ludvigsson JF | The American journal of gastroenterology | 29087398 | Am J Gastroenterol | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29087398 |
| Detecting a bacterial protein to understand cancer risk. | Blaser MJ | Clinical chemistry | 21586641 | Clin Chem | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21586641 |
| The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota. | Cox LM, Cho I, Young SA, Anderson WH, Waters BJ, Hung SC, Gao Z, Mahana D, Bihan M, Alekseyenko AV, Methé BA, Blaser MJ | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23154883 | FASEB J | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23154883 |
| Association between gastric Helicobacter pylori colonization and glycated hemoglobin levels. | Chen Y, Blaser MJ | The Journal of infectious diseases | 22427676 | J Infect Dis | 2012 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/22427676 |
| Host demise as a beneficial function of indigenous microbiota in human hosts. | Blaser MJ, Webb GF | mBio | 25516618 | mBio | 2014 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/25516618 |
| Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project. | Liu M, Koh H, Kurtz ZD, Battaglia T, PeBenito A, Li H, Nazzal L, Blaser MJ | Microbiome | 28841836 | Microbiome | 2017 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/28841836 |
| The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults. | Barnett C, Nazzal L, Goldfarb DS, Blaser MJ | The Journal of urology | 26292041 | J Urol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26292041 |
| Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. | Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko JP, Rom WN, Blaser MJ, Weiden MD | Thorax | 27486204 | Thorax | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27486204 |
| Microbially Produced Acetate: A "Missing Link" in Understanding Obesity? | Trent CM, Blaser MJ | Cell metabolism | 27411005 | Cell Metab | 2016 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/27411005 |
| Maturation of the gut microbiome and risk of asthma in childhood. | Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ, Bisgaard H | Nature communications | 29321519 | Nat Commun | 2018 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/29321519 |
| A highly adaptive microbiome-based association test for survival traits. | Koh H, Livanos AE, Blaser MJ, Li H | BMC genomics | 29558893 | BMC Genomics | 2018 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/29558893 |
| Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women. | Alemán JO, Bokulich NA, Swann JR, Walker JM, De Rosa JC, Battaglia T, Costabile A, Pechlivanis A, Liang Y, Breslow JL, Blaser MJ, Holt PR | Journal of translational medicine | 30176893 | J Transl Med | 2018 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/30176893 |
| Asthma: Undoing millions of years of coevolution in early life? | Dominguez-Bello MG, Blaser MJ | Science translational medicine | 26424565 | Sci Transl Med | 2015 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/26424565 |
| Helminth colonization is associated with increased diversity of the gut microbiota. | Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Loke P | PLoS neglected tropical diseases | 24851867 | PLoS Negl Trop Dis | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24851867 |
| Intergenerational reduction in Helicobacter pylori prevalence is similar between different ethnic groups living in a Western city. | den Hollander WJ, Holster IL, van Gilst B, van Vuuren AJ, Jaddoe VW, Hofman A, Perez-Perez GI, Kuipers EJ, Moll HA, Blaser MJ | Gut | 25192563 | Gut | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25192563 |
| Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibaculum rodentium. | Cox LM, Sohn J, Tyrrell KL, Citron DM, Lawson PA, Patel NB, Iizumi T, Perez-Perez GI, Goldstein EJC, Blaser MJ | International journal of systematic and evolutionary microbiology | 28100298 | Int J Syst Evol Microbiol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28100298 |
| Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course. | Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J, Blaser MJ | Scientific reports | 31705027 | Sci Rep | 2019 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/31705027 |
| Work-related adverse respiratory health outcomes at a machine manufacturing facility with a cluster of bronchiolitis, alveolar ductitis and emphysema (BADE). | Cummings KJ, Stanton ML, Kreiss K, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Edwards NT, Segal LN, Blaser MJ, Weissman DN, Nett RJ | Occupational and environmental medicine | 32132182 | Occup Environ Med | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32132182 |
| Effect of antibiotic treatment on Oxalobacter formigenes colonization of the gut microbiome and urinary oxalate excretion. | Nazzal L, Francois F, Henderson N, Liu M, Li H, Koh H, Wang C, Gao Z, Perez GP, Asplin JR, Goldfarb DS, Blaser MJ | Scientific reports | 34385560 | Sci Rep | 2021 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/34385560 |
| Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. | Falkenberg CV, Blinov ML, Loew LM | Biophysical journal | 24314076 | Biophys J | 2013 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/24314076 |
| Interconnected network motifs control podocyte morphology and kidney function. | Azeloglu EU, Hardy SV, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma'ayan A, Gordon RE, He JC, Iyengar R | Science signaling | 24497609 | Sci Signal | 2014 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/24497609 |
| Compartmentalized PDE4A5 Signaling Impairs Hippocampal Synaptic Plasticity and Long-Term Memory. | Havekes R, Park AJ, Tolentino RE, Bruinenberg VM, Tudor JC, Lee Y, Hansen RT, Guercio LA, Linton E, Neves-Zaph SR, Meerlo P, Baillie GS, Houslay MD, Abel T | The Journal of neuroscience : the official journal of the Society for Neuroscience | 27559174 | J Neurosci | 2016 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/27559174 |
| A biomimetic gelatin-based platform elicits a pro-differentiation effect on podocytes through mechanotransduction. | Hu M, Azeloglu EU, Ron A, Tran-Ba KH, Calizo RC, Tavassoly I, Bhattacharya S, Jayaraman G, Chen Y, Rabinovich V, Iyengar R, Hone JC, He JC, Kaufman LJ | Scientific reports | 28262745 | Sci Rep | 2017 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/28262745 |
| Cross-regulation of Phosphodiesterase 1 and Phosphodiesterase 2 Activities Controls Dopamine-mediated Striatal α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Trafficking. | Song RS, Tolentino R, Sobie EA, Neves-Zaph SR | The Journal of biological chemistry | 27605670 | J Biol Chem | 2016 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/27605670 |
| Computational analysis of Rho GTPase cycling. | Falkenberg CV, Loew LM | PLoS computational biology | 23326220 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23326220 |
| Modeling of spatially-restricted intracellular signaling. | Neves SR | Wiley interdisciplinary reviews. Systems biology and medicine | 21766466 | Wiley Interdiscip Rev Syst Biol Med | 2012 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/21766466 |
| Systems biology of kidney diseases. | He JC, Chuang PY, Ma'ayan A, Iyengar R | Kidney international | 21881558 | Kidney Int | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21881558 |
| ERK regulation of phosphodiesterase 4 enhances dopamine-stimulated AMPA receptor membrane insertion. | Song RS, Massenburg B, Wenderski W, Jayaraman V, Thompson L, Neves SR | Proceedings of the National Academy of Sciences of the United States of America | 23986500 | Proc Natl Acad Sci U S A | 2013 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/23986500 |
| Cell shape information is transduced through tension-independent mechanisms. | Ron A, Azeloglu EU, Calizo RC, Hu M, Bhattacharya S, Chen Y, Jayaraman G, Lee S, Neves-Zaph SR, Li H, Gordon RE, He JC, Hone JC, Iyengar R | Nature communications | 29247198 | Nat Commun | 2017 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/29247198 |
| Obtaining and estimating kinetic parameters from the literature. | Neves SR | Science signaling | 21934111 | Sci Signal | 2011 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/21934111 |
| Modeling of spatial intracellular signaling events in neurons. | Wenderski WC, Neves SR | Methods in enzymology | 22289450 | Methods Enzymol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22289450 |
| G Protein-regulated inducer of neurite outgrowth (GRIN) modulates Sprouty protein repression of mitogen-activated protein kinase (MAPK) activation by growth factor stimulation. | Hwangpo TA, Jordan JD, Premsrirut PK, Jayamaran G, Licht JD, Iyengar R, Neves SR | The Journal of biological chemistry | 22383529 | J Biol Chem | 2012 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/22383529 |
| Developing models in virtual cell. | Neves SR | Science signaling | 21954293 | Sci Signal | 2011 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/21954293 |
| Activation of the Nlrp3 inflammasome in infiltrating macrophages by endocannabinoids mediates beta cell loss in type 2 diabetes. | Jourdan T, Godlewski G, Cinar R, Bertola A, Szanda G, Liu J, Tam J, Han T, Mukhopadhyay B, Skarulis MC, Ju C, Aouadi M, Czech MP, Kunos G | Nature medicine | 23955712 | Nat Med | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23955712 |
| CD40 deficiency in mice exacerbates obesity-induced adipose tissue inflammation, hepatic steatosis, and insulin resistance. | Guo CA, Kogan S, Amano SU, Wang M, Dagdeviren S, Friedline RH, Aouadi M, Kim JK, Czech MP | American journal of physiology. Endocrinology and metabolism | 23482447 | Am J Physiol Endocrinol Metab | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23482447 |
| Local proliferation of macrophages contributes to obesity-associated adipose tissue inflammation. | Amano SU, Cohen JL, Vangala P, Tencerova M, Nicoloro SM, Yawe JC, Shen Y, Czech MP, Aouadi M | Cell metabolism | 24374218 | Cell Metab | 2014 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/24374218 |
| IL-1 signaling in obesity-induced hepatic lipogenesis and steatosis. | Negrin KA, Roth Flach RJ, DiStefano MT, Matevossian A, Friedline RH, Jung D, Kim JK, Czech MP | PloS one | 25216251 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25216251 |
| Insulin signalling mechanisms for triacylglycerol storage. | Czech MP, Tencerova M, Pedersen DJ, Aouadi M | Diabetologia | 23443243 | Diabetologia | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23443243 |
| Glucan particles for selective delivery of siRNA to phagocytic cells in mice. | Tesz GJ, Aouadi M, Prot M, Nicoloro SM, Boutet E, Amano SU, Goller A, Wang M, Guo CA, Salomon WE, Virbasius JV, Baum RA, O'Connor MJ Jr, Soto E, Ostroff GR, Czech MP | The Biochemical journal | 21418037 | Biochem J | 2011 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/21418037 |
| Activated Kupffer cells inhibit insulin sensitivity in obese mice. | Tencerova M, Aouadi M, Vangala P, Nicoloro SM, Yawe JC, Cohen JL, Shen Y, Garcia-Menendez L, Pedersen DJ, Gallagher-Dorval K, Perugini RA, Gupta OT, Czech MP | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 25805830 | FASEB J | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25805830 |
| Insulin action and resistance in obesity and type 2 diabetes. | Czech MP | Nature medicine | 28697184 | Nat Med | 2017 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/28697184 |
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| Alcohol Drinking Without Meals Is Associated With Risk of Gastrointestinal Cancers, Including Early-Onset Cases. | Shi M, Ahmedin NJ, Zong X, Yilmaz ӦH, Bishehsari F, Cao Y | Gastroenterology | 37977310 | Gastroenterology | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37977310 |
| Circadian transcriptome of pancreatic adenocarcinoma unravels chronotherapeutic targets. | Sharma D, Adnan D, Abdel-Reheem MK, Anafi RC, Leary DD, Bishehsari F | JCI insight | 38716727 | JCI Insight | 2024 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/38716727 |
| Early-onset Colon Cancer Shows a Distinct Intestinal Microbiome and a Host-Microbe Interaction. | Adnan D, Trinh JQ, Sharma D, Alsayid M, Bishehsari F | Cancer prevention research (Philadelphia, Pa.) | 37967575 | Cancer Prev Res (Phila) | 2024 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/37967575 |
| Evidence that the loss of colonic anti-microbial peptides may promote dysbiotic Gram-negative inflammaging-associated bacteria in aging mice. | Forsyth CB, Shaikh M, Engen PA, Preuss F, Naqib A, Palmen BA, Green SJ, Zhang L, Bogin ZR, Lawrence K, Sharma D, Swanson GR, Bishehsari F, Voigt RM, Keshavarzian A | Frontiers in aging | 38501032 | Front Aging | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38501032 |
| A Patient-Derived Organ-on-Chip Platform for Modeling the Tumor Microenvironment and Drug Responses in Pancreatic Cancer. | Adnan D, de Barros NR, Santovito LS, Cheng X, Lawrence KM, Barnett MK, Boetto MD, Mehta N, Singh A, Cheng L, Huang X, Bishehsari F | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 41610338 | Adv Sci (Weinh) | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41610338 |
| Defining and detecting global transcriptional amplitude in circadian gene expression. | Saint-Antoine M, Anafi RC | bioRxiv : the preprint server for biology | 41292949 | bioRxiv | 2025 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/41292949 |
| Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis. | Nicoludis JM, Green AG, Walujkar S, May EJ, Sotomayor M, Marks DS, Gaudet R | Proceedings of the National Academy of Sciences of the United States of America | 31431536 | Proc Natl Acad Sci U S A | 2019 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/31431536 |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | bioRxiv : the preprint server for biology | 33200136 | bioRxiv | 2020 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/33200136 |
| Protein design and variant prediction using autoregressive generative models. | Shin JE, Riesselman AJ, Kollasch AW, McMahon C, Simon E, Sander C, Manglik A, Kruse AC, Marks DS | Nature communications | 33893299 | Nat Commun | 2021 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/33893299 |
| Proteome-wide model for human disease genetics. | Orenbuch R, Shearer CA, Kollasch AW, Spinner AD, Hopf T, van Niekerk L, Franceschi D, Dias M, Frazer J, Marks DS | Nature genetics | 41286104 | Nat Genet | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41286104 |
| The M3 Muscarinic Acetylcholine Receptor Can Signal through Multiple G Protein Families. | Smith JS, Hilibrand AS, Skiba MA, Dates AN, Calvillo-Miranda VG, Kruse AC | Molecular pharmacology | 38641412 | Mol Pharmacol | 2024 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/38641412 |
| Evolutionary-Scale Enzymology Enables Biochemical Constant Prediction Across a Multi-Peaked Catalytic Landscape. | Muir DF, Asper GPR, Notin P, Posner JA, Marks DS, Keiser MJ, Pinney MM | bioRxiv : the preprint server for biology | 39484523 | bioRxiv | 2024 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/39484523 |
| Continuous evolution of user-defined genes at 1 million times the genomic mutation rate. | Rix G, Williams RL, Hu VJ, Spinner A, Pisera AO, Marks DS, Liu CC | Science (New York, N.Y.) | 39509492 | Science | 2024 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/39509492 |
| Custom CRISPR-Cas9 PAM variants via scalable engineering and machine learning. | Silverstein RA, Kim N, Kroell AS, Walton RT, Delano J, Butcher RM, Pacesa M, Smith BK, Christie KA, Ha LL, Meis RJ, Clark AB, Spinner AD, Lazzarotto CR, Li Y, Matsubara A, Urbina EO, Dahl GA, Correia BE, Marks DS, Tsai SQ, Pinello L, De Ravin SS, Liu Q, Kleinstiver BP | Nature | 40262634 | Nature | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40262634 |
| Proteome-wide model for human disease genetics. | Orenbuch R, Shearer CA, Kollasch AW, Spinner HD, Hopf TA, van Niekerk L, Franceschi D, Dias M, Frazer J, Marks DS | medRxiv : the preprint server for health sciences | 38076790 | medRxiv | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/38076790 |
| Discovery of VH domains that allosterically inhibit ENPP1. | Solomon PE, Bracken CJ, Carozza JA, Wang H, Young EP, Wellner A, Liu CC, Sweet-Cordero EA, Li L, Wells JA | Nature chemical biology | 37400538 | Nat Chem Biol | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37400538 |
| Rapidly inducible yeast surface display for antibody evolution with OrthoRep. | Paulk AM, Williams RL, Liu CC | bioRxiv : the preprint server for biology | 38826191 | bioRxiv | 2024 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/38826191 |
| An in silico method to assess antibody fragment polyreactivity. | Harvey EP, Shin JE, Skiba MA, Nemeth GR, Hurley JD, Wellner A, Shaw AY, Miranda VG, Min JK, Liu CC, Marks DS, Kruse AC | Nature communications | 36477674 | Nat Commun | 2022 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/36477674 |
| ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. | Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS | bioRxiv : the preprint server for biology | 38106144 | bioRxiv | 2023 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/38106144 |
| ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers. | Notin P, Marks DS, Weitzman R, Gal Y | bioRxiv : the preprint server for biology | 38106034 | bioRxiv | 2023 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/38106034 |
| Protein design using structure-based residue preferences. | Ding D, Shaw AY, Sinai S, Rollins N, Prywes N, Savage DF, Laub MT, Marks DS | Nature communications | 38388493 | Nat Commun | 2024 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/38388493 |
| Evolutionary-scale enzymology enables exploration of a rugged catalytic landscape. | Muir DF, Asper GPR, Notin P, Posner JA, Marks DS, Keiser MJ, Pinney MM | Science (New York, N.Y.) | 40504906 | Science | 2025 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/40504906 |
| β-arrestin recruitment facilitates a direct association with G proteins. | Lee CY, Smith JS, Kohlmann T, Meara EM, Pham U, Kwarcinski F, Dates AN, Choi I, Hilibrand AS, Gillikin A, Blacklow SC, Tall GG, Kruse AC, Rajagopal S | bioRxiv : the preprint server for biology | 40631328 | bioRxiv | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40631328 |
| Ultra-efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids. | Pisera AO, Yu Y, Williams RL, Liu CC | ACS synthetic biology | 40127237 | ACS Synth Biol | 2025 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/40127237 |
| Machine learning enables efficient and effective affinity maturation of nanobodies. | Paul S, Harvey EP, Osei-Owusu J, Kollasch AW, Riesselman AJ, McMahon C, Gazizov A, Anuganti M, Belay F, Kieu MA, Zhu H, Hollingsworth LR, Harper JW, Moshinsky DJ, Teixeira AAR, Marks DS, Kruse AC | bioRxiv : the preprint server for biology | 41648218 | bioRxiv | 2026 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/41648218 |
| Co-evolution of interacting proteins through non-contacting and non-specific mutations. | Ding D, Green AG, Wang B, Lite TV, Weinstein EN, Marks DS, Laub MT | Nature ecology & evolution | 35361892 | Nat Ecol Evol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35361892 |
| Atomically accurate de novo design of antibodies with RFdiffusion. | Bennett NR, Watson JL, Ragotte RJ, Borst AJ, See DL, Weidle C, Biswas R, Yu Y, Shrock EL, Ault R, Leung PJY, Huang B, Goreshnik I, Tam J, Carr KD, Singer B, Criswell C, Wicky BIM, Vafeados D, Sanchez MG, Kim HM, Torres SV, Chan S, Sun SM, Spear T, Sun Y, O'Reilly K, Maris JM, Sgourakis NG, Melnyk RA, Liu CC, Baker D | bioRxiv : the preprint server for biology | 38562682 | bioRxiv | 2025 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/38562682 |
| Guidelines for releasing a variant effect predictor. | Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA | ArXiv | 38699161 | ArXiv | 2024 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/38699161 |
| Epitope-directed selection of GPCR nanobody ligands with evolvable function. | Skiba MA, Canavan C, Nemeth GR, Liu J, Kanso A, Kruse AC | Proceedings of the National Academy of Sciences of the United States of America | 40067891 | Proc Natl Acad Sci U S A | 2025 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/40067891 |
| Rapidly Inducible Yeast Surface Display for Antibody Evolution with OrthoRep. | Paulk AM, Williams RL, Liu CC | ACS synthetic biology | 39052526 | ACS Synth Biol | 2024 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/39052526 |
| G Protein Selectivity in Dopamine Receptors is Determined before GDP Release. | Tawfeeq C, Hilibrand AS, Smith JS, Portillo J, Kruse AC, Abrol R | Biochemistry | 40358213 | Biochemistry | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/40358213 |
| Decoding protein-peptide interactions using a large, target-agnostic yeast surface display library. | Hurley JD, Shlosman I, Lakshminarayan M, Zhao Z, Yue H, Nowak RP, Fischer ES, Kruse AC | bioRxiv : the preprint server for biology | 40475574 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475574 |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Hu VJ, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | Nature chemical biology | 34168368 | Nat Chem Biol | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34168368 |
| Antibodies expand the scope of angiotensin receptor pharmacology. | Skiba MA, Sterling SM, Rawson S, Zhang S, Xu H, Jiang H, Nemeth GR, Gilman MSA, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Rockman HA, Barth P, Wingler LM, Kruse AC | Nature chemical biology | 38744986 | Nat Chem Biol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38744986 |
| The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. | Erlandson SC, Rawson S, Osei-Owusu J, Brock KP, Liu X, Paulo JA, Mintseris J, Gygi SP, Marks DS, Cong X, Kruse AC | Nature chemical biology | 37081311 | Nat Chem Biol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37081311 |
| An Atlas of Variant Effects to understand the genome at nucleotide resolution. | Fowler DM, Adams DJ, Gloyn AL, Hahn WC, Marks DS, Muffley LA, Neal JT, Roth FP, Rubin AF, Starita LM, Hurles ME | Genome biology | 37394429 | Genome Biol | 2023 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/37394429 |
| Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate. | Rix G, Williams RL, Spinner H, Hu VJ, Marks DS, Liu CC | bioRxiv : the preprint server for biology | 38014077 | bioRxiv | 2023 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/38014077 |
| Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders. | Orenbuch R, Kollasch AW, Spinner HD, Shearer CA, Hopf TA, Franceschi D, Dias M, Frazer J, Marks DS | Research square | 38260496 | Res Sq | 2024 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/38260496 |
| Antibodies Expand the Scope of Angiotensin Receptor Pharmacology. | Skiba MA, Sterling SM, Rawson S, Gilman MSA, Xu H, Nemeth GR, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Wingler LM, Kruse AC | bioRxiv : the preprint server for biology | 37662341 | bioRxiv | 2023 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/37662341 |
| Learning from prepandemic data to forecast viral escape. | Thadani NN, Gurev S, Notin P, Youssef N, Rollins NJ, Ritter D, Sander C, Gal Y, Marks DS | Nature | 37821700 | Nature | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37821700 |
| Guidelines for releasing a variant effect predictor. | Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA | Genome biology | 40234898 | Genome Biol | 2025 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/40234898 |
| Atomically accurate de novo design of antibodies with RFdiffusion. | Bennett NR, Watson JL, Ragotte RJ, Borst AJ, See DL, Weidle C, Biswas R, Yu Y, Shrock EL, Ault R, Leung PJY, Huang B, Goreshnik I, Tam J, Carr KD, Singer B, Criswell C, Wicky BIM, Vafeados D, Garcia Sanchez M, Kim HM, Vázquez Torres S, Chan S, Sun SM, Spear TT, Sun Y, O'Reilly K, Maris JM, Sgourakis NG, Melnyk RA, Liu CC, Baker D | Nature | 41193805 | Nature | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41193805 |
| Metal Ion Requirement for Catalysis by 3'-5' RNA Polymerases. | Iwaniec BWJ, Allegretti MM, Jackman JE | Biochemistry | 40774528 | Biochemistry | 2025 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/40774528 |
| Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity. | Boys IN, Johnson AG, Quinlan MR, Kranzusch PJ, Elde NC | Cell reports | 37494187 | Cell Rep | 2023 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/37494187 |
| C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. | Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL | bioRxiv : the preprint server for biology | 37790392 | bioRxiv | 2024 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/37790392 |
| Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses. | Boys IN, Johnson AG, Quinlan M, Kranzusch PJ, Elde NC | bioRxiv : the preprint server for biology | 36909515 | bioRxiv | 2023 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/36909515 |
| A comparison of Dictyostelium discoideum 3'-5' RNA polymerases reveals a conserved tRNA(His) guanylyltransferase residue that plays a dual role in catalysis. | Johnecheck GN, Kihm KJ, Jackman JE | bioRxiv : the preprint server for biology | 41279222 | bioRxiv | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41279222 |
| The competitive landscape of the dsRNA world. | Cottrell KA, Andrews RJ, Bass BL | Molecular cell | 38118451 | Mol Cell | 2024 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/38118451 |
| Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis. | Jayasinghe MI, Patel KJ, Jackman JE | RNA (New York, N.Y.) | 38997129 | RNA | 2024 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/38997129 |
| Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. | Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL | eLife | 38747717 | Elife | 2024 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/38747717 |
| Detection of Orsay viral replication intermediates reveals spatial and regulatory links to Caenorhabditis elegans innate immune responses. | Ranganathan S, Aruscavage PJ, Bass BL | bioRxiv : the preprint server for biology | 41000914 | bioRxiv | 2025 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/41000914 |
| Mitochondrial tRNA processing: a neutral evolutionary ratchet innovation. | Lai LB, Jackman JE, Daniels CJ, Gopalan V | Trends in biochemical sciences | 40581570 | Trends Biochem Sci | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40581570 |
| Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. | Aderounmu AM, Aruscavage PJ, Kolaczkowski B, Bass BL | eLife | 37068011 | Elife | 2023 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/37068011 |
| A trove of antiviral TRIM family E3 ligases in reptiles. | Boys IN, Quinlan MR, Elde NC | bioRxiv : the preprint server for biology | 40667304 | bioRxiv | 2025 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/40667304 |
| Metal ion requirement for catalysis by 3'-5' RNA polymerases. | Iwaniec BWJ, Allegretti MM, Jackman JE | bioRxiv : the preprint server for biology | 40166239 | bioRxiv | 2025 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/40166239 |
| Characterization of Orsay virus replication intermediates in Caenorhabditis elegans reveals links to antiviral RNA interference. | Ranganathan S, Aruscavage PJ, Bass BL | Molecular biology of the cell | 41705949 | Mol Biol Cell | 2026 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/41705949 |
| The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont. | Dunning Hotopp JC, Klasson L | G3 (Bethesda, Md.) | 29301977 | G3 (Bethesda) | 2018 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/29301977 |
| Pim kinase inhibitor co-treatment decreases alternative non-homologous end-joining DNA repair and genomic instability induced by topoisomerase 2 inhibitors in cells with FLT3 internal tandem duplication. | Scarpa M, Kapoor S, Tvedte ES, Doshi KA, Zou YS, Singh P, Lee JK, Chatterjee A, Ali MKM, Bromley RE, Hotopp JCD, Rassool FV, Baer MR | Oncotarget | 34504649 | Oncotarget | 2021 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/34504649 |
| Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement. | Tvedte ES, Gasser M, Zhao X, Tallon LJ, Sadzewicz L, Bromley RE, Chung M, Mattick J, Sparklin BC, Dunning Hotopp JC | Current biology : CB | 35671755 | Curr Biol | 2022 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/35671755 |
| Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes. | Tvedte ES, Gasser M, Sparklin BC, Michalski J, Hjelmen CE, Johnston JS, Zhao X, Bromley R, Tallon LJ, Sadzewicz L, Rasko DA, Dunning Hotopp JC | G3 (Bethesda, Md.) | 33768248 | G3 (Bethesda) | 2021 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/33768248 |
| Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics. | Shetty AC, Mattick J, Chung M, McCracken C, Mahurkar A, Filler SG, Fraser CM, Rasko DA, Bruno VM, Dunning Hotopp JC | Microbial genomics | 31851607 | Microb Genom | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31851607 |
| Grafting or pruning in the animal tree: lateral gene transfer and gene loss? | Dunning Hotopp JC | BMC genomics | 29914363 | BMC Genomics | 2018 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/29914363 |
| Aligner optimization increases accuracy and decreases compute times in multi-species sequence data. | Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC | Microbial genomics | 29114401 | Microb Genom | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29114401 |
| Updated annotation and meta-analysis of Brugia malayi transcriptomics data reveals consistent transcriptional profiles across time and space with some study-specific differences in adult female worm transcriptional profiles. | Holt CI, Dunning Hotopp JC | PLoS neglected tropical diseases | 39325836 | PLoS Negl Trop Dis | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39325836 |
| Modeling the integration of bacterial rRNA fragments into the human cancer genome. | Sieber KB, Gajer P, Dunning Hotopp JC | BMC bioinformatics | 27001685 | BMC Bioinformatics | 2016 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/27001685 |
| Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae. | Gasser MT, Chung M, Bromley RE, Nadendla S, Dunning Hotopp JC | Microbiology resource announcements | 31649084 | Microbiol Resour Announc | 2019 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/31649084 |
| Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data. | Robinson KM, Crabtree J, Mattick JS, Anderson KE, Dunning Hotopp JC | Microbiome | 28118849 | Microbiome | 2017 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/28118849 |
| Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements. | Dunning Hotopp JC, Baltrus DA, Bruno VM, Dennehy JJ, Gill SR, Maresca JA, Matthijnssens J, Newton ILG, Putonti C, Rasko DA, Rokas A, Roux S, Stajich JE, Stedman KM, Stewart FJ, Thrash JC | Microbiology resource announcements | 32883786 | Microbiol Resour Announc | 2020 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/32883786 |
| TwinBLAST: When Two Is Better than One. | Dunning Hotopp JC, Matsumura J, Bromley RE, Riley DR, Agrawal S, Sparklin B, Mattick J, Crabtree J, Mahurkar A | Microbiology resource announcements | 31467106 | Microbiol Resour Announc | 2019 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/31467106 |
| Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences. | Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O'Connor TD | Cancer | 30865299 | Cancer | 2019 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/30865299 |
| Lateral gene transfer between prokaryotes and eukaryotes. | Sieber KB, Bromley RE, Dunning Hotopp JC | Experimental cell research | 28189637 | Exp Cell Res | 2017 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/28189637 |
| Innovations in Instrumentation for Positron Emission Tomography. | Berg E, Cherry SR | Seminars in nuclear medicine | 29852942 | Semin Nucl Med | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29852942 |
| Total-Body Quantitative Parametric Imaging of Early Kinetics of (18)F-FDG. | Feng T, Zhao Y, Shi H, Li H, Zhang X, Wang G, Price PM, Badawi RD, Cherry SR, Jones T | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 32948679 | J Nucl Med | 2021 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/32948679 |
| Oncologic Applications of Long Axial Field-of-View PET/Computed Tomography. | Nardo L, Pantel AR | PET clinics | 33218605 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218605 |
| Numerical observer study of lesion detectability for a long axial field-of-view whole-body PET imager using the PennPET Explorer. | Viswanath V, Daube Witherspoon ME, Karp JS, Surti S | Physics in medicine and biology | 31816616 | Phys Med Biol | 2020 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/31816616 |
| Quantitative accuracy in total-body imaging using the uEXPLORER PET/CT scanner. | Leung EK, Berg E, Omidvari N, Spencer BA, Li E, Abdelhafez YG, Schmall JP, Liu W, He L, Tang S, Liu Y, Dong Y, Jones T, Cherry SR, Badawi RD | Physics in medicine and biology | 34544074 | Phys Med Biol | 2021 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/34544074 |
| PET Parametric Imaging: Past, Present, and Future. | Wang G, Rahmim A, Gunn RN | IEEE transactions on radiation and plasma medical sciences | 33763624 | IEEE Trans Radiat Plasma Med Sci | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33763624 |
| Exploring Vessel Wall Biology In Vivo by Ultrasensitive Total-Body PET. | Derlin T, Spencer BA, Mamach M, Abdelhafez Y, Nardo L, Badawi RD, Cherry SR, Bengel FM | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 36175139 | J Nucl Med | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36175139 |
| Performance Characteristics of Long Axial Field-of-View PET Scanners with Axial Gaps. | Daube-Witherspoon ME, Viswanath V, Werner ME, Karp JS | IEEE transactions on radiation and plasma medical sciences | 34179595 | IEEE Trans Radiat Plasma Med Sci | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/34179595 |
| Beyond skin deep: total-body positron emission tomography to illuminate systemic inflammation in psoriatic arthritis. | Chaudhari AJ, Abdelhafez YG, Nardo L, Raychaudhuri SP | Current opinion in immunology | 40543379 | Curr Opin Immunol | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40543379 |
| Optimization-derived blood input function using a kernel method and its evaluation with total-body PET for brain parametric imaging. | Zhu Y, Tran Q, Wang Y, Badawi RD, Cherry SR, Qi J, Abbaszadeh S, Wang G | NeuroImage | 38643890 | Neuroimage | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38643890 |
| Multimodal positron emission tomography (PET) imaging in non-oncologic musculoskeletal radiology. | Kogan F, Yoon D, Teeter MG, Chaudhari AJ, Hales L, Barbieri M, Gold GE, Vainberg Y, Goyal A, Watkins L | Skeletal radiology | 38492029 | Skeletal Radiol | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38492029 |
| Total-Body (18)F-FDG PET/CT in Autoimmune Inflammatory Arthritis at Ultra-Low Dose: Initial Observations. | Abdelhafez Y, Raychaudhuri SP, Mazza D, Sarkar S, Hunt HL, McBride K, Nguyen M, Caudle DT, Spencer BA, Omidvari N, Bang H, Cherry SR, Nardo L, Badawi RD, Chaudhari AJ | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 35589405 | J Nucl Med | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35589405 |
| Facial Anonymization and Privacy Concerns in Total-Body PET/CT. | Selfridge AR, Spencer BA, Abdelhafez YG, Nakagawa K, Tupin JD, Badawi RD | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37268426 | J Nucl Med | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37268426 |
| Total-Body Multiparametric PET Quantification of (18)F-FDG Delivery and Metabolism in the Study of Coronavirus Disease 2019 Recovery. | Wang Y, Nardo L, Spencer BA, Abdelhafez YG, Li EJ, Omidvari N, Chaudhari AJ, Badawi RD, Jones T, Cherry SR, Wang G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37591539 | J Nucl Med | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37591539 |
| First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody. | Omidvari N, Jones T, Price PM, Ferre AL, Lu J, Abdelhafez YG, Sen F, Cohen SH, Schmiedehausen K, Badawi RD, Shacklett BL, Wilson I, Cherry SR | Science advances | 37824612 | Sci Adv | 2023 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/37824612 |
| Total-Body Dynamic Reconstruction and Parametric Imaging on the uEXPLORER. | Zhang X, Xie Z, Berg E, Judenhofer MS, Liu W, Xu T, Ding Y, Lv Y, Dong Y, Deng Z, Tang S, Shi H, Hu P, Chen S, Bao J, Li H, Zhou J, Wang G, Cherry SR, Badawi RD, Qi J | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31302637 | J Nucl Med | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31302637 |
| Scanner Design Considerations for Long Axial Field-of-View PET Systems. | Daube-Witherspoon ME, Cherry SR | PET clinics | 33160929 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33160929 |
| Update on the PennPET Explorer: A Whole-body Imager with Scalable Axial Field-of-View. | Pantel AR, Viswanath V, Karp JS | PET clinics | 33218602 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218602 |
| 3D/4D Reconstruction and Quantitative Total Body Imaging. | Qi J, Matej S, Wang G, Zhang X | PET clinics | 33218603 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218603 |
| Development and Evaluation of mini-EXPLORER: A Long Axial Field-of-View PET Scanner for Nonhuman Primate Imaging. | Berg E, Zhang X, Bec J, Judenhofer MS, Patel B, Peng Q, Kapusta M, Schmand M, Casey ME, Tarantal AF, Qi J, Badawi RD, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 29419483 | J Nucl Med | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29419483 |
| Mini EXPLORER II: a prototype high-sensitivity PET/CT scanner for companion animal whole body and human brain scanning. | Lv Y, Lv X, Liu W, Judenhofer MS, Zwingenberger A, Wisner E, Berg E, McKenney S, Leung E, Spencer BA, Cherry SR, Badawi RD | Physics in medicine and biology | 30620929 | Phys Med Biol | 2019 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/30620929 |
| PennPET Explorer: Human Imaging on a Whole-Body Imager. | Pantel AR, Viswanath V, Daube-Witherspoon ME, Dubroff JG, Muehllehner G, Parma MJ, Pryma DA, Schubert EK, Mankoff DA, Karp JS | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31562224 | J Nucl Med | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31562224 |
| Total-Body PET: Maximizing Sensitivity to Create New Opportunities for Clinical Research and Patient Care. | Cherry SR, Jones T, Karp JS, Qi J, Moses WW, Badawi RD | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 28935835 | J Nucl Med | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28935835 |
| Total-body imaging: Transforming the role of positron emission tomography. | Cherry SR, Badawi RD, Karp JS, Moses WW, Price P, Jones T | Science translational medicine | 28298419 | Sci Transl Med | 2017 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/28298419 |
| Reaching 200-ps timing resolution in a time-of-flight and depth-of-interaction positron emission tomography detector using phosphor-coated crystals and high-density silicon photomultipliers. | Kwon SI, Ferri A, Gola A, Berg E, Piemonte C, Cherry SR, Roncali E | Journal of medical imaging (Bellingham, Wash.) | 27921069 | J Med Imaging (Bellingham) | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27921069 |
| First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody. | Omidvari N, Jones T, Price PM, Ferre AL, Lu J, Abdelhafez YG, Sen F, Cohen SH, Schmiedehausen K, Badawi RD, Shacklett BL, Wilson I, Cherry SR | medRxiv : the preprint server for health sciences | 36993568 | medRxiv | 2023 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/36993568 |
| Quantitative PET imaging and modeling of molecular blood-brain barrier permeability. | Chung KJ, Abdelhafez YG, Spencer BA, Jones T, Tran Q, Nardo L, Chen MS Jr, Sarkar S, Medici V, Lyo V, Badawi RD, Cherry SR, Wang G | Nature communications | 40159510 | Nat Commun | 2025 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/40159510 |
| Total-body positron emission tomography: a tool for systemic, quantitative evaluation of the inflammatory burden of psoriatic arthritis. | Raychaudhuri SP, Abdelhafez YG, Mazza DF, Raychaudhuri SK, Cherry SR, Nardo L, Badawi RD, Chaudhari AJ | Rheumatology (Oxford, England) | 39714258 | Rheumatology (Oxford) | 2025 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/39714258 |
| Parallax error in long-axial field-of-view PET scanners-a simulation study. | Schmall JP, Karp JS, Werner M, Surti S | Physics in medicine and biology | 27367971 | Phys Med Biol | 2016 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/27367971 |
| First Human Imaging Studies with the EXPLORER Total-Body PET Scanner. | Badawi RD, Shi H, Hu P, Chen S, Xu T, Price PM, Ding Y, Spencer BA, Nardo L, Liu W, Bao J, Jones T, Li H, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 30733314 | J Nucl Med | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30733314 |
| Theoretical study of the benefit of long axial field-of-view PET on region of interest quantification. | Zhang X, Badawi RD, Cherry SR, Qi J | Physics in medicine and biology | 29799814 | Phys Med Biol | 2018 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/29799814 |
| Performance assessment of a software-based coincidence processor for the EXPLORER total-body PET scanner. | Leung EK, Judenhofer MS, Cherry SR, Badawi RD | Physics in medicine and biology | 30152793 | Phys Med Biol | 2018 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/30152793 |
| Practical joint reconstruction of activity and attenuation with autonomous scaling for time-of-flight PET. | Li Y, Matej S, Karp JS | Physics in medicine and biology | 32340014 | Phys Med Biol | 2020 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/32340014 |
| Performance Evaluation of the uEXPLORER Total-Body PET/CT Scanner Based on NEMA NU 2-2018 with Additional Tests to Characterize PET Scanners with a Long Axial Field of View. | Spencer BA, Berg E, Schmall JP, Omidvari N, Leung EK, Abdelhafez YG, Tang S, Deng Z, Dong Y, Lv Y, Bao J, Liu W, Li H, Jones T, Badawi RD, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 33008932 | J Nucl Med | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/33008932 |
| Total-Body PET Kinetic Modeling and Potential Opportunities Using Deep Learning. | Wang Y, Li E, Cherry SR, Wang G | PET clinics | 34353745 | PET Clin | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34353745 |
| Total Body PET: Why, How, What for? | Surti S, Pantel AR, Karp JS | IEEE transactions on radiation and plasma medical sciences | 33134653 | IEEE Trans Radiat Plasma Med Sci | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/33134653 |
| Total-body PET/CT - First Clinical Experiences and Future Perspectives. | Ng QK, Triumbari EKA, Omidvari N, Cherry SR, Badawi RD, Nardo L | Seminars in nuclear medicine | 35272853 | Semin Nucl Med | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35272853 |
| Total-body Dynamic Imaging and Kinetic Modeling of (18)F-AraG in Healthy Individuals and a Non-Small Cell Lung Cancer Patient Undergoing Anti-PD-1 Immunotherapy. | Omidvari N, Levi J, Abdelhafez YG, Wang Y, Nardo L, Daly ME, Wang G, Cherry SR | medRxiv : the preprint server for health sciences | 37790461 | medRxiv | 2023 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/37790461 |
| Cloud-based serverless computing enables accelerated monte carlo simulations for nuclear medicine imaging. | Bayerlein R, Swarnakar V, Selfridge A, Spencer BA, Nardo L, Badawi RD | Biomedical physics & engineering express | 38876087 | Biomed Phys Eng Express | 2024 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/38876087 |
| Sharing a whole-/total-body [18F]FDG-PET/CT dataset with CT-derived segmentations: an ENHANCE.PET initiative. | Ferrara D, Pires M, Gutschmayer S, Yu J, Abdelhafez YG, Abenavoli E, Badawi RD, Chaudhari AJ, Chen MS Jr, Cherry SR, Frille A, Geist BK, Gruenert S, Hacker M, Hesse S, Kerkhoff T, Linder P, Pappisch J, Pusitz S, Raslan OA, Rausch I, Raychaudhuri SP, Sabri O, Schmidt F, Sciagrà R, Spencer B, Wang G, Wirtz H, Beyer T, Sundar LKS | Research square | 40799763 | Res Sq | 2025 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/40799763 |
| Advances in PET Diagnostics for Guiding Targeted Cancer Therapy and Studying In Vivo Cancer Biology. | Mankoff DA, Pantel AR, Viswanath V, Karp JS | Current pathobiology reports | 37092138 | Curr Pathobiol Rep | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37092138 |
| The role of brown adipose tissue in branched-chain amino acid clearance in people. | Abdelhafez YG, Wang G, Li S, Pellegrinelli V, Chaudhari AJ, Ramirez A, Sen F, Vidal-Puig A, Sidossis LS, Klein S, Badawi RD, Chondronikola M | iScience | 39175781 | iScience | 2024 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/39175781 |
| Quantitative Total-Body Imaging of Blood Flow with High Temporal Resolution Early Dynamic (18)F-Fluorodeoxyglucose PET Kinetic Modeling. | Chung KJ, Chaudhari AJ, Nardo L, Jones T, Chen MS Jr, Badawi RD, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 39252929 | medRxiv | 2024 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/39252929 |
| Quantitative image reconstruction for total-body PET imaging using the 2-meter long EXPLORER scanner. | Zhang X, Zhou J, Cherry SR, Badawi RD, Qi J | Physics in medicine and biology | 28240215 | Phys Med Biol | 2017 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/28240215 |
| Subsecond total-body imaging using ultrasensitive positron emission tomography. | Zhang X, Cherry SR, Xie Z, Shi H, Badawi RD, Qi J | Proceedings of the National Academy of Sciences of the United States of America | 31964808 | Proc Natl Acad Sci U S A | 2020 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/31964808 |
| Lutetium background radiation in total-body PET-A simulation study on opportunities and challenges in PET attenuation correction. | Omidvari N, Cheng L, Leung EK, Abdelhafez YG, Badawi RD, Ma T, Qi J, Cherry SR | Frontiers in nuclear medicine | 36172601 | Front Nucl Med | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36172601 |
| Quantitative PET imaging and modeling of molecular blood-brain barrier permeability. | Chung KJ, Abdelhafez YG, Spencer BA, Jones T, Tran Q, Nardo L, Chen MS Jr, Sarkar S, Medici V, Lyo V, Badawi RD, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 39108503 | medRxiv | 2024 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/39108503 |
| Role of Total Body PET/CT in Inflammatory Disorders. | Zoghi S, Mingels C, Badawi RD, Spencer BA, Yarbrough TL, Nardo L, Chaudhari AJ | Seminars in nuclear medicine | 39578110 | Semin Nucl Med | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39578110 |
| Clinical Implementation of Total-Body PET/CT at University of California, Davis. | Nardo L, Abdelhafez YG, Spencer BA, Badawi RD | PET clinics | 33218600 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218600 |
| Analysis of Four-Dimensional Data for Total Body PET Imaging. | Viswanath V, Chitalia R, Pantel AR, Karp JS, Mankoff DA | PET clinics | 33218604 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218604 |
| Quantitative PET in the 2020s: a roadmap. | Meikle SR, Sossi V, Roncali E, Cherry SR, Banati R, Mankoff D, Jones T, James M, Sutcliffe J, Ouyang J, Petibon Y, Ma C, El Fakhri G, Surti S, Karp JS, Badawi RD, Yamaya T, Akamatsu G, Schramm G, Rezaei A, Nuyts J, Fulton R, Kyme A, Lois C, Sari H, Price J, Boellaard R, Jeraj R, Bailey DL, Eslick E, Willowson KP, Dutta J | Physics in medicine and biology | 33339012 | Phys Med Biol | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/33339012 |
| PennPET Explorer: Design and Preliminary Performance of a Whole-Body Imager. | Karp JS, Viswanath V, Geagan MJ, Muehllehner G, Pantel AR, Parma MJ, Perkins AE, Schmall JP, Werner ME, Daube-Witherspoon ME | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31227573 | J Nucl Med | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31227573 |
| Impact of event positioning algorithm on performance of a whole-body PET scanner using one-to-one coupled detectors. | Surti S, Karp JS | Physics in medicine and biology | 29411709 | Phys Med Biol | 2018 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/29411709 |
| Total-Body Multiparametric PET Quantification of (18) F-FDG Delivery and Metabolism in the Study of COVID-19 Recovery. | Wang Y, Nardo L, Spencer BA, Abdelhafez YG, Li EJ, Omidvari N, Chaudhari AJ, Badawi RD, Jones T, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 37034643 | medRxiv | 2023 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/37034643 |
| High-Temporal-Resolution Lung Kinetic Modeling Using Total-Body Dynamic PET with Time-Delay and Dispersion Corrections. | Wang Y, Spencer BA, Schmall J, Li E, Badawi RD, Jones T, Cherry SR, Wang G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37116916 | J Nucl Med | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37116916 |
| Relating(18)F-FDG image signal-to-noise ratio to time-of-flight noise-equivalent count rate in total-body PET using the uEXPLORER scanner. | Leung EK, Abdelhafez YG, Berg E, Xie Z, Zhang X, Bayerlein R, Spencer B, Li E, Omidvari N, Selfridge A, Cherry SR, Qi J, Badawi RD | Physics in medicine and biology | 35609588 | Phys Med Biol | 2022 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/35609588 |
| EXPLORing Arthritis with Total-body Positron Emission Tomography. | Chaudhari AJ, Abdelhafez YG, Nardo L, Raychaudhuri SP | Seminars in musculoskeletal radiology | 37935209 | Semin Musculoskelet Radiol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37935209 |
| Total-Body Perfusion Imaging with [(11)C]-Butanol. | Li EJ, López JE, Spencer BA, Abdelhafez Y, Badawi RD, Wang G, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37652544 | J Nucl Med | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37652544 |
| Numerical investigation reveals challenges in measuring the contrast recovery coefficients in PET. | Bayerlein R, Spencer BA, Abdelhafez YG, Cherry SR, Badawi RD, Omidvari N | Physics in medicine and biology | 37802064 | Phys Med Biol | 2023 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/37802064 |
| CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. | Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A | Scientific reports | 28389661 | Sci Rep | 2017 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/28389661 |
| Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. | Roybal KT, Williams JZ, Morsut L, Rupp LJ, Kolinko I, Choe JH, Walker WJ, McNally KA, Lim WA | Cell | 27693353 | Cell | 2016 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/27693353 |
| T cells selectively filter oscillatory signals on the minutes timescale. | O'Donoghue GP, Bugaj LJ, Anderson W, Daniels KG, Rawlings DJ, Lim WA | Proceedings of the National Academy of Sciences of the United States of America | 33627405 | Proc Natl Acad Sci U S A | 2021 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/33627405 |
| Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies. | Dannenfelser R, Allen GM, VanderSluis B, Koegel AK, Levinson S, Stark SR, Yao V, Tadych A, Troyanskaya OG, Lim WA | Cell systems | 32916097 | Cell Syst | 2020 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/32916097 |
| Engineering cytokines and cytokine circuits. | Li AW, Lim WA | Science (New York, N.Y.) | 33243875 | Science | 2020 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/33243875 |
| Precise T cell recognition programs designed by transcriptionally linking multiple receptors. | Williams JZ, Allen GM, Shah D, Sterin IS, Kim KH, Garcia VP, Shavey GE, Yu W, Puig-Saus C, Tsoi J, Ribas A, Roybal KT, Lim WA | Science (New York, N.Y.) | 33243890 | Science | 2020 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/33243890 |
| The Principles of Engineering Immune Cells to Treat Cancer. | Lim WA, June CH | Cell | 28187291 | Cell | 2017 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/28187291 |
| Modular engineering of cellular signaling proteins and networks. | Gordley RM, Bugaj LJ, Lim WA | Current opinion in structural biology | 27423114 | Curr Opin Struct Biol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27423114 |
| Synthetic cytokine circuits that drive T cells into immune-excluded tumors. | Allen GM, Frankel NW, Reddy NR, Bhargava HK, Yoshida MA, Stark SR, Purl M, Lee J, Yee JL, Yu W, Li AW, Garcia KC, El-Samad H, Roybal KT, Spitzer MH, Lim WA | Science (New York, N.Y.) | 36520915 | Science | 2022 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/36520915 |
| Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits. | Roybal KT, Rupp LJ, Morsut L, Walker WJ, McNally KA, Park JS, Lim WA | Cell | 26830879 | Cell | 2016 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/26830879 |
| Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. | Roybal KT, Lim WA | Annual review of immunology | 28446063 | Annu Rev Immunol | 2017 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/28446063 |
| Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials. | Esensten JH, Bluestone JA, Lim WA | Annual review of pathology | 27959633 | Annu Rev Pathol | 2017 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/27959633 |
| Remote control of therapeutic T cells through a small molecule-gated chimeric receptor. | Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA | Science (New York, N.Y.) | 26405231 | Science | 2015 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/26405231 |
| Synthetic biology approaches to engineer T cells. | Wu CY, Rupp LJ, Roybal KT, Lim WA | Current opinion in immunology | 26218616 | Curr Opin Immunol | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26218616 |
| Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. | Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA | Cell | 26830878 | Cell | 2016 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/26830878 |
| T cell circuits that sense antigen density with an ultrasensitive threshold. | Hernandez-Lopez RA, Yu W, Cabral KA, Creasey OA, Lopez Pazmino MDP, Tonai Y, De Guzman A, Mäkelä A, Saksela K, Gartner ZJ, Lim WA | Science (New York, N.Y.) | 33632893 | Science | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/33632893 |
| SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma. | Choe JH, Watchmaker PB, Simic MS, Gilbert RD, Li AW, Krasnow NA, Downey KM, Yu W, Carrera DA, Celli A, Cho J, Briones JD, Duecker JM, Goretsky YE, Dannenfelser R, Cardarelli L, Troyanskaya O, Sidhu SS, Roybal KT, Okada H, Lim WA | Science translational medicine | 33910979 | Sci Transl Med | 2021 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/33910979 |
| Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. | Boettcher M, McManus MT | Molecular cell | 26000843 | Mol Cell | 2015 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/26000843 |
| Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. | Loh KH, Stawski PS, Draycott AS, Udeshi ND, Lehrman EK, Wilton DK, Svinkina T, Deerinck TJ, Ellisman MH, Stevens B, Carr SA, Ting AY | Cell | 27565350 | Cell | 2016 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/27565350 |
| Directed Evolution of Split APEX2 Peroxidase. | Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A | ACS chemical biology | 30848125 | ACS Chem Biol | 2019 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/30848125 |
| Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. | Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC | eLife | 31535972 | Elife | 2019 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/31535972 |
| A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. | Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY | Nature biotechnology | 27240195 | Nat Biotechnol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27240195 |
| Proximity labeling: spatially resolved proteomic mapping for neurobiology. | Han S, Li J, Ting AY | Current opinion in neurobiology | 29125959 | Curr Opin Neurobiol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29125959 |
| Atlas of Subcellular RNA Localization Revealed by APEX-Seq. | Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY | Cell | 31230715 | Cell | 2019 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/31230715 |
| Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics. | Kim TW, Park CH, Hsu CC, Kim YW, Ko YW, Zhang Z, Zhu JY, Hsiao YC, Branon T, Kaasik K, Saldivar E, Li K, Pasha A, Provart NJ, Burlingame AL, Xu SL, Ting AY, Wang ZY | The Plant cell | 36660928 | Plant Cell | 2023 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/36660928 |
| Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. | Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY | eLife | 28441135 | Elife | 2017 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/28441135 |
| Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. | Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY | eLife | 29239719 | Elife | 2017 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/29239719 |
| Efficient proximity labeling in living cells and organisms with TurboID. | Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY | Nature biotechnology | 30125270 | Nat Biotechnol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30125270 |
| Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. | Martell JD, Deerinck TJ, Lam SS, Ellisman MH, Ting AY | Nature protocols | 28796234 | Nat Protoc | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28796234 |
| Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. | Han S, Udeshi ND, Deerinck TJ, Svinkina T, Ellisman MH, Carr SA, Ting AY | Cell chemical biology | 28238724 | Cell Chem Biol | 2017 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/28238724 |
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| Nanoparticle-mediated combinatorial targeting of multiple human dendritic cell (DC) subsets leads to enhanced T cell activation via IL-15-dependent DC crosstalk. | Sehgal K, Ragheb R, Fahmy TM, Dhodapkar MV, Dhodapkar KM | Journal of immunology (Baltimore, Md. : 1950) | 25080481 | J Immunol | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/25080481 |
| Human hemato-lymphoid system mice: current use and future potential for medicine. | Rongvaux A, Takizawa H, Strowig T, Willinger T, Eynon EE, Flavell RA, Manz MG | Annual review of immunology | 23330956 | Annu Rev Immunol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23330956 |
| Clonal Immunoglobulin against Lysolipids in the Origin of Myeloma. | Nair S, Branagan AR, Liu J, Boddupalli CS, Mistry PK, Dhodapkar MV | The New England journal of medicine | 26863356 | N Engl J Med | 2016 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/26863356 |
| inv(16) and NPM1mut AMLs engraft human cytokine knock-in mice. | Ellegast JM, Rauch PJ, Kovtonyuk LV, Müller R, Wagner U, Saito Y, Wildner-Verhey van Wijk N, Fritz C, Rafiei A, Lysenko V, Dudkiewicz E, Theocharides AP, Soldini D, Goede JS, Flavell RA, Manz MG | Blood | 27581357 | Blood | 2016 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/27581357 |
| The Ability of Narrative Communication to Address Health-related Social Norms. | Moran MB, Murphy ST, Frank L, Baezconde-Garbanati L | International Review of Social Research | 24179677 | Int Rev Soc Res | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24179677 |
| Reducing the Excess Burden of Cervical Cancer Among Latinas: Translating Science into Health Promotion Initiatives. | Baezconde-Garbanati L, Murphy ST, Moran MB, Cortessis VK | Californian journal of health promotion | 24587769 | Calif J Health Promot | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24587769 |
| Narrative versus Non-narrative: The Role of Identification, Transportation and Emotion in Reducing Health Disparities. | Murphy ST, Frank LB, Chatterjee JS, Baezconde-Garbanati L | The Journal of communication | 24347679 | J Commun | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24347679 |
| Self-Construal as a Predictor of Korean American Women's Intention to Vaccinate Daughters against Human Papillomavirus. | Zhao N, Huh J, Murphy ST, Chatterjee JS, Baezconde-Garbanati L | Asian American journal of psychology | 25558309 | Asian Am J Psychol | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25558309 |
| Barriers and innovative interventions for early detection of cervical cancer. | Baezconde-Garbanati L, Agurto I, Gravitt PE, Luciani S, Murphy S, Ochoa C, Gallegos K, Barahona R, Rodríguez Y | Salud publica de Mexico | 31430087 | Salud Publica Mex | 2019 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/31430087 |
| Implementation of HPV vaccination guidelines in a diverse population in Los Angeles: Results from an environmental scan of local HPV resources and needs. | Baezconde-Garbanati L, Lienemann BA, Robles M, Johnson E, Sanchez K, Singhal R, Steinberg J, Jaque JM, Pentz MA, Gruber S | Vaccine | 28774559 | Vaccine | 2017 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/28774559 |
| A pilot test of the acceptability and efficacy of narrative and non-narrative health education materials in a low health literacy population. | Moran MB, Frank LB, Chatterjee JS, Murphy ST, Baezconde-Garbanati L | Journal of communication in healthcare | 27872657 | J Commun Healthc | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27872657 |
| Information scanning and vaccine safety concerns among African American, Mexican American, and non-Hispanic White women. | Moran MB, Frank LB, Chatterjee JS, Murphy ST, Baezconde-Garbanati L | Patient education and counseling | 26321294 | Patient Educ Couns | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26321294 |
| Public Diplomacy in Prime Time: Exploring the Potential of Entertainment Education in International Public Diplomacy. | Murphy ST, Hether HJ, Felt LJ, de Castro Buffington S | American journal of media psychology | 24489980 | Am J Media Psychol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/24489980 |
| Portrayals of reproductive and sexual health on prime-time television. | Pariera KL, Hether HJ, Murphy ST, Buffington Sde C, Baezconde-Garbanati L | Health communication | 24156468 | Health Commun | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24156468 |
| Each Medium Tells a Different Story: The Effect of Message Channel on Narrative Persuasion. | Walter N, Murphy ST, Frank LB, Baezconde-Garbanati L | Communication research reports : CRR | 30739986 | Commun Res Rep | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/30739986 |
| Assessing impact of a community-based screening campaign to address social determinants of cervical cancer. | Po J, Bookstein A, Lee W, Barahona R, Baezconde-Garbanati L | JNCI cancer spectrum | 39888858 | JNCI Cancer Spectr | 2025 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/39888858 |
| Comparing the Relative Efficacy of Narrative vs Nonnarrative Health Messages in Reducing Health Disparities Using a Randomized Trial. | Murphy ST, Frank LB, Chatterjee JS, Moran MB, Zhao N, Amezola de Herrera P, Baezconde-Garbanati LA | American journal of public health | 25905845 | Am J Public Health | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25905845 |
| Telling stories, saving lives: creating narrative health messages. | Frank LB, Murphy ST, Chatterjee JS, Moran MB, Baezconde-Garbanati L | Health communication | 25470440 | Health Commun | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25470440 |
| Using a Culturally Tailored Narrative to Increase Cervical Cancer Detection Among Spanish-Speaking Mexican-American Women. | Ochoa CY, Murphy ST, Frank LB, Baezconde-Garbanati LA | Journal of cancer education : the official journal of the American Association for Cancer Education | 31020621 | J Cancer Educ | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31020621 |
| The strategy, organization, and progress of the HUPO Human Proteome Project. | Omenn GS | Journal of proteomics | 24145142 | J Proteomics | 2014 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/24145142 |
| Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. | Menon R, Im H, Zhang EY, Wu SL, Chen R, Snyder M, Hancock WS, Omenn GS | Journal of proteome research | 24111759 | J Proteome Res | 2014 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/24111759 |
| Expression of human endogenous retrovirus type K (HML-2) is activated by the Tat protein of HIV-1. | Gonzalez-Hernandez MJ, Swanson MD, Contreras-Galindo R, Cookinham S, King SR, Noel RJ Jr, Kaplan MH, Markovitz DM | Journal of virology | 22593154 | J Virol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22593154 |
| Human endogenous retrovirus K Gag coassembles with HIV-1 Gag and reduces the release efficiency and infectivity of HIV-1. | Monde K, Contreras-Galindo R, Kaplan MH, Markovitz DM, Ono A | Journal of virology | 22855497 | J Virol | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22855497 |
| Characterization of human endogenous retroviral elements in the blood of HIV-1-infected individuals. | Contreras-Galindo R, Kaplan MH, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Ferlenghi I, Giusti F, Lorenzo E, Gitlin SD, Dosik MH, Yamamura Y, Markovitz DM | Journal of virology | 22031938 | J Virol | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22031938 |
| Rapid molecular assays to study human centromere genomics. | Contreras-Galindo R, Fischer S, Saha AK, Lundy JD, Cervantes PW, Mourad M, Wang C, Qian B, Dai M, Meng F, Chinnaiyan A, Omenn GS, Kaplan MH, Markovitz DM | Genome research | 29141960 | Genome Res | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29141960 |
| NGSQC: cross-platform quality analysis pipeline for deep sequencing data. | Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F | BMC genomics | 21143816 | BMC Genomics | 2010 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/21143816 |
| Expansion of a novel endogenous retrovirus throughout the pericentromeres of modern humans. | Zahn J, Kaplan MH, Fischer S, Dai M, Meng F, Saha AK, Cervantes P, Chan SM, Dube D, Omenn GS, Markovitz DM, Contreras-Galindo R | Genome biology | 25886262 | Genome Biol | 2015 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/25886262 |
| Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. | Omenn GS, Menon R, Zhang Y | Journal of proteomics | 23603631 | J Proteomics | 2013 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/23603631 |
| Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein. | Gonzalez-Hernandez MJ, Cavalcoli JD, Sartor MA, Contreras-Galindo R, Meng F, Dai M, Dube D, Saha AK, Gitlin SD, Omenn GS, Kaplan MH, Markovitz DM | Journal of virology | 24872592 | J Virol | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24872592 |
| HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. | Contreras-Galindo R, Kaplan MH, He S, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Kappes F, Dube D, Chan SM, Robinson D, Meng F, Dai M, Gitlin SD, Chinnaiyan AM, Omenn GS, Markovitz DM | Genome research | 23657884 | Genome Res | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23657884 |
| Genomic flexibility of human endogenous retrovirus type K. | Dube D, Contreras-Galindo R, He S, King SR, Gonzalez-Hernandez MJ, Gitlin SD, Kaplan MH, Markovitz DM | Journal of virology | 24920813 | J Virol | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/24920813 |
| Susceptibility of Human Endogenous Retrovirus Type K to Reverse Transcriptase Inhibitors. | Contreras-Galindo R, Dube D, Fujinaga K, Kaplan MH, Markovitz DM | Journal of virology | 28931682 | J Virol | 2017 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/28931682 |
| Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. | Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS | Journal of proteome research | 24364385 | J Proteome Res | 2014 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/24364385 |
| A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. | Omenn GS, Guan Y, Menon R | Journal of proteomics | 24802673 | J Proteomics | 2014 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/24802673 |
| "Reverse genomics" and human endogenous retroviruses. | Markovitz DM | Transactions of the American Clinical and Climatological Association | 25125718 | Trans Am Clin Climatol Assoc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25125718 |
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| Strategies for Genomic and Proteomic Profiling of Cancers. | Omenn GS | Statistics in biosciences | 27594925 | Stat Biosci | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27594925 |
| The Genomic Landscape of Centromeres in Cancers. | Saha AK, Mourad M, Kaplan MH, Chefetz I, Malek SN, Buckanovich R, Markovitz DM, Contreras-Galindo R | Scientific reports | 31375789 | Sci Rep | 2019 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/31375789 |
| Genetic Variants in Epigenetic Pathways and Risks of Multiple Cancers in the GAME-ON Consortium. | Toth R, Scherer D, Kelemen LE, Risch A, Hazra A, Balavarca Y, Issa JJ, Moreno V, Eeles RA, Ogino S, Wu X, Ye Y, Hung RJ, Goode EL, Ulrich CM, OCAC, CORECT, TRICL, ELLIPSE, DRIVE, and GAME-ON consortia | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 28115406 | Cancer Epidemiol Biomarkers Prev | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28115406 |
| A Germline Variant on Chromosome 4q31.1 Associates with Susceptibility to Developing Colon Cancer Metastasis. | Markowitz SD, Nock NL, Schmit SL, Stadler ZK, Joseph V, Zhang L, Willis JE, Scacheri P, Veigl M, Adams MD, Raskin L, Sullivan JF, Stratton K, Shia J, Ellis N, Rennert HS, Manschreck C, Li L, Offit K, Elston RC, Rennert G, Gruber SB | PloS one | 26751797 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26751797 |
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| Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects. | Guo X, Lin W, Wen W, Huyghe J, Bien S, Cai Q, Harrison T, Chen Z, Qu C, Bao J, Long J, Yuan Y, Wang F, Bai M, Abecasis GR, Albanes D, Berndt SI, Bézieau S, Bishop DT, Brenner H, Buch S, Burnett-Hartman A, Campbell PT, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Cho SH, Conti DV, Chapelle A, Feskens EJM, Gallinger SJ, Giles GG, Goodman PJ, Gsur A, Guinter M, Gunter MJ, Hampe J, Hampel H, Hayes RB, Hoffmeister M, Kampman E, Kang HM, Keku TO, Kim HR, Le Marchand L, Lee SC, Li CI, Li L, Lindblom A, Lindor N, Milne RL, Moreno V, Murphy N, Newcomb PA, Nickerson DA, Offit K, Pearlman R, Pharoah PDP, Platz EA, Potter JD, Rennert G, Sakoda LC, Schafmayer C, Schmit SL, Schoen RE, Schumacher FR, Slattery ML, Su YR, Tangen CM, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Wang X, White E, Wolk A, Woods MO, Casey G, Hsu L, Jenkins MA, Gruber SB, Peters U, Zheng W | Gastroenterology | 33058866 | Gastroenterology | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33058866 |
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| Nonadditive Effects of Common Genetic Variants Have a Negligent Contribution to Cancer Heritability. | Hammermeister Suger A, Harrison TA, Henning B, Turman C, Kraft P, Lindström S | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 39018351 | Cancer Epidemiol Biomarkers Prev | 2024 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/39018351 |
| IgG-seq identifies immune-reactive enteric bacteria in Crohn's disease with spondyloarthritis. | Maldarelli GA, Metz M, Oguntunmibi S, Tran N, Xiang G, Lukin D, Scherl EJ, Longman RS | Gut microbes | 39949039 | Gut Microbes | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39949039 |
| Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity. | Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ | Cell | 40239649 | Cell | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40239649 |
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| Precision microbiota therapy for IBD: premise and promise. | Nagayama M, Gogokhia L, Longman RS | Gut microbes | 40190259 | Gut Microbes | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/40190259 |
| Microbiota-mediated mechanisms of mucosal immunity across the lifespan. | Iliev ID, Blander JM, Collins N, Guo CJ, Longman RS, Sonnenberg GF, Zeng MY, Artis D | Nature immunology | 40957908 | Nat Immunol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40957908 |
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| Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions. | Omelchenko AA, Siwek JC, Chhibbar P, Arshad S, Nazarali I, Nazarali K, Rosengart A, Rahimikollu J, Tilstra J, Shlomchik MJ, Koes DR, Joglekar AV, Das J | bioRxiv : the preprint server for biology | 38746274 | bioRxiv | 2024 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/38746274 |
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| Predicting Differentially Methylated Cytosines in TET and DNMT3 Knockout Mutants via a Large Language Model. | Sereshki S, Lonardi S | bioRxiv : the preprint server for biology | 39282350 | bioRxiv | 2024 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/39282350 |
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| Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights. | Barroso da Silva FL, Paco K, Laaksonen A, Ray A | Biophysical reviews | 40376405 | Biophys Rev | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40376405 |
| Genome resource announcement of a Leptodophora sp. fungus isolated from roots of broadleaf plants in Wisconsin, USA. | Yang T, Certano A, Lakshmanan V, Bassi S, Purushotham N, Nock T, Chaudhury A, Ray A | Microbiology resource announcements | 40698949 | Microbiol Resour Announc | 2025 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/40698949 |
| Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model. | Sereshki S, Lonardi S | Briefings in bioinformatics | 40079264 | Brief Bioinform | 2025 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/40079264 |
| RAmbler resolves complex repeats in human Chromosomes 8, 19, and X. | Chakravarty S, Logsdon G, Lonardi S | Genome research | 40037839 | Genome Res | 2025 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/40037839 |
| A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters. | Chaturvedi S, Beutler N, Vasen G, Pablo M, Chen X, Calia G, Buie L, Rodick R, Smith D, Rogers T, Weinberger LS | Proceedings of the National Academy of Sciences of the United States of America | 36074824 | Proc Natl Acad Sci U S A | 2022 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/36074824 |
| Identification of a therapeutic interfering particle-A single-dose SARS-CoV-2 antiviral intervention with a high barrier to resistance. | Chaturvedi S, Vasen G, Pablo M, Chen X, Beutler N, Kumar A, Tanner E, Illouz S, Rahgoshay D, Burnett J, Holguin L, Chen PY, Ndjamen B, Ott M, Rodick R, Rogers T, Smith DM, Weinberger LS | Cell | 34838159 | Cell | 2021 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/34838159 |
| Myeloperoxidase Inhibition Ameliorates Plaque Psoriasis in Mice. | Neu SD, Strzepa A, Martin D, Sorci-Thomas MG, Pritchard KA Jr, Dittel BN | Antioxidants (Basel, Switzerland) | 34572970 | Antioxidants (Basel) | 2021 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/34572970 |
| Negative Data, Oh No What Should I Do? How Publication of Negative Data Removes Roadblocks to Productive Research from the Perspective of Scientists Who Perform the Experiments. | Beltrame AK, Caldon JJ, Gurski CJ, Hajiyeva Z, Meinhardt NJ, Sommers KC, Neu SD, Dittel BN | ImmunoHorizons | 37252801 | Immunohorizons | 2023 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/37252801 |
| Ingested (Oral) Adrenocorticotropic Hormone Inhibits IL-17 in the Central Nervous System in the Mouse Model of Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis. | Dittel LJ, Dittel BN, Brod SA | ImmunoHorizons | 35868840 | Immunohorizons | 2022 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/35868840 |
| Characterization of Definitive Regulatory B Cell Subsets by Cell Surface Phenotype, Function and Context. | Neu SD, Dittel BN | Frontiers in immunology | 34987513 | Front Immunol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34987513 |
| Conserved Gammaherpesvirus Protein Kinase Counters the Antiviral Effects of Myeloid Cell-Specific STAT1 Expression To Promote the Establishment of Splenic B Cell Latency. | Sylvester PA, Jondle CN, Stoltz KP, Lanham J, Dittel BN, Tarakanova VL | Journal of virology | 34132573 | J Virol | 2021 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/34132573 |
| Myeloperoxidase as a Marker to Differentiate Mouse Monocyte/Macrophage Subsets. | Gurski CJ, Dittel BN | International journal of molecular sciences | 35897821 | Int J Mol Sci | 2022 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/35897821 |
| T Cell-Specific STAT1 Expression Promotes Lytic Replication and Supports the Establishment of Gammaherpesvirus Latent Reservoir in Splenic B Cells. | Sylvester PA, Jondle CN, Schmalzriedt DL, Dittel BN, Tarakanova VL | mBio | 35968944 | mBio | 2022 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/35968944 |
| Elevated frequencies of activated memory B cells in multiple sclerosis are reset to healthy control levels after B cell depletion with Ocrelizumab. | Gurski CJ, Hajiyeva Z, Veltri AJ, Fenton K, O'Dell S, Obeidat AZ, Dittel BN | Journal of neuroimmunology | 39643951 | J Neuroimmunol | 2025 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/39643951 |
| Gut IgA-antibody secreting cells segregate into four Blimp1+ subsets based on differential expression of IgA and Ki-67 and are retained following prolonged αCD20 B cell depletion in mice. | Neu SD, Gurski CJ, Meinhardt NJ, Jennings KC, Dittel BN | Journal of immunology (Baltimore, Md. : 1950) | 40073093 | J Immunol | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40073093 |
| Targeting transmembrane-domain-less MOG expression to platelets prevents disease development in experimental autoimmune encephalomyelitis. | Cai Y, Schroeder JA, Jing W, Gurski C, Williams CB, Wang S, Dittel BN, Shi Q | Frontiers in immunology | 36389708 | Front Immunol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36389708 |
| 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 |
| 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 |
| Tracking and predicting the African COVID-19 pandemic. | Ssentongo P, Fronterre C, Geronimo A, Greybush SJ, Mbabazi PK, Muvawala J, Nahalamba SB, Omadi PO, Opar BT, Sinnar SA, Wang Y, Whalen AJ, Held L, Jewell C, Muwanguzi AJB, Greatrex H, Norton MM, Diggle P, Schiff SJ | medRxiv : the preprint server for health sciences | 33236036 | medRxiv | 2020 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/33236036 |
| 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 |
| Normal childhood brain growth and a universal sex and anthropomorphic relationship to cerebrospinal fluid. | Peterson MR, Cherukuri V, Paulson JN, Ssentongo P, Kulkarni AV, Warf BC, Monga V, Schiff SJ | Journal of neurosurgery. Pediatrics | 34243147 | J Neurosurg Pediatr | 2021 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/34243147 |
| Short-term and Long-term Rates of Postacute Sequelae of SARS-CoV-2 Infection: A Systematic Review. | Groff D, Sun A, Ssentongo AE, Ba DM, Parsons N, Poudel GR, Lekoubou A, Oh JS, Ericson JE, Ssentongo P, Chinchilli VM | JAMA network open | 34643720 | JAMA Netw Open | 2021 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/34643720 |
| Differential richness inference for 16S rRNA marker gene surveys. | Kumar MS, Slud EV, Hehnly C, Zhang L, Broach J, Irizarry RA, Schiff SJ, Paulson JN | Genome biology | 35915508 | Genome Biol | 2022 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/35915508 |
| Brain growth after surgical treatment for infant postinfectious hydrocephalus in Sub-Saharan Africa: 2-year results of a randomized trial. | Schiff SJ, Kulkarni AV, Mbabazi-Kabachelor E, Mugamba J, Ssenyonga P, Donnelly R, Levenbach J, Monga V, Peterson M, Cherukuri V, Warf BC | Journal of neurosurgery. Pediatrics | 34243157 | J Neurosurg Pediatr | 2021 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/34243157 |
| Rates and risk factors for suicidal ideation, suicide attempts and suicide deaths in persons with HIV: a systematic review and meta-analysis. | Pelton M, Ciarletta M, Wisnousky H, Lazzara N, Manglani M, Ba DM, Chinchillli VM, Du P, Ssentongo AE, Ssentongo P | General psychiatry | 33912798 | Gen Psychiatr | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33912798 |
| Poisson Kalman filter for disease surveillance. | Ebeigbe D, Berry T, Schiff SJ, Sauer T | Physical review research | 39211287 | Phys Rev Res | 2020 Oct-Dec | https://www.ncbi.nlm.nih.gov/pubmed/39211287 |
| Engineering Principles and Bioengineering in Global Health. | Harper JR, Schiff SJ | Neurosurgery clinics of North America | 39244320 | Neurosurg Clin N Am | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39244320 |
| Infection diagnosis in hydrocephalus CT images: a domain enriched attention learning approach. | Yu M, Peterson MR, Cherukuri V, Hehnly C, Mbabazi-Kabachelor E, Mulondo R, Nsubuga Kaaya B, Broach JR, Schiff SJ, Monga V | Journal of neural engineering | 37253355 | J Neural Eng | 2023 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/37253355 |
| 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 | |
| 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 |
| Pan-African evolution of within- and between-country COVID-19 dynamics. | Ssentongo P, Fronterre C, Geronimo A, Greybush SJ, Mbabazi PK, Muvawala J, Nahalamba SB, Omadi PO, Opar BT, Sinnar SA, Wang Y, Whalen AJ, Held L, Jewell C, Muwanguzi AJB, Greatrex H, Norton MM, Diggle PJ, Schiff SJ | Proceedings of the National Academy of Sciences of the United States of America | 34187879 | Proc Natl Acad Sci U S A | 2021 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/34187879 |
| Congenital Cytomegalovirus Infection Burden and Epidemiologic Risk Factors in Countries With Universal Screening: A Systematic Review and Meta-analysis. | Ssentongo P, Hehnly C, Birungi P, Roach MA, Spady J, Fronterre C, Wang M, Murray-Kolb LE, Al-Shaar L, Chinchilli VM, Broach JR, Ericson JE, Schiff SJ | JAMA network open | 34424308 | JAMA Netw Open | 2021 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/34424308 |
| A Generalized Unscented Transformation for Probability Distributions. | Ebeigbe D, Berry T, Norton MM, Whalen AJ, Simon D, Sauer T, Schiff SJ | ArXiv | 33850954 | ArXiv | 2021 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/33850954 |
| Prevalence and determinants of cervical cancer screening in five sub-Saharan African countries: A population-based study. | Ba DM, Ssentongo P, Musa J, Agbese E, Diakite B, Traore CB, Wang S, Maiga M | Cancer epidemiology | 33756434 | Cancer Epidemiol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33756434 |
| 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 |
| Brain imaging with portable low-field MRI. | Kimberly WT, Sorby-Adams AJ, Webb AG, Wu EX, Beekman R, Bowry R, Schiff SJ, de Havenon A, Shen FX, Sze G, Schaefer P, Iglesias JE, Rosen MS, Sheth KN | Nature reviews bioengineering | 37705717 | Nat Rev Bioeng | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37705717 |
| 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 |
| Verification of operational numerical weather prediction model forecasts of precipitation using satellite rainfall estimates over Africa. | Wang Y, Gueye M, Greybush SJ, Greatrex H, Whalen AJ, Ssentongo P, Zhang F, Jenkins GS, Schiff SJ | Meteorological applications | 39554903 | Meteorol Appl | 2023 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/39554903 |
| Five-year outcomes after surgical treatment of infant postinfectious hydrocephalus in sub-Saharan Africa: results of a randomized trial. | Mbabazi-Kabachelor E, Peterson MR, Mugamba J, Ssenyonga P, Onen J, Nalule E, Magombe J, Cherukuri V, Monga V, Schiff SJ, Kulkarni AV, Warf BC | Journal of neurosurgery. Pediatrics | 40315611 | J Neurosurg Pediatr | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/40315611 |
| Generalized unscented transformation for forecasting non-Gaussian processes. | Ebeigbe D, Berry T, Whalen AJ, Norton MM, Simon D, Sauer TD, Schiff SJ | Physical review. E | 40533957 | Phys Rev E | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40533957 |
| Gun violence incidence during the COVID-19 pandemic is higher than before the pandemic in the United States. | Ssentongo P, Fronterre C, Ssentongo AE, Advani S, Heilbrunn ES, Hazelton JP, Oh JS, McCall-Hosenfeld JS, Chinchilli VM | Scientific reports | 34675321 | Sci Rep | 2021 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/34675321 |
| 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 |
| 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 |
| 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 |
| IDENTIFIABILITY OF INFECTION MODEL PARAMETERS EARLY IN AN EPIDEMIC. | Sauer T, Berry T, Ebeigbe D, Norton MM, Whalen AJ, Schiff SJ | SIAM journal on control and optimization | 36338855 | SIAM J Control Optim | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36338855 |
| Stabilizing the return to normal behavior in an epidemic. | Berry T, Ferrari M, Sauer T, Greybush SJ, Ebeigbe D, Whalen AJ, Schiff SJ | medRxiv : the preprint server for health sciences | 36993470 | medRxiv | 2023 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/36993470 |
| 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 |
| Preconception and Prenatal Environment and Growth Faltering Among Children in Uganda. | Ssentongo P, Fronterre C, Ericson JE, Wang M, Al-Shaar L, Greatrex H, Omadi PO, Muvawala J, Greybush SJ, Mbabazi PK, Murray-Kolb LE, Muwanguzi AJB, Schiff SJ | JAMA network open | 40105840 | JAMA Netw Open | 2025 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/40105840 |
| 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 |
| Paediatric hydrocephalus. | Kahle KT, Klinge PM, Koschnitzky JE, Kulkarni AV, MacAulay N, Robinson S, Schiff SJ, Strahle JM | Nature reviews. Disease primers | 38755194 | Nat Rev Dis Primers | 2024 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/38755194 |
| 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 |
| 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 |
| 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 |
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| Identification of White Matter Hyperintensities in Routine Emergency Department Visits Using Portable Bedside Magnetic Resonance Imaging. | de Havenon A, Parasuram NR, Crawford AL, Mazurek MH, Chavva IR, Yadlapalli V, Iglesias JE, Rosen MS, Falcone GJ, Payabvash S, Sze G, Sharma R, Schiff SJ, Safdar B, Wira C, Kimberly WT, Sheth KN | Journal of the American Heart Association | 37218590 | J Am Heart Assoc | 2023 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/37218590 |
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| Aβ-targeting synNotch Receptor for Alzheimer's Disease: Expanding Applications to Extracellular Protein Aggregates. | Bergo NJ, Lee S, Siebrand CJ, Andersen JK, Walton CC | bioRxiv : the preprint server for biology | 39464071 | bioRxiv | 2024 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/39464071 |
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| Circadian disruption of hippocampus in an early senescence male mouse model. | Davis JA, Paul JR, Mokashi MV, Yates SA, Mount DJ, Munir HA, Goode LK, Young ME, Allison DB, Gamble KL | Pharmacology, biochemistry, and behavior | 35447158 | Pharmacol Biochem Behav | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35447158 |
| Positive and negative gustatory inputs affect Drosophila lifespan partly in parallel to dFOXO signaling. | Ostojic I, Boll W, Waterson MJ, Chan T, Chandra R, Pletcher SD, Alcedo J | Proceedings of the National Academy of Sciences of the United States of America | 24847072 | Proc Natl Acad Sci U S A | 2014 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/24847072 |
| Water sensor ppk28 modulates Drosophila lifespan and physiology through AKH signaling. | Waterson MJ, Chung BY, Harvanek ZM, Ostojic I, Alcedo J, Pletcher SD | Proceedings of the National Academy of Sciences of the United States of America | 24821805 | Proc Natl Acad Sci U S A | 2014 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/24821805 |
| Second-hand eating? Maternal perception of the food environment affects reproductive investment in mice. | Schwartz TS, Gainer R, Dohm ED, Johnson MS, Wyss JM, Allison DB | Obesity (Silver Spring, Md.) | 25864567 | Obesity (Silver Spring) | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25864567 |
| Adaptive Physiological Response to Perceived Scarcity as a Mechanism of Sensory Modulation of Life Span. | Waterson MJ, Chan TP, Pletcher SD | The journals of gerontology. Series A, Biological sciences and medical sciences | 25878032 | J Gerontol A Biol Sci Med Sci | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25878032 |
| Effect of Food Predictability on Life Span in Male Mice. | Rowland NE, Robertson KL, Minaya D, Minervini V, Cervantez M, Kaiser KA, Allison DB | The journals of gerontology. Series A, Biological sciences and medical sciences | 30289438 | J Gerontol A Biol Sci Med Sci | 2019 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/30289438 |
| Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis. | Razzoli M, Frontini A, Gurney A, Mondini E, Cubuk C, Katz LS, Cero C, Bolan PJ, Dopazo J, Vidal-Puig A, Cinti S, Bartolomucci A | Molecular metabolism | 26844204 | Mol Metab | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26844204 |
| Effects of fluctuating temperature and food availability on reproduction and lifespan. | Schwartz TS, Pearson P, Dawson J, Allison DB, Gohlke JM | Experimental gerontology | 27364192 | Exp Gerontol | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27364192 |
| Sex-dependent Differences in Liver and Gut Metabolomic Profiles With Acarbose and Calorie Restriction in C57BL/6 Mice. | Gibbs VK, Brewer RA, Miyasaki ND, Patki A, Smith DL Jr | The journals of gerontology. Series A, Biological sciences and medical sciences | 28651373 | J Gerontol A Biol Sci Med Sci | 2018 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/28651373 |
| No Significant Effect of Maternal Perception of the Food Environment on Reproductive Success or Pup Outcomes in C57BL/6J Mice. | Gibbs VK, Schwartz TS, Johnson MS, Patki A, Nagy TR, George BJ, Allison DB | Obesity (Silver Spring, Md.) | 29476611 | Obesity (Silver Spring) | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29476611 |
| Body Mass Index and Subjective Social Status: The Coronary Artery Risk Development in Young Adults Study. | Dhurandhar EJ, Pavela G, Kaiser KA, Dutton GR, Fontaine KR, Kim D, Shikany JM, Allison DB, Lewis CE | Obesity (Silver Spring, Md.) | 29280341 | Obesity (Silver Spring) | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29280341 |
| Calories or protein? The effect of dietary restriction on lifespan in rodents is explained by calories alone. | Speakman JR, Mitchell SE, Mazidi M | Experimental gerontology | 27006163 | Exp Gerontol | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27006163 |
| The effect of a pharmaceutical ghrelin agonist on lifespan in C57BL/6J male mice: A controlled experiment. | Kaiser KA, Kadish I, van Groen T, Smith DL Jr, Dickinson S, Henschel B, Parker ES, Brown AW, Allison DB | Aging cell | 36734122 | Aging Cell | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36734122 |
| The multiple roles of life stress in metabolic disorders. | Kivimäki M, Bartolomucci A, Kawachi I | Nature reviews. Endocrinology | 36224493 | Nat Rev Endocrinol | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36224493 |
| A computational approach to studying ageing at the individual level. | Harvanek ZM, Mourão MA, Schnell S, Pletcher SD | Proceedings. Biological sciences | 26865300 | Proc Biol Sci | 2016 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/26865300 |
| The Dichotomous Effect of Chronic Stress on Obesity. | Razzoli M, Bartolomucci A | Trends in endocrinology and metabolism: TEM | 27162125 | Trends Endocrinol Metab | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27162125 |
| Social stress shortens lifespan in mice. | Razzoli M, Nyuyki-Dufe K, Gurney A, Erickson C, McCallum J, Spielman N, Marzullo M, Patricelli J, Kurata M, Pope EA, Touma C, Palme R, Largaespada DA, Allison DB, Bartolomucci A | Aging cell | 29806171 | Aging Cell | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29806171 |
| Innovative approaches in cognitive aging. | Austad SN, Wood MA, Villeda SA, Voss JL, Sahay A, Albert M | Neurobiology of aging | 31277894 | Neurobiol Aging | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31277894 |
| Serotonin signaling mediates protein valuation and aging. | Ro J, Pak G, Malec PA, Lyu Y, Allison DB, Kennedy RT, Pletcher SD | eLife | 27572262 | Elife | 2016 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/27572262 |
| Oxidative costs of reproduction in mouse strains selected for different levels of food intake and which differ in reproductive performance. | Jothery AH, Vaanholt LM, Mody N, Arnous A, Lykkesfeldt J, Bünger L, Hill WG, Mitchell SE, Allison DB, Speakman JR | Scientific reports | 27841266 | Sci Rep | 2016 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/27841266 |
| Targeting glucose metabolism for healthy aging. | Brewer RA, Gibbs VK, Smith DL Jr | Nutrition and healthy aging | 28035340 | Nutr Healthy Aging | 2016 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/28035340 |
| Diurnal, metabolic and thermogenic alterations in a murine model of accelerated aging. | Allison DB, Ren G, Peliciari-Garcia RA, Mia S, McGinnis GR, Davis J, Gamble KL, Kim JA, Young ME | Chronobiology international | 32819176 | Chronobiol Int | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32819176 |
| Acute Dietary Restriction Acts via TOR, PP2A, and Myc Signaling to Boost Innate Immunity in Drosophila. | Lee JE, Rayyan M, Liao A, Edery I, Pletcher SD | Cell reports | 28700947 | Cell Rep | 2017 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/28700947 |
| Nutrition and energetics in rodent longevity research. | Gibbs VK, Smith DL Jr | Experimental gerontology | 27073168 | Exp Gerontol | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27073168 |
| Sex Differences in Lifespan. | Austad SN, Fischer KE | Cell metabolism | 27304504 | Cell Metab | 2016 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/27304504 |
| Stress, overeating, and obesity: Insights from human studies and preclinical models. | Razzoli M, Pearson C, Crow S, Bartolomucci A | Neuroscience and biobehavioral reviews | 28292531 | Neurosci Biobehav Rev | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28292531 |
| Ghrelin agonist does not foster insulin resistance but improves cognition in an Alzheimer's disease mouse model. | Kunath N, van Groen T, Allison DB, Kumar A, Dozier-Sharpe M, Kadish I | Scientific reports | 26090621 | Sci Rep | 2015 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/26090621 |
| FLIC: high-throughput, continuous analysis of feeding behaviors in Drosophila. | Ro J, Harvanek ZM, Pletcher SD | PloS one | 24978054 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24978054 |
| Reproduction has immediate effects on female mortality, but no discernible lasting physiological impacts: A test of the disposable soma theory. | Mitchell SE, Simpson M, Coulet L, Gouedard S, Hambly C, Morimoto J, Allison DB, Speakman JR | Proceedings of the National Academy of Sciences of the United States of America | 39374394 | Proc Natl Acad Sci U S A | 2024 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/39374394 |
| Contextual modifiers of healthspan, lifespan, and epigenome in mice under chronic social stress. | Razzoli M, Nyuyki-Dufe K, Chen BH, Bartolomucci A | Proceedings of the National Academy of Sciences of the United States of America | 37043532 | Proc Natl Acad Sci U S A | 2023 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/37043532 |
| Not feeling the heat? Effects of dietary protein on satiation and satiety in mice are not due to its impact on body temperature. | Osorio M J, Mitchell SE, Hambly C, Allison DB, Speakman JR | Appetite | 38759755 | Appetite | 2024 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/38759755 |
| A fully automated microfluidic femtosecond laser axotomy platform for nerve regeneration studies in C. elegans. | Gokce SK, Guo SX, Ghorashian N, Everett WN, Jarrell T, Kottek A, Bovik AC, Ben-Yakar A | PloS one | 25470130 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25470130 |
| An automated microfluidic multiplexer for fast delivery of C. elegans populations from multiwells. | Ghorashian N, Gökçe SK, Guo SX, Everett WN, Ben-Yakar A | PloS one | 24069313 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24069313 |
| Microfluidics for the analysis of behavior, nerve regeneration, and neural cell biology in C. elegans. | Ben-Yakar A, Chronis N, Lu H | Current opinion in neurobiology | 19896831 | Curr Opin Neurobiol | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19896831 |
| Axonal regeneration proceeds through specific axonal fusion in transected C. elegans neurons. | Neumann B, Nguyen KC, Hall DH, Ben-Yakar A, Hilliard MA | Developmental dynamics : an official publication of the American Association of Anatomists | 21416556 | Dev Dyn | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21416556 |
| Femtosecond laser nanoaxotomy lab-on-a-chip for in vivo nerve regeneration studies. | Guo SX, Bourgeois F, Chokshi T, Durr NJ, Hilliard MA, Chronis N, Ben-Yakar A | Nature methods | 18408725 | Nat Methods | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18408725 |
| Ultrasound measurements of cavitation bubble radius for femtosecond laser-induced breakdown in water. | Aglyamov SR, Karpiouk AB, Bourgeois F, Ben-Yakar A, Emelianov SY | Optics letters | 18552957 | Opt Lett | 2008 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/18552957 |
| Quantitative ultrasound method to detect and monitor laser-induced cavitation bubbles. | Karpiouk AB, Aglyamov SR, Bourgeois F, Ben-Yakar A, Emelianov SY | Journal of biomedical optics | 18601556 | J Biomed Opt | 2008 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/18601556 |
| Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model. | Mondal S, Hegarty E, Martin C, Gökçe SK, Ghorashian N, Ben-Yakar A | Nature communications | 27725672 | Nat Commun | 2016 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/27725672 |
| An automated microfluidic device for time-lapse imaging of mouse embryonic stem cells. | Laing AF, Tirumala V, Hegarty E, Mondal S, Zhao P, Hamilton WB, Brickman JM, Ben-Yakar A | Biomicrofluidics | 31558920 | Biomicrofluidics | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31558920 |
| Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene egl-1 in a Living Neuron Pair in Caenorhabditis elegans. | Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT | G3 (Bethesda, Md.) | 31519744 | G3 (Bethesda) | 2019 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/31519744 |
| Small molecule modulator of sigma 2 receptor is neuroprotective and reduces cognitive deficits and neuroinflammation in experimental models of Alzheimer's disease. | Yi B, Sahn JJ, Ardestani PM, Evans AK, Scott LL, Chan JZ, Iyer S, Crisp A, Zuniga G, Pierce JT, Martin SF, Shamloo M | Journal of neurochemistry | 27926996 | J Neurochem | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27926996 |
| Planar Laser Activated Neuronal Scanning (PLANS) System for in vivo Flow Cytometry. | Watson N, Mondal S, DuPlissis A, Kim KH, Ben-Yakar A | Frontiers in optics. Annual Meeting of the Optical Society of America | 35350105 | Front Opt | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35350105 |
| Ultrafast laser nanosurgery in microfluidics for genome-wide screenings. | Ben-Yakar A, Bourgeois F | Current opinion in biotechnology | 19278850 | Curr Opin Biotechnol | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19278850 |
| Small-molecule-mediated axonal branching in Caenorhabditis elegans. | Zlotkowski K, Pierce-Shimomura J, Siegel D | Chembiochem : a European journal of chemical biology | 23362121 | Chembiochem | 2013 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/23362121 |
| Systematic Functional Characterization of Human 21st Chromosome Orthologs in Caenorhabditis elegans. | Nordquist SK, Smith SR, Pierce JT | G3 (Bethesda, Md.) | 29367452 | G3 (Bethesda) | 2018 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/29367452 |
| A multi-trap microfluidic chip enabling longitudinal studies of nerve regeneration in Caenorhabditis elegans. | Gokce SK, Hegarty EM, Mondal S, Zhao P, Ghorashian N, Hilliard MA, Ben-Yakar A | Scientific reports | 28852096 | Sci Rep | 2017 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/28852096 |
| Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans. | Vidal-Gadea A, Ward K, Beron C, Ghorashian N, Gokce S, Russell J, Truong N, Parikh A, Gadea O, Ben-Yakar A, Pierce-Shimomura J | eLife | 26083711 | Elife | 2015 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/26083711 |
| APP-Induced Patterned Neurodegeneration Is Exacerbated by APOE4 in Caenorhabditis elegans. | Sae-Lee W, Scott LL, Brose L, Encarnacion AJ, Shi T, Kore P, Oyibo LO, Ye C, Rozmiarek SK, Pierce JT | G3 (Bethesda, Md.) | 32580938 | G3 (Bethesda) | 2020 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/32580938 |
| Femtosecond laser nanoaxotomy properties and their effect on axonal recovery in C. elegans. | Bourgeois F, Ben-Yakar A | Optics express | 18725955 | Opt Express | 2008 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/18725955 |
| Worming our way to Alzheimer's disease drug discovery. | Iyer S, Pierce-Shimomura JT | Biological psychiatry | 23399470 | Biol Psychiatry | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23399470 |
| High-Content Microfluidic Screening Platform Used To Identify σ2R/Tmem97 Binding Ligands that Reduce Age-Dependent Neurodegeneration in C. elegans SC_APP Model. | Mondal S, Hegarty E, Sahn JJ, Scott LL, Gökçe SK, Martin C, Ghorashian N, Satarasinghe PN, Iyer S, Sae-Lee W, Hodges TR, Pierce JT, Martin SF, Ben-Yakar A | ACS chemical neuroscience | 29426225 | ACS Chem Neurosci | 2018 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/29426225 |
| Line excitation array detection fluorescence microscopy at 0.8 million frames per second. | Martin C, Li T, Hegarty E, Zhao P, Mondal S, Ben-Yakar A | Nature communications | 30374138 | Nat Commun | 2018 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/30374138 |
| Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron. | Cohn JA, Cebul ER, Valperga G, Brose L, de Bono M, Heiman MG, Pierce JT | Developmental biology | 31945343 | Dev Biol | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/31945343 |
