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Author Details

Chun Jimmie Ye
University of California san francisco
2013
62
36
Nevan J Krogan (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37066254Reply to Barton et al: signatures of natural selection during the Black Death.bioRxiv2023
37803001Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq.Nat Commun2023
37735198Functional characterization of Alzheimer's disease genetic variants in microglia.Nat Genet2023
37563329Genome-wide prediction of disease variant effects with a deep protein language model.Nat Genet2023
36993359Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.bioRxiv2023
37188663Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy.Nat Commun2023
35322231The development and evolution of inhibitory neurons in primate cerebrum.Nature2022
35799782Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity.Front Immunol2022
35672358Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure.Nat Commun2022
35389781Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus.Science2022
35389779Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease.Science2022
35355021Obesity alters pathology and treatment response in inflammatory disease.Nature2022
36171194Multi-context genetic modeling of transcriptional regulation resolves novel disease loci.Nat Commun2022
36130508Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis.Cell Rep2022
36350984Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies.Sci Transl Med2022
36261521Evolution of immune genes is associated with the Black Death.Nature2022
34890161CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq.Pac Symp Biocomput2022
35309349Combined Single Cell Transcriptome and Surface Epitope Profiling Identifies Potential Biomarkers of Psoriatic Arthritis and Facilitates Diagnosis <i>via</i> Machine Learning.Front Immunol2022
35113687CRISPR activation and interference screens decode stimulation responses in primary human T cells.Science2022
33128032Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.Nat Protoc2021
33883687Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures.Commun Biol2021
33883145XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.Sci Adv2021
33597545Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla.Nat Commun2021
33758859Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19: Anti-IFN antibodies in critical COVID-19 correlate with poor ISG response and upregulation of LAIR1 surface protein in PBMCs.bioRxiv2021
34702736Monoclonal antibody-mediated neutralization of SARS-CoV-2 in an IRF9-deficient child.Proc Natl Acad Sci U S A2021
34429372Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19.Sci Transl Med2021
34324441The effect of low-dose IL-2 and Treg adoptive cell therapy in patients with type 1 diabetes.JCI Insight2021
34341540Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19.Nature2021
33406429Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells.Cell Rep2021
33472616No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells.BMC Biol2021
32497499Intratumoral CD4<sup>+</sup> T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer.Cell2020
33057163Author Correction: Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.Nat Biotechnol2020
32855547Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.Nat Biotechnol2020
32797036On the cross-population generalizability of gene expression prediction models.PLoS Genet2020
32620816Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM.Sci Rep2020
32989329Functional CRISPR dissection of gene networks controlling human regulatory T cell identity.Nat Immunol2020
32641802lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.Nat Protoc2020
31477931Ultrarare variants drive substantial cis heritability of human gene expression.Nat Genet2019
31558714Functional interpretation of single cell similarity maps.Nat Commun2019
31308526How mutations express themselves in blood-cell production.Nature2019
31538139Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans.Nat Metab2019
29114909An ancestry-based approach for detecting interactions.Genet Epidemiol2018
29988122Genetic determinants of co-accessible chromatin regions in activated T cells across humans.Nat Genet2018
30254276Lineage dynamics of murine pancreatic development at single-cell resolution.Nat Commun2018
29899441Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation.Nature2018
30446528Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of <i>ERAP2</i> transcripts under balancing selection.Genome Res2018
29752062Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity.Immunity2018
29227470Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.Nat Biotechnol2018
28854172Discovery of stimulation-responsive immune enhancers with CRISPR activation.Nature2017
28389661CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells.Sci Rep2017
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Collaborators

Alexander Marson
Gladstone-UCSF Institute of Genomic Immunology
Co-authored papers 13
Noah Zaitlen
Co-authored papers 11
Aviv Regev
Broad Institute of MIT and Harvard
Co-authored papers 9
Nir Hacohen
Broad Institute of MIT and Harvard
Co-authored papers 6
Philip L De Jager
Columbia University Medical Center
Co-authored papers 6
Kathrin Schumann
Institute for Medical Microbiology, Technical University of Munich (TUM)
Co-authored papers 5
Jonathan M Woo
University of California san francisco
Co-authored papers 5
Sara Mostafavi
University of British Columbia and BC Children's Hospital
Co-authored papers 4
Barbara E Stranger
Center for Genetic Medicine, Northwestern University Feinberg School of Medicine
Co-authored papers 4
Theodore L Roth
Stanford University
Co-authored papers 4
Lenka Maliskova
Co-authored papers 4
Dimitre R Simeonov
University of California San Francisco
Co-authored papers 4
Cody T Mowery
University of California san francisco
Co-authored papers 4
Howard Y Chang
Center for Personal Dynamic Regulomes, Stanford University
Co-authored papers 4
Lindsey A Criswell
Co-authored papers 4
Youjin V Lee
University of Chicago
Co-authored papers 4
Lawrence Fong
University of California san francisco
Co-authored papers 3
Ansuman T Satpathy
Stanford University
Co-authored papers 3
Mark S Anderson
Diabetes Center, University of California san francisco
Co-authored papers 3
Eran Halperin
Co-authored papers 3
Kara L Lynch
University of California San Francisco
Co-authored papers 3
Carolyn S Calfee
University of California San Francisco
Co-authored papers 3
Mark J Daly
Massachusetts General Hospital
Co-authored papers 3
Nir Yosef
Center for Computational Biology, University of California berkeley
Co-authored papers 3
Michelle Nguyen
School of Medicine Stanford University
Co-authored papers 3
Joseph L DeRisi
University of California San Francisco
Co-authored papers 3
Soumya Raychaudhuri
Brigham and Women's Hospital and Harvard Medical School
Co-authored papers 2
Martin Kircher
Berlin Institute of Health (BIH) at Charite-Universitatsmedizin Berlin
Co-authored papers 2
Feng Zhang
Massachusetts Institute of Technology, USA Broad Institute
Co-authored papers 2
Jacob E Corn
Co-authored papers 2
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