Jimmie Ye, PhD
Associate Professor
Medicine
School of Medicine

The lab develops novel experimental approaches that enable the large-scale collection of functional genomic data en masse and computational approaches that translate the data into novel biological insights. This approach is used to initially study primary human immune cells in both healthy and diseased patients to understand host pathogen interactions and its role in autoimmunity.

• Functional genomics in inborn errors of immunity.
  Immunological reviews 2024 Hurabielle C, LaFlam TN, Gearing M, Ye CJ
• Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs.
  Science immunology 2023 Bastard P, Vazquez SE, Liu J, Laurie MT, Wang CY, Gervais A, Le Voyer T, Bizien L, Zamecnik C, Philippot Q, Rosain J, Catherinot E, Willmore A, Mitchell AM, Bair R, Garçon P, Kenney H, Fekkar A, …
• Protracted neuronal recruitment in the temporal lobes of young children.
  Nature 2023 Nascimento MA, Biagiotti S, Herranz-Pérez V, Santiago S, Bueno R, Ye CJ, Abel TJ, Zhang Z, Rubio-Moll JS, Kriegstein AR, Yang Z, Garcia-Verdugo JM, Huang EJ, Alvarez-Buylla A, Sorrells SF
• Base-editing mutagenesis maps alleles to tune human T cell functions.
  Nature 2023 Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, …
• Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics.
  bioRxiv : the preprint server for biology 2023 Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Ye CJ, Kim S, Gartner Z, Sirota M, Neely J
• Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq.
  Nature communications 2023 Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY
• Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.
  Cell 2023 Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Hofman L, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June …
• Functional characterization of Alzheimer's disease genetic variants in microglia.
  Nature genetics 2023 Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang MZ, Chan CSY, Ye CJ, …
• Genome-wide prediction of disease variant effects with a deep protein language model.
  Nature genetics 2023 Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V
• Reply to Barton et al: signatures of natural selection during the Black Death.
  bioRxiv : the preprint server for biology 2023 Vilgalys TP, Klunk J, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, …
• Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.
  bioRxiv : the preprint server for biology 2023 Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang …
• Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies.
  Science translational medicine 2022 Goodman DB, Azimi CS, Kearns K, Talbot A, Garakani K, Garcia J, Patel N, Hwang B, Lee D, Park E, Vykunta VS, Shy BR, Ye CJ, Eyquem J, Marson A, Bluestone JA, Roybal KT
• Evolution of immune genes is associated with the Black Death.
  Nature 2022 Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, …
• Multi-context genetic modeling of transcriptional regulation resolves novel disease loci.
  Nature communications 2022 Thompson M, Gordon MG, Lu A, Tandon A, Halperin E, Gusev A, Ye CJ, Balliu B, Zaitlen N
• Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis.
  Cell reports 2022 Keenan BP, McCarthy EE, Ilano A, Yang H, Zhang L, Allaire K, Fan Z, Li T, Lee DS, Sun Y, Cheung A, Luong D, Chang H, Chen B, Marquez J, Sheldon B, Kelley RK, Ye CJ, Fong L
• Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity.
  Frontiers in immunology 2022 Neely J, Hartoularos G, Bunis D, Sun Y, Lee D, Kim S, Ye CJ, Sirota M
• Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure.
  Nature communications 2022 Oelen R, de Vries DH, Brugge H, Gordon MG, Vochteloo M, single-cell eQTLGen consortium, BIOS Consortium, Ye CJ, Westra HJ, Franke L, van der Wijst MGP
• Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus.
  Science (New York, N.Y.) 2022 Perez RK, Gordon MG, Subramaniam M, Kim MC, Hartoularos GC, Targ S, Sun Y, Ogorodnikov A, Bueno R, Lu A, Thompson M, Rappoport N, Dahl A, Lanata CM, Matloubian M, Maliskova L, Kwek SS, Li T, Slyper M,…
• Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease.
  Science (New York, N.Y.) 2022 Yazar S, Alquicira-Hernandez J, Wing K, Senabouth A, Gordon MG, Andersen S, Lu Q, Rowson A, Taylor TRP, Clarke L, Maccora K, Chen C, Cook AL, Ye CJ, Fairfax KA, Hewitt AW, Powell JE
• Obesity alters pathology and treatment response in inflammatory disease.
  Nature 2022 Bapat SP, Whitty C, Mowery CT, Liang Y, Yoo A, Jiang Z, Peters MC, Zhang LJ, Vogel I, Zhou C, Nguyen VQ, Li Z, Chang C, Zhu WS, Hastie AT, He H, Ren X, Qiu W, Gayer SG, Liu C, Choi EJ, Fassett M, …
• The development and evolution of inhibitory neurons in primate cerebrum.
  Nature 2022 Schmitz MT, Sandoval K, Chen CP, Mostajo-Radji MA, Seeley WW, Nowakowski TJ, Ye CJ, Paredes MF, Pollen AA
• Combined Single Cell Transcriptome and Surface Epitope Profiling Identifies Potential Biomarkers of Psoriatic Arthritis and Facilitates Diagnosis via Machine Learning.
  Frontiers in immunology 2022 Liu J, Kumar S, Hong J, Huang ZM, Paez D, Castillo M, Calvo M, Chang HW, Cummins DD, Chung M, Yeroushalmi S, Bartholomew E, Hakimi M, Ye CJ, Bhutani T, Matloubian M, Gensler LS, Liao W
• CRISPR activation and interference screens decode stimulation responses in primary human T cells.
  Science (New York, N.Y.) 2022 Schmidt R, Steinhart Z, Layeghi M, Freimer JW, Bueno R, Nguyen VQ, Blaeschke F, Ye CJ, Marson A
• CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2022 He B, Thomson M, Subramaniam M, Perez R, Ye CJ, Zou J
• Monoclonal antibody-mediated neutralization of SARS-CoV-2 in an IRF9-deficient child.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Lévy R, Zhang P, Bastard P, Dorgham K, Melki I, Hadchouel A, Hartoularos GC, Neven B, Castelle M, Roy C, Toin T, Berteloot L, Bizien L, Abid H, Burgard M, Houhou-Fidouh N, Rozenberg F, Jouanguy E, Ye …
• The effect of low-dose IL-2 and Treg adoptive cell therapy in patients with type 1 diabetes.
  JCI insight 2021 Dong S, Hiam-Galvez KJ, Mowery CT, Herold KC, Gitelman SE, Esensten JH, Liu W, Lares AP, Leinbach AS, Lee M, Nguyen V, Tamaki SJ, Tamaki W, Tamaki CM, Mehdizadeh M, Putnam AL, Spitzer MH, Ye CJ, Tang …
• CCR2 deficiency alters activation of microglia subsets in traumatic brain injury.
  Cell reports 2021 Somebang K, Rudolph J, Imhof I, Li L, Niemi EC, Shigenaga J, Tran H, Gill TM, Lo I, Zabel BA, Schmajuk G, Wipke BT, Gyoneva S, Jandreski L, Craft M, Benedetto G, Plowey ED, Charo I, Campbell J, Ye CJ,…
• Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19.
  Science translational medicine 2021 van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, …
• SCITO-seq: single-cell combinatorial indexed cytometry sequencing.
  Nature methods 2021 Hwang B, Lee DS, Tamaki W, Sun Y, Ogorodnikov A, Hartoularos GC, Winters A, Yeung BZ, Nazor KL, Song YS, Chow ED, Spitzer MH, Ye CJ
• Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis.
  Blood cancer discovery 2021 Wang VE, Blaser BW, Patel RK, Behbehani GK, Rao AA, Durbin-Johnson B, Jiang T, Logan AC, Settles M, Mannis GN, Olin R, Damon LE, Martin TG, Sayre PH, Gaensler KM, McMahon E, Flanders M, Weinberg V, Ye…
• Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree.
  eLife 2021 Hendley AM, Rao AA, Leonhardt L, Ashe S, Smith JA, Giacometti S, Peng XL, Jiang H, Berrios DI, Pawlak M, Li LY, Lee J, Collisson EA, Anderson MS, Fragiadakis GK, Yeh JJ, Ye CJ, Kim GE, Weaver VM, …
• Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures.
  Communications biology 2021 Andreoletti G, Lanata CM, Trupin L, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Dall'Era M, Yazdany J, Criswell LA, Sirota M
• XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.
  Science advances 2021 Lee Y, Bogdanoff D, Wang Y, Hartoularos GC, Woo JM, Mowery CT, Nisonoff HM, Lee DS, Sun Y, Lee J, Mehdizadeh S, Cantlon J, Shifrut E, Ngyuen DN, Roth TL, Song YS, Marson A, Chow ED, Ye CJ
• Longitudinal 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.
  bioRxiv : the preprint server for biology 2021 van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, …
• Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla.
  Nature communications 2021 Bautista JL, Cramer NT, Miller CN, Chavez J, Berrios DI, Byrnes LE, Germino J, Ntranos V, Sneddon JB, Burt TD, Gardner JM, Ye CJ, Anderson MS, Parent AV
• Global absence and targeting of protective immune states in severe COVID-19.
  Nature 2021 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells.
  BMC biology 2021 McGinnis CS, Siegel DA, Xie G, Hartoularos G, Stone M, Ye CJ, Gartner ZJ, Roan NR, Lee SA
• Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells.
  Cell reports 2021 Bunis DG, Bronevetsky Y, Krow-Lucal E, Bhakta NR, Kim CC, Nerella S, Jones N, Mendoza VF, Bryson YJ, Gern JE, Rutishauser RL, Ye CJ, Sirota M, McCune JM, Burt TD
• Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.
  Nature communications 2020 Mandric I, Schwarz T, Majumdar A, Hou K, Briscoe L, Perez R, Subramaniam M, Hafemeister C, Satija R, Ye CJ, Pasaniuc B, Halperin E
• Global Absence and Targeting of Protective Immune States in Severe COVID-19.
  Research square 2020 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• Functional CRISPR dissection of gene networks controlling human regulatory T cell identity.
  Nature immunology 2020 Schumann K, Raju SS, Lauber M, Kolb S, Shifrut E, Cortez JT, Skartsis N, Nguyen VQ, Woo JM, Roth TL, Yu R, Nguyen MLT, Simeonov DR, Nguyen DN, Targ S, Gate RE, Tang Q, Bluestone JA, Spitzer MH, Ye CJ,…
• Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.
  Nature biotechnology 2020 Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong …
• lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
  Nature protocols 2020 Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N
• Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM.
  Scientific reports 2020 Alvarez M, Rahmani E, Jew B, Garske KM, Miao Z, Benhammou JN, Ye CJ, Pisegna JR, Pietiläinen KH, Halperin E, Pajukanta P
• IL-27: An endogenous constitutive repressor of human monocytes.
  Clinical immunology (Orlando, Fla.) 2020 Frangieh M, McHenry A, Phillips R, Ye C, Bernier A, Laffel L, Elyaman W, Bradshaw EM
• Test performance evaluation of SARS-CoV-2 serological assays.
  medRxiv : the preprint server for health sciences 2020 Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong …
• Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies.
  Cell 2020 Roth TL, Li PJ, Blaeschke F, Nies JF, Apathy R, Mowery C, Yu R, Nguyen MLT, Lee Y, Truong A, Hiatt J, Wu D, Nguyen DN, Goodman D, Bluestone JA, Ye CJ, Roybal K, Shifrut E, Marson A
• Functional interpretation of single cell similarity maps.
  Nature communications 2019 DeTomaso D, Jones MG, Subramaniam M, Ashuach T, Ye CJ, Yosef N
• Ultrarare variants drive substantial cis heritability of human gene expression.
  Nature genetics 2019 Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N
• How mutations express themselves in blood-cell production.
  Nature 2019 Raju S, Ye CJ
• Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans.
  Nature metabolism 2019 Garske KM, Pan DZ, Miao Z, Bhagat YV, Comenho C, Robles CR, Benhammou JN, Alvarez M, Ko A, Ye CJ, Pisegna JR, Mohlke KL, Sinsheimer JS, Laakso M, Pajukanta P
• Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity.
  Cell 2019 Binnewies M, Mujal AM, Pollack JL, Combes AJ, Hardison EA, Barry KC, Tsui J, Ruhland MK, Kersten K, Abushawish MA, Spasic M, Giurintano JP, Chan V, Daud AI, Ha P, Ye CJ, Roberts EW, Krummel MF
• EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.
  Genome biology 2019 Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st Human Cell Atlas Jamboree, Marioni JC
• Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection.
  Genome research 2018 Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL…
• Lineage dynamics of murine pancreatic development at single-cell resolution.
  Nature communications 2018 Byrnes LE, Wong DM, Subramaniam M, Meyer NP, Gilchrist CL, Knox SM, Tward AD, Ye CJ, Sneddon JB
• Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity.
  Immunity 2018 Rodda LB, Lu E, Bennett ML, Sokol CL, Wang X, Luther SA, Barres BA, Luster AD, Ye CJ, Cyster JG
• Principles of Systems Biology, No. 27.
  Cell systems 2018
• An ancestry-based approach for detecting interactions.
  Genetic epidemiology 2017 Park DS, Eskin I, Kang EY, Gamazon ER, Eng C, Gignoux CR, Galanter JM, Burchard E, Ye CJ, Aschard H, Eskin E, Halperin E, Zaitlen N
• Reconstructing the Molecular Function of Genetic Variation in Regulatory Networks.
  Genetics 2017 Wilentzik R, Ye CJ, Gat-Viks I
• Covariate selection for association screening in multiphenotype genetic studies.
  Nature genetics 2017 Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N
• Discovery of stimulation-responsive immune enhancers with CRISPR activation.
  Nature 2017 Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, …
• CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells.
  Scientific reports 2017 Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A
• A tissue checkpoint regulates type 2 immunity.
  Nature immunology 2016 Van Dyken SJ, Nussbaum JC, Lee J, Molofsky AB, Liang HE, Pollack JL, Gate RE, Haliburton GE, Ye CJ, Marson A, Erle DJ, Locksley RM
• Transethnic Genetic-Correlation Estimates from Summary Statistics.
  American journal of human genetics 2016 Brown BC, Asian Genetic Epidemiology Network Type 2 Diabetes Consortium, Ye CJ, Price AL, Zaitlen N
• Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.
  Genome research 2016 Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD
• Parsing the Interferon Transcriptional Network and Its Disease Associations.
  Cell 2016 Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, Hacohen N, De Jager PL, Regev A, Mathis D, …
• Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A
• A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
  Cell 2015 Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A
• Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.
  Science (New York, N.Y.) 2014 Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, …
• Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies.
  Genome biology 2014 Joo JW, Sul JH, Han B, Ye C, Eskin E
• Common genetic variants modulate pathogen-sensing responses in human dendritic cells.
  Science (New York, N.Y.) 2014 Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, …
• Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches.
  PLoS genetics 2013 Sul JH, Han B, Ye C, Choi T, Eskin E
• Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.
  Nature genetics 2013 Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hulková H, Sovová J, Vylet'al P, Antignac…
• Integrated computational and experimental analysis of the neuroendocrine transcriptome in genetic hypertension identifies novel control points for the cardiometabolic syndrome.
  Circulation. Cardiovascular genetics 2012 Friese RS, Ye C, Nievergelt CM, Schork AJ, Mahapatra NR, Rao F, Napolitan PS, Waalen J, Ehret GB, Munroe PB, Schmid-Schönbein GW, Eskin E, O'Connor DT
• Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity.
  Bioinformatics (Oxford, England) 2011 Furlotte NA, Kang HM, Ye C, Eskin E
• Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples.
  Journal of computational biology : a journal of computational molecular cell biology 2010 Kang EY, Ye C, Shpitser I, Eskin E
• Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast.
  PLoS computational biology 2009 Ye C, Galbraith SJ, Liao JC, Eskin E
• Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots.
  Genetics 2008 Kang HM, Ye C, Eskin E
• Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.
  Bioinformatics (Oxford, England) 2007 Ye C, Eskin E
• Orthologous repeats and mammalian phylogenetic inference.
  Genome research 2005 Bashir A, Ye C, Price AL, Bafna V
• Assessing computational tools for the discovery of transcription factor binding sites.
  Nature biotechnology 2005 Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J,…