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Chun Ye, Ph.D. - Publications

Affiliations: 
2009 Bioinformatics University of California, San Diego, La Jolla, CA 
Area:
Biostatistics Biology, Bioinformatics Biology, Systematic Biology
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ. Method of moments framework for differential expression analysis of single-cell RNA sequencing data. Cell. PMID 39454576 DOI: 10.1016/j.cell.2024.09.044  0.362
2024 Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, ... ... Ye CJ, et al. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature Genetics. PMID 38811842 DOI: 10.1038/s41588-024-01743-5  0.325
2024 Fujita M, Gao Z, Zeng L, McCabe C, White CC, Ng B, Green GS, Rozenblatt-Rosen O, Phillips D, Amir-Zilberstein L, Lee H, Pearse RV, Khan A, Vardarajan BN, Kiryluk K, ... Ye CJ, et al. Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature Genetics. PMID 38514782 DOI: 10.1038/s41588-024-01685-y  0.325
2024 Zhou Z, Du J, Wang J, Liu L, Gordon MG, Ye CJ, Powell JE, Li MJ, Rao S. SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. Database : the Journal of Biological Databases and Curation. 2024. PMID 38459946 DOI: 10.1093/database/baae010  0.379
2024 Gordon MG, Kathail P, Choy B, Kim MC, Mazumder T, Gearing M, Ye CJ. Population Diversity at the Single-Cell Level. Annual Review of Genomics and Human Genetics. PMID 38382493 DOI: 10.1146/annurev-genom-021623-083207  0.312
2024 Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biology. 25: 28. PMID 38254214 DOI: 10.1186/s13059-023-03152-z  0.384
2022 Thompson M, Gordon MG, Lu A, Tandon A, Halperin E, Gusev A, Ye CJ, Balliu B, Zaitlen N. Multi-context genetic modeling of transcriptional regulation resolves novel disease loci. Nature Communications. 13: 5704. PMID 36171194 DOI: 10.1038/s41467-022-33212-0  0.674
2022 Oelen R, de Vries DH, Brugge H, Gordon MG, Vochteloo M, Ye CJ, Westra HJ, Franke L, van der Wijst MGP. Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nature Communications. 13: 3267. PMID 35672358 DOI: 10.1038/s41467-022-30893-5  0.391
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, ... ... Ye CJ, et al. Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. Science (New York, N.Y.). 376: eabf1970. PMID 35389781 DOI: 10.1126/science.abf1970  0.588
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, et al. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. Science (New York, N.Y.). 376: eabf3041. PMID 35389779 DOI: 10.1126/science.abf3041  0.314
2020 Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, ... Ye CJ, et al. Author Correction: Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nature Biotechnology. PMID 33057163 DOI: 10.1038/s41587-020-0715-9  0.536
2019 Hernandez RD, Uricchio LH, Hartman K, Ye C, Dahl A, Zaitlen N. Ultrarare variants drive substantial cis heritability of human gene expression. Nature Genetics. 51: 1349-1355. PMID 31477931 DOI: 10.1038/S41588-019-0487-7  0.619
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, et al. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of transcripts under balancing selection. Genome Research. PMID 30446528 DOI: 10.1101/Gr.240390.118  0.376
2018 Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, ... ... Ye CJ, et al. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nature Genetics. PMID 29988122 DOI: 10.1038/S41588-018-0156-2  0.388
2017 Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, ... Ye CJ, et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nature Biotechnology. PMID 29227470 DOI: 10.1038/Nbt.4042  0.585
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. An ancestry-based approach for detecting interactions. Genetic Epidemiology. PMID 29114909 DOI: 10.1002/Gepi.22087  0.712
2017 Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N. Covariate selection for association screening in multiphenotype genetic studies. Nature Genetics. PMID 29038595 DOI: 10.1038/Ng.3975  0.589
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, ... ... Ye CJ, et al. Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature. PMID 28854172 DOI: 10.1038/Nature23875  0.301
2016 Brown BC, Ye CJ, Price AL, Zaitlen N. Transethnic Genetic-Correlation Estimates from Summary Statistics. American Journal of Human Genetics. PMID 27321947 DOI: 10.1016/J.Ajhg.2016.05.001  0.611
2016 Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Research. PMID 27197206 DOI: 10.1101/Gr.202440.115  0.579
2014 Ye CJ, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, McCabe C, Lee MH, Frohlich I, Paik HI, Zaitlen N, Hacohen N, Stranger B, De Jager P, Mathis D, et al. Intersection of population variation and autoimmunity genetics in human T cell activation. Science (New York, N.Y.). 345: 1254665. PMID 25214635 DOI: 10.1126/Science.1254665  0.567
2014 Joo JW, Sul JH, Han B, Ye C, Eskin E. Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. Genome Biology. 15: r61. PMID 24708878 DOI: 10.1186/Gb-2014-15-4-R61  0.746
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, et al. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science (New York, N.Y.). 343: 1246980. PMID 24604203 DOI: 10.1126/Science.1246980  0.305
2013 Sul JH, Han B, Ye C, Choi T, Eskin E. Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches. Plos Genetics. 9: e1003491. PMID 23785294 DOI: 10.1371/Journal.Pgen.1003491  0.712
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. Integrated computational and experimental analysis of the neuroendocrine transcriptome in genetic hypertension identifies novel control points for the cardiometabolic syndrome. Circulation. Cardiovascular Genetics. 5: 430-40. PMID 22670052 DOI: 10.1161/Circgenetics.111.962415  0.565
2011 Furlotte NA, Kang HM, Ye C, Eskin E. Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. Bioinformatics (Oxford, England). 27: i288-94. PMID 21685083 DOI: 10.1093/bioinformatics/btr221  0.716
2010 Kang EY, Ye C, Shpitser I, 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. 17: 533-46. PMID 20377462 DOI: 10.1089/Cmb.2009.0176  0.73
2009 Ye C, Galbraith SJ, Liao JC, Eskin E. Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. Plos Computational Biology. 5: e1000311. PMID 19300475 DOI: 10.1371/Journal.Pcbi.1000311  0.641
2008 Kang HM, Ye C, Eskin E. Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics. 180: 1909-25. PMID 18791227 DOI: 10.1534/Genetics.108.094201  0.641
2007 Ye C, Eskin E. Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. Bioinformatics (Oxford, England). 23: e84-90. PMID 17237110 DOI: 10.1093/Bioinformatics/Btl315  0.653
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, ... ... Ye C, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology. 23: 137-44. PMID 15637633 DOI: 10.1038/Nbt1053  0.497
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