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Chun Ye
Researcher at University of California, San Diego
Publications - 41
Citations - 2308
Chun Ye is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Biology & Medicine. The author has an hindex of 9, co-authored 10 publications receiving 1692 citations. Previous affiliations of Chun Ye include University of California, Los Angeles & Broad Institute.
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Journal ArticleDOI
Assessing computational tools for the discovery of transcription factor binding sites.
Martin Tompa,Nan Li,Timothy L. Bailey,George M. Church,Bart De Moor,Eleazar Eskin,Alexander V. Favorov,Martin C. Frith,Yutao Fu,W. James Kent,Vsevolod J. Makeev,Andrei A. Mironov,William Stafford Noble,Giulio Pavesi,Graziano Pesole,Mireille Régnier,Nicolas Simonis,Saurabh Sinha,Gert Thijs,Jacques van Helden,Mathias Vandenbogaert,Zhiping Weng,Christopher T. Workman,Chun Ye,Zhou Zhu +24 more
TL;DR: The purpose of the current assessment is to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.
Journal ArticleDOI
Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots.
TL;DR: Applying the intersample correlation emended (ICE) eQTL mapping method to mouse, yeast, and human identifies many more cis associations while eliminating most of the spurious trans associations, demonstrating the higher accuracy of the method to identify real genetic effects.
Journal ArticleDOI
Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches.
TL;DR: This paper develops a framework that leverages two popular meta-analysis methods that address effect size heterogeneity to detect eQTLs across multiple tissues and provides an interpretation framework that accurately predicts whether an eQ TL has an effect in a particular tissue.
Journal ArticleDOI
Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease
Seyhan Yazar,José Alquicira-Hernandez,Kristof Wing,Anne Senabouth,M. Grace Gordon,Stacey B. Andersen,Qinyi Lu,Antonia Rowson,Thomas R P Taylor,Linda Clarke,Katia Maccora,Christine Y. Chen,Anthony L. Cook,Chun Ye,Kirsten A. Fairfax,Alex W. Hewitt,Joseph E. Powell +16 more
TL;DR: This work brings together genetic epidemiology with scRNA-seq to uncover drivers of interindividual variation in the immune system and investigates how eQTLs affect the expression variation of essential immune genes in specific cell types and provided experimental support for established hypotheses of cellular mechanisms in complex autoimmune diseases.
Journal ArticleDOI
Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus
Richard Perez,M. Grace Gordon,Meena Subramaniam,Min Cheol Kim,George C. Hartoularos,Sasha Targ,Yang Sun,Anton Ogorodnikov,Raymund Bueno,Andrew Lu,Mike Thompson,Nadav Rappoport,Andrew Dahl,Cristina Lanata,Mehrdad Matloubian,Lenka Maliskova,Serena S. Kwek,Tony Li,Michal Slyper,Julia Waldman,Danielle Dionne,Orit Rozenblatt-Rosen,Lawrence Fong,Maria Dall'Era,Brunilda Balliu,Aviv Regev,Jinoos Yazdany,Lindsey A. Criswell,Noah Zaitlen,Chun Ye +29 more
TL;DR: Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) holds potential as a comprehensive and unbiased approach to simultaneously profile the composition and transcriptional states of circulating immune cells.