Chun Jimmie Ye
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Assessing computational tools for the discovery of transcription factor binding sites
M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, ...
Nature Biotechnology 23 (1), 137, 2005
Generation of knock-in primary human T cells using Cas9 ribonucleoproteins
K Schumann, S Lin, E Boyer, DR Simeonov, M Subramaniam, RE Gate, ...
Proceedings of the National Academy of Sciences 112 (33), 10437-10442, 2015
Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes
T Raj, K Rothamel, S Mostafavi, C Ye, MN Lee, JM Replogle, T Feng, ...
Science 344 (6183), 519-523, 2014
Common genetic variants modulate pathogen-sensing responses in human dendritic cells
MN Lee, C Ye, AC Villani, T Raj, W Li, TM Eisenhaure, SH Imboywa, ...
Science 343 (6175), 2014
A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks
O Parnas, M Jovanovic, TM Eisenhaure, RH Herbst, A Dixit, CJ Ye, ...
Cell 162 (3), 675-686, 2015
CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells
LJ Rupp, K Schumann, KT Roybal, RE Gate, CJ Ye, WA Lim, A Marson
Scientific Reports 7 (1), 737, 2017
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
HM Kang, M Subramaniam, S Targ, M Nguyen, L Maliskova, E McCarthy, ...
Nature Biotechnology 36 (1), 89, 2018
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
A Kirby, A Gnirke, DB Jaffe, V Barešová, N Pochet, B Blumenstiel, C Ye, ...
Nature Genetics 45 (3), 299, 2013
Intersection of population variation and autoimmunity genetics in human T cell activation
CJ Ye, T Feng, HK Kwon, T Raj, MT Wilson, N Asinovski, C McCabe, ...
Science 345 (6202), 2014
Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots
HM Kang, C Ye, E Eskin
Genetics 180 (4), 1909-1925, 2008
Discovery of stimulation-responsive immune enhancers with CRISPR activation
DR Simeonov, BG Gowen, M Boontanrart, TL Roth, JD Gagnon, ...
Nature 549 (7670), 111, 2017
Parsing the interferon transcriptional network and its disease associations
S Mostafavi, H Yoshida, D Moodley, H LeBoité, K Rothamel, T Raj, CJ Ye, ...
Cell 164 (3), 564-578, 2016
Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity
LB Rodda, E Lu, ML Bennett, CL Sokol, X Wang, SA Luther, BA Barres, ...
Immunity 48 (5), 1014-1028. e6, 2018
A tissue checkpoint regulates type 2 immunity
SJ Van Dyken, JC Nussbaum, J Lee, AB Molofsky, HE Liang, JL Pollack, ...
Nature Immunology 17 (12), 1381, 2016
Transethnic genetic-correlation estimates from summary statistics
BC Brown, CJ Ye, AL Price, N Zaitlen, ...
The American Journal of Human Genetics 99 (1), 76-88, 2016
Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches
JH Sul, B Han, C Ye, T Choi, E Eskin
PLoS Genet 9 (6), e1003491, 2013
EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
ATL Lun, S Riesenfeld, T Andrews, T Gomes, JC Marioni
Genome Biology 20 (1), 63, 2019
Unleashing type-2 dendritic cells to drive protective antitumor CD4+ T cell immunity
M Binnewies, AM Mujal, JL Pollack, AJ Combes, EA Hardison, KC Barry, ...
Cell 177 (3), 556-571. e16, 2019
Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants
LH Uricchio, NA Zaitlen, CJ Ye, JS Witte, RD Hernandez
Genome Research 26 (7), 863-873, 2016
Genetic determinants of co-accessible chromatin regions in activated T cells across humans
RE Gate, CS Cheng, AP Aiden, A Siba, M Tabaka, D Lituiev, I Machol, ...
Nature Genetics 50 (8), 1140, 2018
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