Human

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

Chun Jimmie Ye, Jenny Chen, Alexandra-Chloé Villani, Rachel E Gate, Meena Subramaniam, Tushar Bhangale, Mark N Lee, Towfique Raj, Raktima Raychowdhury, Weibo Li, Noga Rogel, Sean Simmons, Selina H Imboywa, Portia I Chipendo, Cristin McCabe, Michelle H Lee, Irene Y Frohlich, Barbara E Stranger, Philip L De Jager, Aviv Regev, Tim Behrens, Nir Hacohen

Genome Research 2018

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

Hyun Min Kang*, Meena Subramaniam*, Sasha Targ*, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata, Rachel E Gate, Sara Mostafavi, Alexander Marson, Noah Zaitlen, Lindsey A Criswell, Chun Jimmie Ye

Nature Biotechnology 2017

Discovery of stimulation-responsive immune enhancers with CRISPR activation

Discovery of stimulation-responsive immune enhancers with CRISPR activation

Dimitre R. Simeonov, Benjamin G. Gowen, Mandy Boontanrart, Theodore L. Roth, John D. Gagnon, Maxwell R. Mumbach, Ansuman T. Satpathy, Youjin Lee, Nicolas L. Bray, Alice Y. Chan, Dmytro S. Lituiev, Michelle L. Nguyen, Rachel E. Gate, Meena Subramaniam, Zhongmei Li, Jonathan M. Woo, Therese Mitros, Graham J. Ray, Gemma L. Curie, Nicki Naddaf, Julia S. Chu, Hong Ma, Eric Boyer, Frederic Van Gool, Hailiang Huang, Ruize Liu, Victoria R. Tobin, Kathrin Schumann, Mark J. Daly, Kyle K. Farh, K. Mark Ansel, Chun Jimmie Ye, William J. Greenleaf, Mark S. Anderson, Jeffrey A. Bluestone, Howard Y. Chang, Jacob E. Corn, Alexander Marson

Nature 2017

Parsing the interferon transcriptional network and its disease associations

Parsing the interferon transcriptional network and its disease associations

Sara Mostafavi, Hideyuki Yoshida, Devapregasan Moodley, Hugo LeBoité, Katherine Rothamel, Towfique Raj, Chun Jimmie Ye, Nicolas Chevrier, Shen-Ying Zhang, Ting Feng, Mark Lee, Jean-Laurent Casanova, James D Clark, Martin Hegen, Jean-Baptiste Telliez, Nir Hacohen, Philip L De Jager, Aviv Regev, Diane Mathis, Christophe Benoist, Immunological Genome Project Consortium

Cell 2016

Intersection of population variation and autoimmunity genetics in human T cell activation

Intersection of population variation and autoimmunity genetics in human T cell activation

Chun Jimmie Ye, Ting Feng, Ho-Keun Kwon, Towfique Raj, Michael T Wilson, Natasha Asinovski, Cristin McCabe, Michelle H Lee, Irene Frohlich, Hyun-il Paik, Noah Zaitlen, Nir Hacohen, Barbara Stranger, Philip De Jager, Diane Mathis, Aviv Regev, Christophe Benoist

Science 2014

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes

Towfique Raj, Katie Rothamel, Sara Mostafavi, Chun Ye, Mark N Lee, Joseph M Replogle, Ting Feng, Michelle Lee, Natasha Asinovski, Irene Frohlich, Selina Imboywa, Alina Von Korff, Yukinori Okada, Nikolaos A Patsopoulos, Scott Davis, Cristin McCabe, Hyun-il Paik, Gyan P Srivastava, Soumya Raychaudhuri, David A Hafler, Daphne Koller, Aviv Regev, Nir Hacohen, Diane Mathis, Christophe Benoist, Barbara E Stranger, Philip L De Jager

Science 2014

Common genetic variants modulate pathogen-sensing responses in human dendritic cells

Common genetic variants modulate pathogen-sensing responses in human dendritic cells

Mark N Lee, Chun Ye, Alexandra-Chloé Villani, Towfique Raj, Weibo Li, Thomas M Eisenhaure, Selina H Imboywa, Portia I Chipendo, F Ann Ran, Kamil Slowikowski, Lucas D Ward, Khadir Raddassi, Cristin McCabe, Michelle H Lee, Irene Y Frohlich, David A Hafler, Manolis Kellis, Soumya Raychaudhuri, Feng Zhang, Barbara E Stranger, Christophe O Benoist, Philip L De Jager, Aviv Regev, Nir Hacohen

Science 2014

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Andrew Kirby, Andreas Gnirke, David B Jaffe, Veronika Barešová, Nathalie Pochet, Brendan Blumenstiel, Chun Ye, Daniel Aird, Christine Stevens, James T Robinson, Moran N Cabili, Irit Gat-Viks, Edward Kelliher, Riza Daza, Matthew DeFelice, Helena Hůlková, Jana Sovová, Petr Vylet'al, Corinne Antignac, Mitchell Guttman, Robert E Handsaker, Danielle Perrin, Scott Steelman, Snaevar Sigurdsson, Steven J Scheinman, Carrie Sougnez, Kristian Cibulskis, Melissa Parkin, Todd Green, Elizabeth Rossin, Michael C Zody, Ramnik J Xavier, Martin R Pollak, Seth L Alper, Kerstin Lindblad-Toh, Stacey Gabriel, P Suzanne Hart, Aviv Regev, Chad Nusbaum, Stanislav Kmoch, Anthony J Bleyer, Eric S Lander, Mark J Daly

Nature Genetics 2013

Integrated Computational and Experimental Analysis of the Neuroendocrine Transcriptome in Genetic Hypertension Identifies Novel Control Points for the Cardio-Metabolic Syndrome

Integrated Computational and Experimental Analysis of the Neuroendocrine Transcriptome in Genetic Hypertension Identifies Novel Control Points for the Cardio-Metabolic Syndrome

Ryan S. Friese, Chun Ye, Caroline M. Nievergelt, Andrew J. Schork, Nitish R. Mahapatra, Fangwen Rao, Philip S. Napolitan, Jill Waalen, Geert W. Schmid-Schönbein, Eleazar Eskin, Daniel T. O'Connor

Circulation: Cardiovascular Genetics 2012