Publications

Links to all papers from the lab are organized by year of publication.

XYZeq: Spatially-resolved single-cell RNA-sequencing reveals expression heterogeneity in the tumor microenvironment

Youjin Lee, Derek Bogdanoff, Yutong Wang, George Hartoularos, Jonathan M. Woo, Cody T. Mowery, Hunter M. Nisonoff, David S. Lee, Yang Sun, James Lee, Sadaf Mehdizadeh, Joshua Cantlon, Eric Shifrut, David N. Ngyuen, Yun S. Song, Alexander Marson, Eric D. Chow, and Chun J. Ye

Science Advances. 2021

 

Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Hematopoiesis

Daniel Bunis, Yelena Bronevetsky, Elisabeth Krow-Lucal, Nirav R Bhakta, Charles C Kim, Srilaxmi Nerella, Norman Jones, Ventura F Mendoza, Yvonne J Bryson, James E Gern, Rachel L Rutishauser, Chun Jimmie Ye, Marina Sirota, Joseph M McCune, Trevor D Burt.

Cell Reports. 2021

 

Single-Cell Transcriptional Profiling of Human Thymic Stroma Uncovers Novel Cellular Heterogeneity in the Thymic Medulla

Jhoanne L. Bautista, Nathan T. Cramer, Corey N. Miller, Jessica Chavez, David I. Berrios, Lauren E. Byrnes, Joe Germino, Vasilis Ntranos, Julie B. Sneddon, Trevor D. Burt, James M. Gardner, Chun J. Ye, Mark S. Anderson & Audrey V. Parent 

Nature Communications. 2021

 

No Detectable Alloreactive Transcriptional Responses under Standard Sample Preparation Conditions during Donor-Multiplexed Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells

McGinnis, Christopher S., David A. Siegel, Guorui Xie, George Hartoularos, Mars Stone, Chun J. Ye, Zev J. Gartner, Nadia R. Roan, and Sulggi A. Lee. 

BMC Biology. 2021

 

Single-Cell RNA Sequencing of Tocilizumab-Treated Peripheral Blood Mononuclear Cells as an in Vitro Model of Inflammation

Arya Zarinsefat, George Hartoularos, Dmitry Rychkov, Priyanka Rashmi, Sindhu Chandran, Flavio Vincenti, Chun J. Ye, Minnie M. Sarwal

Frontiers in Genetics. 2021

 

Global Absence and Targeting of Protective Immune States in Severe COVID-19

Alexis J. Combes, Tristan Courau, Nicholas F. Kuhn, Kenneth H. Hu, Arja Ray, William S. Chen, Simon J. Cleary, Nayvin W. Chew, Divyashree Kushnoor, Gabriella C. Reeder, Alan Shen, Jessica Tsui, Kamir J. Hiam-Galvez, Priscila Muñoz-Sandoval, Wandi S Zhu, David S. Lee, Yang Sun, Ran You, Mélia Magnen, Lauren Rodriguez, Aleksandra Leligdowicz, Colin R. Zamecnik, Rita P. Loudermilk, Michael R. Wilson, Chun J. Ye, Gabriela K. Fragiadakis, Mark R. Looney, Vincent Chan, Alyssa Ward, Sidney Carrillo, Michael Matthay, David J. Erle, Prescott G. Woodruff, Charles Langelier, Kirsten Kangelaris, Carolyn M. Hendrickson, Carolyn Calfee, Arjun Arkal Rao, and Matthew F. Krummel

Nature. 2021

Intratumoral CD4+ T Cells Mediate Anti-Tumor Cytotoxicity in Human Bladder Cancer

David Y Oh, Serena S Kwek, Siddharth S Raju, Tony Li, Elizabeth McCarthy, Eric Chow, Dvir Aran, Arielle Ilano, Chien-Chun Steven Pai, Chiara Rancan, Kathryn Allaire, Arun Burra, Yang Sun, Matthew H Spitzer, Serghei Mangul, Sima Porten, Maxwell V Meng, Terence W Friedlander, Chun Jimmie Ye, Lawrence Fong

Cell. 2020

 

Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies

Theodore L Roth, P Jonathan Li, Franziska Blaeschke, Jasper F Nies, Ryan Apathy, Cody Mowery, Ruby Yu, Michelle L T Nguyen, Youjin Lee, Anna Truong, Joseph Hiatt, David Wu, David N Nguyen, Daniel Goodman, Jeffrey A Bluestone, Chun Jimmie Ye, Kole Roybal, Eric Shifrut, Alexander Marson

Cell. 2020

 

Functional CRISPR Dissection of Gene Networks Controlling Human Regulatory T Cell Identity

Kathrin Schumann, Siddharth S. Raju, Michael Lauber, Saskia Kolb, Eric Shifrut, Jessica T. Cortez, Nikolaos Skartsis, Vinh Q. Nguyen, Jonathan M. Woo, Theodore L. Roth, Ruby Yu, Michelle L. T. Nguyen, Dimitre R. Simeonov, David N. Nguyen, Sasha Targ, Rachel E. Gate, Qizhi Tang, Jeffrey A. Bluestone, Matthew H. Spitzer, Chun Jimmie Ye & Alexander Marson

Nature Immunology. 2020

 

Evaluation of SARS-CoV-2 Serology Assays Reveals a Range of Test Performance

Jeffrey D. Whitman, Joseph Hiatt, Cody T. Mowery, Brian R. Shy, Ruby Yu, Tori N. Yamamoto, Ujjwal Rathore, Gregory M. Goldgof, Caroline Whitty, Jonathan M. Woo, Antonia E. Gallman, Tyler E. Miller, Andrew G. Levine, David N. Nguyen, Sagar P. Bapat, Joanna Balcerek, Sophia A. Bylsma, Ana M. Lyons, Stacy Li, Allison Wai-yi Wong, Eva Mae Gillis-Buck, Zachary B. Steinhart, Youjin Lee, Ryan Apathy, Mitchell J. Lipke, Jennifer Anne Smith, Tina Zheng, Ian C. Boothby, Erin Isaza, Jackie Chan, Dante D. Acenas II, Jinwoo Lee, Trisha A. Macrae, Than S. Kyaw, David Wu, Dianna L. Ng, Wei Gu, Vanessa A. York, Haig Alexander Eskandarian, Perri C. Callaway, Lakshmi Warrier, Mary E. Moreno, Justine Levan, Leonel Torres, Lila A. Farrington, Rita P. Loudermilk, Kanishka Koshal, Kelsey C. Zorn, Wilfredo F. Garcia-Beltran, Diane Yang, Michael G. Astudillo, Bradley E. Bernstein, Jeffrey A. Gelfand, Edward T. Ryan, Richelle C. Charles, A. John Iafrate, Jochen K. Lennerz, Steve Miller, Charles Y. Chiu, Susan L. Stramer, Michael R. Wilson, Aashish Manglik, Chun Jimmie Ye, Nevan J. Krogan, Mark S. Anderson, Jason G. Cyster, Joel D. Ernst, Alan H. B. Wu, Kara L. Lynch, Caryn Bern, Patrick D. Hsu & Alexander Marson

Nature Biotechnology. 2020

 

lentiMPRA and MPRAflow for High-Throughput Functional Characterization of Gene Regulatory ElementsGrace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Georgakopoulos-Soares, Nir Yosef, Chun Jimmie Ye, Katherine S. Pollard, Jay Shendure, Martin Kircher & Nadav Ahituv

Nature Protocols. 2020

 

Enhancing Droplet-Based Single-Nucleus RNA-Seq Resolution Using the Semi-Supervised Machine Learning Classifier DIEM

Marcus Alvarez, Elior Rahmani, Brandon Jew, Kristina M. Garske, Zong Miao, Jihane N. Benhammou, Chun Jimmie Ye, Joseph R. Pisegna, Kirsi H. Pietiläinen, Eran Halperin & Päivi Pajukanta. 

Scientific Reports. 2020

 

IL-27: An Endogenous Constitutive Repressor of Human Monocytes

Frangieh, Michael, Allison McHenry, Roxanne Phillips, Chun Ye, Angelina Bernier, Lori Laffel, Wassim Elyaman, and Elizabeth M. Bradshaw

Clinical Immunology. 2020

 

On the Cross-Population Generalizability of Gene Expression Prediction Models

Kevin L. Keys, Angel C. Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew W. Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. Lenoir, Jimmie C. Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard, Christopher R. Gignoux

PLoS Genetics. 2020

 

Optimized Design of Single-Cell RNA Sequencing Experiments for Cell-Type-Specific eQTL Analysis

Igor Mandric, Tommer Schwarz, Arunabha Majumdar, Kangcheng Hou, Leah Briscoe, Richard Perez, Meena Subramaniam, Christoph Hafemeister, Rahul Satija, Chun Jimmie Ye, Bogdan Pasaniuc & Eran Halperin

Nature Communications. 2020

 

The Single-Cell eQTLGen Consortium

MGP van der Wijst, DH de Vries, HE Groot, G Trynka, CC Hon, MJ Bonder, O Stegle, MC Nawijn, Y Idaghdour, P van der Harst, CJ Ye, J Powell, FJ Theis, A Mahfouz, M Heinig, L Franke

eLife. 2020

 

SCITO-Seq: Single-Cell Combinatorial Indexed Cytometry Sequencing

Byungjin Hwang, David S. Lee, Whitney Tamaki, Yang Sun, Anton Ogorodnikov, George Hartoularos, Aidan Winters, Yun S. Song, Eric D. Chow, Matthew H. Spitzer, Chun Jimmie Ye

bioRxiv. 2020

 

Improved Covid-19 Serology Test Performance by Integrating Multiple Lateral Flow Assays Using Machine Learning

Mowery, C. T., A. Marson, Y. S. Song, and C. J. Ye

medRxiv. 2020

 

Ethnicity-Specific Transcriptomic Variation in Immune Cells and Correlation with Disease Activity in Systemic Lupus Erythematosus

Gaia Andreoletti, Cristina M. Lanata, Ishan Paranjpe, Tia S. Jain, Joanne Nititham, Kimberly E. Taylor, Alexis J Combes, Lenka Maliskova, Chun Jimmie Ye, Patricia Katz, Maria Dall’Era, Jinoos Yazdany, Lindsey A. Criswell, Marina Sirota. 

bioRxiv. 2020

 

Single Cell Transcriptome Analysis Defines Novel Heterogeneity within the Pancreatic Ductal Tree

Audrey M. Hendley, Arjun A. Rao, Laura Leonhardt, Sudipta Ashe, Jennifer A. Smith, Simone Giacometti, Xianlu L Peng, Honglin Jiang, David I. Berrios, Mathias Pawlak, Lucia Y. Li, Jonghyun Lee, Eric A. Collisson, Mark Anderson, Gabriela K. Fragiadakis, Jen Jen Yeh, Jimmie Ye Chun, Grace E. Kim, Valerie M. Weaver, Matthias Hebrok

bioRxiv. 2020

Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity

Mikhail Binnewies, Adriana M Mujal, Joshua L Pollack, Alexis J Combes, Emily A Hardison, Kevin C Barry, Jessica Tsui, Megan K Ruhland, Kelly Kersten, Marwan A Abushawish, Marko Spasic, Jonathan P Giurintano, Vincent Chan, Adil I Daud, Patrick Ha, Chun J Ye, Edward W Roberts, Matthew F Krummel. 

Cell. 2019

 

Reverse Gene–environment Interaction Approach to Identify Variants Influencing Body-Mass Index in Humans

Kristina M. Garske, David Z. Pan, Zong Miao, Yash V. Bhagat, Caroline Comenho, Christopher R. Robles, Jihane N. Benhammou, Marcus Alvarez, Arthur Ko, Chun Jimmie Ye, Joseph R. Pisegna, Karen L. Mohlke, Janet S. Sinsheimer, Markku Laakso & Päivi Pajukanta

Nature Metabolism. 2019

 

Ultrarare Variants Drive Substantial Cis-Heritability of Human Gene Expression

Ryan D. Hernandez, Lawrence H. Uricchio, Kevin Hartman, Chun Ye, Andrew Dahl & Noah Zaitlen

Nature Genetics. 2019

 

Functional Interpretation of Single Cell Similarity Maps

DeTomaso, David, Matthew G. Jones, Meena Subramaniam, Tal Ashuach, Chun J. Ye, and Nir Yosef

Nature Communication. 2019

 

Mapping Gene Regulatory Networks of Primary CD4+ T Cells Using Single-Cell Genomics and Genome Engineering

Rachel E. Gate, Min Cheol Kim, Andrew Lu, David Lee, Eric Shifrut, Meena Subramaniam, Alexander Marson, Chun J. Ye

bioRxiv. 2019

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. 2018

 

Genetic Determinants of Co-Accessible Chromatin Regions in Activated T Cells across Humans

Rachel E. Gate, Christine S. Cheng, Aviva P. Aiden, Atsede Siba, Marcin Tabaka, Dmytro Lituiev, Ido Machol, M. Grace Gordon, Meena Subramaniam, Muhammad Shamim, Kendrick L. Hougen, Ivo Wortman, Su-Chen Huang, Neva C. Durand, Ting Feng, Philip L. De Jager, Howard Y. Chang, Erez Lieberman Aiden, Christophe Benoist, Michael A. Beer, Chun J. Ye & Aviv Regev

Nature Genetics. 2018

 

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

 

Lineage Dynamics of Murine Pancreatic Development at Single-Cell Resolution

Byrnes, Lauren E., Daniel M. Wong, Meena Subramaniam, Nathaniel P. Meyer, Caroline L. Gilchrist, Sarah M. Knox, Aaron D. Tward, Chun J. Ye, and Julie B. Sneddon. 

Nature Communications. 2018

 

An Ancestry‐based Approach for Detecting Interactions

Danny S. Park, Itamar Eskin, Eun Yong Kang, Eric R. Gamazon, Celeste Eng, Christopher R. Gignoux, Joshua M. Galanter, Esteban Burchard, Chun J. Ye, Hugues Aschard, Eleazar Eskin, Eran Halperin, Noah Zaitlen

Genetic. 2018

 

Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity

Lauren B Rodda, Erick Lu, Mariko L Bennett, Caroline L Sokol, Xiaoming Wang, Sanjiv A Luther, Ben A Barres, Andrew D Luster, Chun Jimmie Ye, Jason G Cyster

Immunity. 2018

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 J. Ye, William J. Greenleaf, Mark S. Anderson, Jeffrey A. Bluestone, Howard Y. Chang, Jacob E. Corn & Alexander Marson

Nature. 2017

 

CRISPR/Cas9-Mediated PD-1 Disruption Enhances Anti-Tumor Efficacy of Human Chimeric Antigen Receptor T Cells

Rupp, Levi J., Kathrin Schumann, Kole T. Roybal, Rachel E. Gate, Chun J. Ye, Wendell A. Lim, and Alexander Marson

Scientific Reports. 2017

 

Covariate Selection for Association Screening in Multiphenotype Genetic Studies

Aschard, Hugues, Vincent Guillemot, Bjarni Vilhjalmsson, Chirag J. Patel, David Skurnik, Chun J. Ye, Brian Wolpin, Peter Kraft, and Noah Zaitlen. 

Nature Genetics. 2017

 

PhAT-QTL: A Phase-Aware Test for QTL Detection

Subramaniam, Meena, Noah Zaitlen, and Jimmie Ye

Bioinformatics Research and Applications. 2017

 

Reconstructing the Molecular Function of Genetic Variation in Regulatory Networks

Wilentzik, Roni, Chun Jimmie Ye, and Irit Gat-Viks

Genetics. 2017

Transethnic Genetic-Correlation Estimates from Summary Statistics

Brown, Brielin C., Asian Genetic Epidemiology Network Type 2 Diabetes Consortium, Chun Jimmie Ye, Alkes L. Price, and Noah Zaitlen. 

American Journal of Human Genetics. 2016

 

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

 

Selection and Explosive Growth Alter Genetic Architecture and Hamper the Detection of Causal Rare Variants

Uricchio, Lawrence H., Noah A. Zaitlen, Chun Jimmie Ye, John S. Witte, and Ryan D. Hernandez

Genome Research. 2016

 

A Tissue Checkpoint Regulates Type 2 Immunity

Steven J Van Dyken, Jesse C Nussbaum, Jinwoo Lee, Ari B Molofsky, Hong-Erh Liang, Joshua L Pollack, Rachel E Gate, Genevieve E Haliburton, Chun J Ye, Alexander Marson, David J Erle & Richard M Locksley

Nature Immunology. 2016

A Genome-Wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Oren Parnas, Marko Jovanovic, Thomas M Eisenhaure, Rebecca H Herbst, Atray Dixit, Chun Jimmie Ye, Dariusz Przybylski, Randall J Platt, Itay Tirosh, Neville E Sanjana, Ophir Shalem, Rahul Satija, Raktima Raychowdhury, Philipp Mertins, Steven A Carr, Feng Zhang, Nir Hacohen, Aviv Regev

Cell. 2015

 

Generation of Knock-in Primary Human T Cells Using Cas9 Ribonucleoproteins

Kathrin Schumann, Steven Lin, Eric Boyer, Dimitre R. Simeonov, Meena Subramaniam, Rachel E. Gate, Genevieve E. Haliburton, Chun J. Ye, Jeffrey A. Bluestone, Jennifer A. Doudna, and Alexander Marson

PNAS. 2015

Intersection of Population Variation and Autoimmunity Genetics in Human T Cell Activation

Ye, Chun Jimmie, Ting Feng, Ho-Keun Kwon, Towfique Raj, Michael T. Wilson, Natasha Asinovski, Cristin McCabe, et al

Science. 2014

 

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

Lee, Mark N., Chun Ye, Alexandra-Chloé Villani, Towfique Raj, Weibo Li, Thomas M. Eisenhaure, Selina H. Imboywa, et al.

Science. 2014

 

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

Raj, Towfique, Katie Rothamel, Sara Mostafavi, Chun Ye, Mark N. Lee, Joseph M. Replogle, Ting Feng, et al

Science. 2014

News

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