Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity by Jessica Neely, George Hartoularos, George Hartoularos, George Hartoularos, Daniel Bunis, Daniel Bunis, Yang Sun, David Lee, David Lee, Susan Kim, Chun Jimmie Ye, Chun Jimmie Ye, Chun Jimmie Ye, Chun Jimmie Ye, Chun Jimmie Ye, Chun Jimmie Ye, Marina Sirota, Marina Sirota

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2105 UCSF AutoImmunoProfiler – Understanding the Immunomes of Autoimmune diseases by Vincent Chan, Jeroen Roose, Eli Lilly, Jimmie Ye, Andy Gross, Max Krummel

SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models by Benjamin J. Strober, Karl Tayeb, Joshua Popp, Guanghao Qi, M. Grace Gordon, Richard Perez, Chun Jimmie Ye, Alexis Battle

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Multi-context genetic modeling of transcriptional regulation resolves novel disease loci by Mike Thompson, Mary Grace Gordon, Andrew Lu, Anchit Tandon, Eran Halperin, Alexander Gusev, Chun Jimmie Ye, Brunilda Balliu, Noah Zaitlen

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606 Cell-specific human endogenous retrovirus expression, host gene expression and SLE phenotypes by Maria Dall’Era, Lindsey A Criswell, Jinoos Yazdany, Marina Sirota, Cristina Lanata, Chun Jimmie Ye, Zachary Cutts, Sarah Patterson, Lenka Maliskova, Chaz Langelier

Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods by Drew Neavin, Anne Senabouth, Himanshi Arora, Jimmy Tsz Hang Lee, Aida Ripoll-Cladellas, sc-eQTLGen Consortium, Lude Franke, Shyam Prabhakar, Chun Jimmie Ye, Davis J. McCarthy, Marta Melé, Martin Hemberg, Joseph E. Powell

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Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures by Gaia Andreoletti, Cristina M. Lanata, Laura Trupin, 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

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Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq by Sara Sunshine, Andreas S. Puschnik, Joseph M. Replogle, Matthew T. Laurie, Jamin Liu, Beth Shoshana Zha, James K. Nuñez, Janie R. Byrum, Aidan H. McMorrow, Matthew B. Frieman, Juliane Winkler, Xiaojie Qiu, Oren S. Rosenberg, Manuel D. Leonetti, Chun Jimmie Ye, Jonathan S. Weissman, Joseph L. DeRisi, Marco Y. Hein

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Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree by 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 S Anderson, Gabriela K Fragiadakis, Jen Jen Yeh, Chun Jimmie Ye, Grace E Kim, Valerie M Weaver, Matthias Hebrok

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The effect of low-dose IL-2 and Treg adoptive cell therapy in patients with type 1 diabetes by Shen Dong, Kamir J. Hiam-Galvez, Cody T. Mowery, Kevan C. Herold, Stephen E. Gitelman, Jonathan H. Esensten, Weihong Liu, Angela P. Lares, Ashley S. Leinbach, Michael Lee, Vinh Nguyen, Stanley J. Tamaki, Whitney Tamaki, Courtney M. Tamaki, Morvarid Mehdizadeh, Amy L. Putnam, Matthew H. Spitzer, Chun Jimmie Ye, Qizhi Tang, Jeffrey A. Bluestone

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CCR2 deficiency alters activation of microglia subsets in traumatic brain injury by Kerri Somebang, Joshua Rudolph, Isabella Imhof, Luyi Li, Erene C. Niemi, Judy Shigenaga, Huy Tran, T. Michael Gill, Iris Lo, Brian A. Zabel, Gabriela Schmajuk, Brian T. Wipke, Stefka Gyoneva, Luke Jandreski, Michael Craft, Gina Benedetto, Edward D. Plowey, Israel Charo, James Campbell, Chun Jimmie Ye, S. Scott Panter, Mary C. Nakamura, Walter Eckalbar, Christine L. Hsieh

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Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy by Hanna M. Ollila, Eilon Sharon, Ling Lin, Nasa Sinnott-Armstrong, Aditya Ambati, Selina M. Yogeshwar, Ryan P. Hillary, Otto Jolanki, Juliette Faraco, Mali Einen, Guo Luo, Jing Zhang, Fang Han, Han Yan, Xiao Song Dong, Jing Li, Jun Zhang, Seung-Chul Hong, Tae Won Kim, Yves Dauvilliers, Lucie Barateau, Gert Jan Lammers, Rolf Fronczek, Geert Mayer, Joan Santamaria, Isabelle Arnulf, Stine Knudsen-Heier, May Kristin Lyamouri Bredahl, Per Medbøe Thorsby, Giuseppe Plazzi, Fabio Pizza, Monica Moresco, Catherine Crowe, Stephen K. Van den Eeden, Michel Lecendreux, Patrice Bourgin, Takashi Kanbayashi, Francisco J. Martínez-Orozco, Rosa Peraita-Adrados, Antonio Benetó, Jacques Montplaisir, Alex Desautels, Yu-Shu Huang, FinnGen, Poul Jennum, Sona Nevsimalova, David Kemlink, Alex Iranzo, Sebastiaan Overeem, Aleksandra Wierzbicka, Peter Geisler, Karel Sonka, Makoto Honda, Birgit Högl, Ambra Stefani, Fernando Morgadinho Coelho, Vilma Mantovani, Eva Feketeova, Mia Wadelius, Niclas Eriksson, Hans Smedje, Pär Hallberg, Per Egil Hesla, David Rye, Zerrin Pelin, Luigi Ferini-Strambi, Claudio L. Bassetti, Johannes Mathis, Ramin Khatami, Adi Aran, Sheela Nampoothiri, Tomas Olsson, Ingrid Kockum, Markku Partinen, Markus Perola, Birgitte R. Kornum, Sina Rueger, Juliane Winkelmann, Taku Miyagawa, Hiromi Toyoda, Seik-Soon Khor, Mihoko Shimada, Katsushi Tokunaga, Manuel Rivas, Jonathan K. Pritchard, Neil Risch, Zoltan Kutalik, Ruth O’Hara, Joachim Hallmayer, Chun Jimmie Ye, Emmanuel J. Mignot

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A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling by Jason A. Hackney, Haridha Shivram, Jason Vander Heiden, Chris Overall, Luz Orozco, Xia Gao, Eugene Kim, Nathan West, Aditi Qamra, Diana Chang, Arindam Chakrabarti, David F. Choy, Alexis J. Combes, Tristan Courau, Gabriela K. Fragiadakis, Arjun Arkal Rao, Arja Ray, Jessica Tsui, Kenneth Hu, Nicholas F. Kuhn, Matthew F. Krummel, David J. Erle, Kirsten Kangelaris, Aartik Sarma, Zoe Lyon, Carolyn S. Calfee, Prescott G. Woodruff, Rajani Ghale, Eran Mick, Ashley Byrne, Beth Shoshana Zha, Charles Langelier, Carolyn M. Hendrickson, Monique G.P. van der Wijst, George C. Hartoularos, Tianna Grant, Raymund Bueno, David S. Lee, John R. Greenland, Yang Sun, Richard Perez, Anton Ogorodnikov, Alyssa Ward, Chun Jimmie Ye, Thiru Ramalingam, Jacqueline M. McBride, Fang Cai, Anastasia Teterina, Min Bao, Larry Tsai, Ivan O. Rosas, Aviv Regev, Sharookh B. Kapadia, Rebecca N. Bauer, Carrie M. Rosenberger, Yumiko Abe-Jones, Michael Adkisson, K. Mark Ansel, Saurabh Asthana, Alexander Beagle, Sharvari Bhide, Cathy Cai, Saharai Caldera, Maria Calvo, Sidney A. Carrillo, Suzanna Chak, Stephanie Christenson, Zachary Collins, Spyros Darmanis, Angela Detweiler, Catherine DeVoe, Walter Eckalbar, Jeremy Giberson, Ana Gonzalez, Gracie Gordon, Paula Hayakawa Serpa, Alejandra Jauregui, Chayse Jones, Serena Ke, Divya Kushnoor, Tasha Lea, Deanna Lee, Aleksandra Leligdowicz, Yale Liu, Salman Mahboob, Lenka Maliskova, Michael Matthay, Elizabeth McCarthy, Priscila Muñoz-Sandoval, Norma Neff, Viet Nguyen, Nishita Nigam, Randy Parada, Maira Phelps, Logan Pierce, Priya Prasad, Sadeed Rashid, Gabriella Reeder, Nicklaus Rodriguez, Bushra Samad, Andrew Schroeder, Cole Shaw, Alan Shen, Austin Sigman, Pratik Sinha, Matthew Spitzer, Sara Sunshine, Kevin Tang, Luz Torres Altamirano, Alexandra Tsitsiklis, Erden Tumurbaatar, Vaibhav Upadhyay, Alexander Whatley, Andrew Willmore, Michael Wilson, Juliane Winkler, Kristine Wong, Kimberly Yee, Michelle Yu, Mingyue Zhou, Wandi S. Zhu

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