Chun Jimmie Ye (Chun J Ye, Chun Ye, Jimmie C Ye, Chun J Yee)

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 74

Top Topics

Genome Wide Association

Systemic Lupus Erythematosus

Gene Expression

Top Venues

Nature genetics

bioRxiv : the preprint server for biology

Nature communications

This page only lists publications with an associated author ORCID identifier.

Publications

Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics 56 (4) (2024)
Gabriel B Loeb, Pooja Kathail, Richard W Shuai, Ryan Chung, Reinier J Grona, Sailaja Peddada, Volkan Sevim, Scot Federman, Karl Mader, Audrey Y Chu, Jonathan Davitte, Juan Du, Alexander R Gupta, Chun Jimmie Ye, Shawn Shafer, Laralynne Przybyla, Radu Rapiteanu, Nilah M Ioannidis, Jeremy F Reiter
Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. Nature genetics (2024)
Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics (2024)
Charlotte Hurabielle, Taylor N LaFlam, Melissa Gearing, Chun Jimmie Ye
Functional genomics in inborn errors of immunity. Immunological reviews 322 (1) (2024)
Cody T Mowery, Jacob W Freimer, Zeyu Chen, Salvador Casaní-Galdón, Jennifer M Umhoefer, Maya M Arce, Ketrin Gjoni, Bence Daniel, Katalin D Sandor, Benjamin G Gowen, Vinh Nguyen, Dimitre R Simeonov, Christian M Garrido, Gemma L Curie, Ralf Schmidt, Zachary Steinhart, Ansuman T Satpathy, Katherine S Pollard, Jacob E Corn, Bradley E Bernstein, Chun Jimmie Ye, Alexander Marson
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature genetics 56 (6) (2024)
Cody T Mowery, Jacob W Freimer, Zeyu Chen, Salvador Casaní-Galdón, Jennifer M Umhoefer, Maya M Arce, Ketrin Gjoni, Bence Daniel, Katalin D Sandor, Benjamin G Gowen, Vinh Nguyen, Dimitre R Simeonov, Christian M Garrido, Gemma L Curie, Ralf Schmidt, Zachary Steinhart, Ansuman T Satpathy, Katherine S Pollard, Jacob E Corn, Bradley E Bernstein, Chun Jimmie Ye, Alexander Marson
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature genetics 56 (6) (2024)
Cody T Mowery, Jacob W Freimer, Zeyu Chen, Salvador Casaní-Galdón, Jennifer M Umhoefer, Maya M Arce, Ketrin Gjoni, Bence Daniel, Katalin D Sandor, Benjamin G Gowen, Vinh Nguyen, Dimitre R Simeonov, Christian M Garrido, Gemma L Curie, Ralf Schmidt, Zachary Steinhart, Ansuman T Satpathy, Katherine S Pollard, Jacob E Corn, Bradley E Bernstein, Chun Jimmie Ye, Alexander Marson
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature genetics (2024)
Charlotte Hurabielle, Taylor N LaFlam, Melissa Gearing, Chun Jimmie Ye
Functional genomics in inborn errors of immunity. Immunological reviews 322 (1) (2024)
Cody T Mowery, Jacob W Freimer, Zeyu Chen, Salvador Casaní-Galdón, Jennifer M Umhoefer, Maya M Arce, Ketrin Gjoni, Bence Daniel, Katalin D Sandor, Benjamin G Gowen, Vinh Nguyen, Dimitre R Simeonov, Christian M Garrido, Gemma L Curie, Ralf Schmidt, Zachary Steinhart, Ansuman T Satpathy, Katherine S Pollard, Jacob E Corn, Bradley E Bernstein, Chun Jimmie Ye, Alexander Marson
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature genetics 56 (6) (2024)
Gabriel B Loeb, Pooja Kathail, Richard Shuai, Ryan Chung, Reinier J Grona, Sailaja Peddada, Volkan Sevim, Scot Federman, Karl Mader, Audrey Chu, Jonathan Davitte, Juan Du, Alexander R Gupta, Chun Jimmie Ye, Shawn Shafer, Laralynne Przybyla, Radu Rapiteanu, Nilah Ioannidis, Jeremy F Reiter
Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. bioRxiv : the preprint server for biology (2024)
Pooja Kathail, Richard W Shuai, Ryan Chung, Chun Jimmie Ye, Gabriel B Loeb, Nilah M Ioannidis
Current genomic deep learning models display decreased performance in cell type specific accessible regions. bioRxiv : the preprint server for biology (2024)
Charlotte Hurabielle, Taylor N LaFlam, Melissa Gearing, Chun Jimmie Ye
Functional genomics in inborn errors of immunity. Immunological reviews 322 (1) (2024)
Cody T Mowery, Jacob W Freimer, Zeyu Chen, Salvador Casaní-Galdón, Jennifer M Umhoefer, Maya M Arce, Ketrin Gjoni, Bence Daniel, Katalin D Sandor, Benjamin G Gowen, Vinh Nguyen, Dimitre R Simeonov, Christian M Garrido, Gemma L Curie, Ralf Schmidt, Zachary Steinhart, Ansuman T Satpathy, Katherine S Pollard, Jacob E Corn, Bradley E Bernstein, Chun Jimmie Ye, Alexander Marson
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature genetics 56 (6) (2024)
Cody T Mowery, Jacob W Freimer, Zeyu Chen, Salvador Casaní-Galdón, Jennifer M Umhoefer, Maya M Arce, Ketrin Gjoni, Bence Daniel, Katalin D Sandor, Benjamin G Gowen, Vinh Nguyen, Dimitre R Simeonov, Christian M Garrido, Gemma L Curie, Ralf Schmidt, Zachary Steinhart, Ansuman T Satpathy, Katherine S Pollard, Jacob E Corn, Bradley E Bernstein, Chun Jimmie Ye, Alexander Marson
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature genetics 56 (6) (2024)
Pooja Kathail, Richard W Shuai, Ryan Chung, Chun Jimmie Ye, Gabriel B Loeb, Nilah M Ioannidis
Current genomic deep learning models display decreased performance in cell type specific accessible regions. bioRxiv : the preprint server for biology (2024)
Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics 56 (4) (2024)
Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics 56 (4) (2024)
Charlotte Hurabielle, Taylor N LaFlam, Melissa Gearing, Chun Jimmie Ye
Functional genomics in inborn errors of immunity. Immunological reviews 322 (1) (2024)
Charlotte Hurabielle, Taylor N LaFlam, Melissa Gearing, Chun Jimmie Ye
Functional genomics in inborn errors of immunity. Immunological reviews 322 (1) (2024)
Pooja Kathail, Richard W Shuai, Ryan Chung, Chun Jimmie Ye, Gabriel B Loeb, Nilah M Ioannidis
Current genomic deep learning models display decreased performance in cell type specific accessible regions. bioRxiv : the preprint server for biology (2024)
Gabriel B Loeb, Pooja Kathail, Richard Shuai, Ryan Chung, Reinier J Grona, Sailaja Peddada, Volkan Sevim, Scot Federman, Karl Mader, Audrey Chu, Jonathan Davitte, Juan Du, Alexander R Gupta, Chun Jimmie Ye, Shawn Shafer, Laralynne Przybyla, Radu Rapiteanu, Nilah Ioannidis, Jeremy F Reiter
Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. bioRxiv : the preprint server for biology (2024)
Charlotte Hurabielle, Taylor N LaFlam, Melissa Gearing, Chun Jimmie Ye
Functional genomics in inborn errors of immunity. Immunological reviews (2024)
Pooja Kathail, Richard W Shuai, Ryan Chung, Chun Jimmie Ye, Gabriel B Loeb, Nilah M Ioannidis
Current genomic deep learning models display decreased performance in cell type specific accessible regions. bioRxiv : the preprint server for biology (2024)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature 626 (8001) (2023)
Nadav Brandes, Grant Goldman, Charlotte H Wang, Chun Jimmie Ye, Vasilis Ntranos
Genome-wide prediction of disease variant effects with a deep protein language model. Nature genetics (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature 626 (8001) (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobe of young children. Nature (2023)
Xiaoyu Yang, Jia Wen, Han Yang, Ian R Jones, Xiaodong Zhu, Weifang Liu, Bingkun Li, Claire D Clelland, Wenjie Luo, Man Ying Wong, Xingjie Ren, Xiekui Cui, Michael Song, Hongjiang Liu, Cady Chen, Nicolas Eng, Mirunalini Ravichandran, Yang Sun, David S Lee, Eric Van Buren, Min-Zhi Jiang, Candace S Y Chan, Chun Jimmie Ye, Rushika M Perera, Li Gan, Yun Li, Yin Shen
Functional characterization of Alzheimer's disease genetic variants in microglia. Nature genetics (2023)
Tauras P Vilgalys, Jennifer Klunk, Christian E Demeure, Xiaoheng Cheng, Mari Shiratori, Julien Madej, Rémi Beau, Derek Elli, Maria I Patino, Rebecca Redfern, Sharon N DeWitte, Julia A Gamble, Jesper L Boldsen, Ann G Carmichael, Nükhet Varlik, Katherine Eaton, Jean-Christophe Grenier, G Brian Golding, Alison Devault, Jean-Marie Rouillard, Vania Yotova, Renata Sindeaux, Chun Jimmie Ye, Matin Bikaran, Anne Dumaine, Jessica F Brinkworth, Dominique Missiakas, Guy A Rouleau, Matthias Steinrücken, Javier Pizarro-Cerdá, Hendrik N Poinar, Luis B Barreiro
Reply to Barton et al: signatures of natural selection during the Black Death. bioRxiv : the preprint server for biology (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature 626 (8001) (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature 626 (8001) (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature (2023)
Sara Sunshine, Andreas S Puschnik, Joseph M Replogle, Matthew T Laurie, Jamin Liu, Beth Shoshanna Zha, James K Nuñez, Janie R Byrum, Aidan H McMorrow, Matthew B Friemann, Juliane Winkler, Xiaojie Qiu, Oren S Rosenberg, Manuel D Leonetti, Chun Jimmie Ye, Jonathan S Weissman, Joseph L DeRisi, Marco Y Hein
Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nature communications 14 (1) (2023)
Gabrielle Rabadam, Camilla Wibrand, Emily Flynn, George C Hartoularos, Yang Sun, Chun Jimmie Ye, Susan Kim, Zev Gartner, Marina Sirota, Jessica Neely
Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics. bioRxiv : the preprint server for biology (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature 626 (8001) (2023)
Hanna M Ollila, Eilon Sharon, Ling Lin, Nicholas A 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, null null, 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, Lukrécia Mertová, 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 Rahbek Kornum, Sina Rueger, Juliane Winkelmann, Taku Miyagawa, Hiromi Toyoda, Seik-Soon Khor, Mihoko Shimada, Katsushi Tokunaga, Manuel A Rivas, Jonathan K Pritchard, Neil Risch, Zoltán Kutalik, Ruth O'Hara, Joachim Hallmayer, Chun Jimmie Ye, Emmanuel Jean-Marie Mignot
Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy. Nature communications 14 (1) (2023)
Connor A Tsuchida, Nadav Brandes, Raymund Bueno, Marena I Trinidad, Thomas Mazumder, Bingfei Yu, Byungjin Hwang, Christopher Chang, Jamin Liu, Yang Sun, Caitlin R Hopkins, Kevin R Parker, Yanyan Qi, Ansuman T Satpathy, Edward A Stadtmauer, Jamie H D Cate, Justin Eyquem, Joseph A Fraietta, Carl H June, Howard Y Chang, Chun Jimmie Ye, Jennifer A Doudna
Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. bioRxiv : the preprint server for biology (2023)
Marcos Assis Nascimento, Sean Biagiotti, Vicente Herranz-Pérez, Samara Santiago, Raymund Bueno, Chun Jimmie Ye, Taylor J Abel, Zhuangzhi Zhang, Juan S Rubio-Moll, Arnold R Kriegstein, Zhengang Yang, Jose Manuel García-Verdugo, Eric J Huang, Arturo Alvarez-Buylla, Shawn F Sorrells
Protracted neuronal recruitment in the temporal lobes of young children. Nature (2023)
Kotdaji Ha, Gabriel B Loeb, Meyeon Park, Aide Pinedo, Christine Haewon Park, Nadav Brandes, F Ritu, Chun Jimmie Ye, Jeremy F Reiter, Markus Delling
ADPKD-Causing Missense Variants in Polycystin-1 Disrupt Cell Surface Localization or Polycystin Channel Function. bioRxiv : the preprint server for biology (2023)
Zachary Cutts, Sarah Patterson, Lenka Maliskova, Kimberly E Taylor, Chun Jimmie Ye, Maria Dall'Era, Jinoos Yazdany, Lindsey Criswell, Gabriela K Fragiadakis, Charles Langelier, Anthony Capra, Marina Sirota, Cristina M Lanata
Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. bioRxiv : the preprint server for biology (2023)
Hanna M Ollila, Eilon Sharon, Ling Lin, Nicholas A 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, null null, 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, Lukrécia Mertová, 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 Rahbek Kornum, Sina Rueger, Juliane Winkelmann, Taku Miyagawa, Hiromi Toyoda, Seik-Soon Khor, Mihoko Shimada, Katsushi Tokunaga, Manuel A Rivas, Jonathan K Pritchard, Neil Risch, Zoltán Kutalik, Ruth O'Hara, Joachim Hallmayer, Chun Jimmie Ye, Emmanuel Jean-Marie Mignot
Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy. Nature communications 14 (1) (2023)
Hanna M Ollila, Eilon Sharon, Ling Lin, Nicholas A 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, null null, 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, Lukrécia Mertová, 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 Rahbek Kornum, Sina Rueger, Juliane Winkelmann, Taku Miyagawa, Hiromi Toyoda, Seik-Soon Khor, Mihoko Shimada, Katsushi Tokunaga, Manuel A Rivas, Jonathan K Pritchard, Neil Risch, Zoltán Kutalik, Ruth O'Hara, Joachim Hallmayer, Chun Jimmie Ye, Emmanuel Jean-Marie Mignot
Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy. Nature communications 14 (1) (2023)
Mike Thompson, Mary Grace Gordon, Andrew Lu, Anchit Tandon, Eran Halperin, Alexander Gusev, Chun Jimmie Ye, Brunilda Balliu, Noah A Zaitlen
Multi-context genetic modeling of transcriptional regulation resolves novel disease loci. Nature communications 13 (1) (2022)
Seyhan Yazar, Jose Alquicira Hernandez, Kristof Wing, Anne Senabouth, M Grace Gordon, Stacey Andersen, Qinyi Lu, Antonia Rowson, Thomas R P Taylor, Linda Clarke, Katia Maccora, Christine Chen, Anthony L Cook, Chun Jimmie Ye, Kirsten A Fairfax, Alex W Hewitt, Joseph E Powell
Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. Science (New York, N.Y.) 376 (6589) (2022)
Jennifer Klunk, Tauras P Vilgalys, Christian E Demeure, Xiaoheng Cheng, Mari Shiratori, Julien Madej, Rémi Beau, Derek Elli, Maria I Patino, Rebecca Redfern, Sharon N DeWitte, Julia A Gamble, Jesper L Boldsen, Ann G Carmichael, Nükhet Varlik, Katherine Eaton, Jean-Christophe Grenier, G Brian Golding, Alison Devault, Jean-Marie Rouillard, Vania Yotova, Renata Sindeaux, Chun Jimmie Ye, Matin Bikaran, Anne Dumaine, Jessica F Brinkworth, Dominique Missiakas, Guy A Rouleau, Matthias Steinrücken, Javier Pizarro-Cerdá, Hendrik N Poinar, Luis B Barreiro
Evolution of immune genes is associated with the Black Death. Nature 611 (7935) (2022)
Ralf Schmidt, Zachary Steinhart, Madeline Layeghi, Jacob W Freimer, Raymund Bueno, Vinh Q Nguyen, Franziska Blaeschke, Chun Jimmie Ye, Alexander Marson
CRISPR activation and interference screens decode stimulation responses in primary human T cells. Science (New York, N.Y.) 375 (6580) (2022)
Matthew T Schmitz, Kadellyn Sandoval, Christopher P Chen, Mohammed A Mostajo-Radji, William W Seeley, Tomasz Jan Nowakowski, Chun Jimmie Ye, Mercedes F Paredes, Alex Aaron Pollen
The development and evolution of inhibitory neurons in primate cerebrum. Nature 603 (7903) (2022)
Roy Oelen, Dylan H de Vries, Harm Brugge, M Grace Gordon, Martijn Vochteloo, null null, null null, Chun Jimmie Ye, Harm-Jan Westra, Lude Franke, Monique G P van der Wijst
Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nature communications 13 (1) (2022)
Richard K 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 W Dahl, Cristina M 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, Rebecca Grainger, Lindsey A Criswell, Noah A Zaitlen, Chun Jimmie Ye
Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. Science (New York, N.Y.) 376 (6589) (2022)
Sagar P Bapat, Caroline Whitty, Cody T Mowery, Yuqiong Liang, Arum Yoo, Zewen Jiang, Michael C Peters, Ling-Juan Zhang, Ian Vogel, Carmen Zhou, Vinh Q Nguyen, Zhongmei Li, Christina Chang, Wandi S Zhu, Annette T Hastie, Helen He, Xin Ren, Wenli Qiu, Sarah G Gayer, Chang Liu, Eun Jung Choi, Marlys S Fassett, Jarish N Cohen, Jamie L Sturgill, Laura E Crotty Alexander, Jae Myoung Suh, Christopher Liddle, Annette R Atkins, Ruth T Yu, Michael Downes, Sihao Liu, Barbara S Nikolajczyk, In-Kyu Lee, Emma Guttman-Yassky, Karl Mark Ansel, Prescott G Woodruff, John V Fahy, Dean Sheppard, Richard L Gallo, Chun Jimmie Ye, Ronald M Evans, Ye Zheng, Alexander Marson
Obesity alters pathology and treatment response in inflammatory disease. Nature 604 (7905) (2022)
Daniel B Goodman, Camillia S Azimi, Kendall Kearns, Alexis Talbot, Kiavash Garakani, Julie M Garcia, Nisarg A Patel, Byungjin Hwang, David S Lee, Minhee Park, Vivasvan S Vykunta, Brian R Shy, Chun Jimmie Ye, Justin Eyquem, Alexander Marson, Jeffrey A Bluestone, Kole T Roybal
Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies. Science translational medicine 14 (670) (2022)
Priyanka Rashmi, Swastika Sur, Tara K Sigdel, Patrick Boada, Andrew W Schroeder, Izabella Damm, Matthias Kretzler, Jeff Hodgin, George Hartoularos, Chun Jimmie Ye, Minnie M Sarwal, null null
Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons (2021)
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
Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures. Communications biology 4 (1) (2021)
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 Jimmie Ye, Mark S Anderson, Audrey V Parent
Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nature communications 12 (1) (2021)
Youjin Lee, Derek Bogdanoff, Yutong Wang, George C Hartoularos, Jonathan M Woo, Cody T Mowery, Hunter M Nisonoff, David S Lee, Yang Sun, James C Lee, Sadaf Mehdizadeh, Joshua Cantlon, Eric Shifrut, David N Nguyen, Theodore L Roth, Yun S Song, Alexander Marson, Eric D Chow, Chun Jimmie Ye
XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment. Science advances 7 (17) (2021)
Byungjin Hwang, David S Lee, Whitney Tamaki, Yang Sun, Anton Ogorodnikov, George C Hartoularos, Aidan Winters, Bertrand Z Yeung, Kristopher L Nazor, Yun S Song, Eric D Chow, Matthew H Spitzer, Chun Jimmie Ye
SCITO-seq: single-cell combinatorial indexed cytometry sequencing. Nature methods 18 (8) (2021)
Monique G P van der Wijst, Sara E Vazquez, George C Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno, David S Lee, John R Greenland, Yang Sun, Richard Perez, Anton Ogorodnikov, Alyssa Ward, Sabrina A Mann, Kara L Lynch, Cassandra Yun, Diane V Havlir, Gabriel Chamie, Carina Marquez, Bryan Greenhouse, Michail S Lionakis, Philip J Norris, Larry J Dumont, Kathleen Kelly, Peng Zhang, Qian Zhang, Adrian Gervais, Tom Le Voyer, Alexander Whatley, Yichen Si, Ashley Byrne, Alexis J Combes, Arjun Arkal Rao, Yun S Song, null null, Gabriela K Fragiadakis, Kirsten Kangelaris, Carolyn S Calfee, David J Erle, Carolyn Hendrickson, Matthew F Krummel, Prescott G Woodruff, Charles R Langelier, Jean-Laurent Casanova, Joseph L Derisi, Mark S Anderson, Chun Jimmie Ye
Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv : the preprint server for biology (2021)
Alexis J Combes, Tristan Courau, Nicholas F Kuhn, Kenneth H Hu, Arja Ray, William S Chen, Nayvin W Chew, Simon J Cleary, 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, K W Im, Nina Kathrin Serwas, Aleksandra Leligdowicz, Colin R Zamecnik, Rita P Loudermilk, Michael R Wilson, Chun Jimmie Ye, Gabriela K Fragiadakis, Mark R Looney, Vincent Chan, Alyssa Ward, Sidney Carrillo, null null, Michael A Matthay, David J Erle, Prescott G Woodruff, Charles Langelier, Kirsten Kangelaris, Carolyn M Hendrickson, Carolyn Calfee, Arjun Arkal Rao, Matthew F Krummel
Global absence and targeting of protective immune states in severe COVID-19. Nature 591 (7848) (2021)
Monique G P van der Wijst, Sara E Vazquez, George C Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno, David S Lee, John R Greenland, Yang Sun, Richard K Perez, Anton Ogorodnikov, Alyssa Ward, Sabrina A Mann, Kara L Lynch, Cassandra Yun, Diane V Havlir, Gabriel Chamie, Carina Marquez, Bryan Greenhouse, Michail S Lionakis, Phillip J Norris, Larry J Dumont, Kathleen K Kelly, Peng Zhang, Qian Zhang, Adrian Gervais, Tom Le Voyer, Alexander Whatley, Yichen Si, Ashley Byrne, Alexis J Combes, Arjun Arkal Rao, Yun S Song, Gabriela K Fragiadakis, Kirsten Kangelaris, Carolyn S Calfee, David J Erle, Carolyn M Hendrickson, Matthew F Krummel, Prescott G Woodruff, Charles R Langelier, Jean Laurent Casanova, Joseph L Derisi, Mark S Anderson, Chun Jimmie Ye, null null
Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Science translational medicine 13 (612) (2021)
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 Jimmie 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, Matthew F Krummel
Global Absence and Targeting of Protective Immune States in Severe COVID-19. bioRxiv : the preprint server for biology (2020)
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 Anna 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, 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
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nature biotechnology 38 (10) (2020)
Arya Zarinsefat, George C Hartoularos, Sindhu Chandran, Chun Jimmie Ye, Flavio Vincenti, Minnie M Sarwal
Single-cell RNA sequencing of Tocilizumab-treated peripheral blood mononuclear cells as an in vitro model of inflammation. bioRxiv : the preprint server for biology (2020)
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
Functional CRISPR dissection of gene networks controlling human regulatory T cell identity. Nature immunology 21 (11) (2020)
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
Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis. Nature communications 11 (1) (2020)
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, Chun Jimmie Ye, Timothy A Thornton, Noah Zaitlen, Esteban González Burchard, Christopher R Gignoux
On the cross-population generalizability of gene expression prediction models. PLoS genetics 16 (8) (2020)
M Grace 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
lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature protocols 15 (8) (2020)
M Grace 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
Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature protocols (2020)
David DeTomaso, Matthew G Jones, Meena Subramaniam, Tal Ashuach, Chun Jimmie Ye, Nir Yosef
Functional interpretation of single cell similarity maps. Nature communications 10 (1) (2019)
Ryan D Hernandez, Lawrence H Uricchio, Kevin Hartman, Chun Jimmie Ye, Andrew W Dahl, Noah A Zaitlen
Ultrarare variants drive substantial cis heritability of human gene expression. Nature genetics 51 (9) (2019)
Rachel E Gate, Christine S Cheng, Aviva P Aiden, Atsede Siba, Marcin Tabaka, Dmytro Sergiiovych Lituiev, Ido Machol, M Grace Gordon, Meena Subramaniam, Muhammad Saad Shamim, Kendrick L Hougen, Ivo Wortman, Su-Chen Huang, Neva C Durand, Ting Feng, Philip Lawrence De Jager, Howard Y Chang, Erez Lieberman Aiden, Christophe Benoist, Michael A Beer, Chun Jimmie Ye, Aviv Regev
Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nature genetics 50 (8) (2018)
Lauren E Byrnes, Daniel M Wong, Meena Subramaniam, Nathaniel P Meyer, Caroline L Gilchrist, Sarah M Knox, Aaron D Tward, Chun Jimmie Ye, Julie B Sneddon
Lineage dynamics of murine pancreatic development at single-cell resolution. Nature communications 9 (1) (2018)