Z
Zhengyu Ouyang
Researcher at University of California, San Diego
Publications - 36
Citations - 3539
Zhengyu Ouyang is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Immune system & Innate immune system. The author has an hindex of 19, co-authored 35 publications receiving 2772 citations. Previous affiliations of Zhengyu Ouyang include Ragon Institute of MGH, MIT and Harvard & New Mexico State University.
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Wisdom of crowds for robust gene network inference
Daniel Marbach,James C. Costello,Robert Küffner,Nicole M. Vega,Robert J. Prill,Diogo M. Camacho,Kyle R. Allison,Andrej Aderhold,Richard Bonneau,Yukun Chen,James J. Collins,Francesca Cordero,Martin Crane,Frank Dondelinger,Mathias Drton,Roberto Esposito,Rina Foygel,Alberto de la Fuente,Jan Gertheiss,Pierre Geurts,Alex Greenfield,Marco Grzegorczyk,Anne-Claire Haury,Benjamin Holmes,Torsten Hothorn,Dirk Husmeier,Vân Anh Huynh-Thu,Alexandre Irrthum,Manolis Kellis,Guy Karlebach,Sophie Lèbre,Vincenzo De Leo,Aviv Madar,Subramani Mani,Fantine Mordelet,Harry Ostrer,Zhengyu Ouyang,Ravi Pandya,Tobias Petri,Andrea Pinna,Christopher S. Poultney,Serena Rezny,Heather J. Ruskin,Yvan Saeys,Ron Shamir,Alina Sîrbu,Mingzhou Song,Nicola Soranzo,Alexander Statnikov,Gustavo Stolovitzky,Nicci Vega,Paola Vera-Licona,Jean-Philippe Vert,Alessia Visconti,Haizhou Wang,Louis Wehenkel,Lukas Windhager,Yang Zhang,Ralf Zimmer +58 more
TL;DR: A comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data defines the performance, data requirements and inherent biases of different inference approaches, and provides guidelines for algorithm application and development.
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HIV-1 persistence in CD4+ T cells with stem cell-like properties
Maria J. Buzon,Hong Sun,Chun Li,Amy Shaw,Katherine Seiss,Zhengyu Ouyang,Enrique Martin-Gayo,Jin Leng,Timothy J. Henrich,Jonathan Z. Li,Florencia Pereyra,Ryan Zurakowski,Bruce D. Walker,Eric S. Rosenberg,Xu G. Yu,Mathias Lichterfeld +15 more
TL;DR: HIV-1 may exploit the stem cell characteristics of cellular immune memory to promote long-term viral persistence of viral quasispecies in CD4+ TSCM cells.
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Long-Term Antiretroviral Treatment Initiated at Primary HIV-1 Infection Affects the Size, Composition, and Decay Kinetics of the Reservoir of HIV-1-Infected CD4 T Cells
Maria J. Buzon,Enrique Martin-Gayo,Florencia Pereyra,Zhengyu Ouyang,Hong Sun,Jonathan Z. Li,Michael J. Piovoso,Amy Shaw,Judith Dalmau,Nadine Zangger,Javier Martinez-Picado,Ryan Zurakowski,Xu G. Yu,Amalio Telenti,Bruce D. Walker,Eric S. Rosenberg,Mathias Lichterfeld +16 more
TL;DR: It is suggested that early HIV-1 treatment initiation, even when continued for >10 years, is unlikely to lead to viral eradication, but the presence of low viral reservoirs and durable HIV-2 T cell responses may make such patients good candidates for future interventional studies aiming at HIV- 1 eradication and cure.
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Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells
Guinevere Q. Lee,Nina Orlova-Fink,Kevin Einkauf,Fatema Z. Chowdhury,Xiaoming Sun,Sean Harrington,Hsiao-Hsuan Kuo,Hsiao-Hsuan Kuo,Stephane Hua,Hsiao-Rong Chen,Zhengyu Ouyang,Kavidha Reddy,Krista L. Dong,Thumbi Ndung'u,Bruce D. Walker,Bruce D. Walker,Eric S. Rosenberg,Xu G. Yu,Xu G. Yu,Mathias Lichterfeld,Mathias Lichterfeld +20 more
TL;DR: massive single-genome, near-full-length next-generation sequencing of HIV-1 DNA derived from unfractionated peripheral blood mononuclear cells, ex vivo-isolated CD4+ T cells, and subsets of functionally polarized memory CD4- T cells suggests that clonal proliferation of Th1-polarized CD4+.
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Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis.
Jason S. Seidman,Ty D. Troutman,Mashito Sakai,Anita Gola,Nathanael J. Spann,Hunter Bennett,Cassi M. Bruni,Zhengyu Ouyang,Rick Z. Li,Xiaoli Sun,Bao Chau T. Vu,Martina P. Pasillas,Kaori M. Ego,David Gosselin,Verena M. Link,Ling Wa Chong,Ronald M. Evans,Bonne M. Thompson,Jeffrey G. McDonald,Mojgan Hosseini,Joseph L. Witztum,Ronald N. Germain,Christopher K. Glass +22 more
TL;DR: Findings reveal mechanisms by which disease-associated environmental signals instruct resident and recruited macrophages to acquire distinct gene expression programs and corresponding functions.