S
Serghei Mangul
Researcher at University of Southern California
Publications - 136
Citations - 5362
Serghei Mangul is an academic researcher from University of Southern California. The author has contributed to research in topics: Computer science & Biology. The author has an hindex of 19, co-authored 115 publications receiving 2832 citations. Previous affiliations of Serghei Mangul include University of California, Los Angeles & University of California, Berkeley.
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Journal ArticleDOI
The GTEx Consortium atlas of genetic regulatory effects across human tissues
François Aguet,Alvaro N. Barbeira,Rodrigo Bonazzola,Andrew A. Brown,SE Castel,Brian Jo,Silva Kasela,Sarah Kim-Hellmuth,Yanyu Liang,Meritxell Oliva,Elise D. Flynn,Princy Parsana,Laure Fresard,Eric R. Gamazon,Andrew R. Hamel,Yuan He,Farhad Hormozdiari,Pejman Mohammadi,Manuel Muñoz-Aguirre,YoSon Park,Ashis Saha,Ayellet V. Segrè,Benjamin J. Strober,Xiaoquan Wen,Wucher,Kristin G. Ardlie,Alexis Battle,Christopher D. Brown,Nancy J. Cox,Souvik Das,Emmanouil T. Dermitzakis,Barbara E. Engelhardt,D Garrido-Martin,Gad Getz,Roderic Guigó,Robert E. Handsaker,Paul J. Hoffman,Hae Kyung Im,Seva Kashin,Alan Kwong,Lappalainen T,Xiao Li,Daniel G. MacArthur,Stephen B. Montgomery,John M. Rouhana,Matthew Stephens,Barbara E. Stranger,Ellen Todres,Ana Viñuela,Gao Wang,Yuxin Zou,Shankara Anand,S. Gabriel,Aaron Graubert,Kane Hadley,Katherine H. Huang,Meier,Jared L. Nedzel,Duyen T. Nguyen,Brunilda Balliu,Donald F. Conrad,Daniel J. Cotter,OM deGoede,Jonah Einson,Eskin E,Tiffany Eulalio,Nicole M. Ferraro,Michael J. Gloudemans,Lei Hou,Serghei Mangul,Daniel Nachun,Andrew B. Nobel,Abhiram Rao,Ferran Reverter,Chiara Sabatti,Andrew D Skol,Nicole A. Teran,Fred A. Wright,Pedro G. Ferreira,Gen Li,Marta Melé,Esti Yeger-Lotem,Mary Barcus,Debra Bradbury,T Krubit,Jeffrey McLean,Liqun Qi,Karna Robinson,Nancy Roche,Anna M. Smith,David E. Tabor,Anita H. Undale,Jason Bridge,Lori E. Brigham,Barbara A. Foster,Bryan Gillard,Rick Hasz,Marcus Hunter,Christopher Johns,Mark H. Johnson,Ellen Karasik,Gene Kopen,William F. Leinweber,Alisa McDonald,Mike Moser,Kevin Myer,Kimberly Ramsey,Bruce A. Roe,Saboor Shad,Jeffrey A. Thomas,Gary Walters,Michael Washington,Jessica Wheeler,Scott D. Jewell,Daniel C. Rohrer,David A. Davis,Deborah C. Mash,Leslie H. Sobin,Laura Barker,HM Gardiner,Maghboeba Mosavel,Laura A. Siminoff,Paul Flicek,Maximilian Haeussler,Thomas Juettemann,W. J. Kent,Christopher Lee,CC Powell,Kate R. Rosenbloom,Magali Ruffier,Dan Sheppard,Kieron Taylor,Stephen J. Trevanion,Zerbino,Nathan S. Abell,Joshua M. Akey,Lin Chen,Kathryn Demanelis,Jennifer A. Doherty,Andrew P. Feinberg,Kasper D. Hansen,Peter Hickey,Farzana Jasmine,Lihua Jiang,Rajinder Kaul,Manolis Kellis,Muhammad G. Kibriya,Jin Billy Li,Qin Li,Shin Lin,Sandra Linder,Brandon L. Pierce,Lindsay F. Rizzardi,Kevin S. Smith,Michael Snyder,John A. Stamatoyannopoulos,Hua Tang,Meng Wang,Phillip Branton,Latarsha J. Carithers,Ping Guan,Susan E. Koester,AR Little,Helen M. Moore,Concepcion R. Nierras,Abhi Rao,Jimmie B. Vaught,Simona Volpi +167 more
Journal ArticleDOI
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics.
Alvaro N. Barbeira,Scott P. Dickinson,Rodrigo Bonazzola,Jiamao Zheng,Heather E. Wheeler,Jason M. Torres,Eric S. Torstenson,Kaanan P. Shah,Tzintzuni Garcia,Todd L. Edwards,Eli A. Stahl,Laura M. Huckins,François Aguet,Kristin G. Ardlie,Beryl B. Cummings,Ellen Gelfand,Gad Getz,Kane Hadley,Robert E. Handsaker,Katherine H. Huang,Seva Kashin,Konrad J. Karczewski,Monkol Lek,Xiao Li,Xiao Li,Daniel G. MacArthur,Jared L. Nedzel,Duyen T. Nguyen,Michael S. Noble,Ayellet V. Segrè,Casandra A. Trowbridge,Taru Tukiainen,Nathan S. Abell,Brunilda Balliu,Ruth Barshir,Omer Basha,Alexis Battle,Gireesh K. Bogu,Andrew A. Brown,Andrew A. Brown,Christopher D. Brown,Stephane E. Castel,Lin Chen,Colby Chiang,Donald F. Conrad,Farhan N. Damani,Joe R. Davis,Olivier Delaneau,Olivier Delaneau,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis,Barbara E. Engelhardt,Eleazar Eskin,Pedro G. Ferreira,Laure Fresard,Eric R. Gamazon,Eric R. Gamazon,Diego Garrido-Martín,Ariel D. H. Gewirtz,Genna Gliner,Michael J. Gloudemans,Roderic Guigó,Ira M. Hall,Buhm Han,Yuan He,Farhad Hormozdiari,Cédric Howald,Cédric Howald,Brian Jo,Eun Yong Kang,Yungil Kim,Sarah Kim-Hellmuth,Tuuli Lappalainen,Gen Li,Xin Li,Boxiang Liu,Serghei Mangul,Mark I. McCarthy,Ian C. McDowell,Pejman Mohammadi,Jean Monlong,Jean Monlong,Stephen B. Montgomery,Manuel Muñoz-Aguirre,Manuel Muñoz-Aguirre,Anne Ndungu,Andrew B. Nobel,Meritxell Oliva,Halit Ongen,Halit Ongen,John Palowitch,Nikolaos I Panousis,Nikolaos I Panousis,Panagiotis Papasaikas,YoSon Park,Princy Parsana,Anthony Payne,Christine B. Peterson,Jie Quan,Ferran Reverter,Ferran Reverter,Chiara Sabatti,Ashis Saha,Michael Sammeth,Alexandra J. Scott,Andrey A. Shabalin,Reza Sodaei,Matthew Stephens,Barbara E. Stranger,Benjamin J. Strober,Jae Hoon Sul,Emily K. Tsang,Sarah Urbut,Martijn van de Bunt,Gao Wang,Xiaoquan Wen,Fred A. Wright,Hualin S. Xi,Esti Yeger-Lotem,Zachary Zappala,Judith B. Zaugg,Yi-Hui Zhou,Joshua M. Akey,Daniel Bates,Joanne Chan,Melina Claussnitzer,Melina Claussnitzer,Kathryn Demanelis,Morgan Diegel,Jennifer A. Doherty,Andrew P. Feinberg,Marian S. Fernando,Jessica Halow,Kasper D. Hansen,Eric Haugen,Peter Hickey,Lei Hou,Lei Hou,Farzana Jasmine,Ruiqi Jian,Lihua Jiang,Audra K. Johnson,Rajinder Kaul,Manolis Kellis,Manolis Kellis,Muhammad G. Kibriya,Kristen Lee,Jin Billy Li,Qin Li,Jessica Lin,Jessica Lin,Shin Lin,Shin Lin,Sandra Linder,Caroline Linke,Yaping Liu,Yaping Liu,Matthew T. Maurano,Benoit Molinie,Jemma Nelson,Fidencio J. Neri,Yongjin Park,Yongjin Park,Brandon L. Pierce,Nicola J. Rinaldi,Nicola J. Rinaldi,Lindsay F. Rizzardi,Richard Sandstrom,Andrew D. Skol,Kevin S. Smith,Michael Snyder,John A. Stamatoyannopoulos,Hua Tang,Li Wang,Meng Wang,Nicholas Van Wittenberghe,Fan Wu,Rui Zhang,Concepcion R. Nierras,Philip A. Branton,Latarsha J. Carithers,Ping Guan,Helen M. Moore,Abhi Rao,Jimmie B. Vaught,Sarah E. Gould,Nicole C. Lockart,Casey Martin,Jeffery P. Struewing,Simona Volpi,Anjené M. Addington,Susan E. Koester,A. Roger Little,Lori E. Brigham,Richard Hasz,Marcus Hunter,Christopher Johns,Mark H. Johnson,Gene Kopen,William F. Leinweber,John T. Lonsdale,Alisa McDonald,Bernadette Mestichelli,Kevin Myer,Brian Roe,Michael F. Salvatore,Saboor Shad,Jeffrey A. Thomas,Gary Walters,Michael Washington,Joseph Wheeler,Jason Bridge,Barbara A. Foster,Bryan Gillard,Ellen Karasik,Rachna Kumar,Mark Miklos,Michael T. Moser,Scott D. Jewell,Robert G. Montroy,Daniel C. Rohrer,Dana R. Valley,David A. Davis,Deborah C. Mash,Anita H. Undale,Anna M. Smith,David E. Tabor,Nancy Roche,Jeffrey McLean,Negin Vatanian,Karna Robinson,Leslie H. Sobin,Mary Barcus,Kimberly M. Valentino,Liqun Qi,Steven Hunter,Pushpa Hariharan,Shilpi Singh,Ki Sung Um,Takunda Matose,Maria M. Tomaszewski,Laura Barker,Maghboeba Mosavel,Laura A. Siminoff,Heather M. Traino,Paul Flicek,Thomas Juettemann,Magali Ruffier,Dan Sheppard,Kieron Taylor,Stephen J. Trevanion,Daniel R. Zerbino,Brian Craft,Mary Goldman,Maximilian Haeussler,W. James Kent,Christopher Lee,Benedict Paten,Kate R. Rosenbloom,John Vivian,Jingchun Zhu,Dan L. Nicolae,Nancy J. Cox,Hae Kyung Im +263 more
TL;DR: A mathematical expression is derived to compute PrediXcan results using summary data, and the effects of gene expression variation on human phenotypes in 44 GTEx tissues and >100 phenotypes are investigated.
Journal ArticleDOI
Cell type–specific genetic regulation of gene expression across human tissues
Sarah Kim-Hellmuth,Sarah Kim-Hellmuth,François Aguet,Meritxell Oliva,Manuel Muñoz-Aguirre,Silva Kasela,Valentin Wucher,Stephane E. Castel,Andrew R. Hamel,Andrew R. Hamel,Ana Viñuela,Amy L. Roberts,Serghei Mangul,Serghei Mangul,Xiaoquan Wen,Gao Wang,Alvaro N. Barbeira,Diego Garrido-Martín,Brian B. Nadel,Yuxin Zou,Rodrigo Bonazzola,Jie Quan,Andrew A. Brown,Andrew A. Brown,Angel Martinez-Perez,José Manuel Soria,Gad Getz,Gad Getz,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis,Kerrin S. Small,Matthew Stephens,Hualin S. Xi,Hae Kyung Im,Roderic Guigó,Ayellet V. Segrè,Ayellet V. Segrè,Barbara E. Stranger,Barbara E. Stranger,Kristin G. Ardlie,Tuuli Lappalainen +40 more
TL;DR: A growing number of in silico cell type deconvolution methods and associated reference panels with cell type–specific marker genes enable the robust estimation of the enrichment of specific cell types from bulk tissue gene expression data.
Journal ArticleDOI
Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer.
David Y. Oh,Serena S. Kwek,Siddharth S. Raju,Tony Li,Elizabeth E. McCarthy,Eric D. Chow,Dvir Aran,Arielle Ilano,Chien-Chun Steven Pai,Chiara Rancan,Kathryn Allaire,Arun Burra,Yang Sun,Matthew H. Spitzer,Serghei Mangul,Sima P. Porten,Maxwell V. Meng,Terence W. Friedlander,Chun Jimmie Ye,Lawrence Fong +19 more
TL;DR: A gene signature of cytotoxic CD4+ T cells in tumors predicts a clinical response in 244 metastatic bladder cancer patients treated with anti-PD-L1, and several tumor-specific states are found, including multiple distinct states of regulatory T cells.
Journal ArticleDOI
Estimation of alternative splicing isoform frequencies from RNA-Seq data
TL;DR: A novel expectation-maximization algorithm for inference of isoform- and gene-specific expression levels from RNA-Seq data, referred to as IsoEM, is based on disambiguating information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand and read pairing information when available.