N
Ni Zhao
Researcher at Johns Hopkins University
Publications - 76
Citations - 7725
Ni Zhao is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Medicine & Microbiome. The author has an hindex of 23, co-authored 59 publications receiving 5907 citations. Previous affiliations of Ni Zhao include National Institutes of Health & University of North Carolina at Chapel Hill.
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Journal ArticleDOI
Comprehensive genomic characterization of head and neck squamous cell carcinomas
Michael S. Lawrence,Carrie Sougnez,Lee Lichtenstein,Kristian Cibulskis,Eric S. Lander,Stacey Gabriel,Gad Getz,Adrian Ally,Miruna Balasundaram,Inanc Birol,Reanne Bowlby,Denise Brooks,Yaron S.N. Butterfield,Rebecca Carlsen,Dean Cheng,Andy Chu,Noreen Dhalla,Ranabir Guin,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Haiyan I. Li,Marco A. Marra,Michael Mayo,Richard A. Moore,Andrew J. Mungall,A. Gordon Robertson,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Nina Thiessen,Tina Wong,Alexei Protopopov,Netty Santoso,Semin Lee,Michael Parfenov,Jianhua Zhang,Harshad S. Mahadeshwar,Jiabin Tang,Xiaojia Ren,Sahil Seth,Psalm Haseley,Dong Zeng,Lixing Yang,Andrew Wei Xu,Xingzhi Song,Angeliki Pantazi,Christopher A. Bristow,Angela Hadjipanayis,Jonathan G. Seidman,Lynda Chin,Peter J. Park,Raju Kucherlapati,Rehan Akbani,Tod D. Casasent,Wenbin Liu,Yiling Lu,Gordon B. Mills,Thomas C. Motter,John N. Weinstein,Lixia Diao,Jing Wang,You Hong Fan,Jinze Liu,Kai Wang,J. Todd Auman,Saianand Balu,Thomas Bodenheimer,Elizabeth Buda,D. Neil Hayes,Katherine A. Hoadley,Alan P. Hoyle,Stuart R. Jefferys,Corbin D. Jones,Patrick K. Kimes,Yufeng Liu,James Stephen Marron,Shaowu Meng,Piotr A. Mieczkowski,Lisle E. Mose,Joel S. Parker,Charles M. Perou,Jan F. Prins,Jeffrey Roach,Yan Shi,Janae V. Simons,Darshan Singh,Matthew G. Soloway,Donghui Tan,Umadevi Veluvolu,Vonn Walter,Scot Waring,Matthew D. Wilkerson,Junyuan Wu,Ni Zhao,Andrew D. Cherniack,Peter S. Hammerman,Aaron D. Tward,Chandra Sekhar Pedamallu,Gordon Saksena,Joonil Jung,Akinyemi I. Ojesina,Scott L. Carter,Travis I. Zack,Steven E. Schumacher,Rameen Beroukhim,Samuel S. Freeman,Matthew Meyerson,Juok Cho,Michael S. Noble,Daniel DiCara,Hailei Zhang,David I. Heiman,Nils Gehlenborg,Doug Voet,Pei Lin,Scott Frazer,Petar Stojanov,Yingchun Liu,Lihua Zou,Jaegil Kim,Donna M. Muzny,Harshavardhan Doddapaneni,Christie Kovar,Jeffrey S. Reid,Donna Morton,Yi Han,Walker Hale,Hsu Chao,Kyle Chang,Jennifer Drummond,Richard A. Gibbs,Nipun Kakkar,David A. Wheeler,Liu Xi,Giovanni Ciriello,Marc Ladanyi,William Lee,Ricardo Ramirez,Chris Sander,Ronglai Shen,Rileen Sinha,Nils Weinhold,Barry S. Taylor,B. Arman Aksoy,Gideon Dresdner,Jianjiong Gao,Benjamin Gross,Anders Jacobsen,Boris Reva,Nikolaus Schultz,S. Onur Sumer,Yichao Sun,Timothy A. Chan,Luc G. T. Morris,Joshua M. Stuart,Stephen C. Benz,Sam Ng,Christopher C. Benz,Christina Yau,Stephen B. Baylin,Leslie Cope,Ludmila Danilova,James G. Herman,Moiz S. Bootwalla,Dennis T. Maglinte,Peter W. Laird,Timothy J. Triche,Daniel J. Weisenberger,David Van Den Berg,Nishant Agrawal,Justin A. Bishop,Paul C. Boutros,Jeff Bruce,Lauren Averett Byers,Joseph A. Califano,Thomas E. Carey,Zhong Chen,Hui Cheng,Simion I. Chiosea,Ezra E.W. Cohen,Brenda Diergaarde,Ann Marie Egloff,Adel K. El-Naggar,Robert L. Ferris,Mitchell J. Frederick,Jennifer R. Grandis,Yan Guo,Robert I. Haddad,Thomas M. Harris,Angela B.Y. Hui,J. Jack Lee,Scott M. Lippman,Fei-Fei Liu,Jonathan B. McHugh,Jeffrey N. Myers,Patrick Kwok Shing Ng,Bayardo Perez-Ordonez,Curtis R. Pickering,Michael B. Prystowsky,Marjorie Romkes,Anthony Saleh,Maureen A. Sartor,Raja R. Seethala,Tanguy Y. Seiwert,Han Si,Carter Van Waes,Daryl Waggott,Maciej Wiznerowicz,Wendell G. Yarbrough,Jiexin Zhang,Zhixiang Zuo,Ken Burnett,Daniel Crain,Johanna Gardner,Kevin Lau,David Mallery,Scott Morris,Joseph Paulauskis,Robert Penny,Candace Shelton,Troy Shelton,Mark E. Sherman,Peggy Yena,Aaron D. Black,Jay Bowen,Jessica Frick,Julie M. Gastier-Foster,Hollie A. Harper,Kristen M. Leraas,Tara M. Lichtenberg,Nilsa C. Ramirez,Lisa Wise,Erik Zmuda,Julien Baboud,Mark A. Jensen,Ari B. Kahn,Todd Pihl,David Pot,Deepak Srinivasan,Jessica Walton,Yunhu Wan,Robert A. Burton,Tanja Davidsen,John A. Demchok,Greg Eley,Martin L. Ferguson,Kenna R. Mills Shaw,Bradley A. Ozenberger,Margi Sheth,Heidi J. Sofia,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean C. Zenklusen,Charles Saller,Katherine Tarvin,Chu Chen,Roni J. Bollag,Paul M. Weinberger,Wojciech Golusiński,Paweł Golusiński,Matthew Ibbs,Konstanty Korski,Andrzej Mackiewicz,Wiktoria Maria Suchorska,Bartosz Szybiak,Erin Curley,Christina Beard,Colleen Mitchell,George E. Sandusky,Julie Ahn,Zubair Khan,Jonathan C. Irish,John Waldron,William N. William,Sophie C. Egea,Carmen Gomez-Fernandez,Lynn M. Herbert,Carol R. Bradford,Douglas B. Chepeha,Andrea Haddad,Tamara R. Jones,Christine M. Komarck,Mayya Malakh,Jeffrey S. Moyer,Ariane Nguyen,Lisa A. Peterson,Mark E. Prince,Laura S. Rozek,Evan G. Taylor,Heather M. Walline,Gregory T. Wolf,Lori Boice,Bhishamjit S. Chera,William K. Funkhouser,Margaret L. Gulley,Trevor Hackman,Michele C. Hayward,Mei Huang,W. Kimryn Rathmell,Ashley H. Salazar,William W. Shockley,Carol G. Shores,Leigh B. Thorne,Mark C. Weissler,Sylvia Wrenn,Adam M. Zanation,Brandee T. Brown,Michelle Q. Pham +309 more
TL;DR: It is shown that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1.
Journal ArticleDOI
Integrated Genomic Characterization of Papillary Thyroid Carcinoma
Nishant Agrawal,Rehan Akbani,B. Arman Aksoy,Adrian Ally,Harindra Arachchi,Sylvia L. Asa,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Stephen B. Baylin,Madhusmita Behera,Brady Bernard,Rameen Beroukhim,Justin A. Bishop,Aaron D. Black,Tom Bodenheimer,Lori Boice,Moiz S. Bootwalla,Jay Bowen,Reanne Bowlby,Christopher A. Bristow,Robin Brookens,Denise Brooks,Robert Bryant,Elizabeth Buda,Yaron S.N. Butterfield,Tobias Carling,Rebecca Carlsen,Scott L. Carter,Sally E. Carty,Timothy A. Chan,Amy Chen,Andrew D. Cherniack,Dorothy Cheung,Lynda Chin,Juok Cho,Andy Chu,Eric Chuah,Kristian Cibulskis,Giovanni Ciriello,Amanda Clarke,Gary L. Clayman,Leslie Cope,John A. Copland,Kyle R. Covington,Ludmila Danilova,Tanja Davidsen,John A. Demchok,Daniel DiCara,Noreen Dhalla,Rajiv Dhir,Sheliann S. Dookran,Gideon Dresdner,Jonathan V. Eldridge,Greg Eley,Adel K El-Naggar,Stephanie Eng,James A. Fagin,Timothy R. Fennell,Robert L. Ferris,Sheila Fisher,Scott Frazer,Jessica Frick,Stacey Gabriel,Ian Ganly,Jianjiong Gao,Levi A. Garraway,Julie M. Gastier-Foster,Gad Getz,Nils Gehlenborg,Ronald Ghossein,Richard A. Gibbs,Thomas J. Giordano,Karen Gomez-Hernandez,Jonna Grimsby,Benjamin Gross,Ranabir Guin,Angela Hadjipanayis,Hollie A. Harper,D. Neil Hayes,David I. Heiman,James G. Herman,Katherine A. Hoadley,Matan Hofree,Robert A. Holt,Alan P. Hoyle,Franklin W. Huang,Mei Huang,Carolyn M. Hutter,Trey Ideker,Lisa Iype,Anders Jacobsen,Stuart R. Jefferys,Corbin D. Jones,Steven J.M. Jones,Katayoon Kasaian,Electron Kebebew,Fadlo R. Khuri,Jaegil Kim,Roger Kramer,Richard Kreisberg,Raju Kucherlapati,David J. Kwiatkowski,Marc Ladanyi,Phillip H. Lai,Peter W. Laird,Eric S. Lander,Michael S. Lawrence,Darlene Lee,Eunjung Lee,Semin Lee,William Lee,Kristen M. Leraas,Tara M. Lichtenberg,Lee Lichtenstein,Pei Lin,Shiyun Ling,Jinze Liu,Wen-Bin Liu,Yingchun Liu,Virginia A. LiVolsi,Yiling Lu,Yussanne Ma,Harshad S. Mahadeshwar,Marco A. Marra,Michael Mayo,David G. McFadden,Shaowu Meng,Matthew Meyerson,Piotr A. Mieczkowski,Michael L. Miller,Gordon B. Mills,Richard A. Moore,Lisle E. Mose,Andrew J. Mungall,Bradley A. Murray,Yuri E. Nikiforov,Michael S. Noble,Akinyemi I. Ojesina,Taofeek K. Owonikoko,Bradley A. Ozenberger,Angeliki Pantazi,Michael Parfenov,Peter J. Park,Joel S. Parker,Evan O. Paull,Chandra Sekhar Pedamallu,Charles M. Perou,Jan F. Prins,Alexei Protopopov,Suresh Ramalingam,Nilsa C. Ramirez,Ricardo Ramirez,Benjamin J. Raphael,W. Kimryn Rathmell,Xiaojia Ren,Sheila Reynolds,Esther Rheinbay,Matthew D. Ringel,Michael Rivera,Jeffrey Roach,A. Gordon Robertson,Mara Rosenberg,Matthew Rosenthal,Sara Sadeghi,Gordon Saksena,Chris Sander,Netty Santoso,Jacqueline E. Schein,Nikolaus Schultz,Steven E. Schumacher,Raja R. Seethala,Jonathan G. Seidman,Yasin Senbabaoglu,Sahil Seth,Samantha Sharpe,Kenna R. Mills Shaw,John Paul Shen,Ronglai Shen,Steven I. Sherman,Margi Sheth,Yan Shi,Ilya Shmulevich,Gabriel Sica,Janae V. Simons,Rileen Sinha,Payal Sipahimalani,Robert C. Smallridge,Heidi J. Sofia,Matthew G. Soloway,Xingzhi Song,Carrie Sougnez,Chip Stewart,Petar Stojanov,Joshua M. Stuart,S. Onur Sumer,Yichao Sun,Barbara Tabak,Angela Tam,Donghui Tan,Jiabin Tang,Roy Tarnuzzer,Barry S. Taylor,Nina Thiessen,Leigh B. Thorne,Vesteinn Thorsson,R. Michael Tuttle,Christopher B. Umbricht,David Van Den Berg,Fabio Vandin,Umadevi Veluvolu,Roeland Verhaak,Michelle Vinco,Doug Voet,Vonn Walter,Zhining Wang,Scot Waring,Paul M. Weinberger,Nils Weinhold,John N. Weinstein,Daniel J. Weisenberger,David A. Wheeler,Matthew D. Wilkerson,Jocelyn Wilson,Michelle D. Williams,Daniel A. Winer,Lisa Wise,Junyuan Wu,Liu Xi,Andrew Wei Xu,Liming Yang,Lixing Yang,Travis I. Zack,Martha A. Zeiger,Dong Zeng,Jean C. Zenklusen,Ni Zhao,Hailei Zhang,Jianhua Zhang,Jiashan Zhang,Wei Zhang,Erik Zmuda,Lihua Zou +242 more
TL;DR: The genomic landscape of 496 PTCs is described and a reclassification of thyroid cancers into molecular subtypes that better reflect their underlying signaling and differentiation properties is proposed, which has the potential to improve their pathological classification and better inform the management of the disease.
Journal ArticleDOI
Characterization of HPV and host genome interactions in primary head and neck cancers.
Michael Parfenov,Chandra Sekhar Pedamallu,Nils Gehlenborg,Nils Gehlenborg,Samuel S. Freeman,Ludmila Danilova,Christopher A. Bristow,Semin Lee,Angela Hadjipanayis,Elena Ivanova,Matthew D. Wilkerson,Alexei Protopopov,Lixing Yang,Sahil Seth,Xingzhi Song,Jiabin Tang,Xiaojia Ren,Jianhua Zhang,Angeliki Pantazi,Netty Santoso,Andrew Wei Xu,Harshad S. Mahadeshwar,D Wheeler,Robert I. Haddad,Joonil Jung,Akinyemi I. Ojesina,Natalia Issaeva,Wendell G. Yarbrough,D. Neil Hayes,Jennifer R. Grandis,Adel K. El-Naggar,Matthew Meyerson,Peter J. Park,Lynda Chin,Jon G. Seidman,Peter S. Hammerman,Raju Kucherlapati,Adrian Ally,Miruna Balasundaram,Inanc Birol,Reanne Bowlby,Yaron S.N. Butterfield,Rebecca Carlsen,Dean Cheng,Andy Chu,Noreen Dhalla,Ranabir Guin,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Haiyan I. Li,Marco A. Marra,Michael Mayo,Richard A. Moore,Andrew J. Mungall,A. Gordon Robertson,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Nina Thiessen,Tina Wong,Harshad S. Mahadeshwar,Psalm Haseley,Dong Zeng,Christopher A. Bristow,Angela Hadjipanayis,Jonathan G. Seidman,Rehan Akbani,Tod D. Casasent,Wen-Bin Liu,Yiling Lu,Gordon B. Mills,Thomas C. Motter,John N. Weinstein,Lixia Diao,Jing Wang,You Hong Fan,Jinze Liu,Kai Wang,J. Todd Auman,Saianand Balu,Tom Bodenheimer,Elizabeth Buda,Katherine A. Hoadley,Alan P. Hoyle,Stuart R. Jefferys,Corbin D. Jones,Patrick K. Kimes,James Stephen Marron,Shaowu Meng,Piotr A. Mieczkowski,Lisle E. Mose,Joel S. Parker,Charles M. Perou,Jan F. Prins,Jeffrey Roach,Yan Shi,Janae V. Simons,Darshan Singh,Mathew G. Soloway,Donghui Tan,Umadevi Veluvolu,Vonn Walter,Scot Waring,Junyuan Wu,Ni Zhao,Andrew D. Cherniack,Aaron D. Tward,Gordon Saksena,Scott L. Carter,Travis I. Zack,Steven E. Schumacher,Rameen Beroukhim,Juok Cho,Gad Getz,Michael S. Noble,Daniel DiCara,Hailei Zhang,David I. Heiman,Doug Voet,Pei Lin,Scott Frazer,Petar Stojanov,Yingchun Liu,Lihua Zou,Jaegil Kim,Michael S. Lawrence,Carrie Sougnez,Lee Lichtenstein,Kristian Cibulskis,Eric S. Lander,Stacey Gabriel,Donna M. Muzny,Harshavardhan Doddapaneni,Christie Kovar,Jeffrey S. Reid,Donna Morton,Yi Han,Walker Hale,Hsu Chao,Kyle Chang,Jennifer Drummond,Richard A. Gibbs,Nipun Kakkar,David A. Wheeler,Liu Xi,Giovanni Ciriello,Marc Ladanyi,William Lee,Ricardo Ramirez,Chris Sander,Ronglai Shen,Rileen Sinha,Nils Weinhold,Barry S. Taylor,B. Arman Aksoy,Gideon Dresdner,Jianjiong Gao,Benjamin Gross,Anders Jacobsen,Boris Reva,Nikolaus Schultz,S. Onur Sumer,Yichao Sun,Timothy M. Chan,Luc G. T. Morris,Joshua M. Stuart,Stephen C. Benz,Sam Ng,Christopher C. Benz,Christina Yau,Stephen B. Baylin,Leslie Cope,James G. Herman,Moiz S. Bootwalla,Dennis T. Maglinte,Peter W. Laird,Timothy J. Triche,Daniel J. Weisenberger,David Van Den Berg,Nishant Agrawal,Justin A. Bishop,Paul C. Boutros,Jeff Bruce,Lauren Averett Byers,Joseph A. Califano,Thomas E. Carey,Zhong Chen,Hui Cheng,Simion I. Chiosea,Ezra E.W. Cohen,Brenda Diergaarde,Ann Marie Egloff,Robert L. Ferris,Mitchell J. Frederick,Yan Guo,Thomas M. Harris,Angela By Hui,J. Jack Lee,Scott M. Lippman,Fei-Fei Liu,Jonathan B. McHugh,Jeffrey N. Myers,Patrick Kwok Shing Ng,Bayardo Perez-Ordonez,Curtis R. Pickering,Michael B. Prystowsky,Marjorie Romkes,Anthony Saleh,Maureen A. Sartor,Raja R. Seethala,Tanguy Y. Seiwert,Han Si,Carter Van Waes,Daryl Waggott,Maciej Wiznerowicz,Wendell G. Yarbrough,Jiexin Zhang,Zhixiang Zuo,Ken Burnett,Daniel Crain,Johanna Gardner,Kevin Lau,David Mallery,Scott J. Morris,Joseph Paulauskis,Robert Penny,Candance Shelton,Troy Shelton,Mark E. Sherman,Peggy Yena,Aaron D. Black,Jay Bowen,Jessica Frick,Julie M. Gastier-Foster,Hollie A. Harper,Tara M. Lichtenberg,Nilsa C. Ramirez,Lisa Wise,Erik Zmuda,Julien Baboud,Mark A. Jensen,Ari B. Kahn,Todd Pihl,David A. Pot,Deepak Srinivasan,Jessica Walton,Yunhu Wan,Robert A. Burton,Tanja M. Davidsen,John A. Demchok,Greg Eley,Martin L. Ferguson,Kenna R. Mills Shaw,Bradley A. Ozenberger,Margi Sheth,Heidi J. Sofia,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean C. Zenklusen,Charles Saller,Katherine Tarvin,Chu Chen,Roni J. Bollag,Paul M. Weinberger,Wojciech Golusiński,Paweł Golusiński,Matthiew Ibbs,Konstanty Korski,Andrzej Mackiewicz,Wiktoria Maria Suchorska,Bartosz Szybiak,Erin Curley,Christina Beard,Colleen Mitchell,George E. Sandusky,Julie Ahn,Zubair Khan,Jonathan M. Irish,John W.F. Waldron,Sophie C. Egea,Carmen Gomez-Fernandez,Lynn M. Herbert,Carol R. Bradford,Douglas B. Chepeha,Andrea Haddad,Tamara R. Jones,Christine M. Komarck,Mayya Malakh,Jeffrey S. Moyer,Ariane Nguyen,Lisa A. Peterson,Mark E. Prince,Laura S. Rozek,Evan G. Taylor,Heather M. Walline,Gregory T. Wolf,Lori Boice,Bhishamjit S. Chera,William K. Funkhouser,Margaret L. Gulley,Trevor Hackman,Michele C. Hayward,Mei Huang,W. Kimryn Rathmell,Ashley H. Salazar,William W. Shockley,Carol G. Shores,Leigh B. Thorne,Mark C. Weissler,Sylvia Wrenn,Adam M. Zanation,Brandee T. Brown,Michelle Q. Pham +314 more
TL;DR: A cohort of 279 head and neck cancers with next generation RNA and DNA sequencing is profiled to provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viraloncogenesis.
Journal ArticleDOI
Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes.
Vonn Walter,Xiaoying Yin,Matthew D. Wilkerson,Christopher R. Cabanski,Christopher R. Cabanski,Ni Zhao,Ying Du,Mei Kim Ang,Michele C. Hayward,Ashley H. Salazar,Katherine A. Hoadley,Karen J. Fritchie,Charles G. Sailey,Mark C. Weissler,William W. Shockley,Adam M. Zanation,Trevor Hackman,Leigh B. Thorne,William D. Funkhouser,Kenneth L. Muldrew,Andrew F. Olshan,Scott H. Randell,Fred A. Wright,Carol G. Shores,D. Neil Hayes +24 more
TL;DR: Four molecular classes of HNSCC are confirmed consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR.
Journal ArticleDOI
Testing in microbiome-profiling studies with MiRKAT, the microbiome regression-based kernel association test
Ni Zhao,Jun Chen,Ian M. Carroll,Tamar Ringel-Kulka,Michael P. Epstein,Hua Zhou,Jin Zhou,Yehuda Ringel,Hongzhe Li,Michael C. Wu +9 more
TL;DR: The microbiome regression-based kernel association test (MiRKAT), which directly regresses the outcome on the microbiome profiles via the semi-parametric kernel machine regression framework, is proposed and applied to real microbiome datasets to show that microbial communities are associated with smoking and with fecal protease levels after confounders are controlled for.