C
Chris Sander
Researcher at Harvard University
Publications - 730
Citations - 273726
Chris Sander is an academic researcher from Harvard University. The author has contributed to research in topics: Large Hadron Collider & Protein structure. The author has an hindex of 178, co-authored 713 publications receiving 233287 citations. Previous affiliations of Chris Sander include Purdue University & University of Leeds.
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Journal ArticleDOI
Integration of biological networks and gene expression data using Cytoscape
Melissa S. Cline,Michael E. Smoot,Ethan Cerami,Allan Kuchinsky,Nerius Landys,Christopher T. Workman,Rowan H. Christmas,Iliana Avila-Campilo,Iliana Avila-Campilo,Michael L. Creech,Benjamin Gross,Kristina Hanspers,Ruth Isserlin,Ryan Kelley,Sarah Killcoyne,Samad Lotia,Steven Maere,John H. Morris,Keiichiro Ono,Vuk Pavlovic,Alexander R. Pico,Aditya Vailaya,Peng-Liang Wang,Annette M. Adler,Bruce R. Conklin,Leroy Hood,Martin Kuiper,Chris Sander,Ilya Schmulevich,Benno Schwikowski,Guy J. Warner,Trey Ideker,Gary D. Bader +32 more
TL;DR: This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Journal ArticleDOI
Comprehensive molecular characterization of urothelial bladder carcinoma
John N. Weinstein,Rehan Akbani,Bradley M. Broom,Wenyi Wang,Roeland Verhaak,David J. McConkey,Seth P. Lerner,Margaret Morgan,Chad J. Creighton,Carolyn L. Smith,Andrew D. Cherniack,Jaegil Kim,Chandra Sekhar Pedamallu,Michael S. Noble,Hikmat Al-Ahmadie,Victor E. Reuter,Jonathan E. Rosenberg,Dean F. Bajorin,Bernard H. Bochner,David B. Solit,Theresa M. Koppie,Brian D. Robinson,Dmitry A. Gordenin,David C. Fargo,Leszek J. Klimczak,Steven A. Roberts,Jessie Au,Peter W. Laird,Toshinori Hinoue,Nikolaus Schultz,Ricardo Ramirez,Donna E. Hansel,Katherine A. Hoadley,William Y. Kim,Jeffrey S. Damrauer,Stephen B. Baylin,Andrew J. Mungall,A. Gordon Robertson,Andy Chu,David J. Kwiatkowski,Carrie Sougnez,Kristian Cibulskis,Lee Lichtenstein,Andrey Sivachenko,Chip Stewart,Michael S. Lawrence,Gad Getz,Eric S. Lander,Stacey B. Gabrie,Lawrence A. Donehower,Scott L. Carter,Gordon Saksena,Steven E. Schumacher,Samuel S. Freeman,Joonil Jung,Ami S. Bhatt,Trevor J. Pugh,Rameen Beroukhim,Matthew Meyerson,Adrian Ally,Miruna Balasundaram,Yaron S.N. Butterfield,Noreen Dhalla,Carrie Hirst,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Haiyan I. Li,Marco A. Marra,Michael Mayo,Richard A. Moore,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Nina Thiessen,Tina Wong,Natasja Wye,Reanne Bowlby,Eric Chuah,Ranabir Guin,Hui Shen,Moiz S. Bootwalla,Timothy J. Triche,Phillip H. Lai,David Van Den Berg,Daniel J. Weisenberger,Saianand Balu,Tom Bodenheimer,Alan P. Hoyle,Stuart R. Jefferys,Shaowu Meng,Lisle E. Mose,Janae V. Simons,Mathew G. Soloway,Junyuan Wu,Joel S. Parker,D. Neil Hayes,Jeffrey Roach,Elizabeth Buda,Corbin D. Jones,Piotr A. Mieczkowski,Donghui Tan,Umadevi Veluvolu,Scot Waring,J. Todd Auman,Charles M. Perou,Matthew D. Wilkerson,Netty Santoso,Michael Parfenov,Xiaojia Ren,Angeliki Pantazi,Angela Hadjipanayis,Jonathan G. Seidman,Raju Kucherlapati,Semin Lee,Lixing Yang,Peter J. Park,Andrew Wei Xu,Alexei Protopopov,Jianhua Zhang,Christopher A. Bristow,Harshad S. Mahadeshwar,Sahil Seth,Xingzhi Song,Jiabin Tang,Dong Zeng,Lynda Chin,Lynda Chin,Charles C. Guo,Tod D. Casasent,Wenbin Liu,Zhenlin Ju,Thomas C. Motter,Bo Peng,Michael Ryan,Xiaoping Su,Ji Yeon Yang,Philip L. Lorenzi,Hui Yao,Nianxiang Zhang,Jiexin Zhang,Gordon B. Mills,Juok Cho,Daniel DiCara,Scott Frazer,Nils Gehlenborg,David I. Heiman,Pei Lin,Yingchun Liu,Petar Stojanov,Doug Voet,Hailei Zhang,Lihua Zou,Brady Bernard,Dick Kreisberg,Sheila Reynolds,Hector Rovira,Ilya Shmulevich,Jianjiong Gao,Anders Jacobsen,B. Arman Aksoy,Yevgeniy Antipin,Giovanni Ciriello,Gideon Dresdner,Benjamin Gross,William Lee,Boris Reva,Ronglai Shen,Rileen Sinha,S. Onur Sumer,Nils Weinhold,Marc Ladanyi,Chris Sander,Christopher C. Benz,Daniel E. Carlin,David Haussler,Sam Ng,Evano Paull,Joshua M. Stuart,Jing Zhu,Yuexin Liu,Wei Zhang,Barry S. Taylor,Tara M. Lichtenberg,Erik Zmuda,Thomas Barr,Aaron D. Black,Myra M. George,Benjamin Hanf,Carmen Helsel,Cynthia McAllister,Nilsa C. Ramirez,Nilsa C. Ramirez,Teresa R. Tabler,Stephanie Weaver,Lisa Wise,Jay Bowen,Julie M. Gastier-Foster,Julie M. Gastier-Foster,Weiguo Jian,Sebrina A Tello,Michael Ittman,Patricia Castro,Whitney D. McClenden,Richard A. Gibbs,Charles Saller,Katherine Tarvin,Jennifer DiPiero,Jennifer Owens,Roni J. Bollag,Qiang Li,Paul M. Weinberger,Christine Czerwinski,Lori Huelsenbeck-Dill,Mary Iacocca,Nicholas J. Petrelli,Brenda Rabeno,Pat Swanson,Troy Shelton,Erin Curley,Johanna Gardner,David Mallery,Robert Penny,Nguyen Van Bang,Phan Thi Hanh,Bernard Kohl,Xuan Van Le,Bui Duc Phu,Richard Thorp,Nguyen Viet Tien,Le Quang Vinh,George E. Sandusky,Eric J. Burks,Kimberly R. Christ,Jason R. Gee,Antonia H. Holway,Alireza Moinzadeh,Andrea Sorcini,Travis Sullivan,Ilana Rebecca Garcia-Grossman,Ashley Marie Regazzi,Lori Boice,W.K. Rathmell,Leigh B. Thorne,Sheldon I. Bastacky,Benjamin Davies,Rajiv Dhir,Jeffrey R. Gingrich,Ronald L. Hrebinko,Jodi K. Maranchie,Joel B. Nelson,Anil V. Parwani,Wiam Bshara,Carmelo Gaudioso,Carl Morrison,Vina Alexopoulou,John M. S. Bartlett,Jay Engel,Sugy Kodeeswaran,Tatjana Antic,Peter H. O'Donnell,Norm D. Smith,Gary D. Steinberg,Sophie C. Egea,Carmen Gomez-Fernandez,Lynn M. Herbert,Merce Jorda,Mark S. Soloway,Allison Beaver,Suzie Carter,Payal Kapur,Cheryl M. Lewis,Yair Lotan,Jolanta Bondaruk,Bogdan Czerniak,Eila C. Skinner,Kenneth Aldape,Mark A. Jensen,Ari B. Kahn,Todd Pihl,David Pot,Deepak Srinivasan,Yunhu Wan,Martin L. Ferguson,Jean C. Zenklusen,Tanja Davidsen,John A. Demchok,Kenna R. Mills Shaw,Kenna R. Mills Shaw,Margi Sheth,Roy Tarnuzzer,Zhining Wang,Liming Yang,Carolyn M. Hutter,Bradley A. Ozenberger,Heidi J. Sofia,Greg Eley +296 more
TL;DR: Ch Chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any other common cancer studied so far, indicating the future possibility of targeted therapy for chromatin abnormalities.
Journal ArticleDOI
Errors in protein structures
Journal ArticleDOI
The Molecular Taxonomy of Primary Prostate Cancer
Adam Abeshouse,Jaeil Ahn,Rehan Akbani,Adrian Ally,Samirkumar B. Amin,Christopher D. Andry,Matti Annala,Armen Aprikian,Joshua Armenia,Arshi Arora,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Christopher E. Barbieri,Thomas L. Bauer,Christopher C. Benz,Alain Bergeron,Rameen Beroukhim,Mario Berrios,Adrian Bivol,Tom Bodenheimer,Lori Boice,Moiz S. Bootwalla,Rodolfo Borges Dos Reis,Paul C. Boutros,Jay Bowen,Reanne Bowlby,Jeff Boyd,Robert K. Bradley,Anne Breggia,Fadi Brimo,Christopher A. Bristow,Denise Brooks,Bradley M. Broom,Alan H. Bryce,Glenn Bubley,Eric J. Burks,Yaron S.N. Butterfield,Michael Button,David Canes,Carlos Gilberto Carlotti,Rebecca Carlsen,Michel Carmel,Peter R. Carroll,Scott L. Carter,Richard Cartun,Brett S. Carver,June M. Chan,Matthew T. Chang,Yu Chen,Andrew D. Cherniack,Simone Chevalier,Lynda Chin,Juok Cho,Andy Chu,Eric Chuah,Sudha Chudamani,Kristian Cibulskis,Giovanni Ciriello,Amanda Clarke,Matthew R. Cooperberg,Niall M. Corcoran,Anthony J. Costello,Janet E. Cowan,Daniel Crain,Erin Curley,Kerstin David,John A. Demchok,Francesca Demichelis,Noreen Dhalla,Rajiv Dhir,Alexandre Doueik,Bettina F. Drake,Heidi Dvinge,Natalya Dyakova,Ina Felau,Martin L. Ferguson,Scott Frazer,Stephen J. Freedland,Yao Fu,Stacey Gabriel,Jianjiong Gao,Johanna Gardner,Julie M. Gastier-Foster,Nils Gehlenborg,Mark Gerken,Mark Gerstein,Gad Getz,Andrew K. Godwin,Anuradha Gopalan,Markus Graefen,Kiley Graim,Thomas Gribbin,Ranabir Guin,Manaswi Gupta,Angela Hadjipanayis,Syed Haider,Lucie Hamel,D. Neil Hayes,David I. Heiman,Julian M. Hess,Katherine A. Hoadley,Andrea Holbrook,Robert A. Holt,Antonia H. Holway,Christopher M. Hovens,Alan P. Hoyle,Mei Huang,Carolyn M. Hutter,Michael Ittmann,Lisa Iype,Stuart R. Jefferys,Corbin D. Jones,Steven J.M. Jones,Hartmut Juhl,Andre Kahles,Christopher J. Kane,Katayoon Kasaian,Michael Kerger,Ekta Khurana,Jaegil Kim,Robert J. Klein,Raju Kucherlapati,Louis Lacombe,Marc Ladanyi,Phillip H. Lai,Peter W. Laird,Eric S. Lander,Mathieu Latour,Michael S. Lawrence,Kevin Lau,Tucker W. LeBien,Darlene Lee,Semin Lee,Kjong-Van Lehmann,Kristen M. Leraas,Ignaty Leshchiner,Robert Leung,John A. Libertino,Tara M. Lichtenberg,Pei Lin,W. Marston Linehan,Shiyun Ling,Scott M. Lippman,Jia Liu,Wen-Bin Liu,Lucas Lochovsky,Massimo Loda,Christopher J. Logothetis,Laxmi Lolla,Teri A. Longacre,Yiling Lu,Jianhua Luo,Yussanne Ma,Harshad S. Mahadeshwar,David Mallery,Armaz Mariamidze,Marco A. Marra,Michael Mayo,Shannon J. McCall,Ginette McKercher,Shaowu Meng,Anne Marie Mes-Masson,Maria J. Merino,Matthew Meyerson,Piotr A. Mieczkowski,Gordon B. Mills,Kenna R. Mills Shaw,Sarah Minner,Alireza Moinzadeh,Richard A. Moore,Scott Morris,Carl Morrison,Lisle E. Mose,Andrew J. Mungall,Bradley A. Murray,Jerome Myers,Rashi Naresh,Joel Nelson,Mark Nelson,Peter S. Nelson,Yulia Newton,Michael S. Noble,Houtan Noushmehr,Matti Nykter,Angeliki Pantazi,Michael Parfenov,Peter J. Park,Joel S. Parker,Joseph Paulauskis,Robert Penny,Charles M. Perou,Alain Piché,Todd Pihl,Peter A. Pinto,Davide Prandi,Alexei Protopopov,Nilsa C. Ramirez,Arvind Rao,W. Kimryn Rathmell,Gunnar Rätsch,Xiaojia Ren,Victor E. Reuter,Sheila Reynolds,Suhn K. Rhie,Kimberly Rieger-Christ,Jeffrey Roach,A. Gordon Robertson,Brian D. Robinson,Mark A. Rubin,Fred Saad,Sara Sadeghi,Gordon Saksena,Charles Saller,Andrew Salner,Francisco Sanchez-Vega,Chris Sander,George E. Sandusky,Guido Sauter,Andrea Sboner,Peter T. Scardino,Eleonora Scarlata,Jacqueline E. Schein,Thorsten Schlomm,Laura S. Schmidt,Nikolaus Schultz,Steven E. Schumacher,Jonathan G. Seidman,Luciano Neder,Sahil Seth,Alexis Sharp,Candace Shelton,Troy Shelton,Hui Shen,Ronglai Shen,Mark E. Sherman,Margi Sheth,Yan Shi,Juliann Shih,Ilya Shmulevich,Jeffry Simko,Ronald Simon,Janae V. Simons,Payal Sipahimalani,Tara Skelly,Heidi J. Sofia,Matthew G. Soloway,Xingzhi Song,Andrea Sorcini,Carrie Sougnez,Serghei Stepa,Chip Stewart,John A. Stewart,Joshua M. Stuart,Travis Sullivan,Charlie Sun,Huandong Sun,Angela Tam,Donghui Tan,Jiabin Tang,Roy Tarnuzzer,Katherine Tarvin,Barry S. Taylor,Patrick Teebagy,Imelda Tenggara,Bernard Têtu,Ashutosh Tewari,Nina Thiessen,Timothy C. Thompson,Leigh B. Thorne,Daniela P. Tirapelli,Scott A. Tomlins,Felipe Amstalden Trevisan,Patricia Troncoso,Lawrence D. True,Maria Christina Tsourlakis,Svitlana Tyekucheva,Eliezer M. Van Allen,David Van Den Berg,Umadevi Veluvolu,Roeland Verhaak,Cathy D. Vocke,Doug Voet,Yunhu Wan,Qingguo Wang,Wenyi Wang,Zhining Wang,Nils Weinhold,John N. Weinstein,Daniel J. Weisenberger,Matthew D. Wilkerson,Lisa Wise,John S. Witte,Chia Chin Wu,Junyuan Wu,Ye Wu,Andrew Wei Xu,Shalini S. Yadav,Liming Yang,Lixing Yang,Christina Yau,Huihui Ye,Peggy Yena,Thomas Zeng,Jean C. Zenklusen,Hailei Zhang,Jianhua Zhang,Jiashan Zhang,Wei Zhang,Yi Zhong,Kelsey Zhu,Erik Zmuda +311 more
TL;DR: The Cancer Genome Atlas (TCGA) has been used for a comprehensive molecular analysis of primary prostate carcinomas as discussed by the authors, revealing substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course.
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.