A
Andrea Sboner
Researcher at Cornell University
Publications - 215
Citations - 30060
Andrea Sboner is an academic researcher from Cornell University. The author has contributed to research in topics: Prostate cancer & Cancer. The author has an hindex of 57, co-authored 191 publications receiving 24496 citations. Previous affiliations of Andrea Sboner include Yale University & National Institutes of Health.
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An integrated encyclopedia of DNA elements in the human genome
Ian Dunham,Anshul Kundaje,Shelley Force Aldred,Patrick J. Collins,Carrie A. Davis,Francis Doyle,Charles B. Epstein,Seth Frietze,Jennifer Harrow,Rajinder Kaul,Jainab Khatun,Bryan R. Lajoie,Stephen G. Landt,Bum Kyu Lee,Florencia Pauli,Kate R. Rosenbloom,Peter J. Sabo,Alexias Safi,Amartya Sanyal,Noam Shoresh,Jeremy M. Simon,Lingyun Song,Nathan D. Trinklein,Robert C. Altshuler,Ewan Birney,James B. Brown,Chao Cheng,Sarah Djebali,Xianjun Dong,Jason Ernst,Terrence S. Furey,Mark Gerstein,Belinda Giardine,Melissa C. Greven,Ross C. Hardison,Robert S. Harris,Javier Herrero,Michael M. Hoffman,Sowmya Iyer,Manolis Kellis,Pouya Kheradpour,Timo Lassmann,Qiang Li,Xinying Lin,Georgi K. Marinov,Angelika Merkel,Ali Mortazavi,Stephen C. J. Parker,Timothy E. Reddy,Joel Rozowsky,Felix Schlesinger,Robert E. Thurman,Jie Wang,Lucas D. Ward,Troy W. Whitfield,Steven P. Wilder,Weisheng Wu,Hualin S. Xi,Kevin Y. Yip,Jiali Zhuang,Bradley E. Bernstein,Eric D. Green,Chris Gunter,Michael Snyder,Michael J. Pazin,Rebecca F. Lowdon,Laura A.L. Dillon,Leslie B. Adams,Caroline J. Kelly,Julia Zhang,Judith R. Wexler,Peter J. Good,Elise A. Feingold,Gregory E. Crawford,Job Dekker,Laura Elnitski,Peggy J. Farnham,Morgan C. Giddings,Thomas R. Gingeras,Roderic Guigó,Tim Hubbard,W. James Kent,Jason D. Lieb,Elliott H. Margulies,Richard M. Myers,John A. Stamatoyannopoulos,Scott A. Tenenbaum,Zhiping Weng,Kevin P. White,Barbara J. Wold,Yanbao Yu,John A. Wrobel,Brian A. Risk,Harsha P. Gunawardena,Heather C. Kuiper,Christopher W. Maier,Ling Xie,Xian Chen,Tarjei S. Mikkelsen,Shawn M. Gillespie,Alon Goren,Oren Ram,Xiaolan Zhang,Li Wang,Robbyn Issner,Michael Coyne,Timothy Durham,Manching Ku,Thanh Truong,Matthew L. Eaton,Alexander Dobin,Andrea Tanzer,Julien Lagarde,Wei Lin,Chenghai Xue,Brian A. Williams,Chris Zaleski,Marion S. Röder,Felix Kokocinski,Rehab F. Abdelhamid,Tyler Alioto,Igor Antoshechkin,Michael T. Baer,Philippe Batut,Ian Bell,Kimberly Bell,Sudipto K. Chakrabortty,Jacqueline Chrast,Joao Curado,Thomas Derrien,Jorg Drenkow,Erica Dumais,Jackie Dumais,Radha Duttagupta,Megan Fastuca,Kata Fejes-Toth,Pedro G. Ferreira,Sylvain Foissac,Melissa J. Fullwood,Hui Gao,David Gonzalez,Assaf Gordon,Cédric Howald,Sonali Jha,Rory Johnson,Philipp Kapranov,Brandon King,Colin Kingswood,Guoliang Li,Oscar Junhong Luo,Eddie Park,Jonathan B. Preall,Kimberly Presaud,Paolo Ribeca,Daniel Robyr,Xiaoan Ruan,Michael Sammeth,Kuljeet Singh Sandhu,Lorain Schaeffer,Lei-Hoon See,Atif Shahab,Jørgen Skancke,Ana Maria Suzuki,Hazuki Takahashi,Hagen Tilgner,Diane Trout,Nathalie Walters,Huaien Wang,Yoshihide Hayashizaki,Alexandre Reymond,Stylianos E. Antonarakis,Gregory J. Hannon,Yijun Ruan,Piero Carninci,Cricket A. Sloan,Katrina Learned,Venkat S. Malladi,Matthew C. Wong,Galt P. Barber,Melissa S. Cline,Timothy R. Dreszer,Steven G. Heitner,Donna Karolchik,Vanessa M. Kirkup,Laurence R. Meyer,Jeffrey C. Long,Morgan Maddren,Brian J. Raney,Linda L. Grasfeder,Paul G. Giresi,Anna Battenhouse,Nathan C. Sheffield,Kimberly A. Showers,Darin London,Akshay Bhinge,Christopher Shestak,Matthew R. Schaner,Seul K.C. Kim,Zhuzhu Zhang,Piotr A. Mieczkowski,Joanna O. Mieczkowska,Zheng Liu,Ryan M. McDaniell,Yunyun Ni,Naim U. Rashid,Min Jae Kim,Sheera Adar,Zhancheng Zhang,Tianyuan Wang,Deborah R. Winter,Damian Keefe,Vishwanath R. Iyer,Meizhen Zheng,Ping Wang,Jason Gertz,Jost Vielmetter,Partridge Ec,Katherine E. Varley,Clarke Gasper,Anita Bansal,Shirley Pepke,Preti Jain,Henry Amrhein,Kevin M. Bowling,Michael Anaya,Marie K. Cross,Michael Muratet,Kimberly M. Newberry,Kenneth McCue,Amy S. Nesmith,Katherine I. Fisher-Aylor,Barbara N. Pusey,Gilberto DeSalvo,Stephanie L. Parker,Sreeram Balasubramanian,Nicholas S. Davis,Sarah Meadows,Tracy Eggleston,J. Scott Newberry,Shawn Levy,Devin Absher,Wing Hung Wong,Matthew J. Blow,Axel Visel,Len A. Pennachio,Hanna Petrykowska,Alexej Abyzov,Bronwen Aken,Daniel Barrell,Gemma Barson,Andrew Berry,Alexandra Bignell,Veronika Boychenko,Giovanni Bussotti,Claire Davidson,Gloria Despacio-Reyes,Mark Diekhans,Iakes Ezkurdia,Adam Frankish,James Gilbert,José M. González,Ed Griffiths,Rachel A. Harte,David A. Hendrix,Toby Hunt,Irwin Jungreis,M. Kay,Ekta Khurana,Jing Leng,Michael F. Lin,Jane E. Loveland,Zhi Lu,Deepa Manthravadi,Marco Mariotti,Jonathan M. Mudge,Gaurab Mukherjee,Cedric Notredame,Baikang Pei,Jose Manuel Rodriguez,Gary Saunders,Andrea Sboner,Stephen M. J. Searle,Cristina Sisu,Catherine E. Snow,Charles A. Steward,Electra Tapanari,Michael L. Tress,Marijke J. van Baren,Stefan Washietl,Laurens G. Wilming,Amonida Zadissa,Zhengdong D. Zhang,Michael R. Brent,David Haussler,Alfonso Valencia,Nicholas Addleman,Roger P. Alexander,Raymond K. Auerbach,Suganthi Balasubramanian,Keith Bettinger,Nitin Bhardwaj,Alan P. Boyle,Alina R. Cao,Philip Cayting,Alexandra Charos,Yong Cheng,Catharine L. Eastman,Ghia Euskirchen,Joseph D. Fleming,Fabian Grubert,Lukas Habegger,Manoj Hariharan,Arif Harmanci,Sushma Iyengar,Victor X. Jin,Konrad J. Karczewski,Maya Kasowski,Phil Lacroute,Hugo Y. K. Lam,Nathan Lamarre-Vincent,Jin Lian,Marianne Lindahl-Allen,Renqiang Min,Benoit Miotto,Hannah Monahan,Zarmik Moqtaderi,Xinmeng J. Mu,Henriette O'Geen,Zhengqing Ouyang,Dorrelyn Patacsil,Debasish Raha,Lucía Ramírez,Brian Reed,Minyi Shi,Teri Slifer,Heather Witt,Linfeng Wu,Xiaoqin Xu,Koon-Kiu Yan,Xinqiong Yang,Kevin Struhl,Sherman M. Weissman,Luiz O. F. Penalva,Subhradip Karmakar,Raj R. Bhanvadia,Alina Choudhury,Marc Domanus,Lijia Ma,Jennifer L. Moran,Alec Victorsen,Thomas O. Auer,Lazaro Centanin,Michael P. Eichenlaub,Franziska Gruhl,Stephan Heermann,Burkhard Hoeckendorf,Daigo Inoue,Tanja Kellner,Stephan Kirchmaier,Claudia Mueller,Robert Reinhardt,Lea Schertel,Stephanie Schneider,Rebecca Sinn,Beate Wittbrodt,Jochen Wittbrodt,E. Christopher Partridge,Gaurav Jain,Gayathri Balasundaram,Daniel Bates,Rachel Byron,Theresa K. Canfield,Morgan Diegel,Douglas Dunn,Abigail K. Ebersol,Tristan Frum,Kavita Garg,Erica Gist,R. Scott Hansen,Lisa Boatman,Eric Haugen,Richard Humbert,Audra K. Johnson,Ericka M. Johnson,Tattyana V. Kutyavin,Kristen Lee,Dimitra Lotakis,Matthew T. Maurano,Shane Neph,Fiedencio V. Neri,Eric D. Nguyen,Hongzhu Qu,Alex Reynolds,Vaughn Roach,Eric Rynes,Minerva E. Sanchez,Richard Sandstrom,Anthony Shafer,Andrew B. Stergachis,Sean Thomas,Benjamin Vernot,Jeff Vierstra,Shinny Vong,Hao Wang,Molly Weaver,Yongqi Yan,Miaohua Zhang,Joshua M. Akey,M. A. Bender,Michael O. Dorschner,Mark Groudine,Michael J. MacCoss,Patrick A. Navas,George Stamatoyannopoulos,Kathryn Beal,Alvis Brazma,Paul Flicek,Nathan R. Johnson,Margus Lukk,Nicholas M. Luscombe,Daniel Sobral,Juan M. Vaquerizas,Serafim Batzoglou,Arend Sidow,Nadine Hussami,Sofia Kyriazopoulou-Panagiotopoulou,Max Libbrecht,Marc A. Schaub,Webb Miller,Peter J. Bickel,Balazs Banfai,Nathan Boley,Haiyan Huang,Jingyi Jessica Li,William Stafford Noble,Jeff A. Bilmes,Orion J. Buske,Avinash Das Sahu,Peter V. Kharchenko,Peter J. Park,Dannon Baker,James Taylor,Lucas Lochovsky +442 more
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
Integrative clinical genomics of advanced prostate cancer
Dan R. Robinson,Eliezer M. Van Allen,Eliezer M. Van Allen,Yi-Mi Wu,Nikolaus Schultz,Robert J. Lonigro,Juan Miguel Mosquera,Bruce Montgomery,Mary-Ellen Taplin,Colin C. Pritchard,Gerhardt Attard,Gerhardt Attard,Himisha Beltran,Wassim Abida,Robert K. Bradley,Jake Vinson,Xuhong Cao,Pankaj Vats,Lakshmi P. Kunju,Maha Hussain,Felix Y. Feng,Scott A. Tomlins,Kathleen A. Cooney,David Smith,Christine Brennan,Javed Siddiqui,Rohit Mehra,Yu Chen,Yu Chen,Dana E. Rathkopf,Dana E. Rathkopf,Michael J. Morris,Michael J. Morris,Stephen B. Solomon,Jeremy C. Durack,Victor E. Reuter,Anuradha Gopalan,Jianjiong Gao,Massimo Loda,Rosina T. Lis,Michaela Bowden,Michaela Bowden,Stephen P. Balk,Glenn C. Gaviola,Carrie Sougnez,Manaswi Gupta,Evan Y. Yu,Elahe A. Mostaghel,Heather H. Cheng,Hyojeong Mulcahy,Lawrence D. True,Stephen R. Plymate,Heidi Dvinge,Roberta Ferraldeschi,Roberta Ferraldeschi,Penny Flohr,Penny Flohr,Susana Miranda,Susana Miranda,Zafeiris Zafeiriou,Zafeiris Zafeiriou,Nina Tunariu,Nina Tunariu,Joaquin Mateo,Joaquin Mateo,Raquel Perez-Lopez,Raquel Perez-Lopez,Francesca Demichelis,Francesca Demichelis,Brian D. Robinson,Marc H. Schiffman,David M. Nanus,Scott T. Tagawa,Alexandros Sigaras,Kenneth Eng,Olivier Elemento,Andrea Sboner,Elisabeth I. Heath,Howard I. Scher,Howard I. Scher,Kenneth J. Pienta,Philip W. Kantoff,Johann S. de Bono,Johann S. de Bono,Mark A. Rubin,Peter S. Nelson,Levi A. Garraway,Levi A. Garraway,Charles L. Sawyers,Arul M. Chinnaiyan +89 more
TL;DR: This cohort study provides clinically actionable information that could impact treatment decisions for affected individuals and identified new genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin, and ZBTB16/PLZF.
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.
The Molecular Taxonomy of Primary Prostate Cancer
Adam Abeshouse,Jaeil Ahn,Rehan Akbani,Adrian Ally,Samirkumar B. Amin,Chris 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,Anne Breggia,Fadi Brimo,Denise Brooks,Bradley M. Broom,Alan H. Bryce,Glenn J. Bubley,Eric J. Burks,Yaron S.N. Butterfield,Michael Button,David Canes,Carlos Gilberto Carlotti,Rebecca Carlsen,Peter R. Carroll,Richard Cartun,Brett S. Carver,June M. Chan,Matthew T. Chang,Yu Chen,Anthony J. Costello,Andrew D. Cherniack,Simone Chevalier,Juok Cho,Andy Chu,Eric Chuah,Sudha Chudamani,Giovanni Ciriello,Amanda Clarke,Matthew R. Cooperberg,Niall M. Corcoran,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,Christopher A. Bristow,Jianjiong Gao,Johanna Gardner,Julie M. Gastier-Foster,Nils Gehlenborg,Mark Gerken,Mark Gerstein,Andrew K. Godwin,Anuradha Gopalan,Markus Graefen,Kiley Graim,Thomas Gribbin,Ranabir Guin,Manaswi Gupta,Angela Hadjipanayis,Syed Haider,Lucie Hamel,D. Neil Hayes,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,André 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,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,W. Marston Linehan,Shiyun Ling,Scott M. Lippman,Jia Liu,Wen-Bin Liu,Lucas Lochovsky,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,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,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 M. 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,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 P. Simko,Ronald Simon,Janae V. Simons,Payal Sipahimalani,Tara Skelly,Heidi J. Sofia,Matthew G. Soloway,Xingzhi Song,Andrea Sorcini,Serghei Stepa,Chip Stewart,John 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 Pretti da Cunha 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,Cathy D. Vocke,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,Jiashan Zhang,Wei Zhang,Yi Zhong,Kelsey Zhu,Erik Zmuda,Robert K. Bradley,Michelle Carmell,Scott L. Carter,Lynda Chin,Kristian Cibulskis,Gad Getz,David I. Heiman,Eric S. Lander,Pei Lin,Massimo Loda,Matthew Meyerson,Peter J. Park,Jonathan G. Seidman,Carrie Sougnez,Roel G.W. Verhaak,Douglas Voet +309 more
TL;DR: A comprehensive molecular analysis of 333 primary prostate carcinomas revealed a molecular taxonomy in which 74% of these tumors fell into one of seven subtypes defined by specific gene fusions (ERG, ETV1/4, and FLI1) or mutations (SPOP, FOXA1, and IDH1).
Journal ArticleDOI
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
Richard M. Myers,John A. Stamatoyannopoulos,Michael Snyder,Ian Dunham,Ross C. Hardison,Bradley E. Bernstein,Bradley E. Bernstein,Thomas R. Gingeras,W. James Kent,Ewan Birney,Barbara J. Wold,Gregory E. Crawford,Charles B. Epstein,Noam Shoresh,Jason Ernst,Jason Ernst,Tarjei S. Mikkelsen,Pouya Kheradpour,Pouya Kheradpour,Xiaolan Zhang,Li Wang,Robbyn Issner,Michael Coyne,Timothy Durham,Manching Ku,Thanh Truong,Lucas D. Ward,Lucas D. Ward,Robert C. Altshuler,Michael F. Lin,Michael F. Lin,Manolis Kellis,Manolis Kellis,Carrie A. Davis,Philipp Kapranov,Alexander Dobin,Chris Zaleski,Felix Schlesinger,Philippe Batut,Sudipto K. Chakrabortty,Sonali Jha,Wei Lin,Jorg Drenkow,Huaien Wang,Kim Bell,Ian Bell,Hui Gao,Erica Dumais,Jacqueline Dumais,Stylianos E. Antonarakis,Catherine Ucla,Christelle Borel,Roderic Guigó,Sarah Djebali,Julien Lagarde,Colin Kingswood,Paolo Ribeca,Micha Sammeth,Tyler Alioto,Angelika Merkel,Hagen Tilgner,Piero Carninci,Yoshihide Hayashizaki,Timo Lassmann,Hazuki Takahashi,Rehab F. Abdelhamid,Gregory J. Hannon,Katalin Toth Fejes,Jonathan B. Preall,Assaf Gordon,Vihra Sotirova,Alexandre Reymond,Cédric Howald,Emilie Aït Yahya Graison,Jacqueline Chrast,Yijun Ruan,Xiaoan Ruan,Atif Shahab,Wan Ting Poh,Chia-Lin Wei,Terrence S. Furey,Alan P. Boyle,Nathan C. Sheffield,Lingyun Song,Yoichiro Shibata,Teresa Vales,Deborah R. Winter,Zhancheng Zhang,Darin London,Tianyuan Wang,Damian Keefe,Vishwanath R. Iyer,Bum Kyu Lee,Ryan M. McDaniell,Zheng Liu,Anna Battenhouse,Akshay Bhinge,Jason D. Lieb,Linda L. Grasfeder,Kimberly A. Showers,Paul G. Giresi,Seul K.C. Kim,Christopher Shestak,Florencia Pauli,Timothy E. Reddy,Jason Gertz,E. Christopher Partridge,Preti Jain,Rebekka O. Sprouse,Anita Bansal,Barbara N. Pusey,Michael Muratet,Katherine E. Varley,Kevin M. Bowling,Kimberly M. Newberry,Amy S. Nesmith,Jason A. Dilocker,Stephanie L. Parker,Lindsay L. Waite,Krista Thibeault,Kevin Roberts,Devin Absher,Ali Mortazavi,Brian Williams,Georgi K. Marinov,Diane Trout,Brandon King,Kenneth McCue,Anthony Kirilusha,Gilberto DeSalvo,Katherine Aylor Fisher,Henry Amrhein,Shirley Pepke,Jost Vielmetter,Gavin Sherlock,Arend Sidow,Serafim Batzoglou,Rami Rauch,Anshul Kundaje,Max Libbrecht,Elliott H. Margulies,Stephen C. J. Parker,Laura Elnitski,Eric D. Green,Tim Hubbard,Jennifer Harrow,Stephen M. J. Searle,Felix Kokocinski,Felix Kokocinski,Browen Aken,Adam Frankish,Toby Hunt,Gloria Despacio-Reyes,M. Kay,Gaurab Mukherjee,Alexandra Bignell,Gary Saunders,Veronika Boychenko,Michael R. Brent,M. van Baren,Randall H. Brown,Mark Gerstein,Mark Gerstein,Ekta Khurana,Suganthi Balasubramanian,Hugo Y. K. Lam,Philip Cayting,Philip Cayting,R. Robilotto,Zhi Lu,Thomas Derrien,Andrea Tanzer,David G. Knowles,Marco Mariotti,David Haussler,Rachel A. Harte,Mark Diekhans,Michael F. Lin,Michael F. Lin,Alfonso Valencia,Michael L. Tress,Stephen G. Landt,Stephen G. Landt,Debasish Raha,Minyi Shi,Ghia Euskirchen,Fabian Grubert,Maya Kasowski,Jin Lian,Phil Lacroute,Youhan Xu,Hannah Monahan,Dorrelyn Patacsil,Teri Slifer,Xinqiong Yang,Alexandra Charos,Brian Reed,Linfeng Wu,Raymond K. Auerbach,Lukas Habegger,Manoj Hariharan,Joel Rozowsky,Alexej Abyzov,Sherman M. Weissman,Kevin Struhl,Nathan Lamarre-Vincent,Marianne Lindahl-Allen,Benoit Miotto,Zarmik Moqtaderi,Joseph D. Fleming,Peter E. Newburger,Peggy J. Farnham,Peggy J. Farnham,Seth Frietze,Seth Frietze,Henriette O'Geen,Xiaoqin Xu,Kim Blahnik,Alina R. Cao,Sushma Iyengar,Rajinder Kaul,Robert E. Thurman,Hao Wang,Patrick A. Navas,Richard Sandstrom,Peter J. Sabo,Molly Weaver,Theresa K. Canfield,Kristen Lee,Shane Neph,Vaughan Roach,Alex Reynolds,Audra K. Johnson,Eric Rynes,Erika Giste,Shinny Vong,Jun Neri,Tristan Frum,Eric D. Nguyen,Abigail K. Ebersol,Minerva E. Sanchez,Hadar H. Sheffer,Dimitra Lotakis,Eric Haugen,Richard Humbert,Tanya Kutyavin,Tony Shafer,William Stafford Noble,Job Dekker,Bryan R. Lajoie,Amartya Sanyal,Kate R. Rosenbloom,Timothy R. Dreszer,Brian J. Raney,Galt P. Barber,Laurence R. Meyer,Cricket A. Sloan,Venkat S. Malladi,Melissa S. Cline,Katrina Learned,Vanessa K. Swing,Ann S. Zweig,Brooke Rhead,Pauline A. Fujita,Krishna M. Roskin,Donna Karolchik,Robert M. Kuhn,Steven P. Wilder,Daniel Sobral,Javier Herrero,Kathryn Beal,Margus Lukk,Alvis Brazma,Juan M. Vaquerizas,Nicholas M. Luscombe,Peter J. Bickel,Nathan Boley,James B. Brown,Qiang Li,Haiyan Huang,Andrea Sboner,Kevin Y. Yip,Chao Cheng,Koon-Kiu Yan,Nitin Bhardwaj,Jing Wang,Lucas Lochovsky,Justin Jee,Theodore Gibson,Jing Leng,Jiang Du,Robert S. Harris,Giltae Song,Webb Miller,Bernard B. Suh,Benedict Paten,Michael M. Hoffman,Orion J. Buske,Zhiping Weng,Xianjun Dong,Jie Wang,Hualin Xi,Scott A. Tenenbaum,Frank Doyle,Sridar V. Chittur,Luiz O. F. Penalva,Thomas D. Tullius,Kevin P. White,Subhradip Karmakar,Alec Victorsen,Nader Jameel,Nick Bild,Robert L. Grossman,Patrick J. Collins,Nathan D. Trinklein,Morgan C. Giddings,Morgan C. Giddings,Jainab Khatun,Christopher W. Maier,Ting Wang,Troy W. Whitfield,Xian Chen,Yanbao Yu,Harsha P. Gunawardena,Elise A. Feingold,Rebecca F. Lowdon,Laura A.L. Dillon,Peter J. Good,Brian A. Risk +328 more
TL;DR: An overview of the project and the resources it is generating and the application of ENCODE data to interpret the human genome are provided.