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Subhradip Karmakar
Researcher at All India Institute of Medical Sciences
Publications - 53
Citations - 6876
Subhradip Karmakar is an academic researcher from All India Institute of Medical Sciences. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 13, co-authored 35 publications receiving 6296 citations. Previous affiliations of Subhradip Karmakar include Argonne National Laboratory & University of Chicago.
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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
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt,Georgi K. Marinov,Anshul Kundaje,Pouya Kheradpour,Florencia Pauli,Serafim Batzoglou,Bradley E. Bernstein,Peter J. Bickel,James B. Brown,Philip Cayting,Yiwen Chen,Gilberto DeSalvo,Charles B. Epstein,Katherine I. Fisher-Aylor,Ghia Euskirchen,Mark Gerstein,Jason Gertz,Alexander J. Hartemink,Michael M. Hoffman,Vishwanath R. Iyer,Youngsook L. Jung,Subhradip Karmakar,Manolis Kellis,Peter V. Kharchenko,Qiang Li,Tao Liu,X. Shirley Liu,Lijia Ma,Aleksandar Milosavljevic,Richard M. Myers,Peter J. Park,Michael J. Pazin,Marc D. Perry,Debasish Raha,Timothy E. Reddy,Joel Rozowsky,Noam Shoresh,Arend Sidow,Matthew Slattery,John A. Stamatoyannopoulos,Michael Y. Tolstorukov,Kevin P. White,Simon Xi,Peggy J. Farnham,Jason D. Lieb,Barbara J. Wold,Michael Snyder +46 more
TL;DR: This work discusses how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data and develops a set of working standards and guidelines for ChIP experiments that are updated routinely.
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.
Journal ArticleDOI
SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer
Guoqiang Li,Guoqiang Li,Weimin Ci,Subhradip Karmakar,Subhradip Karmakar,Ke Chen,Ruby Dhar,Ruby Dhar,Zhixiang Fan,Zhongqiang Guo,Zhongqiang Guo,Jing Zhang,Yuwen Ke,Lu Wang,Lu Wang,Min Zhuang,Shengdi Hu,Xuesong Li,Liqun Zhou,Xianghong Li,Matthew F. Calabrese,Edmond R. Watson,Sandip M. Prasad,Carrie W. Rinker-Schaeffer,Scott E. Eggener,Thomas Stricker,Thomas Stricker,Yong Tian,Brenda A. Schulman,Jiang Liu,Kevin P. White,Kevin P. White +31 more
TL;DR: It is demonstrated that SPOP, which encodes an E3 ubiquitin ligase component, is a direct transcriptional target of HIFs in clear cell renal cell carcinoma (ccRCC), and Knockdown of SPOP specifically kills ccRCC cells, indicating that it may be a promising therapeutic target.
Journal ArticleDOI
CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia.
Megan E. McNerney,Christopher D. Brown,Xiaoyue Wang,Elizabeth T. Bartom,Subhradip Karmakar,Chaitanya Bandlamudi,Shan Yu,Jinkyung Ko,Barry P. Sandall,Thomas Stricker,John Anastasi,Robert L. Grossman,John M. Cunningham,Michelle M. Le Beau,Kevin P. White +14 more
TL;DR: In this article, the authors performed transcriptome sequencing and SNP array analysis on de novo and therapy-related myeloid neoplasms, half with −7/del(7q), and identified a 217-Mb commonly deleted segment on chromosome band 7q221 containing CUX1, a gene encoding a home-domain-containing transcription factor.