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Stefan Bekiranov
Researcher at University of Virginia
Publications - 102
Citations - 12689
Stefan Bekiranov is an academic researcher from University of Virginia. The author has contributed to research in topics: Gene & Human genome. The author has an hindex of 35, co-authored 95 publications receiving 11681 citations. Previous affiliations of Stefan Bekiranov include University of Virginia Health System & Rockefeller University.
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The ENCODE (ENCyclopedia of DNA elements) Project
Elise A. Feingold,Peter J. Good,Mark S. Guyer,S. Kamholz,L. Liefer,Kris A. Wetterstrand,Francis S. Collins,Thomas R. Gingeras,Dione Kampa,E. A. Sekinger,Jill Cheng,H. Hirsch,Srinka Ghosh,Zhou Zhu,Sandeep Patel,Antonio Piccolboni,A. Yang,Hari Tammana,Stefan Bekiranov,Philipp Kapranov,Rhonda Harrison,George M. Church,Kevin Struhl,Bing Ren,Tae Hoon Kim,Leah O. Barrera,Chunxu Qu,S. van Calcar,R. Luna,C. K. Glass,M. G. Rosenfeld,Roderic Guigó,Stylianos E. Antonarakis,Ewan Birney,Michael R. Brent,Lior Pachter,Alexandre Reymond,Emmanouil T. Dermitzakis,Colin N. Dewey,Damian Keefe,F. Denoeud,Julien Lagarde,Jennifer L. Ashurst,Tim Hubbard,Jan-Jaap Wesselink,Robert Castelo,Eduardo Eyras,Richard M. Myers,Arend Sidow,Serafim Batzoglou,Nathan D. Trinklein,Sara J. Hartman,Shelley Force Aldred,Elizabeth Anton,Diane I. Schroeder,S. S. Marticke,Long H. Nguyen,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Gregory M. Cooper,Eric A. Stone,George Asimenos,Michael Brudno,Anindya Dutta,Neerja Karnani,Christopher M. Taylor,H. K. Kim,Gabriel Robins,George Stamatoyannopoulos,John A. Stamatoyannopoulos,Michael O. Dorschner,Peter J. Sabo,Michael Hawrylycz,Richard Humbert,James C. Wallace,Min-Feng Yu,Patrick A. Navas,M. McArthur,William Stafford Noble,Ian Dunham,Christof Koch,Robert M. Andrews,Gayle K. Clelland,Sarah Wilcox,Joanna C. Fowler,Keith D. James,P. Groth,Oliver M. Dovey,Peter D. Ellis,Vicki L. Wraight,Andrew J. Mungall,Pawandeep Dhami,Heike Fiegler,Cordelia Langford,Nigel P. Carter,David Vetrie,Michael Snyder,Ghia Euskirchen,Alexander E. Urban,Ugrappa Nagalakshmi,John L. Rinn,George V. Popescu,Paul Bertone,Stephen Hartman,Joel Rozowsky,Olof Emanuelsson,Thomas Royce,Sambath Chung,Mark Gerstein,Zheng Lian,Jane B. Lian,Y. Nakayama,Sherman M. Weissman,Viktor Stolc,W. Tongprasit,H. Sethi,Steven J.M. Jones,Marco A. Marra,H. Shin,Jacquie Schein,Michele Clamp,Kerstin Lindblad-Toh,Jean L. Chang,David B. Jaffe,Michael Kamal,Eric S. Lander,Tarjei S. Mikkelsen,Jade P. Vinson,Michael C. Zody,P. J. De Jong,Kazutoyo Osoegawa,Mikhail Nefedov,Baoli Zhu,Andreas D. Baxevanis,Tyra G. Wolfsberg,Gregory E. Crawford,James R R Whittle,Ingeborg Holt,T. J. Vasicek,D. Zhou,Shu-Jin Luo,Eric D. Green,Gerry Bouffard,Elliott H. Margulies,Matthew E. Portnoy,Nancy F. Hansen,Pamela J. Thomas,Jenny McDowell,Baishali Maskeri,Alice C. Young,Jacquelyn R. Idol,Robert W. Blakesley,Greg Schuler,Webb Miller,Ross C. Hardison,Laura Elnitski,Prachi Shah,Steven L. Salzberg,Mihaela Pertea,William H. Majoros,David Haussler,Daryl J. Thomas,Kate R. Rosenbloom,Hiram Clawson,Adam Siepel,W. J. Kent,Zhiping Weng,S. Jin,Anason S. Halees,H. Burden,Ulas Karaoz,Yutao Fu,Yong Yu,C. Ding,Charles R. Cantor,Robert E. Kingston,Jonathan H. Dennis,Roland Green,Michael A. Singer,Todd Richmond,J. E. Norton,Peggy J. Farnham,Matthew J. Oberley,D. R. Inman,M. R. McCormick,H. Kim,C. L. Middle,Michael C. Pirrung,Xiang-Dong Fu,Y. S. Kwon,Z. Ye,Job Dekker,Tomoko M. Tabuchi,Nele Gheldof,Josée Dostie,S. C. Harvey +196 more
TL;DR: The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function.
Journal ArticleDOI
Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse
Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Michael Kamal,Kerstin Lindblad-Toh,Stefan Bekiranov,Dione K. Bailey,Dana J. Huebert,Dana J. Huebert,Scott McMahon,Scott McMahon,Elinor K. Karlsson,Edward J. Kulbokas,Thomas R. Gingeras,Stuart L. Schreiber,Stuart L. Schreiber,Eric S. Lander,Eric S. Lander +17 more
TL;DR: Methylation patterns at orthologous loci are strongly conserved between human and mouse even though many methylated sites do not show sequence conservation notably higher than background, which suggests that the DNA elements that direct the methylation represent only a small fraction of the region or lie at some distance from the site.
Journal ArticleDOI
Genome-wide analysis of estrogen receptor binding sites
Jason S. Carroll,Clifford A. Meyer,Jun S. Song,Wei Li,Timothy R. Geistlinger,Jérôme Eeckhoute,Alexander S. Brodsky,Erika Krasnickas Keeton,Kirsten C Fertuck,Giles Hall,Qianben Wang,Stefan Bekiranov,Stefan Bekiranov,Victor Sementchenko,Edward A. Fox,Pamela A. Silver,Thomas R. Gingeras,X. Shirley Liu,Myles Brown +18 more
TL;DR: All estrogen receptor and RNA polymerase II binding sites are mapped on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells, and distinct temporal mechanisms of estrogen-mediated gene regulation are demonstrated.
Journal ArticleDOI
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
Jill Cheng,Philipp Kapranov,Jorg Drenkow,Sujit Dike,Shane Brubaker,Sandeep Patel,Jeffrey Long,David Stern,Hari Tammana,Gregg Helt,Victor Sementchenko,Antonio Piccolboni,Stefan Bekiranov,Dione K. Bailey,Madhavan Ganesh,Srinka Ghosh,Ian Bell,Daniela S. Gerhard,Thomas R. Gingeras +18 more
TL;DR: The transcribed portions of the human genome are predominantly composed of interlaced networks of both poly A+ and poly A– annotated transcripts and unannotated transcripts of unknown function, which has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene.
Journal ArticleDOI
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.
Simon Cawley,Stefan Bekiranov,Huck H Ng,Huck H Ng,Huck H Ng,Philipp Kapranov,Edward A. Sekinger,Dione Kampa,Antonio Piccolboni,Victor Sementchenko,Jill Cheng,Alan Williams,Raymond Wheeler,Brant Wong,Jorg Drenkow,Mark Yamanaka,Sandeep Patel,Shane Brubaker,Hari Tammana,Gregg Helt,Kevin Struhl,Thomas R. Gingeras +21 more
TL;DR: The human genome contains roughly comparable numbers of protein-coding and noncoding genes that are bound by common transcription factors and regulated by common environmental signals.