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Joel Rozowsky
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Displaying results 1-9 of
9
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Research
:
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
Chao Cheng
,
Roger Alexander
,
Renqiang Min
,
Jing Leng
,
Kevin Y. Yip
,
Joel Rozowsky
,
Koon-Kiu Yan
,
Xianjun Dong
,
Sarah Djebali
,
Yijun Ruan
,
Carrie A. Davis
,
Piero Carninci
,
Timo Lassman
,
Thomas R. Gingeras
,
Roderic Guigó
,
Ewan Birney
,
Zhiping Weng
,
Michael Snyder
,
and
Mark Gerstein
Genome Res.
September 2012
22
:
1658
-
1667
;
doi:
10.1101/gr.136838.111
Abstract
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Supplemental Material
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Resource
:
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 Bickel
,
James B. Brown
,
Philip Cayting
,
Yiwen Chen
,
Gilberto DeSalvo
,
Charles 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
,
Qunhua 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
,
and
Michael Snyder
Genome Res.
September 2012
22
:
1813
-
1831
;
doi:
10.1101/gr.136184.111
Abstract
Full Text
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Method
:
Prediction and characterization of noncoding RNAs in
C. elegans
by integrating conservation, secondary structure, and high-throughput sequencing and array data
Zhi John Lu
,
Kevin Y. Yip
,
Guilin Wang
,
Chong Shou
,
LaDeana W. Hillier
,
Ekta Khurana
,
Ashish Agarwal
,
Raymond Auerbach
,
Joel Rozowsky
,
Chao Cheng
,
Masaomi Kato
,
David M. Miller
,
Frank Slack
,
Michael Snyder
,
Robert H. Waterston
,
Valerie Reinke
,
and
Mark B. Gerstein
Genome Res.
February 2011
21
:
276
-
285
;
Published in Advance
December 22, 2010
,
doi:
10.1101/gr.110189.110
Abstract
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LETTER
:
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
David S. Johnson
,
Wei Li
,
D. Benjamin Gordon
,
Arindam Bhattacharjee
,
Bo Curry
,
Jayati Ghosh
,
Leonardo Brizuela
,
Jason S. Carroll
,
Myles Brown
,
Paul Flicek
,
Christoph M. Koch
,
Ian Dunham
,
Mark Bieda
,
Xiaoqin Xu
,
Peggy J. Farnham
,
Philipp Kapranov
,
David A. Nix
,
Thomas R. Gingeras
,
Xinmin Zhang
,
Heather Holster
,
Nan Jiang
,
Roland D. Green
,
Jun S. Song
,
Scott A. McCuine
,
Elizabeth Anton
,
Loan Nguyen
,
Nathan D. Trinklein
,
Zhen Ye
,
Keith Ching
,
David Hawkins
,
Bing Ren
,
Peter C. Scacheri
,
Joel Rozowsky
,
Alexander Karpikov
,
Ghia Euskirchen
,
Sherman Weissman
,
Mark Gerstein
,
Michael Snyder
,
Annie Yang
,
Zarmik Moqtaderi
,
Heather Hirsch
,
Hennady P. Shulha
,
Yutao Fu
,
Zhiping Weng
,
Kevin Struhl
,
Richard M. Myers
,
Jason D. Lieb
,
and
X. Shirley Liu
Genome Res.
March 2008
18
:
393
-
403
;
Published in Advance
February 7, 2008
,
doi:
10.1101/gr.7080508
Abstract
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Methods
:
Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
Ghia M. Euskirchen
,
Joel S. Rozowsky
,
Chia-Lin Wei
,
Wah Heng Lee
,
Zhengdong D. Zhang
,
Stephen Hartman
,
Olof Emanuelsson
,
Viktor Stolc
,
Sherman Weissman
,
Mark B. Gerstein
,
Yijun Ruan
,
and
Michael Snyder
Genome Res.
June 2007
17
:
898
-
909
;
doi:
10.1101/gr.5583007
Abstract
Full Text
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Supplemental Research Data
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ARTICLE
:
The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
Joel S. Rozowsky
,
Daniel Newburger
,
Fred Sayward
,
Jiaqian Wu
,
Greg Jordan
,
Jan O. Korbel
,
Ugrappa Nagalakshmi
,
Jin Yang
,
Deyou Zheng
,
Roderic Guigó
,
Thomas R. Gingeras
,
Sherman Weissman
,
Perry Miller
,
Michael Snyder
,
and
Mark B. Gerstein
Genome Res.
June 2007
17
:
732
-
745
;
doi:
10.1101/gr.5696007
Abstract
Full Text
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Methods
:
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
Olof Emanuelsson
,
Ugrappa Nagalakshmi
,
Deyou Zheng
,
Joel S. Rozowsky
,
Alexander E. Urban
,
Jiang Du
,
Zheng Lian
,
Viktor Stolc
,
Sherman Weissman
,
Michael Snyder
,
and
Mark B. Gerstein
Genome Res.
June 2007
17
:
886
-
897
;
Published in Advance
November 21, 2006
,
doi:
10.1101/gr.5014606
Abstract
Full Text
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PERSPECTIVE
:
What is a gene, post-ENCODE? History and updated definition
Mark B. Gerstein
,
Can Bruce
,
Joel S. Rozowsky
,
Deyou Zheng
,
Jiang Du
,
Jan O. Korbel
,
Olof Emanuelsson
,
Zhengdong D. Zhang
,
Sherman Weissman
,
and
Michael Snyder
Genome Res.
June 2007
17
:
669
-
681
;
doi:
10.1101/gr.6339607
Abstract
Full Text
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Fig._1_Timeline_Poster.pdf
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Methods
:
Design optimization methods for genomic DNA tiling arrays
Paul Bertone
,
Valery Trifonov
,
Joel S. Rozowsky
,
Falk Schubert
,
Olof Emanuelsson
,
John Karro
,
Ming-Yang Kao
,
Michael Snyder
,
and
Mark Gerstein
Genome Res.
February 2006
16
:
271
-
281
;
Published in Advance
December 19, 2005
,
doi:
10.1101/gr.4452906
Abstract
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