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Ewan Birney
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30
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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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Resource
:
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
Jie Wang
,
Jiali Zhuang
,
Sowmya Iyer
,
XinYing Lin
,
Troy W. Whitfield
,
Melissa C. Greven
,
Brian G. Pierce
,
Xianjun Dong
,
Anshul Kundaje
,
Yong Cheng
,
Oliver J. Rando
,
Ewan Birney
,
Richard M. Myers
,
William S. Noble
,
Michael Snyder
,
and
Zhiping Weng
Genome Res.
September 2012
22
:
1798
-
1812
;
doi:
10.1101/gr.139105.112
Abstract
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Research
:
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
Bum-Kyu Lee
,
Akshay A. Bhinge
,
Anna Battenhouse
,
Ryan M. McDaniell
,
Zheng Liu
,
Lingyun Song
,
Yunyun Ni
,
Ewan Birney
,
Jason D. Lieb
,
Terrence S. Furey
,
Gregory E. Crawford
,
and
Vishwanath R. Iyer
Genome Res.
January 2012
22
:
9
-
24
;
Published in Advance
November 16, 2011
,
doi:
10.1101/gr.127597.111
Abstract
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Resource
:
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
Lingyun Song
,
Zhancheng Zhang
,
Linda L. Grasfeder
,
Alan P. Boyle
,
Paul G. Giresi
,
Bum-Kyu Lee
,
Nathan C. Sheffield
,
Stefan Gräf
,
Mikael Huss
,
Damian Keefe
,
Zheng Liu
,
Darin London
,
Ryan M. McDaniell
,
Yoichiro Shibata
,
Kimberly A. Showers
,
Jeremy M. Simon
,
Teresa Vales
,
Tianyuan Wang
,
Deborah Winter
,
Zhuzhu Zhang
,
Neil D. Clarke
,
Ewan Birney
,
Vishwanath R. Iyer
,
Gregory E. Crawford
,
Jason D. Lieb
,
and
Terrence S. Furey
Genome Res.
October 2011
21
:
1757
-
1767
;
Published in Advance
July 12, 2011
,
doi:
10.1101/gr.121541.111
Abstract
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Method
:
Efficient storage of high throughput DNA sequencing data using reference-based compression
Markus Hsi-Yang Fritz
,
Rasko Leinonen
,
Guy Cochrane
,
and
Ewan Birney
Genome Res.
May 2011
21
:
734
-
740
;
Published in Advance
January 18, 2011
,
doi:
10.1101/gr.114819.110
Abstract
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Method
:
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
Alan P. Boyle
,
Lingyun Song
,
Bum-Kyu Lee
,
Darin London
,
Damian Keefe
,
Ewan Birney
,
Vishwanath R. Iyer
,
Gregory E. Crawford
,
and
Terrence S. Furey
Genome Res.
March 2011
21
:
456
-
464
;
Published in Advance
November 24, 2010
,
doi:
10.1101/gr.112656.110
Abstract
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Research
:
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
Santosh S. Atanur
,
İnanç Birol
,
Victor Guryev
,
Martin Hirst
,
Oliver Hummel
,
Catherine Morrissey
,
Jacques Behmoaras
,
Xose M. Fernandez-Suarez
,
Michelle D. Johnson
,
William M. McLaren
,
Giannino Patone
,
Enrico Petretto
,
Charles Plessy
,
Kathleen S. Rockland
,
Charles Rockland
,
Kathrin Saar
,
Yongjun Zhao
,
Piero Carninci
,
Paul Flicek
,
Ted Kurtz
,
Edwin Cuppen
,
Michal Pravenec
,
Norbert Hubner
,
Steven J.M. Jones
,
Ewan Birney
,
and
Timothy J. Aitman
Genome Res.
June 2010
20
:
791
-
803
;
Published in Advance
April 29, 2010
,
doi:
10.1101/gr.103499.109
Abstract
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RESOURCE
:
An effective model for natural selection in promoters
Michael M. Hoffman
and
Ewan Birney
Genome Res.
May 2010
20
:
685
-
692
;
Published in Advance
March 1, 2010
,
doi:
10.1101/gr.096719.109
Abstract
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Methods
:
A new strategy for genome assembly using short sequence reads and reduced representation libraries
Andrew L. Young
,
Hatice Ozel Abaan
,
Daniel Zerbino
,
James C. Mullikin
,
Ewan Birney
,
and
Elliott H. Margulies
Genome Res.
February 2010
20
:
249
-
256
;
doi:
10.1101/gr.097956.109
Abstract
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Resource
:
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
Kim D. Pruitt
,
Jennifer Harrow
,
Rachel A. Harte
,
Craig Wallin
,
Mark Diekhans
,
Donna R. Maglott
,
Steve Searle
,
Catherine M. Farrell
,
Jane E. Loveland
,
Barbara J. Ruef
,
Elizabeth Hart
,
Marie-Marthe Suner
,
Melissa J. Landrum
,
Bronwen Aken
,
Sarah Ayling
,
Robert Baertsch
,
Julio Fernandez-Banet
,
Joshua L. Cherry
,
Val Curwen
,
Michael DiCuccio
,
Manolis Kellis
,
Jennifer Lee
,
Michael F. Lin
,
Michael Schuster
,
Andrew Shkeda
,
Clara Amid
,
Garth Brown
,
Oksana Dukhanina
,
Adam Frankish
,
Jennifer Hart
,
Bonnie L. Maidak
,
Jonathan Mudge
,
Michael R. Murphy
,
Terence Murphy
,
Jeena Rajan
,
Bhanu Rajput
,
Lillian D. Riddick
,
Catherine Snow
,
Charles Steward
,
David Webb
,
Janet A. Weber
,
Laurens Wilming
,
Wenyu Wu
,
Ewan Birney
,
David Haussler
,
Tim Hubbard
,
James Ostell
,
Richard Durbin
,
and
David Lipman
Genome Res.
July 2009
19
:
1316
-
1323
;
Published in Advance
June 4, 2009
,
doi:
10.1101/gr.080531.108
Abstract
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