Searching journal content for Ewan Birney in author.

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  1. 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
    OPEN ACCESS ARTICLE
  2. 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
    OPEN ACCESS ARTICLE
  3. 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
    OPEN ACCESS ARTICLE
  4. 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
    OPEN ACCESS ARTICLE
  5. 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
    OPEN ACCESS ARTICLE
  6. 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
    OPEN ACCESS ARTICLE
  7. 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
  8. 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
    OPEN ACCESS ARTICLE
  9. 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
  10. 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
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