Searching journal content for Webb Miller in author.

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  1. Research: Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
    • Weisheng Wu,
    • Yong Cheng,
    • Cheryl A. Keller,
    • Jason Ernst,
    • Swathi Ashok Kumar,
    • Tejaswini Mishra,
    • Christapher Morrissey,
    • Christine M. Dorman,
    • Kuan-Bei Chen,
    • Daniela Drautz,
    • Belinda Giardine,
    • Yoichiro Shibata,
    • Lingyun Song,
    • Max Pimkin,
    • Gregory E. Crawford,
    • Terrence S. Furey,
    • Manolis Kellis,
    • Webb Miller,
    • James Taylor,
    • Stephan C. Schuster,
    • Yu Zhang,
    • Francesca Chiaromonte,
    • Gerd A. Blobel,
    • Mitchell J. Weiss,
    • and Ross C. Hardison
    Genome Res. October 2011 21: 1659-1671; Published in Advance July 27, 2011, doi:10.1101/gr.125088.111
    OPEN ACCESS ARTICLE
  2. Method: Genome-wide identification of conserved regulatory function in diverged sequences
    • Leila Taher,
    • David M. McGaughey,
    • Samantha Maragh,
    • Ivy Aneas,
    • Seneca L. Bessling,
    • Webb Miller,
    • Marcelo A. Nobrega,
    • Andrew S. McCallion,
    • and Ivan Ovcharenko
    Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
    OPEN ACCESS ARTICLE
  3. Article: Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
    • Yong Cheng,
    • Weisheng Wu,
    • Swathi Ashok Kumar,
    • Duonan Yu,
    • Wulan Deng,
    • Tamara Tripic,
    • David C. King,
    • Kuan-Bei Chen,
    • Ying Zhang,
    • Daniela Drautz,
    • Belinda Giardine,
    • Stephan C. Schuster,
    • Webb Miller,
    • Francesca Chiaromonte,
    • Yu Zhang,
    • Gerd A. Blobel,
    • Mitchell J. Weiss,
    • and Ross C. Hardison
    Genome Res. December 2009 19: 2172-2184; Published in Advance November 3, 2009, doi:10.1101/gr.098921.109
    OPEN ACCESS ARTICLE
  4. LETTER: The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)
    • Webb Miller,
    • Daniela I. Drautz,
    • Jan E. Janecka,
    • Arthur M. Lesk,
    • Aakrosh Ratan,
    • Lynn P. Tomsho,
    • Mike Packard,
    • Yeting Zhang,
    • Lindsay R. McClellan,
    • Ji Qi,
    • Fangqing Zhao,
    • M. Thomas P. Gilbert,
    • Love Dalén,
    • Juan Luis Arsuaga,
    • Per G.P. Ericson,
    • Daniel H. Huson,
    • Kristofer M. Helgen,
    • William J. Murphy,
    • Anders Götherström,
    • and Stephan C. Schuster
    Genome Res. February 2009 19: 213-220; Published in Advance January 12, 2009, doi:10.1101/gr.082628.108
    OPEN ACCESS ARTICLE
  5. LETTER: Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
    • Yong Cheng,
    • David C. King,
    • Louis C. Dore,
    • Xinmin Zhang,
    • Yuepin Zhou,
    • Ying Zhang,
    • Christine Dorman,
    • Demesew Abebe,
    • Swathi A. Kumar,
    • Francesca Chiaromonte,
    • Webb Miller,
    • Roland D. Green,
    • Mitchell J. Weiss,
    • and Ross C. Hardison
    Genome Res. December 2008 18: 1896-1905; Published in Advance September 25, 2008, doi:10.1101/gr.083089.108
    OPEN ACCESS ARTICLE
  6. RESOURCE: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
    • Webb Miller,
    • Kate Rosenbloom,
    • Ross C. Hardison,
    • Minmei Hou,
    • James Taylor,
    • Brian Raney,
    • Richard Burhans,
    • David C. King,
    • Robert Baertsch,
    • Daniel Blankenberg,
    • Sergei L. Kosakovsky Pond,
    • Anton Nekrutenko,
    • Belinda Giardine,
    • Robert S. Harris,
    • Svitlana Tyekucheva,
    • Mark Diekhans,
    • Thomas H. Pringle,
    • William J. Murphy,
    • Arthur Lesk,
    • George M. Weinstock,
    • Kerstin Lindblad-Toh,
    • Richard A. Gibbs,
    • Eric S. Lander,
    • Adam Siepel,
    • David Haussler,
    • and W. James Kent
    Genome Res. December 2007 17: 1797-1808; Published in Advance November 5, 2007, doi:10.1101/gr.6761107
  7. ARTICLE: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    • Elliott H. Margulies,
    • Gregory M. Cooper,
    • George Asimenos,
    • Daryl J. Thomas,
    • Colin N. Dewey,
    • Adam Siepel,
    • Ewan Birney,
    • Damian Keefe,
    • Ariel S. Schwartz,
    • Minmei Hou,
    • James Taylor,
    • Sergey Nikolaev,
    • Juan I. Montoya-Burgos,
    • Ari Löytynoja,
    • Simon Whelan,
    • Fabio Pardi,
    • Tim Massingham,
    • James B. Brown,
    • Peter Bickel,
    • Ian Holmes,
    • James C. Mullikin,
    • Abel Ureta-Vidal,
    • Benedict Paten,
    • Eric A. Stone,
    • Kate R. Rosenbloom,
    • W. James Kent,
    • Gerard G. Bouffard,
    • Xiaobin Guan,
    • Nancy F. Hansen,
    • Jacquelyn R. Idol,
    • Valerie V.B. Maduro,
    • Baishali Maskeri,
    • Jennifer C. McDowell,
    • Morgan Park,
    • Pamela J. Thomas,
    • Alice C. Young,
    • Robert W. Blakesley,
    • Donna M. Muzny,
    • Erica Sodergren,
    • David A. Wheeler,
    • Kim C. Worley,
    • Huaiyang Jiang,
    • George M. Weinstock,
    • Richard A. Gibbs,
    • Tina Graves,
    • Robert Fulton,
    • Elaine R. Mardis,
    • Richard K. Wilson,
    • Michele Clamp,
    • James Cuff,
    • Sante Gnerre,
    • David B. Jaffe,
    • Jean L. Chang,
    • Kerstin Lindblad-Toh,
    • Eric S. Lander,
    • Angie Hinrichs,
    • Heather Trumbower,
    • Hiram Clawson,
    • Ann Zweig,
    • Robert M. Kuhn,
    • Galt Barber,
    • Rachel Harte,
    • Donna Karolchik,
    • Matthew A. Field,
    • Richard A. Moore,
    • Carrie A. Matthewson,
    • Jacqueline E. Schein,
    • Marco A. Marra,
    • Stylianos E. Antonarakis,
    • Serafim Batzoglou,
    • Nick Goldman,
    • Ross Hardison,
    • David Haussler,
    • Webb Miller,
    • Lior Pachter,
    • Eric D. Green,
    • and Arend Sidow
    Genome Res. June 2007 17: 760-774; doi:10.1101/gr.6034307
    OPEN ACCESS ARTICLE
  8. RESOURCE: A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
    • Daniel Blankenberg,
    • James Taylor,
    • Ian Schenck,
    • Jianbin He,
    • Yi Zhang,
    • Matthew Ghent,
    • Narayanan Veeraraghavan,
    • Istvan Albert,
    • Webb Miller,
    • Kateryna D. Makova,
    • Ross C. Hardison,
    • and Anton Nekrutenko
    Genome Res. June 2007 17: 960-964; doi:10.1101/gr.5578007
    OPEN ACCESS ARTICLE
  9. LETTER: Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
    • David C. King,
    • James Taylor,
    • Ying Zhang,
    • Yong Cheng,
    • Heather A. Lawson,
    • Joel Martin,
    • ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
    • Francesca Chiaromonte,
    • Webb Miller,
    • and Ross C. Hardison
    Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
    OPEN ACCESS ARTICLE
  10. LETTER: Using genomic data to unravel the root of the placental mammal phylogeny
    • William J. Murphy,
    • Thomas H. Pringle,
    • Tess A. Crider,
    • Mark S. Springer,
    • and Webb Miller
    Genome Res. April 2007 17: 413-421; Published in Advance February 23, 2007, doi:10.1101/gr.5918807
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