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W. Miller
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42
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Research
:
Epstein–Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci
Ted Hong
,
Sreeja Parameswaran
,
Omer A. Donmez
,
Daniel Miller
,
Carmy Forney
,
Michael Lape
,
Mariana Saint Just Ribeiro
,
Jun Liang
,
Lee E. Edsall
,
Albert F. Magnusen
,
William Miller
,
Iouri Chepelev
,
John B. Harley
,
Bo Zhao
,
Leah C. Kottyan
,
and
Matthew T. Weirauch
Genome Res.
December 2021
31
:
2185
-
2198
;
Published in Advance
November 19, 2021
,
doi:
10.1101/gr.264705.120
Abstract
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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
Abstract
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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
Abstract
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Letter
:
Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus
Biola M. Javierre
,
Agustin F. Fernandez
,
Julia Richter
,
Fatima Al-Shahrour
,
J. Ignacio Martin-Subero
,
Javier Rodriguez-Ubreva
,
Maria Berdasco
,
Mario F. Fraga
,
Terrance P. O'Hanlon
,
Lisa G. Rider
,
Filipe V. Jacinto
,
F. Javier Lopez-Longo
,
Joaquin Dopazo
,
Marta Forn
,
Miguel A. Peinado
,
Luis Carreño
,
Amr H. Sawalha
,
John B. Harley
,
Reiner Siebert
,
Manel Esteller
,
Frederick W. Miller
,
and
Esteban Ballestar
Genome Res.
February 2010
20
:
170
-
179
;
Published in Advance
December 22, 2009
,
doi:
10.1101/gr.100289.109
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
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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
Abstract
Full Text
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OPEN ACCESS ARTICLE
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