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Table of Contents
June 2009; 19 (6)
Next-Generation DNA Sequencing/Review
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Finding the fifth base: Genome-wide sequencing of cytosine methylation
Ryan Lister
and
Joseph R. Ecker
Genome Res.
June 2009
19
:
959
-
966
;
Published in Advance
March 9, 2009
,
doi:
10.1101/gr.083451.108
Abstract
Full Text
Full Text (PDF)
Letter
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Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes
Michael Y. Tolstorukov
,
Peter V. Kharchenko
,
Joseph A. Goldman
,
Robert E. Kingston
,
and
Peter J. Park
Genome Res.
June 2009
19
:
967
-
977
;
Published in Advance
February 26, 2009
,
doi:
10.1101/gr.084830.108
Abstract
Full Text
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Supplemental Material
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Large-scale mRNA sequencing determines global regulation of RNA editing during brain development
Helene Wahlstedt
,
Chammiran Daniel
,
Mats Ensterö
,
and
Marie Öhman
Genome Res.
June 2009
19
:
978
-
986
;
Published in Advance
May 6, 2009
,
doi:
10.1101/gr.089409.108
Abstract
Full Text
Full Text (PDF)
Supplemental Material
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The colorectal cancer risk at 18q21 is caused by a novel variant altering
SMAD7
expression
Alan M. Pittman
,
Silvia Naranjo
,
Emily Webb
,
Peter Broderick
,
Esther H. Lips
,
Tom van Wezel
,
Hans Morreau
,
Kate Sullivan
,
Sarah Fielding
,
Philip Twiss
,
Jayaram Vijayakrishnan
,
Fernando Casares
,
Mobshra Qureshi
,
José Luis Gómez-Skarmeta
,
and
Richard S. Houlston
Genome Res.
June 2009
19
:
987
-
993
;
Published in Advance
April 24, 2009
,
doi:
10.1101/gr.092668.109
Abstract
Full Text
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Supplemental Material
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Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
Alexander W. Bruce
,
Andrés J. López-Contreras
,
Paul Flicek
,
Thomas A. Down
,
Pawandeep Dhami
,
Shane C. Dillon
,
Christoph M. Koch
,
Cordelia F. Langford
,
Ian Dunham
,
Robert M. Andrews
,
and
David Vetrie
Genome Res.
June 2009
19
:
994
-
1005
;
Published in Advance
April 28, 2009
,
doi:
10.1101/gr.089086.108
Abstract
Full Text
Full Text (PDF)
Supplemental Material
OPEN ACCESS ARTICLE
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Genomic mapping of binding regions for the Ecdysone receptor protein complex
Zareen Gauhar
,
Ling V. Sun
,
Sujun Hua
,
Christopher E. Mason
,
Florian Fuchs
,
Tong-Ruei Li
,
Michael Boutros
,
and
Kevin P. White
Genome Res.
June 2009
19
:
1006
-
1013
;
Published in Advance
February 23, 2009
,
doi:
10.1101/gr.081349.108
Abstract
Full Text
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Supplemental Material
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Dynamic reprogramming of transcription factors to and from the subtelomere
H. Craig Mak
,
Lorraine Pillus
,
and
Trey Ideker
Genome Res.
June 2009
19
:
1014
-
1025
;
Published in Advance
April 16, 2009
,
doi:
10.1101/gr.084178.108
Abstract
Full Text
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Supplemental Material
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Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
Xiyin Wang
,
Haibao Tang
,
John E. Bowers
,
and
Andrew H. Paterson
Genome Res.
June 2009
19
:
1026
-
1032
;
Published in Advance
April 16, 2009
,
doi:
10.1101/gr.087288.108
Abstract
Full Text
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Supplemental Material
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Complete genome of the cellulolytic thermophile
Acidothermus cellulolyticus
11B provides insights into its ecophysiological and evolutionary adaptations
Ravi D. Barabote
,
Gary Xie
,
David H. Leu
,
Philippe Normand
,
Anamaria Necsulea
,
Vincent Daubin
,
Claudine Médigue
,
William S. Adney
,
Xin Clare Xu
,
Alla Lapidus
,
Rebecca E. Parales
,
Chris Detter
,
Petar Pujic
,
David Bruce
,
Celine Lavire
,
Jean F. Challacombe
,
Thomas S. Brettin
,
and
Alison M. Berry
Genome Res.
June 2009
19
:
1033
-
1043
;
Published in Advance
March 6, 2009
,
doi:
10.1101/gr.084848.108
Abstract
Full Text
Full Text (PDF)
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Methods
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Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
Alayne L. Brunner
,
David S. Johnson
,
Si Wan Kim
,
Anton Valouev
,
Timothy E. Reddy
,
Norma F. Neff
,
Elizabeth Anton
,
Catherine Medina
,
Loan Nguyen
,
Eric Chiao
,
Chuba B. Oyolu
,
Gary P. Schroth
,
Devin M. Absher
,
Julie C. Baker
,
and
Richard M. Myers
Genome Res.
June 2009
19
:
1044
-
1056
;
Published in Advance
March 9, 2009
,
doi:
10.1101/gr.088773.108
Abstract
Full Text
Full Text (PDF)
Supplemental Material
OPEN ACCESS ARTICLE
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Integrating siRNA and protein–protein interaction data to identify an expanded insulin signaling network
Zhidong Tu
,
Carmen Argmann
,
Kenny K. Wong
,
Lyndon J. Mitnaul
,
Stephen Edwards
,
Iliana C. Sach
,
Jun Zhu
,
and
Eric E. Schadt
Genome Res.
June 2009
19
:
1057
-
1067
;
Published in Advance
March 4, 2009
,
doi:
10.1101/gr.087890.108
Abstract
Full Text
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Supplemental Material
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High-throughput genotyping by whole-genome resequencing
Xuehui Huang
,
Qi Feng
,
Qian Qian
,
Qiang Zhao
,
Lu Wang
,
Ahong Wang
,
Jianping Guan
,
Danlin Fan
,
Qijun Weng
,
Tao Huang
,
Guojun Dong
,
Tao Sang
,
and
Bin Han
Genome Res.
June 2009
19
:
1068
-
1076
;
Published in Advance
May 6, 2009
,
doi:
10.1101/gr.089516.108
Abstract
Full Text
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Supplemental Material
OPEN ACCESS ARTICLE
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Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing
Danielle V. Irvine
,
Derek B. Goto
,
Matthew W. Vaughn
,
Yukinobu Nakaseko
,
W. Richard McCombie
,
Mitsuhiro Yanagida
,
and
Rob Martienssen
Genome Res.
June 2009
19
:
1077
-
1083
;
Published in Advance
May 7, 2009
,
doi:
10.1101/gr.089318.108
Abstract
Full Text
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Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
Antonin Marchais
,
Magali Naville
,
Chantal Bohn
,
Philippe Bouloc
,
and
Daniel Gautheret
Genome Res.
June 2009
19
:
1084
-
1092
;
Published in Advance
February 23, 2009
,
doi:
10.1101/gr.089714.108
Abstract
Full Text
Full Text (PDF)
Supplemental Material
Resource
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Exploring the human genome with functional maps
Curtis Huttenhower
,
Erin M. Haley
,
Matthew A. Hibbs
,
Vanessa Dumeaux
,
Daniel R. Barrett
,
Hilary A. Coller
,
and
Olga G. Troyanskaya
Genome Res.
June 2009
19
:
1093
-
1106
;
Published in Advance
February 26, 2009
,
doi:
10.1101/gr.082214.108
Abstract
Full Text
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Global networks of functional coupling in eukaryotes from comprehensive data integration
Andrey Alexeyenko
and
Erik L.L. Sonnhammer
Genome Res.
June 2009
19
:
1107
-
1116
;
Published in Advance
February 25, 2009
,
doi:
10.1101/gr.087528.108
Abstract
Full Text
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ABySS: A parallel assembler for short read sequence data
Jared T. Simpson
,
Kim Wong
,
Shaun D. Jackman
,
Jacqueline E. Schein
,
Steven J.M. Jones
,
and
İnanç Birol
Genome Res.
June 2009
19
:
1117
-
1123
;
Published in Advance
February 27, 2009
,
doi:
10.1101/gr.089532.108
Abstract
Full Text
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OPEN ACCESS ARTICLE
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SNP detection for massively parallel whole-genome resequencing
Ruiqiang Li
,
Yingrui Li
,
Xiaodong Fang
,
Huanming Yang
,
Jian Wang
,
Karsten Kristiansen
,
and
Jun Wang
Genome Res.
June 2009
19
:
1124
-
1132
;
Published in Advance
May 6, 2009
,
doi:
10.1101/gr.088013.108
Abstract
Full Text
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High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues
Guo-Jen Huang
,
Sagiv Shifman
,
William Valdar
,
Martina Johannesson
,
Binnaz Yalcin
,
Martin S. Taylor
,
Jennifer M. Taylor
,
Richard Mott
,
and
Jonathan Flint
Genome Res.
June 2009
19
:
1133
-
1140
;
Published in Advance
April 17, 2009
,
doi:
10.1101/gr.088120.108
Abstract
Full Text
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June 2009;
19
(6)
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