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Table of Contents
December 2009; 19 (12)
Article
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Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
Timothy E. Reddy
,
Florencia Pauli
,
Rebekka O. Sprouse
,
Norma F. Neff
,
Kimberly M. Newberry
,
Michael J. Garabedian
,
and
Richard M. Myers
Genome Res.
December 2009
19
:
2163
-
2171
;
Published in Advance
October 2, 2009
,
doi:
10.1101/gr.097022.109
Abstract
Full Text
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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
Full Text
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Letter
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Human capacitance to dosage imbalance: Coping with inefficient selection
Ariel Fernández
and
Jianping Chen
Genome Res.
December 2009
19
:
2185
-
2192
;
Published in Advance
October 9, 2009
,
doi:
10.1101/gr.094441.109
Abstract
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DNA methylation programming and reprogramming in primate embryonic stem cells
Netta Mendelson Cohen
,
Vikas Dighe
,
Gilad Landan
,
Sigrún Reynisdóttir
,
Arnar Palsson
,
Shoukhrat Mitalipov
,
and
Amos Tanay
Genome Res.
December 2009
19
:
2193
-
2201
;
Published in Advance
November 3, 2009
,
doi:
10.1101/gr.096685.109
Abstract
Full Text
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Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability
Mark D. Pertile
,
Alison N. Graham
,
K.H. Andy Choo
,
and
Paul Kalitsis
Genome Res.
December 2009
19
:
2202
-
2213
;
Published in Advance
September 8, 2009
,
doi:
10.1101/gr.092080.109
Abstract
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Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
Itai Yanai
and
Craig P. Hunter
Genome Res.
December 2009
19
:
2214
-
2220
;
Published in Advance
September 10, 2009
,
doi:
10.1101/gr.093815.109
Abstract
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Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?
Zhixi Tian
,
Carene Rizzon
,
Jianchang Du
,
Liucun Zhu
,
Jeffrey L. Bennetzen
,
Scott A. Jackson
,
Brandon S. Gaut
,
and
Jianxin Ma
Genome Res.
December 2009
19
:
2221
-
2230
;
Published in Advance
September 29, 2009
,
doi:
10.1101/gr.083899.108
Abstract
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Comparative genomics of the fungal pathogens
Candida dubliniensis
and
Candida albicans
Andrew P. Jackson
,
John A. Gamble
,
Tim Yeomans
,
Gary P. Moran
,
David Saunders
,
David Harris
,
Martin Aslett
,
Jamie F. Barrell
,
Geraldine Butler
,
Francesco Citiulo
,
David C. Coleman
,
Piet W.J. de Groot
,
Tim J. Goodwin
,
Michael A. Quail
,
Jacqueline McQuillan
,
Carol A. Munro
,
Arnab Pain
,
Russell T. Poulter
,
Marie-Adèle Rajandream
,
Hubert Renauld
,
Martin J. Spiering
,
Adrian Tivey
,
Neil A.R. Gow
,
Barclay Barrell
,
Derek J. Sullivan
,
and
Matthew Berriman
Genome Res.
December 2009
19
:
2231
-
2244
;
Published in Advance
September 10, 2009
,
doi:
10.1101/gr.097501.109
Abstract
Full Text
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A positive but complex association between meiotic double-strand break hotspots and open chromatin in
Saccharomyces cerevisiae
Luke E. Berchowitz
,
Sean E. Hanlon
,
Jason D. Lieb
,
and
Gregory P. Copenhaver
Genome Res.
December 2009
19
:
2245
-
2257
;
Published in Advance
October 2, 2009
,
doi:
10.1101/gr.096297.109
Abstract
Full Text
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Genome structure of a
Saccharomyces cerevisiae
strain widely used in bioethanol production
Juan Lucas Argueso
,
Marcelo F. Carazzolle
,
Piotr A. Mieczkowski
,
Fabiana M. Duarte
,
Osmar V.C. Netto
,
Silvia K. Missawa
,
Felipe Galzerani
,
Gustavo G.L. Costa
,
Ramon O. Vidal
,
Melline F. Noronha
,
Margaret Dominska
,
Maria G.S. Andrietta
,
Sílvio R. Andrietta
,
Anderson F. Cunha
,
Luiz H. Gomes
,
Flavio C.A. Tavares
,
André R. Alcarde
,
Fred S. Dietrich
,
John H. McCusker
,
Thomas D. Petes
,
and
Gonçalo A.G. Pereira
Genome Res.
December 2009
19
:
2258
-
2270
;
Published in Advance
October 7, 2009
,
doi:
10.1101/gr.091777.109
Abstract
Full Text
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Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis
Boris U. Stambuk
,
Barbara Dunn
,
Sergio L. Alves, Jr
,
Eduarda H. Duval
,
and
Gavin Sherlock
Genome Res.
December 2009
19
:
2271
-
2278
;
Published in Advance
November 6, 2009
,
doi:
10.1101/gr.094276.109
Abstract
Full Text
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Epidemic multiple drug resistant
Salmonella
Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
Robert A. Kingsley
,
Chisomo L. Msefula
,
Nicholas R. Thomson
,
Samuel Kariuki
,
Kathryn E. Holt
,
Melita A. Gordon
,
David Harris
,
Louise Clarke
,
Sally Whitehead
,
Vartul Sangal
,
Kevin Marsh
,
Mark Achtman
,
Malcolm E. Molyneux
,
Martin Cormican
,
Julian Parkhill
,
Calman A. MacLennan
,
Robert S. Heyderman
,
and
Gordon Dougan
Genome Res.
December 2009
19
:
2279
-
2287
;
Published in Advance
November 9, 2009
,
doi:
10.1101/gr.091017.109
Abstract
Full Text
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Methods
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Predictable dynamic program of timing of DNA replication in human cells
Romain Desprat
,
Danielle Thierry-Mieg
,
Nathalie Lailler
,
Julien Lajugie
,
Carl Schildkraut
,
Jean Thierry-Mieg
,
and
Eric E. Bouhassira
Genome Res.
December 2009
19
:
2288
-
2299
;
Published in Advance
September 18, 2009
,
doi:
10.1101/gr.094060.109
Abstract
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Two-parameter characterization of chromosome-scale recombination rate
Wentian Li
and
Jan Freudenberg
Genome Res.
December 2009
19
:
2300
-
2307
;
Published in Advance
September 14, 2009
,
doi:
10.1101/gr.092676.109
Abstract
Full Text
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Simultaneous assay of every
Salmonella
Typhi gene using one million transposon mutants
Gemma C. Langridge
,
Minh-Duy Phan
,
Daniel J. Turner
,
Timothy T. Perkins
,
Leopold Parts
,
Jana Haase
,
Ian Charles
,
Duncan J. Maskell
,
Sarah E. Peters
,
Gordon Dougan
,
John Wain
,
Julian Parkhill
,
and
A. Keith Turner
Genome Res.
December 2009
19
:
2308
-
2316
;
Published in Advance
October 13, 2009
,
doi:
10.1101/gr.097097.109
Abstract
Full Text
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Resource
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The NIH Human Microbiome Project
The NIH HMP Working Group
,
Jane Peterson
,
Susan Garges
,
Maria Giovanni
,
Pamela McInnes
,
Lu Wang
,
Jeffery A. Schloss
,
Vivien Bonazzi
,
Jean E. McEwen
,
Kris A. Wetterstrand
,
Carolyn Deal
,
Carl C. Baker
,
Valentina Di Francesco
,
T. Kevin Howcroft
,
Robert W. Karp
,
R. Dwayne Lunsford
,
Christopher R. Wellington
,
Tsegahiwot Belachew
,
Michael Wright
,
Christina Giblin
,
Hagit David
,
Melody Mills
,
Rachelle Salomon
,
Christopher Mullins
,
Beena Akolkar
,
Lisa Begg
,
Cindy Davis
,
Lindsey Grandison
,
Michael Humble
,
Jag Khalsa
,
A. Roger Little
,
Hannah Peavy
,
Carol Pontzer
,
Matthew Portnoy
,
Michael H. Sayre
,
Pamela Starke-Reed
,
Samir Zakhari
,
Jennifer Read
,
Bracie Watson
,
and
Mark Guyer
Genome Res.
December 2009
19
:
2317
-
2323
;
Published in Advance
October 9, 2009
,
doi:
10.1101/gr.096651.109
Abstract
Full Text
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The completion of the Mammalian Gene Collection (MGC)
The MGC Project Team
,
Gary Temple
,
Daniela S. Gerhard
,
Rebekah Rasooly
,
Elise A. Feingold
,
Peter J. Good
,
Cristen Robinson
,
Allison Mandich
,
Jeffrey G. Derge
,
Jeanne Lewis
,
Debonny Shoaf
,
Francis S. Collins
,
Wonhee Jang
,
Lukas Wagner
,
Carolyn M. Shenmen
,
Leonie Misquitta
,
Carl F. Schaefer
,
Kenneth H. Buetow
,
Tom I. Bonner
,
Linda Yankie
,
Ming Ward
,
Lon Phan
,
Alex Astashyn
,
Garth Brown
,
Catherine Farrell
,
Jennifer Hart
,
Melissa Landrum
,
Bonnie L. Maidak
,
Michael Murphy
,
Terence Murphy
,
Bhanu Rajput
,
Lillian Riddick
,
David Webb
,
Janet Weber
,
Wendy Wu
,
Kim D. Pruitt
,
Donna Maglott
,
Adam Siepel
,
Brona Brejova
,
Mark Diekhans
,
Rachel Harte
,
Robert Baertsch
,
Jim Kent
,
David Haussler
,
Michael Brent
,
Laura Langton
,
Charles L.G. Comstock
,
Michael Stevens
,
Chaochun Wei
,
Marijke J. van Baren
,
Kourosh Salehi-Ashtiani
,
Ryan R. Murray
,
Lila Ghamsari
,
Elizabeth Mello
,
Chenwei Lin
,
Christa Pennacchio
,
Kirsten Schreiber
,
Nicole Shapiro
,
Amber Marsh
,
Elizabeth Pardes
,
Troy Moore
,
Anita Lebeau
,
Mike Muratet
,
Blake Simmons
,
David Kloske
,
Stephanie Sieja
,
James Hudson
,
Praveen Sethupathy
,
Michael Brownstein
,
Narayan Bhat
,
Joseph Lazar
,
Howard Jacob
,
Chris E. Gruber
,
Mark R. Smith
,
John McPherson
,
Angela M. Garcia
,
Preethi H. Gunaratne
,
Jiaqian Wu
,
Donna Muzny
,
Richard A. Gibbs
,
Alice C. Young
,
Gerard G. Bouffard
,
Robert W. Blakesley
,
Jim Mullikin
,
Eric D. Green
,
Mark C. Dickson
,
Alex C. Rodriguez
,
Jane Grimwood
,
Jeremy Schmutz
,
Richard M. Myers
,
Martin Hirst
,
Thomas Zeng
,
Kane Tse
,
Michelle Moksa
,
Merinda Deng
,
Kevin Ma
,
Diana Mah
,
Johnson Pang
,
Greg Taylor
,
Eric Chuah
,
Athena Deng
,
Keith Fichter
,
Anne Go
,
Stephanie Lee
,
Jing Wang
,
Malachi Griffith
,
Ryan Morin
,
Richard A. Moore
,
Michael Mayo
,
Sarah Munro
,
Susan Wagner
,
Steven J.M. Jones
,
Robert A. Holt
,
Marco A. Marra
,
Sun Lu
,
Shuwei Yang
,
James Hartigan
,
Marcus Graf
,
Ralf Wagner
,
Stanley Letovksy
,
Jacqueline C. Pulido
,
Keith Robison
,
Dominic Esposito
,
James Hartley
,
Vanessa E. Wall
,
Ralph F. Hopkins
,
Osamu Ohara
,
and
Stefan Wiemann
Genome Res.
December 2009
19
:
2324
-
2333
;
Published in Advance
September 18, 2009
,
doi:
10.1101/gr.095976.109
Abstract
Full Text
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Large-scale RACE approach for proactive experimental definition of
C. elegans
ORFeome
Kourosh Salehi-Ashtiani
,
Chenwei Lin
,
Tong Hao
,
Yun Shen
,
David Szeto
,
Xinping Yang
,
Lila Ghamsari
,
HanJoo Lee
,
Changyu Fan
,
Ryan R. Murray
,
Stuart Milstein
,
Nenad Svrzikapa
,
Michael E. Cusick
,
Frederick P. Roth
,
David E. Hill
,
and
Marc Vidal
Genome Res.
December 2009
19
:
2334
-
2342
;
Published in Advance
October 2, 2009
,
doi:
10.1101/gr.098640.109
Abstract
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Errata
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Errata
Genome Res.
December 2009
19
:
2343
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December 2009;
19
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