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ARTICLE

Pseudomonas aeruginosa" > Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

  • Craig Winstanley
  • Morgan G.I. Langille
  • Joanne L. Fothergill
  • Irena Kukavica-Ibrulj
  • Catherine Paradis-Bleau
  • François Sanschagrin Nicholas R. Thomson Geoff L. Winsor Michael A. Quail Nicola Lennard Alexandra Bignell Louise Clarke Kathy Seeger David Saunders David Harris
  • ... [+10 authors] ...,
  • Julian Parkhill
  • Robert E.W. Hancock
  • Fiona S.L. Brinkman
  • Roger C. Levesque
  • First Published December 1, 2008
ARTICLE

Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation

  • Lili Milani
  • Anders Lundmark
  • Jessica Nordlund
  • Anna Kiialainen
  • Trond Flaegstad
  • Gudmundur Jonmundsson Jukka Kanerva
  • ... [+2 authors] ...,
  • Kjeld Schmiegelow
  • Kevin L. Gunderson
  • Gudmar Lönnerholm
  • Ann-Christine Syvänen
  • First Published November 7, 2008
ARTICLE

Copy number variation and evolution in humans and chimpanzees

  • George H. Perry
  • Fengtang Yang
  • Tomas Marques-Bonet
  • Carly Murphy
  • Tomas Fitzgerald
  • Arthur S. Lee Courtney Hyland Anne C. Stone Matthew E. Hurles Chris Tyler-Smith
  • ... [+5 authors] ...,
  • Evan E. Eichler
  • Nigel P. Carter
  • Charles Lee
  • Richard Redon
  • First Published September 4, 2008
ARTICLE

A code for transcription initiation in mammalian genomes

  • Martin C. Frith
  • Eivind Valen
  • Anders Krogh
  • Yoshihide Hayashizaki
  • Piero Carninci
  • Albin Sandelin
  • First Published November 21, 2007
ARTICLE

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

  • Heidi G. Parker
  • Anna V. Kukekova
  • Dayna T. Akey
  • Orly Goldstein
  • Ewen F. Kirkness
  • Kathleen C. Baysac
  • ... [+1 authors] ...,
  • Dana S. Mosher
  • Gustavo D. Aguirre
  • Gregory M. Acland
  • Elaine A. Ostrander
  • First Published October 4, 2007
ARTICLE

A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

  • Xiaoqin Xu
  • Mark Bieda
  • Victor X. Jin
  • Alina Rabinovich
  • Mathew J. Oberley
  • Roland Green
  • Peggy J. Farnham
  • First Published October 1, 2007
ARTICLE

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

  • Minglei Wang
  • Liudmila S. Yafremava
  • Derek Caetano-Anollés
  • Jay E. Mittenthal
  • Gustavo Caetano-Anollés
  • First Published October 1, 2007
ARTICLE

The anatomy of microbial cell state transitions in response to oxygen

  • Amy K. Schmid
  • David J. Reiss
  • Amardeep Kaur
  • Min Pan
  • Nichole King
  • Phu T. Van
  • Laura Hohmann
  • Daniel B. Martin
  • Nitin S. Baliga
  • First Published September 4, 2007
ARTICLE

Gene copy number variation spanning 60 million years of human and primate evolution

  • Laura Dumas
  • Young H. Kim
  • Anis Karimpour-Fard
  • Michael Cox
  • Janet Hopkins
  • Jonathan R. Pollack
  • James M. Sikela
  • First Published July 31, 2007
ARTICLE

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates

  • Yoichiro Nakatani
  • Hiroyuki Takeda
  • Yuji Kohara
  • Shinichi Morishita
  • First Published July 25, 2007
ARTICLE

A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids

  • Daria V. Babushok
  • Kazuhiko Ohshima
  • Eric M. Ostertag
  • Xinsheng Chen
  • Yanfeng Wang
  • Prabhat K. Mandal
  • Norihiro Okada
  • Charles S. Abrams
  • Haig H. Kazazian
  • First Published July 10, 2007
ARTICLE

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

  • Alvaro Rada-Iglesias
  • Stefan Enroth
  • Adam Ameur
  • Christoph M. Koch
  • Gayle K. Clelland
  • Patricia Respuela-Alonso Sarah Wilcox Oliver M. Dovey Peter D. Ellis
  • ... [+4 authors] ...,
  • Cordelia F. Langford
  • Ian Dunham
  • Jan Komorowski
  • Claes Wadelius
  • First Published June 13, 2007
ARTICLE

The landscape of histone modifications across 1% of the human genome in five human cell lines

  • Christoph M. Koch
  • Robert M. Andrews
  • Paul Flicek
  • Shane C. Dillon
  • Ulaş Karaöz
  • Gayle K. Clelland Sarah Wilcox David M. Beare Joanna C. Fowler Phillippe Couttet Keith D. James Gregory C. Lefebvre Alexander W. Bruce Oliver M. Dovey Peter D. Ellis Pawandeep Dhami Cordelia F. Langford Zhiping Weng
  • ... [+13 authors] ...,
  • Ewan Birney
  • Nigel P. Carter
  • David Vetrie
  • Ian Dunham
  • First Published June 13, 2007
ARTICLE

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

  • Joel S. Rozowsky
  • Daniel Newburger
  • Fred Sayward
  • Jiaqian Wu
  • Greg Jordan
  • Jan O. Korbel Ugrappa Nagalakshmi Jin Yang Deyou Zheng Roderic Guigó Thomas R. Gingeras
  • ... [+6 authors] ...,
  • Sherman Weissman
  • Perry Miller
  • Michael Snyder
  • Mark B. Gerstein
  • First Published June 13, 2007
ARTICLE

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

  • Nathan D. Trinklein
  • Ulaş Karaöz
  • Jiaqian Wu
  • Anason Halees
  • Shelley Force Aldred
  • Patrick J. Collins Deyou Zheng Zhengdong D. Zhang
  • ... [+3 authors] ...,
  • Mark B. Gerstein
  • Michael Snyder
  • Richard M. Myers
  • Zhiping Weng
  • First Published June 13, 2007
ARTICLE

Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions

  • France Denoeud
  • Philipp Kapranov
  • Catherine Ucla
  • Adam Frankish
  • Robert Castelo
  • Jorg Drenkow Julien Lagarde Tyler Alioto Caroline Manzano Jacqueline Chrast Sujit Dike Carine Wyss Charlotte N. Henrichsen Nancy Holroyd Mark C. Dickson Ruth Taylor Zahra Hance Sylvain Foissac Richard M. Myers Jane Rogers Tim Hubbard Jennifer Harrow
  • ... [+17 authors] ...,
  • Roderic Guigó
  • Thomas R. Gingeras
  • Stylianos E. Antonarakis
  • Alexandre Reymond
  • First Published June 13, 2007
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
  • ... [+68 authors] ...,
  • Webb Miller
  • Lior Pachter
  • Eric D. Green
  • Arend Sidow
  • First Published June 13, 2007
ARTICLE

Darc) as a BMD QTL gene" > Identification of mouse Duffy Antigen Receptor for Chemokines (Darc) as a BMD QTL gene

  • Bouchra Edderkaoui
  • David J. Baylink
  • Wesley G. Beamer
  • Jon E. Wergedal
  • Ryan Porte
  • Asok Chaudhuri
  • Subburaman Mohan
  • First Published April 6, 2007
ARTICLE

Min 2 (Mom2) locus: Embryonic lethality of a mutation in the Atp5a1 gene suggests a novel mechanism of polyp suppression" > The modifier of Min 2 (Mom2) locus: Embryonic lethality of a mutation in the Atp5a1 gene suggests a novel mechanism of polyp suppression

  • Amy A. Baran
  • Karen A. Silverman
  • Joseph Zeskand
  • Revati Koratkar
  • Ashley Palmer
  • Kristen McCullen
  • ... [+1 authors] ...,
  • Walter J. Curran
  • Tina Bocker Edmonston
  • Linda D. Siracusa
  • Arthur M. Buchberg
  • First Published March 26, 2007
ARTICLE

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates

  • Hiroshi Kikuta
  • Mary Laplante
  • Pavla Navratilova
  • Anna Z. Komisarczuk
  • Pär G. Engström
  • David Fredman Altuna Akalin Mario Caccamo Ian Sealy Kerstin Howe Julien Ghislain Guillaume Pezeron Philippe Mourrain Staale Ellingsen Andrew C. Oates Christine Thisse Bernard Thisse Isabelle Foucher
  • ... [+13 authors] ...,
  • Birgit Adolf
  • Andrea Geling
  • Boris Lenhard
  • Thomas S. Becker
  • First Published March 26, 2007
ARTICLE

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

  • Jasmina Ponjavic
  • Chris P. Ponting
  • Gerton Lunter
  • First Published March 26, 2007
ARTICLE

Frankia sp. strains reflect host range and host plant biogeography" > Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

  • Philippe Normand
  • Pascal Lapierre
  • Louis S. Tisa
  • Johann Peter Gogarten
  • Nicole Alloisio
  • Emilie Bagnarol Carla A. Bassi Alison M. Berry Derek M. Bickhart Nathalie Choisne Arnaud Couloux Benoit Cournoyer Stephane Cruveiller Vincent Daubin Nadia Demange Maria Pilar Francino Eugene Goltsman Ying Huang Olga R. Kopp Laurent Labarre Alla Lapidus Celine Lavire Joelle Marechal Michele Martinez Juliana E. Mastronunzio Beth C. Mullin James Niemann Pierre Pujic Tania Rawnsley Zoe Rouy Chantal Schenowitz Anita Sellstedt Fernando Tavares Jeffrey P. Tomkins David Vallenet Claudio Valverde
  • ... [+31 authors] ...,
  • Luis G. Wall
  • Ying Wang
  • Claudine Medigue
  • David R. Benson
  • First Published December 6, 2006
ARTICLE

Phytophthora" > Amplification generates modular diversity at an avirulence locus in the pathogen Phytophthora

  • Rays H.Y. Jiang
  • Rob Weide
  • Peter J.I. van de Vondervoort
  • Francine Govers
  • First Published July 3, 2006
ARTICLE

Extensive low-affinity transcriptional interactions in the yeast genome

  • Amos Tanay
  • First Published June 29, 2006
ARTICLE

Genomic organization of the sex-determining and adjacent regions of the sex chromosomes of medaka

  • Mariko Kondo
  • Ute Hornung
  • Indrajit Nanda
  • Shuichiro Imai
  • Takashi Sasaki
  • Atsushi Shimizu Shuichi Asakawa
  • ... [+2 authors] ...,
  • Hiroshi Hori
  • Michael Schmid
  • Nobuyoshi Shimizu
  • Manfred Schartl
  • First Published June 2, 2006
ARTICLE

A systems view of haloarchaeal strategies to withstand stress from transition metals

  • Amardeep Kaur
  • Min Pan
  • Megan Meislin
  • Marc T. Facciotti
  • Raafat El-Gewely
  • Nitin S. Baliga
  • First Published June 2, 2006
ARTICLE

A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome

  • Mizuki Ohno
  • Tomofumi Miura
  • Masato Furuichi
  • Yohei Tominaga
  • Daisuke Tsuchimoto
  • Kunihiko Sakumi
  • Yusaku Nakabeppu
  • First Published May 1, 2006
ARTICLE

Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis

  • Gayle K. McEwen
  • Adam Woolfe
  • Debbie Goode
  • Tanya Vavouri
  • Heather Callaway
  • Greg Elgar
  • First Published March 13, 2006
ARTICLE

Drosophila retinal determination protein Eyeless" > Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless

  • Edwin J. Ostrin
  • Yumei Li
  • Kristi Hoffman
  • Jing Liu
  • Keqing Wang
  • Li Zhang
  • Graeme Mardon
  • Rui Chen
  • First Published March 13, 2006
ARTICLE

Sodalis glossinidius in the tsetse host" > Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host

  • Hidehiro Toh
  • Brian L. Weiss
  • Sarah A.H. Perkin
  • Atsushi Yamashita
  • Kenshiro Oshima
  • Masahira Hattori
  • Serap Aksoy
  • First Published December 19, 2005
ARTICLE

Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression" > Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression

  • Wei Deng
  • Xiaopeng Zhu
  • Geir Skogerbø
  • Yi Zhao
  • Zhuo Fu
  • Yudong Wang Housheng He Lun Cai Hong Sun Changning Liu Biao Li Baoyan Bai Jie Wang Dong Jia Shiwei Sun Hang He
  • ... [+11 authors] ...,
  • Yan Cui
  • Yu Wang
  • Dongbo Bu
  • Runsheng Chen
  • First Published December 12, 2005
ARTICLE

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

  • Timothy Ravasi
  • Harukazu Suzuki
  • Ken C. Pang
  • Shintaro Katayama
  • Masaaki Furuno
  • Rie Okunishi Shiro Fukuda Kelin Ru Martin C. Frith M. Milena Gongora
  • ... [+5 authors] ...,
  • Sean M. Grimmond
  • David A. Hume
  • Yoshihide Hayashizaki
  • John S. Mattick
  • First Published December 12, 2005
ARTICLE

Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome

  • Sara J. Cooper
  • Nathan D. Trinklein
  • Elizabeth D. Anton
  • Loan Nguyen
  • Richard M. Myers
  • First Published December 12, 2005
ARTICLE

SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27" > Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27

  • Natalay Kouprina
  • Adam Pavlicek
  • Vladimir N. Noskov
  • Greg Solomon
  • John Otstot
  • William Isaacs John D. Carpten Jeffrey M. Trent
  • ... [+3 authors] ...,
  • Joanna Schleutker
  • J. Carl Barrett
  • Jerzy Jurka
  • Vladimir Larionov
  • First Published October 26, 2005
ARTICLE

Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome

  • Adam Pavlicek
  • Reniqua House
  • Andrew J. Gentles
  • Jerzy Jurka
  • Bernice E. Morrow
  • First Published October 26, 2005
ARTICLE

Measures of human population structure show heterogeneity among genomic regions

  • Bruce S. Weir
  • Lon R. Cardon
  • Amy D. Anderson
  • Dahlia M. Nielsen
  • William G. Hill
  • First Published October 26, 2005
ARTICLE

Natronomonas pharaonis" > Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis

  • Michaela Falb
  • Friedhelm Pfeiffer
  • Peter Palm
  • Karin Rodewald
  • Volker Hickmann
  • Jörg Tittor
  • Dieter Oesterhelt
  • First Published September 16, 2005
ARTICLE

De novo discovery of a tissue-specific gene regulatory module in a chordate

  • David S. Johnson
  • Qing Zhou
  • Kasumi Yagi
  • Nori Satoh
  • Wing Wong
  • Arend Sidow
  • First Published September 16, 2005
ARTICLE

Pseudoalteromonas haloplanktis TAC125" > Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125

  • Claudine Médigue
  • Evelyne Krin
  • Géraldine Pascal
  • Valérie Barbe
  • Andreas Bernsel
  • Philippe N. Bertin Frankie Cheung Stéphane Cruveiller Salvino D'Amico Angela Duilio Gang Fang Georges Feller Christine Ho Sophie Mangenot Gennaro Marino Johan Nilsson Ermenegilda Parrilli Eduardo P.C. Rocha Zoé Rouy Agnieszka Sekowska
  • ... [+15 authors] ...,
  • Maria Luisa Tutino
  • David Vallenet
  • Gunnar von Heijne
  • Antoine Danchin
  • First Published September 16, 2005
ARTICLE

Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23

  • Anna Antonell
  • Oscar de Luis
  • Xavier Domingo-Roura
  • Luis Alberto Pérez-Jurado
  • First Published September 1, 2005
ARTICLE

ATG deserts define a novel core promoter subclass

  • Maxwell P. Lee
  • Kevin Howcroft
  • Aparna Kotekar
  • Howard H. Yang
  • Kenneth H. Buetow
  • Dinah S. Singer
  • First Published August 18, 2005
ARTICLE

Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy" > Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy

  • Junkang Rong
  • John E. Bowers
  • Stefan R. Schulze
  • Vijay N. Waghmare
  • Carl J. Rogers
  • Gary J. Pierce
  • Hua Zhang
  • James C. Estill
  • Andrew H. Paterson
  • First Published August 18, 2005
ARTICLE

Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects" > Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects

  • Patrick H. Degnan
  • Adam B. Lazarus
  • Jennifer J. Wernegreen
  • First Published August 2, 2005
ARTICLE

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

  • Adam Siepel
  • Gill Bejerano
  • Jakob S. Pedersen
  • Angie S. Hinrichs
  • Minmei Hou
  • Kate Rosenbloom Hiram Clawson John Spieth LaDeana W. Hillier Stephen Richards George M. Weinstock Richard K. Wilson
  • ... [+7 authors] ...,
  • Richard A. Gibbs
  • W. James Kent
  • Webb Miller
  • David Haussler
  • First Published July 15, 2005
ARTICLE

Distribution and intensity of constraint in mammalian genomic sequence

  • Gregory M. Cooper
  • Eric A. Stone
  • George Asimenos
  • Eric D. Green
  • Serafim Batzoglou
  • Arend Sidow
  • First Published June 17, 2005
ARTICLE

Dichotomous splicing signals in exon flanks

  • Xiang H-F. Zhang
  • Christina S. Leslie
  • Lawrence A. Chasin
  • First Published June 1, 2005
ARTICLE

Xanthomonas campestris pv. campestris" > Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris

  • Wei Qian
  • Yantao Jia
  • Shuang-Xi Ren
  • Yong-Qiang He
  • Jia-Xun Feng
  • Ling-Feng Lu Qihong Sun Ge Ying Dong-Jie Tang Hua Tang Wei Wu Pei Hao Lifeng Wang Bo-Le Jiang Shenyan Zeng Wen-Yi Gu Gang Lu Li Rong Yingchuan Tian Zhijian Yao Gang Fu Baoshan Chen Rongxiang Fang Boqin Qiang
  • ... [+19 authors] ...,
  • Zhu Chen
  • Guo-Ping Zhao
  • Ji-Liang Tang
  • Chaozu He
  • First Published May 17, 2005
ARTICLE

Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants

  • Christos Noutsos
  • Erik Richly
  • Dario Leister
  • First Published May 2, 2005
ARTICLE

C. elegans daf-2 mutants using serial analysis of gene expression" > Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression

  • Julius Halaschek-Wiener
  • Jaswinder S. Khattra
  • Sheldon McKay
  • Anatoli Pouzyrev
  • Jeff M. Stott
  • George S. Yang Robert A. Holt
  • ... [+2 authors] ...,
  • Steven J.M. Jones
  • Marco A. Marra
  • Angela R. Brooks-Wilson
  • Donald L. Riddle
  • First Published April 18, 2005
ARTICLE

Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation" > The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation

  • Nicholas R. Thomson
  • Corin Yeats
  • Kenneth Bell
  • Matthew T.G. Holden
  • Stephen D. Bentley
  • Morag Livingstone Ana M. Cerdeño-Tárraga Barbara Harris Jon Doggett Doug Ormond Karen Mungall Kay Clarke Theresa Feltwell Zahra Hance Mandy Sanders Michael A. Quail
  • ... [+11 authors] ...,
  • Claire Price
  • Bart G. Barrell
  • Julian Parkhill
  • David Longbottom
  • First Published April 18, 2005
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