Search | Genome Research

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

ARTICLE

Retroviruses and yeast retrotransposons use overlapping sets of host genes

Becky Irwin
Michael Aye
Pierre Baldi
Nadejda Beliakova-Bethell
Henry Cheng
Yimeng Dou
Willy Liou
Suzanne Sandmeyer

First Published April 18, 2005

ARTICLE

Gerbera hybrida (Asteraceae)" > Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae)

Roosa A.E. Laitinen
Juha Immanen
Petri Auvinen
Stephen Rudd
Edward Alatalo
Lars Paulin Miia Ainasoja
... [+2 authors] ...,
Mika Kotilainen
Satu Koskela
Teemu H. Teeri
Paula Elomaa

First Published March 21, 2005

ARTICLE

Disclosing hidden transcripts: Mouse natural sense–antisense transcripts tend to be poly(A) negative and nuclear localized

Hidenori Kiyosawa
Nathan Mise
Shigeru Iwase
Yoshihide Hayashizaki
Kuniya Abe

First Published March 21, 2005

ARTICLE

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

Francisco M. De La Vega
Hadar Isaac
Andrew Collins
Charles R. Scafe
Bjarni V. Halldórsson
Xiaoping Su Ross A. Lippert Yu Wang Marion Laig-Webster Ryan T. Koehler Janet S. Ziegle Lewis T. Wogan Junko F. Stevens Kyle M. Leinen Sheri J. Olson Karl J. Guegler Xiaoqing You Lily H. Xu Heinz G. Hemken Francis Kalush Mitsuo Itakura Yi Zheng Guy de Thé Stephen J. O'Brien Andrew G. Clark
... [+20 authors] ...,
Sorin Istrail
Michael W. Hunkapiller
Eugene G. Spier
Dennis A. Gilbert

First Published March 21, 2005

ARTICLE

Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes" > Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes

Toshiaki Fukui
Haruyuki Atomi
Tamotsu Kanai
Rie Matsumi
Shinsuke Fujiwara
Tadayuki Imanaka

First Published February 14, 2005

ARTICLE

Complex genomic rearrangements lead to novel primate gene function

Francesca D. Ciccarelli
Christian von Mering
Mikita Suyama
Eoghan D. Harrington
Elisa Izaurralde
Peer Bork

First Published February 14, 2005

ARTICLE

Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence

Chen-Shan Chin
Jeffrey H. Chuang
Hao Li

First Published January 14, 2005

ARTICLE

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

Stefan Kirsch
Birgit Weiß
Tracie L. Miner
Robert H. Waterston
Royden A. Clark
Evan E. Eichler
Claudia Münch
Werner Schempp
Gudrun Rappold

First Published January 14, 2005

ARTICLE

Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution" > Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

Stephen Richards
Yue Liu
Brian R. Bettencourt
Pavel Hradecky
Stan Letovsky
Rasmus Nielsen Kevin Thornton Melissa J. Hubisz Rui Chen Richard P. Meisel Olivier Couronne Sujun Hua Mark A. Smith Peili Zhang Jing Liu Harmen J. Bussemaker Marinus F. van Batenburg Sally L. Howells Steven E. Scherer Erica Sodergren Beverly B. Matthews Madeline A. Crosby Andrew J. Schroeder Daniel Ortiz-Barrientos Catharine M. Rives Michael L. Metzker Donna M. Muzny Graham Scott David Steffen David A. Wheeler Kim C. Worley Paul Havlak K. James Durbin Amy Egan Rachel Gill Jennifer Hume Margaret B. Morgan George Miner Cerissa Hamilton Yanmei Huang Lenée Waldron Daniel Verduzco Kerstin P. Clerc-Blankenburg Inna Dubchak Mohamed A.F. Noor Wyatt Anderson Kevin P. White Andrew G. Clark
... [+43 authors] ...,
Stephen W. Schaeffer
William Gelbart
George M. Weinstock
Richard A. Gibbs

First Published January 3, 2005

ARTICLE

A survey of RNA editing in human brain

Matthew Blow
P. Andrew Futreal
Richard Wooster
Michael R. Stratton

First Published November 15, 2004

ARTICLE

Coelacanth genome sequence reveals the evolutionary history of vertebrate genes

James P. Noonan
Jane Grimwood
Joshua Danke
Jeremy Schmutz
Mark Dickson
Chris T. Amemiya
Richard M. Myers

First Published November 15, 2004

ARTICLE

Canis familiaris" > Extensive and breed-specific linkage disequilibrium in Canis familiaris

Nathan B. Sutter
Michael A. Eberle
Heidi G. Parker
Barbara J. Pullar
Ewen F. Kirkness
Leonid Kruglyak
Elaine A. Ostrander

First Published November 15, 2004

ARTICLE

Serial segmental duplications during primate evolution result in complex human genome architecture

Paweł Stankiewicz
Christine J. Shaw
Marjorie Withers
Ken Inoue
James R. Lupski

First Published November 1, 2004

ARTICLE

Haloarcula marismortui: A halophilic archaeon from the Dead Sea" > Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea

Nitin S. Baliga
Richard Bonneau
Marc T. Facciotti
Min Pan
Gustavo Glusman
Eric W. Deutsch Paul Shannon Yulun Chiu Rueyhung Sting Weng Rueichi Richie Gan Pingliang Hung
... [+6 authors] ...,
Shailesh V. Date
Edward Marcotte
Leroy Hood
Wailap Victor Ng

First Published November 1, 2004

ARTICLE

Pattern of Sequence Variation Across 213 Environmental Response Genes

Robert J. Livingston
Andrew von Niederhausern
Anil G. Jegga
Dana C. Crawford
Christopher S. Carlson
Mark J. Rieder
... [+1 authors] ...,
Sivakumar Gowrisankar
Bruce J. Aronow
Robert B. Weiss
Deborah A. Nickerson

First Published September 13, 2004

ARTICLE

Regional Patterns of Gene Expression in Human and Chimpanzee Brains

Philipp Khaitovich
Bjoern Muetzel
Xinwei She
Michael Lachmann
Ines Hellmann
Janko Dietzsch Stephan Steigele Hong-Hai Do Gunter Weiss Wolfgang Enard Florian Heissig
... [+6 authors] ...,
Thomas Arendt
Kay Nieselt-Struwe
Evan E. Eichler
Svante Pääbo

First Published August 2, 2004

ARTICLE

Mycoplasma mobile" > The Complete Genome and Proteome of Mycoplasma mobile

Jacob D. Jaffe
Nicole Stange-Thomann
Cherylyn Smith
David DeCaprio
Sheila Fisher
Jonathan Butler Sarah Calvo Tim Elkins Michael G. FitzGerald Nabil Hafez Chinnappa D. Kodira John Major Shunguang Wang Jane Wilkinson Robert Nicol
... [+10 authors] ...,
Chad Nusbaum
Bruce Birren
Howard C. Berg
George M. Church

First Published August 2, 2004

ARTICLE

Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution" > A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution

Soochin Cho
Suk-Won Jin
Adam Cohen
Ronald E. Ellis

First Published July 1, 2004

ARTICLE

The Insertional History of an Active Family of L1 Retrotransposons in Humans

Stéphane Boissinot
Ali Entezam
Lynn Young
Peter J. Munson
Anthony V. Furano

First Published June 14, 2004

ARTICLE

Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes" > The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes

Bill Wickstead
Klaus Ersfeld
Keith Gull

First Published June 1, 2004

ARTICLE

Genomic Regionality in Rates of Evolution Is Not Explained by Clustering of Genes of Comparable Expression Profile

Martin J. Lercher
Jean-Vincent Chamary
Laurence D. Hurst

First Published June 1, 2004

ARTICLE

The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint

Cristian I. Castillo-Davis
Fyodor A. Kondrashov
Daniel L. Hartl
Rob J. Kulathinal

First Published May 3, 2004

ARTICLE

Analysis of Segmental Duplications and Genome Assembly in the Mouse

Jeffrey A. Bailey
Deanna M. Church
Mario Ventura
Mariano Rocchi
Evan E. Eichler

First Published May 3, 2004

ARTICLE

Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes

Shan Yang
Arian F. Smit
Scott Schwartz
Francesca Chiaromonte
Krishna M. Roskin
David Haussler
Webb Miller
Ross C. Hardison

First Published April 1, 2004

ARTICLE

Comparative Recombination Rates in the Rat, Mouse, and Human Genomes

Michael I. Jensen-Seaman
Terrence S. Furey
Bret A. Payseur
Yontao Lu
Krishna M. Roskin
Chin-Fu Chen
Michael A. Thomas
David Haussler
Howard J. Jacob

First Published April 1, 2004

ARTICLE

Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat

Eray Tuzun
Jeffrey A. Bailey
Evan E. Eichler

First Published April 1, 2004

ARTICLE

Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes

Guillaume Bourque
Pavel A. Pevzner
Glenn Tesler

First Published April 1, 2004

ARTICLE

Comparative Analysis of Protein Domain Organization

Yuzhen Ye
Adam Godzik

First Published March 1, 2004

ARTICLE

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

Dione Kampa
Jill Cheng
Philipp Kapranov
Mark Yamanaka
Shane Brubaker
Simon Cawley Jorg Drenkow Antonio Piccolboni
... [+3 authors] ...,
Stefan Bekiranov
Gregg Helt
Hari Tammana
Thomas R. Gingeras

First Published March 1, 2004

ARTICLE

Strongyloides stercoralis and Caenorhabditis elegans" > Comparative Genomics of Gene Expression in the Parasitic and Free-Living Nematodes Strongyloides stercoralis and Caenorhabditis elegans

Makedonka Mitreva
James P. McCarter
John Martin
Mike Dante
Todd Wylie
Brandi Chiapelli
... [+1 authors] ...,
Deana Pape
Sandra W. Clifton
Thomas B. Nutman
Robert H. Waterston

First Published February 2, 2004

ARTICLE

Escherichia coli" > A Motif Co-Occurrence Approach for Genome-Wide Prediction of Transcription-Factor-Binding Sites in Escherichia coli

Martha L. Bulyk
Abigail M. McGuire
Nobuhisa Masuda
George M. Church

First Published February 2, 2004

ARTICLE

Hox Clusters and Genome Evolution in Ray-Fin Fish" > Developmental Roles of Pufferfish Hox Clusters and Genome Evolution in Ray-Fin Fish

Angel Amores
Tohru Suzuki
Yi-Lin Yan
Jordan Pomeroy
Amy Singer
Chris Amemiya
John H. Postlethwait

First Published January 5, 2004

ARTICLE

Arabidopsis thaliana Genome?" > Does Recombination Shape the Distribution and Evolution of Tandemly Arrayed Genes (TAGs) in the Arabidopsis thaliana Genome?

Liqing Zhang
Brandon S. Gaut

First Published December 1, 2003

ARTICLE

Alu-Mediated Recombination Events During Evolution" > Shuffling of Genes Within Low-Copy Repeats on 22q11 (LCR22) by Alu-Mediated Recombination Events During Evolution

Melanie Babcock
Adam Pavlicek
Elizabeth Spiteri
Catherine D. Kashork
Ilya Ioshikhes
Lisa G. Shaffer
Jerzy Jurka
Bernice E. Morrow

First Published December 1, 2003

ARTICLE

Identification and Characterization of Multi-Species Conserved Sequences

Elliott H. Margulies
Mathieu Blanchette
David Haussler
Eric D. Green

First Published December 1, 2003

ARTICLE

Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network

Daniel E. Zak
Gregory E. Gonye
James S. Schwaber
Francis J. Doyle

First Published November 3, 2003

ARTICLE

A Biophysical Approach to Transcription Factor Binding Site Discovery

Marko Djordjevic
Anirvan M. Sengupta
Boris I. Shraiman

First Published November 3, 2003

ARTICLE

Limitations of Quantitative Gene Regulation Models: A Case Study

Philip M. Kim
Bruce Tidor

First Published November 3, 2003

ARTICLE

Drosophila" > An Evolutionary Analysis of Orphan Genes in Drosophila

Tomislav Domazet-Loso
Diethard Tautz

First Published October 2, 2003

ARTICLE

Trans-Splicing in Drosophila" > Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila

Mariano Labrador
Victor G. Corces

First Published October 2, 2003

ARTICLE

ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus" > Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus

Ningxin Zhang
Annette L. Harrex
Barbara R. Holland
Lauren E. Fenton
Richard D. Cannon
Jan Schmid

First Published September 2, 2003

ARTICLE

Schizosaccharomyces pombe" > Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe

Nathan J. Bowen
I. King Jordan
Jonathan A. Epstein
Valerie Wood
Henry L. Levin

First Published September 2, 2003

ARTICLE

Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome" > Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome

Didier Raoult
Hiroyuki Ogata
Stéphane Audic
Catherine Robert
Karsten Suhre
Michel Drancourt
Jean-Michel Claverie

First Published August 5, 2003

ARTICLE

Cryptosporidium parvum" > Integrated Mapping, Chromosomal Sequencing and Sequence Analysis of Cryptosporidium parvum

Alan T. Bankier
Helen F. Spriggs
Berthold Fartmann
Bernard A. Konfortov
Martin Madera
Christine Vogel
Sarah A. Teichmann
Al Ivens
Paul H. Dear

First Published July 17, 2003

ARTICLE

An Evolutionarily Structured Universe of Protein Architecture

Gustavo Caetano-Anollés
Derek Caetano-Anollés

First Published July 1, 2003

ARTICLE

Corynebacterium efficiens" > Comparative Complete Genome Sequence Analysis of the Amino Acid Replacements Responsible for the Thermostability of Corynebacterium efficiens

Yousuke Nishio
Yoji Nakamura
Yutaka Kawarabayasi
Yoshihiro Usuda
Eiichiro Kimura
Shinichi Sugimoto Kazuhiko Matsui
... [+2 authors] ...,
Akihiko Yamagishi
Hisashi Kikuchi
Kazuho Ikeo
Takashi Gojobori

First Published July 1, 2003

ARTICLE

Archaea Methanogenium frigidum and Methanococcoides burtonii" > Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

Neil F.W. Saunders
Torsten Thomas
Paul M.G. Curmi
John S. Mattick
Elizabeth Kuczek
Rob Slade John Davis Peter D. Franzmann David Boone Karl Rusterholtz Robert Feldman Chris Gates Shellie Bench Kevin Sowers Kristen Kadner Andrea Aerts Paramvir Dehal Chris Detter Tijana Glavina Susan Lucas Paul Richardson
... [+16 authors] ...,
Frank Larimer
Loren Hauser
Miriam Land
Ricardo Cavicchioli

First Published June 12, 2003

ARTICLE

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Piero Carninci
Kazunori Waki
Toshiyuki Shiraki
Hideaki Konno
Kazuhiro Shibata
Masayoshi Itoh Katsunori Aizawa Takahiro Arakawa Yoshiyuki Ishii Daisuke Sasaki Hidemasa Bono Shinji Kondo Yuichi Sugahara Rintaro Saito Naoki Osato Shiro Fukuda Kenjiro Sato Akira Watahiki Tomoko Hirozane-Kishikawa Mari Nakamura Yuko Shibata Ayako Yasunishi Noriko Kikuchi Atsushi Yoshiki Moriaki Kusakabe Stefano Gustincich Kirk Beisel William Pavan Vassilis Aidinis Akira Nakagawara William A. Held Hiroo Iwata Tomohiro Kono Hiromitsu Nakauchi Paul Lyons Christine Wells David A. Hume Michela Fagiolini Takao K. Hensch Michelle Brinkmeier Sally Camper Junji Hirota Peter Mombaerts
... [+38 authors] ...,
Masami Muramatsu
Yasushi Okazaki
Jun Kawai
Yoshihide Hayashizaki

First Published June 2, 2003

ARTICLE

Cytokine-Related Genes Identified From the RIKEN Full-Length Mouse cDNA Data Set

Vladimir Brusic
Rekha S. Pillai
Diego G. Silva
Nikolai Petrovsky
Christian Schönbach

First Published June 2, 2003

ARTICLE

Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome

Mihaela Zavolan
Shinji Kondo
Christian Schönbach
Jun Adachi
David A. Hume
Yoshihide Hayashizaki
Terry Gaasterland

First Published June 2, 2003

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