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Methods

Escherichia coli-K12" > High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12

Christiane Honisch
Anu Raghunathan
Charles R. Cantor
Bernhard Ø. Palsson
Dirk van den Boom

First Published December 1, 2004

ERRATUM

Correction for Volume 14, p. 2279

First Published December 1, 2004

Methods

Marking of specific sequences in double-stranded DNA molecules—SNP detection and direct observation

Yasushi Shigemori
Hirotaka Haruta
Takao Okada
Michio Oishi

First Published December 1, 2004

LETTER

Computing prokaryotic gene ubiquity: Rescuing the core from extinction

Robert L. Charlebois
W. Ford Doolittle

First Published December 1, 2004

LETTER

Sprr loci to identify conserved noncoding sequences involved in coordinate regulation" > Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation

Natalia Martin
Satyakam Patel
Julia A. Segre

First Published December 1, 2004

Methods

MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues

Omer Barad
Eti Meiri
Amir Avniel
Ranit Aharonov
Adi Barzilai
Isaac Bentwich Uri Einav Shlomit Gilad Patrick Hurban Yael Karov Edward K. Lobenhofer Eilon Sharon
... [+7 authors] ...,
Yoel M. Shiboleth
Marat Shtutman
Zvi Bentwich
Paz Einat

First Published December 1, 2004

LETTER

The mouse genome: Experimental examination of gene predictions and transcriptional start sites

Sujit Dike
Vivekanand S. Balija
Lidia U. Nascimento
Zhenyu Xuan
Jacqueline Ou
Theresa Zutavern
... [+1 authors] ...,
Lance E. Palmer
Greg Hannon
Michael Q. Zhang
W. Richard McCombie

First Published December 1, 2004

LETTER

Caenorhabditis elegans muscle genes" > Novel transcription regulatory elements in Caenorhabditis elegans muscle genes

Debraj GuhaThakurta
Lawrence A. Schriefer
Robert H. Waterston
Gary D. Stormo

First Published December 1, 2004

LETTER

Reconstructing large regions of an ancestral mammalian genome in silico

Mathieu Blanchette
Eric D. Green
Webb Miller
David Haussler

First Published December 1, 2004

LETTER

Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence–SNP analysis" > Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence–SNP analysis

Kuniya Abe
Hideki Noguchi
Keiko Tagawa
Misako Yuzuriha
Atsushi Toyoda
Toshio Kojima Kiyoshi Ezawa Naruya Saitou
... [+3 authors] ...,
Masahira Hattori
Yoshiyuki Sakaki
Kazuo Moriwaki
Toshihiko Shiroishi

First Published December 1, 2004

ARTICLE

A survey of RNA editing in human brain

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

First Published November 15, 2004

LETTER

Ciona exhibit strong correspondence between evolutionary constraint and functional importance" > Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance

David S. Johnson
Brad Davidson
Christopher D. Brown
William C. Smith
Arend Sidow

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

LETTER

Intraspecies sequence comparisons for annotating genomes

Dario Boffelli
Claire V. Weer
Li Weng
Keith D. Lewis
Malak I. Shoukry
Lior Pachter
David N. Keys
Edward M. Rubin

First Published November 15, 2004

RESOURCE

OptStrain: A computational framework for redesign of microbial production systems

Priti Pharkya
Anthony P. Burgard
Costas D. Maranas

First Published November 1, 2004

Methods

A novel method for multiple alignment of sequences with repeated and shuffled elements

Benjamin Raphael
Degui Zhi
Haixu Tang
Pavel Pevzner

First Published November 1, 2004

Methods

DNA amplification method tolerant to sample degradation

Gang Wang
Elizabeth Maher
Cameron Brennan
Lynda Chin
Christopher Leo
Manjit Kaur
... [+1 authors] ...,
Penny Zhu
Martha Rook
Jia Liu Wolfe
G. Mike Makrigiorgos

First Published November 1, 2004

Methods

A novel, high-performance random array platform for quantitative gene expression profiling

Kenneth Kuhn
Shawn C. Baker
Eugene Chudin
Minh-Ha Lieu
Steffen Oeser
Holly Bennett
... [+1 authors] ...,
Philippe Rigault
David Barker
Timothy K. McDaniel
Mark S. Chee

First Published November 1, 2004

LETTER

Plasmodium falciparum life cycle" > Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle

Karine G. Le Roch
Jeffrey R. Johnson
Laurence Florens
Yingyao Zhou
Andrey Santrosyan
Munira Grainger S. Frank Yan Kim C. Williamson
... [+3 authors] ...,
Anthony A. Holder
Daniel J. Carucci
John R. Yates
Elizabeth A. Winzeler

First Published November 1, 2004

LETTER

Cyclops kolensis" > The molecular structure of the DNA fragments eliminated during chromatin diminution in Cyclops kolensis

Sergei Degtyarev
Tatiana Boykova
Andrei Grishanin
Stepan Belyakin
Nikolai Rubtsov
Tatiana Karamysheva
Grigory Makarevich
Alexei Akifyev
Igor Zhimulev

First Published November 1, 2004

LETTER

Burkholderia species" > Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species

Catherine Ong
Chia Huey Ooi
Dongling Wang
Hweeling Chong
Kim Chong Ng
Fiona Rodrigues
May Ann Lee
Patrick Tan

First Published November 1, 2004

LETTER

VSG expression site containing telomeres of Trypanosoma brucei 427 using transformation-associated recombination in yeast" > Isolation of the repertoire of VSG expression site containing telomeres of Trypanosoma brucei 427 using transformation-associated recombination in yeast

Marion Becker
Niall Aitcheson
Elaine Byles
Bill Wickstead
Edward Louis
Gloria Rudenko

First Published November 1, 2004

LETTER

Alu repeat elements reveals complex evolutionary history" > Whole-genome analysis of Alu repeat elements reveals complex evolutionary history

Alkes L. Price
Eleazar Eskin
Pavel A. Pevzner

First Published November 1, 2004

LETTER

The human L1 promoter: Variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity

Laurence Lavie
Esther Maldener
Brook Brouha
Eckart U. Meese
Jens Mayer

First Published November 1, 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

LETTER

Properties of overlapping genes are conserved across microbial genomes

Zackary I. Johnson
Sallie W. Chisholm

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

RESOURCE

Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications" > Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications

Pierre Hilson
Joke Allemeersch
Thomas Altmann
Sébastien Aubourg
Alexandra Avon
Jim Beynon Rishikesh P. Bhalerao Frédérique Bitton Michel Caboche Bernard Cannoot Vasil Chardakov Cécile Cognet-Holliger Vincent Colot Mark Crowe Caroline Darimont Steffen Durinck Holger Eickhoff Andéol Falcon de Longevialle Edward E. Farmer Murray Grant Martin T.R. Kuiper Hans Lehrach Céline Léon Antonio Leyva Joakim Lundeberg Claire Lurin Yves Moreau Wilfried Nietfeld Javier Paz-Ares Philippe Reymond Pierre Rouzé Goran Sandberg Maria Dolores Segura Carine Serizet Alexandra Tabrett Ludivine Taconnat Vincent Thareau Paul Van Hummelen Steven Vercruysse Marnik Vuylsteke Magdalena Weingartner Peter J. Weisbeek
... [+37 authors] ...,
Valtteri Wirta
Floyd R.A. Wittink
Marc Zabeau
Ian Small

First Published October 15, 2004

Methods

Systematic Recovery and Analysis of Full-ORF Human cDNA Clones

Ágnes Baross
Yaron S.N. Butterfield
Shaun M. Coughlin
Thomas Zeng
Malachi Griffith
Obi L. Griffith Anca S. Petrescu Duane E. Smailus Jaswinder Khattra Helen L. McDonald
... [+5 authors] ...,
Sheldon J. McKay
Michelle Moksa
Robert A. Holt
Marco A. Marra

First Published October 15, 2004

RESOURCE

Pseudomonas aeruginosa PA01 Gene Collection" > The Pseudomonas aeruginosa PA01 Gene Collection

Joshua LaBaer
QingQing Qiu
Anukanth Anumanthan
Wenhong Mar
Dongmei Zuo
T.V.S. Murthy Helen Taycher
... [+2 authors] ...,
Allison Halleck
Eugenie Hainsworth
Stephen Lory
Leonardo Brizuela

First Published October 15, 2004

Methods

Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones

David L. Cheo
Steven A. Titus
Devon R.N. Byrd
James L. Hartley
Gary F. Temple
Michael A. Brasch

First Published October 15, 2004

LETTER

Caenorhabditis elegans Using a MultiSite Gateway Recombination System" > Feasibility of Genome-Scale Construction of Promoter::Reporter Gene Fusions for Expression in Caenorhabditis elegans Using a MultiSite Gateway Recombination System

Ian A. Hope
Jonathan Stevens
Anna Garner
Josie Hayes
David L. Cheo
Michael A. Brasch
Marc Vidal

First Published October 15, 2004

LETTER

1274 Full-Open Reading Frames of Transcripts Expressed in the Developing Mouse Nervous System

Maria F. Bonaldo
Thomas B. Bair
Todd E. Scheetz
Einat Snir
Ike Akabogu
Jennifer L. Bair Brian Berger Keith Crouch Aja Davis Mari E. Eyestone Catherine Keppel Tamara A. Kucaba Mark Lebeck Jenny L. Lin Anna I.R. de Melo Joshua Rehmann Rebecca S. Reiter Kelly Schaefer Christina Smith Dylan Tack Kurtis Trout
... [+16 authors] ...,
Val C. Sheffield
Jim J-C. Lin
Thomas L. Casavant
Marcelo B. Soares

First Published October 15, 2004

RESOURCE

From ORFeome to Biology: A Functional Genomics Pipeline

Stefan Wiemann
Dorit Arlt
Wolfgang Huber
Ruth Wellenreuther
Simone Schleeger
Alexander Mehrle Stephanie Bechtel Mamatha Sauermann
... [+3 authors] ...,
Ulrike Korf
Rainer Pepperkok
Holger Sültmann
Annemarie Poustka

First Published October 15, 2004

RESOURCE

High-Throughput Computational and Experimental Techniques in Structural Genomics

Mark R. Chance
Andras Fiser
Andrej Sali
Ursula Pieper
Narayanan Eswar
Guiping Xu
J. Eduardo Fajardo
Thirumuruhan Radhakannan
Nebojsa Marinkovic

First Published October 15, 2004

LETTER

Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing

Terrence S. Furey
Mark Diekhans
Yontao Lu
Tina A. Graves
Lachlan Oddy
Jennifer Randall-Maher
LaDeana W. Hillier
Richard K. Wilson
David Haussler

First Published October 15, 2004

RESOURCE

The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)

First Published October 15, 2004

LETTER

P. falciparum Functional Molecules by Recombinational Cloning" > High-Throughput Generation of P. falciparum Functional Molecules by Recombinational Cloning

João Carlos Aguiar
Joshua LaBaer
Peter L. Blair
Victoria Y. Shamailova
Malvika Koundinya
Joshua A. Russell Fengying Huang Wenhong Mar Robert M. Anthony Adam Witney Sonia R. Caruana
... [+6 authors] ...,
Leonardo Brizuela
John B. Sacci
Stephen L. Hoffman
Daniel J. Carucci

First Published October 15, 2004

LETTER

An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression

David N. Messina
Jarret Glasscock
Warren Gish
Michael Lovett

First Published October 15, 2004

RESOURCE

Caenorhabditis elegans Promoterome" > A First Version of the Caenorhabditis elegans Promoterome

Denis Dupuy
Qian-Ru Li
Bart Deplancke
Mike Boxem
Tong Hao
Philippe Lamesch Reynaldo Sequerra Stephanie Bosak Lynn Doucette-Stamm
... [+4 authors] ...,
Ian A. Hope
David E. Hill
Albertha J.M. Walhout
Marc Vidal

First Published October 15, 2004

PERSPECTIVE

ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List

Michael A. Brasch
James L. Hartley
Marc Vidal

First Published October 15, 2004

Insight/Outlook

Academia-Industry Collaboration: An Integral Element for Building “Omic” Resources

David E. Hill
Michael A. Brasch
Anthony A. del Campo
Lynn Doucette-Stamm
James I. Garrels
Judith Glaven
... [+1 authors] ...,
James L. Hartley
James R. Hudson
Troy Moore
Marc Vidal

First Published October 15, 2004

RESOURCE

Human ORFeome Version 1.1: A Platform for Reverse Proteomics

Jean-François Rual
Tomoko Hirozane-Kishikawa
Tong Hao
Nicolas Bertin
Siming Li
Amélie Dricot Ning Li Jennifer Rosenberg Philippe Lamesch Pierre-Olivier Vidalain Tracey R. Clingingsmith James L. Hartley Dominic Esposito David Cheo Troy Moore Blake Simmons Reynaldo Sequerra Stephanie Bosak Lynn Doucette-Stamm Christian Le Peuch Jean Vandenhaute
... [+16 authors] ...,
Michael E. Cusick
Joanna S. Albala
David E. Hill
Marc Vidal

First Published October 15, 2004

RESOURCE

Brucella melitensis ORFeome Version 1.1" > Generation of the Brucella melitensis ORFeome Version 1.1

Amélie Dricot
Jean-François Rual
Philippe Lamesch
Nicolas Bertin
Denis Dupuy
Tong Hao Christophe Lambert Régis Hallez Jean-Marc Delroisse Jean Vandenhaute Ignacio Lopez-Goñi Ignacio Moriyon Juan M. Garcia-Lobo Félix J. Sangari Alastair P. MacMillan Sally J. Cutler Adrian M. Whatmore Stephanie Bozak Reynaldo Sequerra Lynn Doucette-Stamm
... [+15 authors] ...,
Marc Vidal
David E. Hill
Jean-Jacques Letesson
Xavier De Bolle

First Published October 15, 2004

REVIEW

Many Paths to Many Clones: A Comparative Look at High-Throughput Cloning Methods

Gerald Marsischky
Joshua LaBaer

First Published October 15, 2004

Methods

A Gateway-Compatible Yeast One-Hybrid System

Bart Deplancke
Denis Dupuy
Marc Vidal
Albertha J.M. Walhout

First Published October 15, 2004

RESOURCE

Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library" > Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library

Jean-François Rual
Julian Ceron
John Koreth
Tong Hao
Anne-Sophie Nicot
Tomoko Hirozane-Kishikawa Jean Vandenhaute
... [+2 authors] ...,
Stuart H. Orkin
David E. Hill
Sander van den Heuvel
Marc Vidal

First Published October 15, 2004

RESOURCE

C. elegans ORFeome" > WormBase as an Integrated Platform for the C. elegans ORFeome

Nansheng Chen
Daniel Lawson
Keith Bradnam
Todd W. Harris
Lincoln D. Stein

First Published October 15, 2004

Methods

C. elegans Proteins" > High-Throughput Expression of C. elegans Proteins

Chi-Hao Luan
Shihong Qiu
James B. Finley
Mike Carson
Rita J. Gray
Wenying Huang David Johnson Jun Tsao Jérôme Reboul Philippe Vaglio
... [+5 authors] ...,
David E. Hill
Marc Vidal
Lawrence J. DeLucas
Ming Luo

First Published October 15, 2004

LETTER

Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs

Masaaki Oyama
Chiharu Itagaki
Hiroko Hata
Yutaka Suzuki
Tomonori Izumi
Tohru Natsume
Toshiaki Isobe
Sumio Sugano

First Published October 15, 2004

COMMENTARY

The Responsibility to Share: Sharing the Responsibility

Martin Yuille
Bernhard Korn
Troy Moore
Andrew A. Farmer
John Carrino
Christa Prange
Yoshihide Hayashizaki

First Published October 15, 2004

REVIEW

From ORFeomes to Protein Interaction Maps in Viruses

Peter Uetz
Seesandra V. Rajagopala
Yu-An Dong
Jürgen Haas

First Published October 15, 2004

LETTER

C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions" > C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions

Philippe Lamesch
Stuart Milstein
Tong Hao
Jennifer Rosenberg
Ning Li
Reynaldo Sequerra Stephanie Bosak
... [+2 authors] ...,
Lynn Doucette-Stamm
Jean Vandenhaute
David E. Hill
Marc Vidal

First Published October 15, 2004

LETTER

An intermediate grade of finished genomic sequence suitable for comparative analyses

Robert W. Blakesley
Nancy F. Hansen
James C. Mullikin
Pamela J. Thomas
Jennifer C. McDowell
Baishali Maskeri Alice C. Young Beatrice Benjamin Shelise Y. Brooks Bradley I. Coleman Jyoti Gupta Shi-Ling Ho Eric M. Karlins Quino L. Maduro Sirintorn Stantripop Cyrus Tsurgeon Jennifer L. Vogt Michelle A. Walker
... [+13 authors] ...,
Catherine A. Masiello
Xiaobin Guan
Gerard G. Bouffard
Eric D. Green

First Published October 12, 2004

Methods

Gene prediction and verification in a compact genome with numerous small introns

Aaron E. Tenney
Randall H. Brown
Charles Vaske
Jennifer K. Lodge
Tamara L. Doering
Michael R. Brent

First Published October 12, 2004

LETTER

Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization

Eduardo P.C. Rocha

First Published October 12, 2004

LETTER

trans-mobilization" > An active murine transposon family pair: Retrotransposition of “master” MusD copies and ETn trans-mobilization

David Ribet
Marie Dewannieux
Thierry Heidmann

First Published October 12, 2004

LETTER

Ψ-Φ: Exploring the outer limits of bacterial pseudogenes

Emmanuelle Lerat
Howard Ochman

First Published October 12, 2004

LETTER

Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome

Jinsheng Lai
Nrisingha Dey
Cheol-Soo Kim
Arvind K. Bharti
Stephen Rudd
Klaus F.X. Mayer
Brian A. Larkins
Philip Becraft
Joachim Messing

First Published October 1, 2004

RESOURCE

A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites

Naoya Ihara
Akiko Takasuga
Kazunori Mizoshita
Haruko Takeda
Mayumi Sugimoto
Yasushi Mizoguchi Takashi Hirano Tomohito Itoh Toshio Watanabe Kent M. Reed Warren M. Snelling
... [+6 authors] ...,
Steven M. Kappes
Craig W. Beattie
Gary L. Bennett
Yoshikazu Sugimoto

First Published October 1, 2004

LETTER

Close Split of Sorghum and Maize Genome Progenitors

Zuzana Swigoňová
Jinsheng Lai
Jianxin Ma
Wusirika Ramakrishna
Victor Llaca
Jeffrey L. Bennetzen
Joachim Messing

First Published October 1, 2004

Methods

Decoding Human Regulatory Circuits

William Thompson
Michael J. Palumbo
Wyeth W. Wasserman
Jun S. Liu
Charles E. Lawrence

First Published October 1, 2004

Methods

High-Content Screening Microscopy Identifies Novel Proteins With a Putative Role in Secretory Membrane Traffic

Vytaute Starkuviene
Urban Liebel
Jeremy C. Simpson
Holger Erfle
Annemarie Poustka
Stefan Wiemann
Rainer Pepperkok

First Published October 1, 2004

LETTER

Gene Loss and Movement in the Maize Genome

Jinsheng Lai
Jianxin Ma
Zuzana Swigoňová
Wusirika Ramakrishna
Eric Linton
Victor Llaca Bahattin Tanyolac
... [+2 authors] ...,
Yong-Jin Park
O-Young Jeong
Jeffrey L. Bennetzen
Joachim Messing

First Published October 1, 2004

Methods

Predicting Subcellular Localization via Protein Motif Co-Occurrence

Michelle S. Scott
David Y. Thomas
Michael T. Hallett

First Published October 1, 2004

Methods

Quantification of Multiple Gene Expression in Individual Cells

António Peixoto
Marta Monteiro
Benedita Rocha
Henrique Veiga-Fernandes

First Published October 1, 2004

RESOURCE

Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon

Anuj Kumar
Michael Seringhaus
Matthew C. Biery
Robert J. Sarnovsky
Lara Umansky
Stacy Piccirillo Matthew Heidtman Kei-Hoi Cheung
... [+3 authors] ...,
Craig J. Dobry
Mark B. Gerstein
Nancy L. Craig
Michael Snyder

First Published October 1, 2004

ERRATUM

Correction for Volume 14, p. 1516

First Published October 1, 2004

LETTER

Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes

Peter E. Warburton
Joti Giordano
Fanny Cheung
Yefgeniy Gelfand
Gary Benson

First Published October 1, 2004

LETTER

Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan

Masashi Tanaka
Vicente M. Cabrera
Ana M. González
José M. Larruga
Takeshi Takeyasu
Noriyuki Fuku Li-Jun Guo Raita Hirose Yasunori Fujita Miyuki Kurata Ken-ichi Shinoda Kazuo Umetsu Yoshiji Yamada Yoshiharu Oshida Yuzo Sato Nobutaka Hattori Yoshikuni Mizuno Yasumichi Arai Nobuyoshi Hirose Shigeo Ohta Osamu Ogawa Yasushi Tanaka Ryuzo Kawamori Masayo Shamoto-Nagai
... [+19 authors] ...,
Wakako Maruyama
Hiroshi Shimokata
Ryota Suzuki
Hidetoshi Shimodaira

First Published October 1, 2004

LETTER

Genetic and Haplotype Diversity Among Wild-Derived Mouse Inbred Strains

Folami Y. Ideraabdullah
Elena de la Casa-Esperón
Timothy A. Bell
David A. Detwiler
Terry Magnuson
Carmen Sapienza
Fernando Pardo-Manuel de Villena

First Published October 1, 2004

LETTER

Divergence of Spatial Gene Expression Profiles Following Species-Specific Gene Duplications in Human and Mouse

Lukasz Huminiecki
Kenneth H. Wolfe

First Published October 1, 2004

LETTER

Svea36H Mouse" > Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse

Ann-Marie Mallon
Laurens Wilming
Joseph Weekes
James G.R. Gilbert
Jennifer Ashurst
Sandrine Peyrefitte Lucy Matthews Matthew Cadman Richard McKeone Chris A. Sellick Ruth Arkell Marc R.M. Botcherby Mark A. Strivens R. Duncan Campbell Simon Gregory
... [+10 authors] ...,
Paul Denny
John M. Hancock
Jane Rogers
Steve D.M. Brown

First Published September 13, 2004

LETTER

Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation

Shaying Zhao
Jyoti Shetty
Lihua Hou
Arthur Delcher
Baoli Zhu
Kazutoyo Osoegawa
... [+1 authors] ...,
Pieter de Jong
William C. Nierman
Robert L. Strausberg
Claire M. Fraser

First Published September 13, 2004

LETTER

A Novel Class of Mammalian-Specific Tailless Retropseudogenes

Jürgen Schmitz
Gennady Churakov
Hans Zischler
Jürgen Brosius

First Published September 13, 2004

LETTER

Identification of Mammalian microRNA Host Genes and Transcription Units

Antony Rodriguez
Sam Griffiths-Jones
Jennifer L. Ashurst
Allan Bradley

First Published September 13, 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

Retraction

Retraction

First Published September 1, 2004

Methods

De Novo Repeat Classification and Fragment Assembly

Paul A. Pevzner
Haixu Tang
Glenn Tesler

First Published September 1, 2004

Methods

A Benchmark for Methods in Reverse Engineering and Model Discrimination: Problem Formulation and Solutions

Andreas Kremling
Sophia Fischer
Kapil Gadkar
Francis J. Doyle
Thomas Sauter
Eric Bullinger
Frank Allgöwer
Ernst D. Gilles

First Published September 1, 2004

Methods

E. coli Have Multiple Equivalent Phenotypic States: Assessment of Correlated Reaction Subsets That Comprise Network States" > Genome-Scale In Silico Models of E. coli Have Multiple Equivalent Phenotypic States: Assessment of Correlated Reaction Subsets That Comprise Network States

Jennifer L. Reed
Bernhard Ø. Palsson

First Published September 1, 2004

RESOURCE

Indica and Japonica Genome Alignments" > An SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments

F. Alex Feltus
Jun Wan
Stefan R. Schulze
James C. Estill
Ning Jiang
Andrew H. Paterson

First Published September 1, 2004

RESOURCE

An Efficient SNP System for Mouse Genome Scanning and Elucidating Strain Relationships

Petko M. Petkov
Yueming Ding
Megan A. Cassell
Weidong Zhang
Gunjan Wagner
Evelyn E. Sargent Steven Asquith Victor Crew
... [+3 authors] ...,
Kevin A. Johnson
Phil Robinson
Valerie E. Scott
Michael V. Wiles

First Published September 1, 2004

Methods

EGPred: Prediction of Eukaryotic Genes Using Ab Initio Methods After Combining With Sequence Similarity Approaches

Biju Issac
Gajendra Pal Singh Raghava

First Published September 1, 2004

LETTER

Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions

Yutaka Suzuki
Riu Yamashita
Matsuyuki Shirota
Yuta Sakakibara
Joe Chiba
Junko Mizushima-Sugano
Kenta Nakai
Sumio Sugano

First Published September 1, 2004

LETTER

IGF2 in Extant Mammals" > Phylogenetic Footprint Analysis of IGF2 in Extant Mammals

Jennifer R. Weidman
Susan K. Murphy
Catherine M. Nolan
Fred S. Dietrich
Randy L. Jirtle

First Published September 1, 2004

LETTER

Alu Elements in the Human Transcriptome" > Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome

Dennis D.Y. Kim
Thomas T.Y. Kim
Thomas Walsh
Yoshifumi Kobayashi
Tara C. Matise
Steven Buyske
Abram Gabriel

First Published September 1, 2004

LETTER

Recurrent Sites for New Centromere Seeding

Mario Ventura
Stefania Weigl
Lucia Carbone
Maria Francesca Cardone
Doriana Misceo
Mariagrazia Teti Pietro D'Addabbo Annelise Wandall Erik Björck Pieter J. de Jong
... [+5 authors] ...,
Xinwei She
Evan E. Eichler
Nicoletta Archidiacono
Mariano Rocchi

First Published September 1, 2004

LETTER

Evidence for Gradients of Human Genetic Diversity Within and Among Continents

David Serre
Svante Pääbo

First Published September 1, 2004

LETTER

Comparative Analysis of Apicomplexa and Genomic Diversity in Eukaryotes

Thomas J. Templeton
Lakshminarayan M. Iyer
Vivek Anantharaman
Shinichiro Enomoto
Juan E. Abrahante
G.M. Subramanian
Stephen L. Hoffman
Mitchell S. Abrahamsen
L. Aravind

First Published September 1, 2004

LETTER

Preference of DNA Methyltransferases for CpG Islands in Mouse Embryonic Stem Cells

Naka Hattori
Tetsuya Abe
Naoko Hattori
Masako Suzuki
Tomoki Matsuyama
Shigeo Yoshida
En Li
Kunio Shiota

First Published August 12, 2004

Methods

Haplotype Analysis in Multiple Crosses to Identify a QTL Gene

Xiaosong Wang
Ron Korstanje
David Higgins
Beverly Paigen

First Published August 12, 2004

LETTER

A Large Imprinted microRNA Gene Cluster at the Mouse Dlk1-Gtl2 Domain

Hervé Seitz
Hélène Royo
Marie-Line Bortolin
Shau-Ping Lin
Anne C. Ferguson-Smith
Jérôme Cavaillé

First Published August 12, 2004

LETTER

Insertion of Telomeric Repeats at Intrachromosomal Break Sites During Primate Evolution

Solomon G. Nergadze
Mariano Rocchi
Claus M. Azzalin
Chiara Mondello
Elena Giulotto

First Published August 12, 2004

Methods

Role of Excess Inorganic Pyrophosphate in Primer-Extension Genotyping Assays

Ming Xiao
Angie Phong
Kristen L. Lum
Richard A. Greene
Philip R. Buzby
Pui-Yan Kwok

First Published August 12, 2004

Methods

Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies

Bjarni V. Halldórsson
Vineet Bafna
Ross Lippert
Russell Schwartz
Francisco M. De La Vega
Andrew G. Clark
Sorin Istrail

First Published August 2, 2004

RESOURCE

cpnDB: A Chaperonin Sequence Database

Janet E. Hill
Susanne L. Penny
Kenneth G. Crowell
Swee Han Goh
Sean M. Hemmingsen

First Published August 2, 2004

Methods

Indel-Based Evolutionary Distance and Mouse–Human Divergence

Aleksey Y. Ogurtsov
Shamil Sunyaev
Alexey S. Kondrashov

First Published August 2, 2004

RESOURCE

Large-Scale Validation of Single Nucleotide Polymorphisms in Gene Regions

Matthew R. Nelson
George Marnellos
Stefan Kammerer
Carolyn R. Hoyal
Michael M. Shi
Charles R. Cantor
Andreas Braun

First Published August 2, 2004

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