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COMMENTARY

A Guide to the Mammalian Genome

Yasushi Okazaki
David A. Hume

First Published June 2, 2003

LETTER

Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse

Alistair R.R. Forrest
Timothy Ravasi
Darrin Taylor
Thomas Huber
David A. Hume
Sean Grimmond

First Published June 2, 2003

Abstracts

The Mouse Neuronal Protein 15.6 Gene Family

Yuko Watanabe
Seiji Nishiguchi
Makoto Watanabe
Kazunori Shimada
Koji Koyama
Hiromichi Yamanishi

First Published June 2, 2003

LETTER

Mouse Proteome Analysis

Alexander Kanapin
Serge Batalov
Melissa J. Davis
Julian Gough
Sean Grimmond
Hideya Kawaji Michele Magrane
... [+2 authors] ...,
Hideo Matsuda
Christian Schönbach
Rohan D. Teasdale
Zheng Yuan3

First Published June 2, 2003

Methods

Human Disease Genes and Their Cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Data Set

Lynn M. Schriml
David P. Hill
Judith A. Blake
Hidemasa Bono
Anthony Wynshaw-Boris
William J. Pavan
... [+1 authors] ...,
Brian Z. Ring
Kirk Beisel
Mitsutoshi Setou
Yasushi Okazaki

First Published June 2, 2003

Abstracts

Identification of Novel “Pathologs” (Human Disease-Related Gene Candidates) From the RIKEN Full-Length Mouse cDNA Data Set

Diego G. Silva
Christian Schönbach
Vladimir Brusic
Luis A. Socha
Takeshi Nagashima
Nikolai Petrovsky

First Published June 2, 2003

LETTER

Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays

Hidemasa Bono
Ken Yagi
Takeya Kasukawa
Itoshi Nikaido
Naoko Tominaga
Rika Miki Yosuke Mizuno Yasuhiro Tomaru Hitoshi Goto Hiroyuki Nitanda Daisuke Shimizu Hirochika Makino Tomoyuki Morita Junshin Fujiyama Takehito Sakai
... [+10 authors] ...,
Takashi Shimoji
David A. Hume
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

LETTER

The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment

Sean M. Grimmond
Kevin C. Miranda
Zheng Yuan
Melissa J. Davis
David A. Hume
Ken Yagi Naoko Tominaga
... [+2 authors] ...,
Hidemasa Bono
Yoshihide Hayashizaki
Yasushi Okazaki
Rohan D. Teasdale

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

Abstracts

Introduction of RIKEN-GenoMapper, Mapping Viewer System

Hidenori Kiyosawa
Tsugumi Kawashima
Yuki Hasegawa
Itaru Yamanaka
Katsunaga Sakai
Shinji Kondo
Yoshihide Hayashizaki

First Published June 2, 2003

LETTER

Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome

Timothy Ravasi
Thomas Huber
Mihaela Zavolan
Alistair Forrest
Terry Gaasterland
Sean Grimmond
David A. Hume

First Published June 2, 2003

RESOURCE

GeneLynx Mouse: Integrated Portal to the Mouse Genome

Boris Lenhard
Claes Wahlestedt
Wyeth W. Wasserman

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

LETTER

The Comparative Proteomics of Ubiquitination in Mouse

Colin A.M. Semple

First Published June 2, 2003

LETTER

Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System

Stefano Gustincich
Serge Batalov
Kirk W. Beisel
Hidemasa Bono
Piero Carninci
Colin F. Fletcher Sean Grimmond Nobutaka Hirokawa Erich D. Jarvis Tim Jegla Yuka Kawasawa Julianna LeMieux Harukata Miki Elio Raviola Rohan D. Teasdale Naoko Tominaga
... [+11 authors] ...,
Ken Yagi
Andreas Zimmer
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

LETTER

CDS Annotation in Full-Length cDNA Sequence

Masaaki Furuno
Takeya Kasukawa
Rintaro Saito
Jun Adachi
Harukazu Suzuki
Richard Baldarelli
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

LETTER

Gnas Imprinted Complex" > A Comprehensive Transcript Map of the Mouse Gnas Imprinted Complex

Rebecca Holmes
Christine Williamson
Jo Peters
Paul Denny
Christine Wells

First Published June 2, 2003

LETTER

Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome

Khairina Tajul-Arifin
Rohan Teasdale
Timothy Ravasi
David A. Hume
John S. Mattick

First Published June 2, 2003

LETTER

Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome

Hidemasa Bono
Itoshi Nikaido
Takeya Kasukawa
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

Methods

DNA Book

Jun Kawai
Yoshihide Hayashizaki

First Published June 2, 2003

LETTER

G Protein-Coupled Receptor Genes in the FANTOM2 Database

Yuka Kawasawa
Louise M. McKenzie
David P. Hill
Hidemasa Bono
Masashi Yanagisawa

First Published June 2, 2003

Abstracts

Functional Annotation of RIKEN Mouse cDNA Clones Using GNF Expression Atlas

Serge Batalov
Andrew I. Su
Keith A. Ching
Colin F. Fletcher

First Published June 2, 2003

ARTICLE

Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection

Koji Numata
Akio Kanai
Rintaro Saito
Shinji Kondo
Jun Adachi
Laurens G. Wilming
David A. Hume
Yoshihide Hayashizaki
Masaru Tomita

First Published June 2, 2003

LETTER

Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage

Christine A. Wells
Timothy Ravasi
Razvan Sultana
Ken Yagi
Piero Carninci
Hidemasa Bono Geoffrey Faulkner
... [+2 authors] ...,
Yasushi Okazaki
John Quackenbush
David A. Hume
Paul A. Lyons

First Published June 2, 2003

RESOURCE

The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer

Harukazu Suzuki
Rintaro Saito
Mutsumi Kanamori
Chikatoshi Kai
Christian Schönbach
Takeshi Nagashima
Junko Hosaka
Yoshihide Hayashizaki

First Published June 2, 2003

LETTER

Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling

Itoshi Nikaido
Chika Saito
Yosuke Mizuno
Makiko Meguro
Hidemasa Bono
Moritoshi Kadomura Tomohiro Kono Gerard A. Morris
... [+3 authors] ...,
Paul A. Lyons
Mitsuo Oshimura
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

Preface

Special FANTOM2 Issue

Yoshihide Hayashizaki

First Published June 2, 2003

LETTER

Exploration of the Cell-Cycle Genes Found Within the RIKEN FANTOM2 Data Set

Alistair R.R. Forrest
Darrin Taylor
Sean Grimmond

First Published June 2, 2003

Abstracts

Identification of Potential Peroxisomal Proteins in Mouse

Igor V. Kurochkin
Akihiko Konagaya
Takeshi Nagashima
Christian Schönbach

First Published June 2, 2003

RESOURCE

Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System

Takeya Kasukawa
Masaaki Furuno
Itoshi Nikaido
Hidemasa Bono
David A. Hume
Carol Bult David P. Hill Richard Baldarelli Julian Gough Alexander Kanapin Hideo Matsuda
... [+6 authors] ...,
Lynn M. Schriml
Yoshihide Hayashizaki
Yasushi Okazaki
John Quackenbush

First Published June 2, 2003

ERRATUM

Correction for Volume 13, p. 742

First Published June 1, 2003

ARTICLE

Streptococcus pyogenes Reveals a Large-Scale Genomic Rearrangement in Invasive Strains and New Insights into Phage Evolution" > Genome Sequence of an M3 Strain of Streptococcus pyogenes Reveals a Large-Scale Genomic Rearrangement in Invasive Strains and New Insights into Phage Evolution

Ichiro Nakagawa
Ken Kurokawa
Atsushi Yamashita
Masanobu Nakata
Yusuke Tomiyasu
Nobuo Okahashi Shigetada Kawabata Kiyoshi Yamazaki Tadayoshi Shiba
... [+4 authors] ...,
Teruo Yasunaga
Hideo Hayashi
Masahira Hattori
Shigeyuki Hamada

First Published June 1, 2003

ARTICLE

New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes

Georgia Panopoulou
Steffen Hennig
Detlef Groth
Antje Krause
Albert J. Poustka
Ralf Herwig
Martin Vingron
Hans Lehrach

First Published June 1, 2003

LETTER

Saccharomyces cerevisiae Proteome" > Multimeric Threading-Based Prediction of Protein–Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome

Long Lu
Adrian K. Arakaki
Hui Lu
Jeffrey Skolnick

First Published June 1, 2003

RESOURCE

Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps

Christopher D. Fjell
Ian Bosdet
Jacqueline E. Schein
Steven J.M. Jones
Marco A. Marra

First Published June 1, 2003

LETTER

F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586" > Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586

Vinayak Kapatral
Natalia Ivanova
Iain Anderson
Gary Reznik
Anamitra Bhattacharyya
Warren L. Gardner Natalia Mikhailova Alla Lapidus Niels Larsen Mark D'Souza
... [+5 authors] ...,
Theresa Walunas
Robert Haselkorn
Ross Overbeek
Nikos Kyrpides

First Published June 1, 2003

RESOURCE

Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource

Asako Koike
Yoshiyuki Kobayashi
Toshihisa Takagi

First Published June 1, 2003

RESOURCE

Arabidopsis thaliana" > Large-Scale Identification and Analysis of Genome-Wide Single-Nucleotide Polymorphisms for Mapping in Arabidopsis thaliana

Karl J. Schmid
Thomas Rosleff Sörensen
Ralf Stracke
Ottó Törjék
Thomas Altmann
Tom Mitchell-Olds
Bernd Weisshaar

First Published June 1, 2003

LETTER

Hox Gene Clusters" > Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters

Simona Santini
Jeffrey L. Boore
Axel Meyer

First Published June 1, 2003

Methods

Computational Discovery of Internal Micro-Exons

Natalia Volfovsky
Brian J. Haas
Steven L. Salzberg

First Published June 1, 2003

LETTER

The Zebrafish Annexin Gene Family

Steven A. Farber
Robert A. De Rose
Eric S. Olson
Marnie E. Halpern

First Published June 1, 2003

RESOURCE

eVOC: A Controlled Vocabulary for Unifying Gene Expression Data

Janet Kelso
Johann Visagie
Gregory Theiler
Alan Christoffels
Soraya Bardien
Damian Smedley Darren Otgaar Gary Greyling
... [+3 authors] ...,
C. Victor Jongeneel
Mark I. McCarthy
Tania Hide
Winston Hide

First Published June 1, 2003

LETTER

The Pattern of Polymorphism on Human Chromosome 21

Hideki Innan
Badri Padhukasahasram
Magnus Nordborg

First Published June 1, 2003

LETTER

Drosophila" > Extrachromosomal Circular DNA of Tandemly Repeated Genomic Sequences in Drosophila

Sarit Cohen
Keren Yacobi
Daniel Segal

First Published June 1, 2003

ERRATUM

Correction for Volume 13, p. 794

First Published June 1, 2003

ARTICLE

Functional Divergence of Two Zebrafish Midkine Growth Factors Following Fish-Specific Gene Duplication

Christoph Winkler
Matthias Schäfer
Jutta Duschl
Manfred Schartl
Jean-Nicolas Volff

First Published May 12, 2003

Methods

Assessment of SAGE in Transcript Identification

Erin D. Pleasance
Marco A. Marra
Steven J.M. Jones

First Published May 12, 2003

LETTER

Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region

Naoya Yuhki
Thomas Beck
Robert M. Stephens
Yoko Nishigaki
Kymberly Newmann
Stephen J. O'Brien

First Published May 12, 2003

LETTER

Phylogenetically Older Introns Strongly Correlate With Module Boundaries in Ancient Proteins

Alexei Fedorov
Scott Roy
Xiaohong Cao
Walter Gilbert

First Published May 12, 2003

Methods

Human–Mouse Gene Identification by Comparative Evidence Integration and Evolutionary Analysis

Lingang Zhang
Vladimir Pavlovic
Charles R Cantor
Simon Kasif

First Published May 12, 2003

LETTER

Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene Clusters

Mark Shannon
Aaron T. Hamilton
Laurie Gordon
Elbert Branscomb
Lisa Stubbs

First Published May 12, 2003

PERSPECTIVE

Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience

Timothy P. O'Brien
Carol J. Bult
Christoph Cremer
Michael Grunze
Barbara B. Knowles
Jörg Langowski James McNally Thoru Pederson Joan C. Politz
... [+4 authors] ...,
Ana Pombo
Günter Schmahl
Joachim P. Spatz
Roel van Driel

First Published May 12, 2003

LETTER

An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From Duplications to Genome Reduction

Eduardo P.C. Rocha

First Published May 12, 2003

LETTER

Parallel Evolution by Gene Duplication in the Genomes of Two Unicellular Fungi

Austin L. Hughes
Robert Friedman

First Published May 1, 2003

LETTER

Retroposed Copies of the HMG Genes: A Window to Genome Dynamics

Liora Z. Strichman-Almashanu
Michael Bustin
David Landsman

First Published May 1, 2003

LETTER

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes

Gregory M. Cooper
Michael Brudno
NISC Comparative Sequencing Program
Eric D. Green
Serafim Batzoglou
Arend Sidow

First Published May 1, 2003

LETTER

Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes

Sankar Subramanian
Sudhir Kumar

First Published May 1, 2003

LETTER

Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA

Ines Hellmann
Sebastian Zöllner
Wolfgang Enard
Ingo Ebersberger
Birgit Nickel
Svante Pääbo

First Published May 1, 2003

ARTICLE

Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells

Ran Elkon
Chaim Linhart
Roded Sharan
Ron Shamir
Yosef Shiloh

First Published May 1, 2003

ERRATUM

Erratum for vol. 13, p. 485

First Published May 1, 2003

RESOURCE

In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling

Mark G. Carter
Toshio Hamatani
Alexei A. Sharov
Condie E. Carmack
Yong Qian
Kazuhiro Aiba Naomi T. Ko
... [+2 authors] ...,
Dawood B. Dudekula
Pius M. Brzoska
S. Stuart Hwang
Minoru S.H. Ko

First Published May 1, 2003

LETTER

LRP5 Gene" > Haplotype Structure, LD Blocks, and Uneven Recombination Within the LRP5 Gene

Rebecca C.J. Twells
Charles A. Mein
Michael S. Phillips
J. Fred Hess
Riitta Veijola
Matthew Gilbey Matthew Bright Michael Metzker Benedicte A. Lie Amanda Kingsnorth Edward Gregory Yusuke Nakagawa Hywel Snook William Y.S. Wang Jennifer Masters Gillian Johnson Iain Eaves Joanna M.M. Howson David Clayton Heather J. Cordell
... [+15 authors] ...,
Sarah Nutland
Helen Rance
Philippa Carr
John A. Todd

First Published May 1, 2003

METHODS

DNA Analysis by Fluorescence Quenching Detection

Ming Xiao
Pui-Yan Kwok

First Published May 1, 2003

ARTICLE

Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature

Uberto Pozzoli
Greg Elgar
Rachele Cagliani
Laura Riva
Giacomo P. Comi
Nereo Bresolin
Alessandra Bardoni
Manuela Sironi

First Published May 1, 2003

ARTICLE

Complex Evolution of 7E Olfactory Receptor Genes in Segmental Duplications

Tera Newman
Barbara J. Trask

First Published May 1, 2003

LETTER

Genome Size Evolution in Pufferfish: A Comparative Analysis of Diodontid and Tetraodontid Pufferfish Genomes

Daniel E. Neafsey
Stephen R. Palumbi

First Published May 1, 2003

RESOURCE

Analysis of 5′-End Sequences of Chimpanzee cDNAs

Ryuichi Sakate
Naoki Osada
Munetomo Hida
Sumio Sugano
Ikuo Hayasaka
Naoko Shimohira
... [+1 authors] ...,
Shinsuke Yanagi
Yumiko Suto
Katsuyuki Hashimoto
Momoki Hirai

First Published May 1, 2003

ERRATUM

Erratum for vol. 13, p. 264

First Published May 1, 2003

LETTER

Fidelity of the Methylation Pattern and Its Variation in the Genome

Toshikazu Ushijima
Naoko Watanabe
Eriko Okochi
Atsushi Kaneda
Takashi Sugimura
Kazuaki Miyamoto

First Published May 1, 2003

METHODS

Software for Automated Analysis of DNA Fingerprinting Gels

Daniel R. Fuhrmann
Martin I. Krzywinski
Readman Chiu
Parvaneh Saeedi
Jacqueline E. Schein
Ian E. Bosdet Asif Chinwalla LaDeana W. Hillier
... [+3 authors] ...,
Robert H. Waterston
John D. McPherson
Steven J.M. Jones
Marco A. Marra

First Published May 1, 2003

METHODS

Selecting Open Reading Frames From DNA

Paola Zacchi
Daniele Sblattero
Fiorella Florian
Roberto Marzari
Andrew R.M. Bradbury

First Published May 1, 2003

METHODS

cis-Regulatory Motifs Using Functional Networks" > Discovering Novel cis-Regulatory Motifs Using Functional Networks

Laurence M. Ettwiller
Johan Rung
Ewan Birney

First Published May 1, 2003

METHODS

DASH-2: Flexible, Low-Cost, and High-Throughput SNP Genotyping by Dynamic Allele-Specific Hybridization on Membrane Arrays

Magnus Jobs
W. Mathias Howell
Linda Strömqvist
Torsten Mayr
Anthony J. Brookes

First Published May 1, 2003

ARTICLE

The Organization and Rate of Evolution of Wheat Genomes Are Correlated With Recombination Rates Along Chromosome Arms

Eduard D. Akhunov
Andrew W. Goodyear
Shu Geng
Li-Li Qi
Benjamin Echalier
Bikram S. Gill Miftahudin J. Perry Gustafson Gerard Lazo Shiaoman Chao Olin D. Anderson Anna M. Linkiewicz Jorge Dubcovsky Mauricio La Rota Mark E. Sorrells Deshui Zhang Henry T. Nguyen Venugopal Kalavacharla Khwaja Hossain Shahryar F. Kianian Junhua Peng Nora L.V. Lapitan Jose L. Gonzalez-Hernandez James A. Anderson Dong-Woog Choi Timothy J. Close Muharrem Dilbirligi Kulvinder S. Gill M. Kay Walker-Simmons
... [+24 authors] ...,
Camille Steber
Patrick E. McGuire
Calvin O. Qualset
Jan Dvorak

First Published April 14, 2003

METHODS

Exo-Proofreading, A Versatile SNP Scoring Technology

Patrick Cahill
Michele Bakis
James Hurley
Veena Kamath
William Nielsen
Dina Weymouth
Josée Dupuis
Lynn Doucette-Stamm
Douglas R. Smith

First Published April 14, 2003

LETTER

Predicting Human Minisatellite Polymorphism

France Denoeud
Gilles Vergnaud
Gary Benson

First Published April 14, 2003

METHODS

Unbiased Whole-Genome Amplification Directly From Clinical Samples

Seiyu Hosono
A. Fawad Faruqi
Frank B. Dean
Yuefen Du
Zhenyu Sun
Xiaohong Wu
... [+1 authors] ...,
Jing Du
Stephen F. Kingsmore
Michael Egholm
Roger S. Lasken

First Published April 14, 2003

METHODS

Predicting Gene Function From Patterns of Annotation

Oliver D. King
Rebecca E. Foulger
Selina S. Dwight
James V. White
Frederick P. Roth

First Published April 14, 2003

LETTER

Genomic Gene Clustering Analysis of Pathways in Eukaryotes

Jennifer M. Lee
Erik L.L. Sonnhammer

First Published April 14, 2003

METHODS

7-Based Genome-Wide Random Insertional Mutagenesis of Candida glabrata " > Tn7-Based Genome-Wide Random Insertional Mutagenesis of Candida glabrata

Irene Castaño
Rupinder Kaur
Shihjung Pan
Robert Cregg
Alejandro De Las Peñas
Nini Guo
Matthew C. Biery
Nancy L. Craig
Brendan P. Cormack

First Published April 14, 2003

METHODS

Comparing Bacterial Genomes Through Conservation Profiles

Maria J. Martı́n
Javier Herrero
Alvaro Mateos
Joaquin Dopazo

First Published April 14, 2003

METHODS

Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns

Astrid Lægreid
Torgeir R. Hvidsten
Herman Midelfart
Jan Komorowski
Arne K. Sandvik

First Published April 14, 2003

METHODS

LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics

Steve Hampson
Aoife McLysaght
Brandon Gaut
Pierre Baldi

First Published April 14, 2003

ARTICLE

Identification of Novel Imprinted Genes in a Genome-Wide Screen for Maternal Methylation

Rachel J. Smith
Wendy Dean
Galia Konfortova
Gavin Kelsey

First Published April 1, 2003

ARTICLE

Candida spp." > Comparative Evolutionary Genomics Unveils the Molecular Mechanism of Reassignment of the CTG Codon in Candida spp.

Steven E. Massey
Gabriela Moura
Pedro Beltrão
Ricardo Almeida
James R. Garey
Mick F. Tuite
Manuel A.S. Santos

First Published April 1, 2003

LETTER

Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements" > Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

Luiz R. Nunes
Yoko B. Rosato
Nair H. Muto
Giane M. Yanai
Vivian S. da Silva
Daniela B. Leite Edmilson R. Gonçalves Alessandra A. de Souza
... [+3 authors] ...,
Helvécio D. Coletta-Filho
Marcos A. Machado
Silvio A. Lopes
Regina Costa de Oliveira

First Published April 1, 2003

RESOURCE

GALA, a Database for Genomic Sequence Alignments and Annotations

Belinda Giardine
Laura Elnitski
Cathy Riemer
Izabela Makalowska
Scott Schwartz
Webb Miller
Ross C. Hardison

First Published April 1, 2003

LETTER

Nonrandom Tripeptide Sequence Distributions at Protein Carboxyl Termini

Gregory J. Gatto
Jeremy M. Berg

First Published April 1, 2003

RESOURCE

The First-Generation Whole-Genome Radiation Hybrid Map in the Horse Identifies Conserved Segments in Human and Mouse Genomes

Bhanu P. Chowdhary
Terje Raudsepp
Srinivas R. Kata
Glenda Goh
Lee V. Millon
Veronica Allan François Piumi Gérard Guérin June Swinburne Matthew Binns Teri L. Lear Jim Mickelson
... [+7 authors] ...,
James Murray
Douglas F. Antczak
James E. Womack
Loren C. Skow

First Published April 1, 2003

LETTER

Y Chromosome STR Haplotypes and the Genetic Structure of U.S. Populations of African, European, and Hispanic Ancestry

Manfred Kayser
Silke Brauer
Hiltrud Schädlich
Mechthild Prinz
Mark A. Batzer
Peter A. Zimmerman
B. A. Boatin
Mark Stoneking

First Published April 1, 2003

METHODS

Ran's C-terminal, Basic Patch, and Nucleotide Exchange Mechanisms in Light of a Canonical Structure for Rab, Rho, Ras, and Ran GTPases

Andrew F. Neuwald
Natarajan Kannan
Aleksandar Poleksic
Naoya Hata
Jun S. Liu

First Published April 1, 2003

METHODS

Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions

Yuval Kluger
Ronen Basri
Joseph T. Chang
Mark Gerstein

First Published April 1, 2003

LETTER

Drosophila " > Homotypic Regulatory Clusters in Drosophila

Alexander P. Lifanov
Vsevolod J. Makeev
Anna G. Nazina
Dmitri A. Papatsenko

First Published April 1, 2003

LETTER

Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite

Yimin Wu
Xiangyun Wang
Xia Liu
Yufeng Wang

First Published April 1, 2003

METHODS

Informatics for Unveiling Hidden Genome Signatures

Takashi Abe
Shigehiko Kanaya
Makoto Kinouchi
Yuta Ichiba
Tokio Kozuki
Toshimichi Ikemura

First Published April 1, 2003

ARTICLE

Dlx Bigene Clusters" > Regulatory Roles of Conserved Intergenic Domains in Vertebrate Dlx Bigene Clusters

Noël Ghanem
Olga Jarinova
Angel Amores
Qiaoming Long
Gary Hatch
Byung Keon Park
John L.R. Rubenstein
Marc Ekker

First Published April 1, 2003

LETTER

Species-Specific Class I Gene Expansions Formed the Telomeric 1 Mb of the Mouse Major Histocompatibility Complex

Toyoyuki Takada
Attila Kumánovics
Claire Amadou
Masayasu Yoshino
Elsy P. Jones
Maria Athanasiou
Glen A. Evans
Kirsten Fischer Lindahl

First Published April 1, 2003

METHODS

Novel Multilocus Measure of Linkage Disequilibrium to Estimate Past Effective Population Size

Ben J. Hayes
Peter M. Visscher
Helen C. McPartlan
Mike E. Goddard

First Published March 12, 2003

METHODS

The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro

Evelyn Camon
Michele Magrane
Daniel Barrell
David Binns
Wolfgang Fleischmann
Paul Kersey Nicola Mulder
... [+2 authors] ...,
Tom Oinn
John Maslen
Anthony Cox
Rolf Apweiler

First Published March 12, 2003

METHODS

Efficient High-Throughput Resequencing of Genomic DNA

Raymond D. Miller
Shenghui Duan
Elizabeth G. Lovins
Ellen F. Kloss
Pui-Yan Kwok

First Published March 12, 2003

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