Volume 13, Issue 6a | June 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
ARTICLES
- - 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
  - 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
    First Published June 1, 2003
  - 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
LETTERS
- - The Zebrafish Annexin Gene Family
    Steven A. Farber
    Robert A. De Rose
    Eric S. Olson
    Marnie E. Halpern
    First Published June 1, 2003
  - 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
  - Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters
    Simona Santini
    Jeffrey L. Boore
    Axel Meyer
    First Published June 1, 2003
  - 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
  - Extrachromosomal Circular DNA of Tandemly Repeated Genomic Sequences in Drosophila
    Sarit Cohen
    Keren Yacobi
    Daniel Segal
    First Published June 1, 2003
  - 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
  - Phylogenetically Older Introns Strongly Correlate With Module Boundaries in Ancient Proteins
    Alexei Fedorov
    Scott Roy
    Xiaohong Cao
    Walter Gilbert
    First Published May 12, 2003
  - The Pattern of Polymorphism on Human Chromosome 21
    Hideki Innan
    Badri Padhukasahasram
    Magnus Nordborg
    First Published June 1, 2003
  - Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region
    Naoya Yuhki
    Thomas Beck
    Robert M. Stephens
    Yoko Nishigaki
    Kymberly Newmann
    First Published May 12, 2003
  - 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
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
  - Assessment of SAGE in Transcript Identification
    Erin D. Pleasance
    Marco A. Marra
    Steven J.M. Jones
    First Published May 12, 2003
  - Computational Discovery of Internal Micro-Exons
    Natalia Volfovsky
    Brian J. Haas
    Steven L. Salzberg
    First Published June 1, 2003
RESOURCES
- - 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
  - Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource
    Asako Koike
    Yoshiyuki Kobayashi
    Toshihisa Takagi
    First Published June 1, 2003
  - 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
  - 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
    First Published June 1, 2003
ERRATA
- - Correction for Volume 13, p. 742
    First Published June 1, 2003
  - Correction for Volume 13, p. 794
    First Published June 1, 2003

Table of Contents

Volume 13, Issue 6a | June 2003

PERSPECTIVE

Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience

ARTICLES

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

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

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

LETTERS

The Zebrafish Annexin Gene Family

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

Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters

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

Extrachromosomal Circular DNA of Tandemly Repeated Genomic Sequences in Drosophila

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

Phylogenetically Older Introns Strongly Correlate With Module Boundaries in Ancient Proteins

The Pattern of Polymorphism on Human Chromosome 21

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

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

Methods

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

Assessment of SAGE in Transcript Identification

Computational Discovery of Internal Micro-Exons

RESOURCES

eVOC: A Controlled Vocabulary for Unifying Gene Expression Data

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

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

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

ERRATA

Correction for Volume 13, p. 742

Correction for Volume 13, p. 794

Table of Contents

Volume 13, Issue 6a | June 2003

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PERSPECTIVE

ARTICLES

LETTERS

Methods

RESOURCES

ERRATA