Table of Contents

June 2003; 13 (6a)

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,
    • Ana Pombo,
    • Günter Schmahl,
    • Joachim P. Spatz,
    • and Roel van Driel
    Genome Res. June 2003 13: 1029-1041; Published in Advance May 12, 2003, doi:10.1101/gr.946403

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,
    • Teruo Yasunaga,
    • Hideo Hayashi,
    • Masahira Hattori,
    • and Shigeyuki Hamada
    Genome Res. June 2003 13: 1042-1055; doi:10.1101/gr.1096703

  • 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,
    • and Hans Lehrach
    Genome Res. June 2003 13: 1056-1066; doi:10.1101/gr.874803

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

    • Christoph Winkler,
    • Matthias Schäfer,
    • Jutta Duschl,
    • Manfred Schartl,
    • and Jean-Nicolas Volff
    Genome Res. June 2003 13: 1067-1081; Published in Advance May 12, 2003, doi:10.1101/gr.1097503

LETTERS

  • The Zebrafish Annexin Gene Family

    • Steven A. Farber,
    • Robert A. De Rose,
    • Eric S. Olson,
    • and Marnie E. Halpern
    Genome Res. June 2003 13: 1082-1096; doi:10.1101/gr.479603

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

    • Mark Shannon,
    • Aaron T. Hamilton,
    • Laurie Gordon,
    • Elbert Branscomb,
    • and Lisa Stubbs
    Genome Res. June 2003 13: 1097-1110; Published in Advance May 12, 2003, doi:10.1101/gr.963903

  • Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters

    • Simona Santini,
    • Jeffrey L. Boore,
    • and Axel Meyer
    Genome Res. June 2003 13: 1111-1122; doi:10.1101/gr.700503

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

    • Eduardo P.C. Rocha
    Genome Res. June 2003 13: 1123-1132; Published in Advance May 12, 2003, doi:10.1101/gr.966203

  • Extrachromosomal Circular DNA of Tandemly Repeated Genomic Sequences in Drosophila

    • Sarit Cohen,
    • Keren Yacobi,
    • and Daniel Segal
    Genome Res. June 2003 13: 1133-1145; doi:10.1101/gr.907603

  • 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,
    • and Jeffrey Skolnick
    Genome Res. June 2003 13: 1146-1154; doi:10.1101/gr.1145203

  • Phylogenetically Older Introns Strongly Correlate With Module Boundaries in Ancient Proteins

    • Alexei Fedorov,
    • Scott Roy,
    • Xiaohong Cao,
    • and Walter Gilbert
    Genome Res. June 2003 13: 1155-1157; Published in Advance May 12, 2003, doi:10.1101/gr.1008203

  • The Pattern of Polymorphism on Human Chromosome 21

    • Hideki Innan,
    • Badri Padhukasahasram,
    • and Magnus Nordborg
    Genome Res. June 2003 13: 1158-1168; doi:10.1101/gr.466303

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

    • Naoya Yuhki,
    • Thomas Beck,
    • Robert M. Stephens,
    • Yoko Nishigaki,
    • Kymberly Newmann,
    • and Stephen J. O'Brien
    Genome Res. June 2003 13: 1169-1179; Published in Advance May 12, 2003, doi:10.1101/gr.976103

  • 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,
    • Theresa Walunas,
    • Robert Haselkorn,
    • Ross Overbeek,
    • and Nikos Kyrpides
    Genome Res. June 2003 13: 1180-1189; doi:10.1101/gr.566003

Methods

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

    • Lingang Zhang,
    • Vladimir Pavlovic,
    • Charles R Cantor,
    • and Simon Kasif
    Genome Res. June 2003 13: 1190-1202; Published in Advance May 12, 2003, doi:10.1101/gr.703903

  • Assessment of SAGE in Transcript Identification

    • Erin D. Pleasance,
    • Marco A. Marra,
    • and Steven J.M. Jones
    Genome Res. June 2003 13: 1203-1215; Published in Advance May 12, 2003, doi:10.1101/gr.873003

  • Computational Discovery of Internal Micro-Exons

    • Natalia Volfovsky,
    • Brian J. Haas,
    • and Steven L. Salzberg
    Genome Res. June 2003 13: 1216-1221; doi:10.1101/gr.677503

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,
    • C. Victor Jongeneel,
    • Mark I. McCarthy,
    • Tania Hide,
    • and Winston Hide
    Genome Res. June 2003 13: 1222-1230; doi:10.1101/gr.985203

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

    • Asako Koike,
    • Yoshiyuki Kobayashi,
    • and Toshihisa Takagi
    Genome Res. June 2003 13: 1231-1243; doi:10.1101/gr.835903

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

    • Christopher D. Fjell,
    • Ian Bosdet,
    • Jacqueline E. Schein,
    • Steven J.M. Jones,
    • and Marco A. Marra
    Genome Res. June 2003 13: 1244-1249; doi:10.1101/gr.819303

  • 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,
    • and Bernd Weisshaar
    Genome Res. June 2003 13: 1250-1257; doi:10.1101/gr.728603

ERRATA

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This Issue

June 2003; 13 (6a)
Cover
  1. PERSPECTIVE
  2. ARTICLES
  3. LETTERS
  4. Methods
  5. RESOURCES
  6. ERRATA

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