Table of Contents

May 2004; 14 (5)

ARTICLES

  • Analysis of Segmental Duplications and Genome Assembly in the Mouse

    • Jeffrey A. Bailey,
    • Deanna M. Church,
    • Mario Ventura,
    • Mariano Rocchi,
    • and Evan E. Eichler
    Genome Res. May 2004 14: 789-801; doi:10.1101/gr.2238404

  • 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,
    • and Rob J. Kulathinal
    Genome Res. May 2004 14: 802-811; doi:10.1101/gr.2195604

LETTERS

  • The Human MitoChip: A High-Throughput Sequencing Microarray for Mitochondrial Mutation Detection

    • Anirban Maitra,
    • Yoram Cohen,
    • Susannah E.D. Gillespie,
    • Elizabeth Mambo,
    • Noriyoshi Fukushima,
    • Mohammad O. Hoque,
    • Nila Shah,
    • Michael Goggins,
    • Joseph Califano,
    • David Sidransky,
    • and Aravinda Chakravarti
    Genome Res. May 2004 14: 812-819; doi:10.1101/gr.2228504

  • A Medaka Gene Map: The Trace of Ancestral Vertebrate Proto-Chromosomes Revealed by Comparative Gene Mapping

    • Kiyoshi Naruse,
    • Minoru Tanaka,
    • Kazuei Mita,
    • Akihiro Shima,
    • John Postlethwait,
    • and Hiroshi Mitani
    Genome Res. May 2004 14: 820-828; Published in Advance April 12, 2004, doi:10.1101/gr.2004004

  • A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation

    • Amos Tanay,
    • Irit Gat-Viks,
    • and Ron Shamir
    Genome Res. May 2004 14: 829-834; doi:10.1101/gr.2064404

  • Dynamics of a Human Interparalog Gene Conversion Hotspot

    • Elena Bosch,
    • Matthew E. Hurles,
    • Arcadi Navarro,
    • and Mark A. Jobling
    Genome Res. May 2004 14: 835-844; doi:10.1101/gr.2177404

  • Testing the Chromosomal Speciation Hypothesis for Humans and Chimpanzees

    • Jianzhi Zhang,
    • Xiaoxia Wang,
    • and Ondrej Podlaha
    Genome Res. May 2004 14: 845-851; doi:10.1101/gr.1891104

  • Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment

    • Emmanouil T. Dermitzakis,
    • Ewen Kirkness,
    • Scott Schwarz,
    • Ewan Birney,
    • Alexandre Reymond,
    • and Stylianos E. Antonarakis
    Genome Res. May 2004 14: 852-859; Published in Advance April 12, 2004, doi:10.1101/gr.1934904

  • Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice

    • Jianxin Ma,
    • Katrien M. Devos,
    • and Jeffrey L. Bennetzen
    Genome Res. May 2004 14: 860-869; Published in Advance April 12, 2004, doi:10.1101/gr.1466204

Methods

  • Decoding Randomly Ordered DNA Arrays

    • Kevin L. Gunderson,
    • Semyon Kruglyak,
    • Michael S. Graige,
    • Francisco Garcia,
    • Bahram G. Kermani,
    • Chanfeng Zhao,
    • Diping Che,
    • Todd Dickinson,
    • Eliza Wickham,
    • Jim Bierle,
    • Dennis Doucet,
    • Monika Milewski,
    • Robert Yang,
    • Chris Siegmund,
    • Juergen Haas,
    • Lixin Zhou,
    • Arnold Oliphant,
    • Jian-Bing Fan,
    • Steven Barnard,
    • and Mark S. Chee
    Genome Res. May 2004 14: 870-877; Published in Advance April 12, 2004, doi:10.1101/gr.2255804

  • A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices

    • Jian-Bing Fan,
    • Joanne M. Yeakley,
    • Marina Bibikova,
    • Eugene Chudin,
    • Eliza Wickham,
    • Jing Chen,
    • Dennis Doucet,
    • Philippe Rigault,
    • Baohong Zhang,
    • Richard Shen,
    • Celeste McBride,
    • Hai-Ri Li,
    • Xiang-Dong Fu,
    • Arnold Oliphant,
    • David L. Barker,
    • and Mark S. Chee
    Genome Res. May 2004 14: 878-885; doi:10.1101/gr.2167504

  • Compositional Gene Landscapes in Vertebrates

    • Stéphane Cruveiller,
    • Kamel Jabbari,
    • Oliver Clay,
    • and Giorgio Bernardi
    Genome Res. May 2004 14: 886-892; doi:10.1101/gr.2246704

  • Systematic Insertional Mutagenesis of a Streptomycete Genome: A Link Between Osmoadaptation and Antibiotic Production

    • Amy Bishop,
    • Sue Fielding,
    • Paul Dyson,
    • and Paul Herron
    Genome Res. May 2004 14: 893-900; Published in Advance April 12, 2004, doi:10.1101/gr.1710304

  • Two Methods of Whole-Genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel

    • David L. Barker,
    • Mark S.T. Hansen,
    • A. Fawad Faruqi,
    • Diane Giannola,
    • Orlando R. Irsula,
    • Roger S. Lasken,
    • Martin Latterich,
    • Vladimir Makarov,
    • Arnold Oliphant,
    • Jonathon H. Pinter,
    • Richard Shen,
    • Irina Sleptsova,
    • William Ziehler,
    • and Eric Lai
    Genome Res. May 2004 14: 901-907; doi:10.1101/gr.1949704

  • Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies

    • Kui Zhang,
    • Zhaohui S. Qin,
    • Jun S. Liu,
    • Ting Chen,
    • Michael S. Waterman,
    • and Fengzhu Sun
    Genome Res. May 2004 14: 908-916; Published in Advance April 12, 2004, doi:10.1101/gr.1837404

RESOURCE

  • Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery

    • Iwei Yeh,
    • Theodor Hanekamp,
    • Sophia Tsoka,
    • Peter D. Karp,
    • and Russ B. Altman
    Genome Res. May 2004 14: 917-924; Published in Advance April 12, 2004, doi:10.1101/gr.2050304

ENSEMBL Special

  • An Overview of Ensembl

    • Ewan Birney,
    • T. Daniel Andrews,
    • Paul Bevan,
    • Mario Caccamo,
    • Yuan Chen,
    • Laura Clarke,
    • Guy Coates,
    • James Cuff,
    • Val Curwen,
    • Tim Cutts,
    • Thomas Down,
    • Eduardo Eyras,
    • Xose M. Fernandez-Suarez,
    • Paul Gane,
    • Brian Gibbins,
    • James Gilbert,
    • Martin Hammond,
    • Hans-Rudolf Hotz,
    • Vivek Iyer,
    • Kerstin Jekosch,
    • Andreas Kahari,
    • Arek Kasprzyk,
    • Damian Keefe,
    • Stephen Keenan,
    • Heikki Lehvaslaiho,
    • Graham McVicker,
    • Craig Melsopp,
    • Patrick Meidl,
    • Emmanuel Mongin,
    • Roger Pettett,
    • Simon Potter,
    • Glenn Proctor,
    • Mark Rae,
    • Steve Searle,
    • Guy Slater,
    • Damian Smedley,
    • James Smith,
    • Will Spooner,
    • Arne Stabenau,
    • James Stalker,
    • Roy Storey,
    • Abel Ureta-Vidal,
    • K. Cara Woodwark,
    • Graham Cameron,
    • Richard Durbin,
    • Anthony Cox,
    • Tim Hubbard,
    • and Michele Clamp
    Genome Res. May 2004 14: 925-928; Published in Advance April 12, 2004, doi:10.1101/gr.1860604

  • The Ensembl Core Software Libraries

    • Arne Stabenau,
    • Graham McVicker,
    • Craig Melsopp,
    • Glenn Proctor,
    • Michele Clamp,
    • and Ewan Birney
    Genome Res. May 2004 14: 929-933; doi:10.1101/gr.1857204

  • The Ensembl Analysis Pipeline

    • Simon C. Potter,
    • Laura Clarke,
    • Val Curwen,
    • Stephen Keenan,
    • Emmanuel Mongin,
    • Stephen M.J. Searle,
    • Arne Stabenau,
    • Roy Storey,
    • and Michele Clamp
    Genome Res. May 2004 14: 934-941; doi:10.1101/gr.1859804

  • The Ensembl Automatic Gene Annotation System

    • Val Curwen,
    • Eduardo Eyras,
    • T. Daniel Andrews,
    • Laura Clarke,
    • Emmanuel Mongin,
    • Steven M.J. Searle,
    • and Michele Clamp
    Genome Res. May 2004 14: 942-950; doi:10.1101/gr.1858004

  • The Ensembl Web Site: Mechanics of a Genome Browser

    • James Stalker,
    • Brian Gibbins,
    • Patrick Meidl,
    • James Smith,
    • William Spooner,
    • Hans-Rudolf Hotz,
    • and Antony V. Cox
    Genome Res. May 2004 14: 951-955; doi:10.1101/gr.1863004

  • Sockeye: A 3D Environment for Comparative Genomics

    • Stephen B. Montgomery,
    • Tamara Astakhova,
    • Mikhail Bilenky,
    • Ewan Birney,
    • Tony Fu,
    • Maik Hassel,
    • Craig Melsopp,
    • Marcin Rak,
    • A. Gordon Robertson,
    • Monica Sleumer,
    • Asim S. Siddiqui,
    • and Steven J.M. Jones
    Genome Res. May 2004 14: 956-962; doi:10.1101/gr.1890304

  • The Otter Annotation System

    • Stephen M.J. Searle,
    • James Gilbert,
    • Vivek Iyer,
    • and Michele Clamp
    Genome Res. May 2004 14: 963-970; doi:10.1101/gr.1864804

  • The Ensembl Computing Architecture

    • James A. Cuff,
    • Guy M.P. Coates,
    • Tim J.R. Cutts,
    • and Mark Rae
    Genome Res. May 2004 14: 971-975; doi:10.1101/gr.1866304

  • ESTGenes: Alternative Splicing From ESTs in Ensembl

    • Eduardo Eyras,
    • Mario Caccamo,
    • Val Curwen,
    • and Michele Clamp
    Genome Res. May 2004 14: 976-987; doi:10.1101/gr.1862204

  • GeneWise and Genomewise

    • Ewan Birney,
    • Michele Clamp,
    • and Richard Durbin
    Genome Res. May 2004 14: 988-995; doi:10.1101/gr.1865504
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This Issue

May 2004; 14 (5)
Cover
  1. ARTICLES
  2. LETTERS
  3. Methods
  4. RESOURCE
  5. ENSEMBL Special

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