Table of Contents

August 2005; 15 (8)

ARTICLES

  • Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects

    • Patrick H. Degnan,
    • Adam B. Lazarus,
    • and Jennifer J. Wernegreen
    Genome Res. August 2005 15: 1023-1033; doi:10.1101/gr.3771305

  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

    • Adam Siepel,
    • Gill Bejerano,
    • Jakob S. Pedersen,
    • Angie S. Hinrichs,
    • Minmei Hou,
    • Kate Rosenbloom,
    • Hiram Clawson,
    • John Spieth,
    • LaDeana W. Hillier,
    • Stephen Richards,
    • George M. Weinstock,
    • Richard K. Wilson,
    • Richard A. Gibbs,
    • W. James Kent,
    • Webb Miller,
    • and David Haussler
    Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005

LETTERS

  • Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

    • David C. King,
    • James Taylor,
    • Laura Elnitski,
    • Francesca Chiaromonte,
    • Webb Miller,
    • and Ross C. Hardison
    Genome Res. August 2005 15: 1051-1060; Published in Advance July 15, 2005, doi:10.1101/gr.3642605

  • A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts

    • Elisa de la Calle-Mustienes,
    • Cármen Gloria Feijóo,
    • Miguel Manzanares,
    • Juan J. Tena,
    • Elisa Rodríguez-Seguel,
    • Annalisa Letizia,
    • Miguel L. Allende,
    • and José Luis Gómez-Skarmeta
    Genome Res. August 2005 15: 1061-1072; Published in Advance July 15, 2005, doi:10.1101/gr.4004805

  • Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution

    • Sarah J. Wheelan,
    • Yasunori Aizawa,
    • Jeffrey S. Han,
    • and Jef D. Boeke
    Genome Res. August 2005 15: 1073-1078; Published in Advance July 15, 2005, doi:10.1101/gr.3688905

  • Human ribosomal RNA gene arrays display a broad range of palindromic structures

    • Sandrine Caburet,
    • Chiara Conti,
    • Catherine Schurra,
    • Ronald Lebofsky,
    • Stuart J. Edelstein,
    • and Aaron Bensimon
    Genome Res. August 2005 15: 1079-1085; Published in Advance July 15, 2005, doi:10.1101/gr.3970105

  • The scale of mutational variation in the murid genome

    • Daniel J. Gaffney and
    • Peter D. Keightley
    Genome Res. August 2005 15: 1086-1094; Published in Advance July 15, 2005, doi:10.1101/gr.3895005

  • Random mutagenesis of proximal mouse chromosome 5 uncovers predominantly embryonic lethal mutations

    • Lawriston Wilson,
    • Yung-Hao Ching,
    • Michael Farias,
    • Suzanne A. Hartford,
    • Gareth Howell,
    • Hongguang Shao,
    • Maja Bucan,
    • and John C. Schimenti
    Genome Res. August 2005 15: 1095-1105; Published in Advance July 15, 2005, doi:10.1101/gr.3826505

  • An extraordinary retrotransposon family encoding dual endonucleases

    • Kenji K. Kojima and
    • Haruhiko Fujiwara
    Genome Res. August 2005 15: 1106-1117; doi:10.1101/gr.3271405

  • Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias

    • Rong Wang,
    • John T. Prince,
    • and Edward M. Marcotte
    Genome Res. August 2005 15: 1118-1126; doi:10.1101/gr.3994105

Methods

  • Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi

    • Jade P. Vinson,
    • David B. Jaffe,
    • Keith O'Neill,
    • Elinor K. Karlsson,
    • Nicole Stange-Thomann,
    • Scott Anderson,
    • Jill P. Mesirov,
    • Nori Satoh,
    • Yutaka Satou,
    • Chad Nusbaum,
    • Bruce Birren,
    • James E. Galagan,
    • and Eric S. Lander
    Genome Res. August 2005 15: 1127-1135; doi:10.1101/gr.3722605

  • Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis

    • Josephine N. Harada,
    • Kristen E. Bower,
    • Anthony P. Orth,
    • Scott Callaway,
    • Christian G. Nelson,
    • Casey Laris,
    • John B. Hogenesch,
    • Peter K. Vogt,
    • and Sumit K. Chanda
    Genome Res. August 2005 15: 1136-1144; Published in Advance July 15, 2005, doi:10.1101/gr.3889305
    OPEN ACCESS ARTICLE

  • Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics

    • Jason Gertz,
    • Linda Riles,
    • Peter Turnbaugh,
    • Su-Wen Ho,
    • and Barak A. Cohen
    Genome Res. August 2005 15: 1145-1152; doi:10.1101/gr.3859605

  • Estimating the tempo and mode of gene family evolution from comparative genomic data

    • Matthew W. Hahn,
    • Tijl De Bie,
    • Jason E. Stajich,
    • Chi Nguyen,
    • and Nello Cristianini
    Genome Res. August 2005 15: 1153-1160; doi:10.1101/gr.3567505

  • Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations

    • Nicolas Ray,
    • Mathias Currat,
    • Pierre Berthier,
    • and Laurent Excoffier
    Genome Res. August 2005 15: 1161-1167; doi:10.1101/gr.3708505

  • Region-specific detection of neuroblastoma loss of heterozygosity at multiple loci simultaneously using a SNP-based tag-array platform

    • John M. Maris,
    • George Hii,
    • Craig A. Gelfand,
    • Shobha Varde,
    • Peter S. White,
    • Eric Rappaport,
    • Saul Surrey,
    • and Paolo Fortina
    Genome Res. August 2005 15: 1168-1176; doi:10.1101/gr.3865305
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This Issue

August 2005; 15 (8)
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  1. ARTICLES
  2. LETTERS
  3. Methods

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