Table of Contents

October 2005; 15 (10)

ARTICLES

  • De novo discovery of a tissue-specific gene regulatory module in a chordate

    • David S. Johnson,
    • Qing Zhou,
    • Kasumi Yagi,
    • Nori Satoh,
    • Wing Wong,
    • and Arend Sidow
    Genome Res. October 2005 15: 1315-1324; Published in Advance September 16, 2005, doi:10.1101/gr.4062605

  • Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125

    • Claudine Médigue,
    • Evelyne Krin,
    • Géraldine Pascal,
    • Valérie Barbe,
    • Andreas Bernsel,
    • Philippe N. Bertin,
    • Frankie Cheung,
    • Stéphane Cruveiller,
    • Salvino D'Amico,
    • Angela Duilio,
    • Gang Fang,
    • Georges Feller,
    • Christine Ho,
    • Sophie Mangenot,
    • Gennaro Marino,
    • Johan Nilsson,
    • Ermenegilda Parrilli,
    • Eduardo P.C. Rocha,
    • Zoé Rouy,
    • Agnieszka Sekowska,
    • Maria Luisa Tutino,
    • David Vallenet,
    • Gunnar von Heijne,
    • and Antoine Danchin
    Genome Res. October 2005 15: 1325-1335; Published in Advance September 16, 2005, doi:10.1101/gr.4126905

  • Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis

    • Michaela Falb,
    • Friedhelm Pfeiffer,
    • Peter Palm,
    • Karin Rodewald,
    • Volker Hickmann,
    • Jörg Tittor,
    • and Dieter Oesterhelt
    Genome Res. October 2005 15: 1336-1343; Published in Advance September 16, 2005, doi:10.1101/gr.3952905

LETTERS

  • A genome-wide survey of structural variation between human and chimpanzee

    • Tera L. Newman,
    • Eray Tuzun,
    • V. Anne Morrison,
    • Karen E. Hayden,
    • Mario Ventura,
    • Sean D. McGrath,
    • Mariano Rocchi,
    • and Evan E. Eichler
    Genome Res. October 2005 15: 1344-1356; Published in Advance September 16, 2005, doi:10.1101/gr.4338005

  • Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: Clues from human phylogeography

    • Igor Mokrousov,
    • Ho Minh Ly,
    • Tatiana Otten,
    • Nguyen Ngoc Lan,
    • Boris Vyshnevskyi,
    • Sven Hoffner,
    • and Olga Narvskaya
    Genome Res. October 2005 15: 1357-1364; Published in Advance September 16, 2005, doi:10.1101/gr.3840605

  • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states

    • Stephen S. Fong,
    • Andrew R. Joyce,
    • and Bernhard Ø. Palsson
    Genome Res. October 2005 15: 1365-1372; doi:10.1101/gr.3832305

  • Evolutionary constraints in conserved nongenic sequences of mammals

    • Peter D. Keightley,
    • Gregory V. Kryukov,
    • Shamil Sunyaev,
    • Daniel L. Halligan,
    • and Daniel J. Gaffney
    Genome Res. October 2005 15: 1373-1378; doi:10.1101/gr.3942005

  • Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements

    • Florian M. Pauler,
    • Stefan H. Stricker,
    • Katarzyna E. Warczok,
    • and Denise P. Barlow
    Genome Res. October 2005 15: 1379-1387; doi:10.1101/gr.3783805

  • Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels

    • Martin Bengtsson,
    • Anders Ståhlberg,
    • Patrik Rorsman,
    • and Mikael Kubista
    Genome Res. October 2005 15: 1388-1392; doi:10.1101/gr.3820805

  • Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila

    • Doris Bachtrog
    Genome Res. October 2005 15: 1393-1401; Published in Advance September 16, 2005, doi:10.1101/gr.3543605

  • The function and expansion of the Patched- and Hedgehog-related homologs in C. elegans

    • Olivier Zugasti,
    • Jeena Rajan,
    • and Patricia E. Kuwabara
    Genome Res. October 2005 15: 1402-1410; doi:10.1101/gr.3935405

  • Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae

    • Michaël Bekaert,
    • Hugues Richard,
    • Bernard Prum,
    • and Jean-Pierre Rousset
    Genome Res. October 2005 15: 1411-1420; doi:10.1101/gr.4258005

  • Metabolic functions of duplicate genes in Saccharomyces cerevisiae

    • Lars Kuepfer,
    • Uwe Sauer,
    • and Lars M. Blank
    Genome Res. October 2005 15: 1421-1430; doi:10.1101/gr.3992505

  • Differential methylation of genes and repeats in land plants

    • Pablo D. Rabinowicz,
    • Robert Citek,
    • Muhammad A. Budiman,
    • Andrew Nunberg,
    • Joseph A. Bedell,
    • Nathan Lakey,
    • Andrew L. O'Shaughnessy,
    • Lidia U. Nascimento,
    • W. Richard McCombie,
    • and Robert A. Martienssen
    Genome Res. October 2005 15: 1431-1440; doi:10.1101/gr.4100405

Methods

  • Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries

    • John Emberton,
    • Jianxin Ma,
    • Yinan Yuan,
    • Phillip SanMiguel,
    • and Jeffrey L. Bennetzen
    Genome Res. October 2005 15: 1441-1446; doi:10.1101/gr.3362105

  • Simple, robust methods for high-throughput nanoliter-scale DNA sequencing

    • Duane E. Smailus,
    • Andre Marziali,
    • Philip Dextras,
    • Marco A. Marra,
    • and Robert A. Holt
    Genome Res. October 2005 15: 1447-1450; Published in Advance September 16, 2005, doi:10.1101/gr.4221805

RESOURCES

  • Galaxy: A platform for interactive large-scale genome analysis

    • Belinda Giardine,
    • Cathy Riemer,
    • Ross C. Hardison,
    • Richard Burhans,
    • Laura Elnitski,
    • Prachi Shah,
    • Yi Zhang,
    • Daniel Blankenberg,
    • Istvan Albert,
    • James Taylor,
    • Webb Miller,
    • W. James Kent,
    • and Anton Nekrutenko
    Genome Res. October 2005 15: 1451-1455; Published in Advance September 16, 2005, doi:10.1101/gr.4086505

  • The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species

    • Kevin P. Byrne and
    • Kenneth H. Wolfe
    Genome Res. October 2005 15: 1456-1461; Published in Advance September 16, 2005, doi:10.1101/gr.3672305
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This Issue

October 2005; 15 (10)
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  1. ARTICLES
  2. LETTERS
  3. Methods
  4. RESOURCES

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