Table of Contents

June 2008; 18 (6)

Next-Generation DNA Sequencing/Review

  • Next-Generation DNA Sequencing/Review:

    The new paradigm of flow cell sequencing

    • Robert A. Holt
    • and Steven J.M. Jones
    Genome Res. June 2008 18:839-846; doi:10.1101/gr.073262.107

LETTERS

  • LETTER:

    Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair

    • Marijke Bauters,
    • Hilde Van Esch,
    • Michael J. Friez,
    • Odile Boespflug-Tanguy,
    • Martin Zenker,
    • Angela M. Vianna-Morgante,
    • Carla Rosenberg,
    • Jaakko Ignatius,
    • Martine Raynaud,
    • Karen Hollanders,
    • Karen Govaerts,
    • Kris Vandenreijt,
    • Florence Niel,
    • Pierre Blanc,
    • Roger E. Stevenson,
    • Jean-Pierre Fryns,
    • Peter Marynen,
    • Charles E. Schwartz,
    • and Guy Froyen
    Genome Res. June 2008 18:847-858; Published in Advance April 2, 2008, doi:10.1101/gr.075903.107
  • LETTER:

    Translation from nonautonomous type IAP retrotransposon is a critical determinant of transposition activity: Implication for retrotransposon-mediated genome evolution

    • Ei-suke Saito,
    • Vincent W. Keng,
    • Junji Takeda,
    • and Kyoji Horie
    Genome Res. June 2008 18:859-868; Published in Advance May 2, 2008, doi:10.1101/gr.069310.107
  • LETTER:

    Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

    • Keiko Akagi,
    • Jingfeng Li,
    • Robert M. Stephens,
    • Natalia Volfovsky,
    • and David E. Symer
    Genome Res. June 2008 18:869-880; Published in Advance April 1, 2008, doi:10.1101/gr.075770.107
  • LETTER:

    Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias

    • Mikael Brandström
    • and Hans Ellegren
    Genome Res. June 2008 18:881-887; Published in Advance March 20, 2008, doi:10.1101/gr.075242.107
  • LETTER:

    De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring

    • Pontus Larsson,
    • Andrea Hinas,
    • David H. Ardell,
    • Leif A. Kirsebom,
    • Anders Virtanen,
    • and Fredrik Söderbom
    Genome Res. June 2008 18:888-899; Published in Advance March 17, 2008, doi:10.1101/gr.069104.107
  • LETTER:

    Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

    • Byung-Kwan Cho,
    • Eric M. Knight,
    • Christian L. Barrett,
    • and Bernhard Ø. Palsson
    Genome Res. June 2008 18:900-910; Published in Advance March 13, 2008, doi:10.1101/gr.070276.107

Methods

  • Methods:

    Power and SNP tagging in whole mitochondrial genome association studies

    • Allan F. McRae,
    • Enda M. Byrne,
    • Zhen Zhen Zhao,
    • Grant W. Montgomery,
    • and Peter M. Visscher
    Genome Res. June 2008 18:911-917; Published in Advance March 20, 2008, doi:10.1101/gr.074872.107
  • Methods:

    Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

    • Georg Zeller,
    • Richard M. Clark,
    • Korbinian Schneeberger,
    • Anja Bohlen,
    • Detlef Weigel,
    • and Gunnar Rätsch
    Genome Res. June 2008 18:918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
    OPEN ACCESS ARTICLE
  • Methods:

    Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions

    • Mahesh Yaragatti,
    • Claudio Basilico,
    • and Lisa Dailey
    Genome Res. June 2008 18:930-938; Published in Advance April 25, 2008, doi:10.1101/gr.073460.107
  • Methods:

    Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

    • Giusy Della Gatta,
    • Mukesh Bansal,
    • Alberto Ambesi-Impiombato,
    • Dario Antonini,
    • Caterina Missero,
    • and Diego di Bernardo
    Genome Res. June 2008 18:939-948; Published in Advance April 25, 2008, doi:10.1101/gr.073601.107
  • Methods:

    Large-scale analysis of gene clustering in bacteria

    • Qingwu Yang
    • and Sing-Hoi Sze
    Genome Res. June 2008 18:949-956; Published in Advance April 4, 2008, doi:10.1101/gr.072322.107

RESOURCE

  • RESOURCE:

    A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach

    • Evgeny A. Glazov,
    • Pauline A. Cottee,
    • Wesley C. Barris,
    • Robert J. Moore,
    • Brian P. Dalrymple,
    • and Mark L. Tizard
    Genome Res. June 2008 18:957-964; Published in Advance May 9, 2008, doi:10.1101/gr.074740.107

Platypus Special/Letter

  • Platypus Special/Letter:

    Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes

    • Frédéric Veyrunes,
    • Paul D. Waters,
    • Pat Miethke,
    • Willem Rens,
    • Daniel McMillan,
    • Amber E. Alsop,
    • Frank Grützner,
    • Janine E. Deakin,
    • Camilla M. Whittington,
    • Kyriena Schatzkamer,
    • Colin L. Kremitzki,
    • Tina Graves,
    • Malcolm A. Ferguson-Smith,
    • Wes Warren,
    • and Jennifer A. Marshall Graves
    Genome Res. June 2008 18:965-973; Published in Advance May 7, 2008, doi:10.1101/gr.7101908
  • Platypus Special/Letter:

    Origin of INSL3-mediated testicular descent in therian mammals

    • Jae-Il Park,
    • Jenia Semyonov,
    • Chia Lin Chang,
    • Wei Yi,
    • Wesley Warren,
    • and Sheau Yu Teddy Hsu
    Genome Res. June 2008 18:974-985; Published in Advance May 7, 2008, doi:10.1101/gr.7119108
  • Platypus Special/Letter:

    Defensins and the convergent evolution of platypus and reptile venom genes

    • Camilla M. Whittington,
    • Anthony T. Papenfuss,
    • Paramjit Bansal,
    • Allan M. Torres,
    • Emily S.W. Wong,
    • Janine E. Deakin,
    • Tina Graves,
    • Amber Alsop,
    • Kyriena Schatzkamer,
    • Colin Kremitzki,
    • Chris P. Ponting,
    • Peter Temple-Smith,
    • Wesley C. Warren,
    • Philip W. Kuchel,
    • and Katherine Belov
    Genome Res. June 2008 18:986-994; Published in Advance May 7, 2008, doi:10.1101/gr.7149808
    OPEN ACCESS ARTICLE
  • Platypus Special/Letter:

    Conservation of small RNA pathways in platypus

    • Elizabeth P. Murchison,
    • Pouya Kheradpour,
    • Ravi Sachidanandam,
    • Carly Smith,
    • Emily Hodges,
    • Zhenyu Xuan,
    • Manolis Kellis,
    • Frank Grützner,
    • Alexander Stark,
    • and Gregory J. Hannon
    Genome Res. June 2008 18:995-1004; Published in Advance May 7, 2008, doi:10.1101/gr.073056.107
  • Platypus Special/Letter:

    Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs

    • Jürgen Schmitz,
    • Anja Zemann,
    • Gennady Churakov,
    • Heiner Kuhl,
    • Frank Grützner,
    • Richard Reinhardt,
    • and Jürgen Brosius
    Genome Res. June 2008 18:1005-1010; Published in Advance May 7, 2008, doi:10.1101/gr.7177908
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This Issue

June 2008; 18 (6)
Cover
  1. Next-Generation DNA Sequencing/Review
  2. LETTERS
  3. Methods
  4. RESOURCE
  5. Platypus Special/Letter

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