Table of Contents

June 2009; 19 (6)

Next-Generation DNA Sequencing/Review

  • Finding the fifth base: Genome-wide sequencing of cytosine methylation

    • Ryan Lister and
    • Joseph R. Ecker
    Genome Res. June 2009 19: 959-966; Published in Advance March 9, 2009, doi:10.1101/gr.083451.108

Letter

  • Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

    • Michael Y. Tolstorukov,
    • Peter V. Kharchenko,
    • Joseph A. Goldman,
    • Robert E. Kingston,
    • and Peter J. Park
    Genome Res. June 2009 19: 967-977; Published in Advance February 26, 2009, doi:10.1101/gr.084830.108

  • Large-scale mRNA sequencing determines global regulation of RNA editing during brain development

    • Helene Wahlstedt,
    • Chammiran Daniel,
    • Mats Ensterö,
    • and Marie Öhman
    Genome Res. June 2009 19: 978-986; Published in Advance May 6, 2009, doi:10.1101/gr.089409.108

  • The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression

    • Alan M. Pittman,
    • Silvia Naranjo,
    • Emily Webb,
    • Peter Broderick,
    • Esther H. Lips,
    • Tom van Wezel,
    • Hans Morreau,
    • Kate Sullivan,
    • Sarah Fielding,
    • Philip Twiss,
    • Jayaram Vijayakrishnan,
    • Fernando Casares,
    • Mobshra Qureshi,
    • José Luis Gómez-Skarmeta,
    • and Richard S. Houlston
    Genome Res. June 2009 19: 987-993; Published in Advance April 24, 2009, doi:10.1101/gr.092668.109

  • Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level

    • Alexander W. Bruce,
    • Andrés J. López-Contreras,
    • Paul Flicek,
    • Thomas A. Down,
    • Pawandeep Dhami,
    • Shane C. Dillon,
    • Christoph M. Koch,
    • Cordelia F. Langford,
    • Ian Dunham,
    • Robert M. Andrews,
    • and David Vetrie
    Genome Res. June 2009 19: 994-1005; Published in Advance April 28, 2009, doi:10.1101/gr.089086.108
    OPEN ACCESS ARTICLE

  • Genomic mapping of binding regions for the Ecdysone receptor protein complex

    • Zareen Gauhar,
    • Ling V. Sun,
    • Sujun Hua,
    • Christopher E. Mason,
    • Florian Fuchs,
    • Tong-Ruei Li,
    • Michael Boutros,
    • and Kevin P. White
    Genome Res. June 2009 19: 1006-1013; Published in Advance February 23, 2009, doi:10.1101/gr.081349.108

  • Dynamic reprogramming of transcription factors to and from the subtelomere

    • H. Craig Mak,
    • Lorraine Pillus,
    • and Trey Ideker
    Genome Res. June 2009 19: 1014-1025; Published in Advance April 16, 2009, doi:10.1101/gr.084178.108

  • Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization

    • Xiyin Wang,
    • Haibao Tang,
    • John E. Bowers,
    • and Andrew H. Paterson
    Genome Res. June 2009 19: 1026-1032; Published in Advance April 16, 2009, doi:10.1101/gr.087288.108

  • Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

    • Ravi D. Barabote,
    • Gary Xie,
    • David H. Leu,
    • Philippe Normand,
    • Anamaria Necsulea,
    • Vincent Daubin,
    • Claudine Médigue,
    • William S. Adney,
    • Xin Clare Xu,
    • Alla Lapidus,
    • Rebecca E. Parales,
    • Chris Detter,
    • Petar Pujic,
    • David Bruce,
    • Celine Lavire,
    • Jean F. Challacombe,
    • Thomas S. Brettin,
    • and Alison M. Berry
    Genome Res. June 2009 19: 1033-1043; Published in Advance March 6, 2009, doi:10.1101/gr.084848.108

Methods

  • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

    • Alayne L. Brunner,
    • David S. Johnson,
    • Si Wan Kim,
    • Anton Valouev,
    • Timothy E. Reddy,
    • Norma F. Neff,
    • Elizabeth Anton,
    • Catherine Medina,
    • Loan Nguyen,
    • Eric Chiao,
    • Chuba B. Oyolu,
    • Gary P. Schroth,
    • Devin M. Absher,
    • Julie C. Baker,
    • and Richard M. Myers
    Genome Res. June 2009 19: 1044-1056; Published in Advance March 9, 2009, doi:10.1101/gr.088773.108
    OPEN ACCESS ARTICLE

  • Integrating siRNA and protein–protein interaction data to identify an expanded insulin signaling network

    • Zhidong Tu,
    • Carmen Argmann,
    • Kenny K. Wong,
    • Lyndon J. Mitnaul,
    • Stephen Edwards,
    • Iliana C. Sach,
    • Jun Zhu,
    • and Eric E. Schadt
    Genome Res. June 2009 19: 1057-1067; Published in Advance March 4, 2009, doi:10.1101/gr.087890.108

  • High-throughput genotyping by whole-genome resequencing

    • Xuehui Huang,
    • Qi Feng,
    • Qian Qian,
    • Qiang Zhao,
    • Lu Wang,
    • Ahong Wang,
    • Jianping Guan,
    • Danlin Fan,
    • Qijun Weng,
    • Tao Huang,
    • Guojun Dong,
    • Tao Sang,
    • and Bin Han
    Genome Res. June 2009 19: 1068-1076; Published in Advance May 6, 2009, doi:10.1101/gr.089516.108
    OPEN ACCESS ARTICLE

  • Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing

    • Danielle V. Irvine,
    • Derek B. Goto,
    • Matthew W. Vaughn,
    • Yukinobu Nakaseko,
    • W. Richard McCombie,
    • Mitsuhiro Yanagida,
    • and Rob Martienssen
    Genome Res. June 2009 19: 1077-1083; Published in Advance May 7, 2009, doi:10.1101/gr.089318.108

  • Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

    • Antonin Marchais,
    • Magali Naville,
    • Chantal Bohn,
    • Philippe Bouloc,
    • and Daniel Gautheret
    Genome Res. June 2009 19: 1084-1092; Published in Advance February 23, 2009, doi:10.1101/gr.089714.108

Resource

  • Exploring the human genome with functional maps

    • Curtis Huttenhower,
    • Erin M. Haley,
    • Matthew A. Hibbs,
    • Vanessa Dumeaux,
    • Daniel R. Barrett,
    • Hilary A. Coller,
    • and Olga G. Troyanskaya
    Genome Res. June 2009 19: 1093-1106; Published in Advance February 26, 2009, doi:10.1101/gr.082214.108

  • Global networks of functional coupling in eukaryotes from comprehensive data integration

    • Andrey Alexeyenko and
    • Erik L.L. Sonnhammer
    Genome Res. June 2009 19: 1107-1116; Published in Advance February 25, 2009, doi:10.1101/gr.087528.108

  • ABySS: A parallel assembler for short read sequence data

    • Jared T. Simpson,
    • Kim Wong,
    • Shaun D. Jackman,
    • Jacqueline E. Schein,
    • Steven J.M. Jones,
    • and İnanç Birol
    Genome Res. June 2009 19: 1117-1123; Published in Advance February 27, 2009, doi:10.1101/gr.089532.108
    OPEN ACCESS ARTICLE

  • SNP detection for massively parallel whole-genome resequencing

    • Ruiqiang Li,
    • Yingrui Li,
    • Xiaodong Fang,
    • Huanming Yang,
    • Jian Wang,
    • Karsten Kristiansen,
    • and Jun Wang
    Genome Res. June 2009 19: 1124-1132; Published in Advance May 6, 2009, doi:10.1101/gr.088013.108

  • High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues

    • Guo-Jen Huang,
    • Sagiv Shifman,
    • William Valdar,
    • Martina Johannesson,
    • Binnaz Yalcin,
    • Martin S. Taylor,
    • Jennifer M. Taylor,
    • Richard Mott,
    • and Jonathan Flint
    Genome Res. June 2009 19: 1133-1140; Published in Advance April 17, 2009, doi:10.1101/gr.088120.108
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This Issue

June 2009; 19 (6)
Cover
  1. Next-Generation DNA Sequencing/Review
  2. Letter
  3. Methods
  4. Resource

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