Table of Contents

September 2009; 19 (9)

Letter

  • Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans

    • Alison H. Harrill,
    • Paul B. Watkins,
    • Stephen Su,
    • Pamela K. Ross,
    • David E. Harbourt,
    • Ioannis M. Stylianou,
    • Gary A. Boorman,
    • Mark W. Russo,
    • Richard S. Sackler,
    • Stephen C. Harris,
    • Philip C. Smith,
    • Raymond Tennant,
    • Molly Bogue,
    • Kenneth Paigen,
    • Christopher Harris,
    • Tanupriya Contractor,
    • Timothy Wiltshire,
    • Ivan Rusyn,
    • and David W. Threadgill
    Genome Res. September 2009 19: 1507-1515; Published in Advance May 5, 2009, doi:10.1101/gr.090241.108

  • Mobile elements create structural variation: Analysis of a complete human genome

    • Jinchuan Xing,
    • Yuhua Zhang,
    • Kyudong Han,
    • Abdel Halim Salem,
    • Shurjo K. Sen,
    • Chad D. Huff,
    • Qiong Zhou,
    • Ewen F. Kirkness,
    • Samuel Levy,
    • Mark A. Batzer,
    • and Lynn B. Jorde
    Genome Res. September 2009 19: 1516-1526; Published in Advance May 13, 2009, doi:10.1101/gr.091827.109

Methods

  • Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

    • Kevin Judd McKernan,
    • Heather E. Peckham,
    • Gina L. Costa,
    • Stephen F. McLaughlin,
    • Yutao Fu,
    • Eric F. Tsung,
    • Christopher R. Clouser,
    • Cisyla Duncan,
    • Jeffrey K. Ichikawa,
    • Clarence C. Lee,
    • Zheng Zhang,
    • Swati S. Ranade,
    • Eileen T. Dimalanta,
    • Fiona C. Hyland,
    • Tanya D. Sokolsky,
    • Lei Zhang,
    • Andrew Sheridan,
    • Haoning Fu,
    • Cynthia L. Hendrickson,
    • Bin Li,
    • Lev Kotler,
    • Jeremy R. Stuart,
    • Joel A. Malek,
    • Jonathan M. Manning,
    • Alena A. Antipova,
    • Damon S. Perez,
    • Michael P. Moore,
    • Kathleen C. Hayashibara,
    • Michael R. Lyons,
    • Robert E. Beaudoin,
    • Brittany E. Coleman,
    • Michael W. Laptewicz,
    • Adam E. Sannicandro,
    • Michael D. Rhodes,
    • Rajesh K. Gottimukkala,
    • Shan Yang,
    • Vineet Bafna,
    • Ali Bashir,
    • Andrew MacBride,
    • Can Alkan,
    • Jeffrey M. Kidd,
    • Evan E. Eichler,
    • Martin G. Reese,
    • Francisco M. De La Vega,
    • and Alan P. Blanchard
    Genome Res. September 2009 19: 1527-1541; Published in Advance June 22, 2009, doi:10.1101/gr.091868.109
    OPEN ACCESS ARTICLE

  • A probabilistic approach for SNP discovery in high-throughput human resequencing data

    • Rose Hoberman,
    • Joana Dias,
    • Bing Ge,
    • Eef Harmsen,
    • Michael Mayhew,
    • Dominique J. Verlaan,
    • Tony Kwan,
    • Ken Dewar,
    • Mathieu Blanchette,
    • and Tomi Pastinen
    Genome Res. September 2009 19: 1542-1552; Published in Advance July 15, 2009, doi:10.1101/gr.092072.109

  • Identification of deleterious mutations within three human genomes

    • Sung Chun and
    • Justin C. Fay
    Genome Res. September 2009 19: 1553-1561; Published in Advance July 14, 2009, doi:10.1101/gr.092619.109

  • Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

    • Sudhir Kumar,
    • Michael P. Suleski,
    • Glenn J. Markov,
    • Simon Lawrence,
    • Antonio Marco,
    • and Alan J. Filipski
    Genome Res. September 2009 19: 1562-1569; Published in Advance June 22, 2009, doi:10.1101/gr.091991.109

  • Identification of rare cancer driver mutations by network reconstruction

    • Ali Torkamani and
    • Nicholas J. Schork
    Genome Res. September 2009 19: 1570-1578; Published in Advance July 2, 2009, doi:10.1101/gr.092833.109

  • A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease

    • Heather C. Mefford,
    • Gregory M. Cooper,
    • Troy Zerr,
    • Joshua D. Smith,
    • Carl Baker,
    • Neil Shafer,
    • Erik C. Thorland,
    • Cindy Skinner,
    • Charles E. Schwartz,
    • Deborah A. Nickerson,
    • and Evan E. Eichler
    Genome Res. September 2009 19: 1579-1585; Published in Advance June 8, 2009, doi:10.1101/gr.094987.109

  • Sensitive and accurate detection of copy number variants using read depth of coverage

    • Seungtai Yoon,
    • Zhenyu Xuan,
    • Vladimir Makarov,
    • Kenny Ye,
    • and Jonathan Sebat
    Genome Res. September 2009 19: 1586-1592; Published in Advance August 5, 2009, doi:10.1101/gr.092981.109
    OPEN ACCESS ARTICLE

  • High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

    • Emily Hodges,
    • Andrew D. Smith,
    • Jude Kendall,
    • Zhenyu Xuan,
    • Kandasamy Ravi,
    • Michelle Rooks,
    • Michael Q. Zhang,
    • Kenny Ye,
    • Arindam Bhattacharjee,
    • Leonardo Brizuela,
    • W. Richard McCombie,
    • Michael Wigler,
    • Gregory J. Hannon,
    • and James B. Hicks
    Genome Res. September 2009 19: 1593-1605; Published in Advance July 6, 2009, doi:10.1101/gr.095190.109
    OPEN ACCESS ARTICLE

  • Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

    • Jin Billy Li,
    • Yuan Gao,
    • John Aach,
    • Kun Zhang,
    • Gregory V. Kryukov,
    • Bin Xie,
    • Annika Ahlford,
    • Jung-Ki Yoon,
    • Abraham M. Rosenbaum,
    • Alexander Wait Zaranek,
    • Emily LeProust,
    • Shamil R. Sunyaev,
    • and George M. Church
    Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109

  • Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing

    • Daniel Summerer,
    • Haiguo Wu,
    • Bettina Haase,
    • Yang Cheng,
    • Nadine Schracke,
    • Cord F. Stähler,
    • Mark S. Chee,
    • Peer F. Stähler,
    • and Markus Beier
    Genome Res. September 2009 19: 1616-1621; Published in Advance July 28, 2009, doi:10.1101/gr.091942.109
    OPEN ACCESS ARTICLE

Resource

  • The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

    • Sung-Min Ahn,
    • Tae-Hyung Kim,
    • Sunghoon Lee,
    • Deokhoon Kim,
    • Ho Ghang,
    • Dae-Soo Kim,
    • Byoung-Chul Kim,
    • Sang-Yoon Kim,
    • Woo-Yeon Kim,
    • Chulhong Kim,
    • Daeui Park,
    • Yong Seok Lee,
    • Sangsoo Kim,
    • Rohit Reja,
    • Sungwoong Jho,
    • Chang Geun Kim,
    • Ji-Young Cha,
    • Kyung-Hee Kim,
    • Bonghee Lee,
    • Jong Bhak,
    • and Seong-Jin Kim
    Genome Res. September 2009 19: 1622-1629; Published in Advance May 26, 2009, doi:10.1101/gr.092197.109
    OPEN ACCESS ARTICLE

  • JBrowse: A next-generation genome browser

    • Mitchell E. Skinner,
    • Andrew V. Uzilov,
    • Lincoln D. Stein,
    • Christopher J. Mungall,
    • and Ian H. Holmes
    Genome Res. September 2009 19: 1630-1638; Published in Advance July 1, 2009, doi:10.1101/gr.094607.109
    OPEN ACCESS ARTICLE

  • Circos: An information aesthetic for comparative genomics

    • Martin Krzywinski,
    • Jacqueline Schein,
    • İnanç Birol,
    • Joseph Connors,
    • Randy Gascoyne,
    • Doug Horsman,
    • Steven J. Jones,
    • and Marco A. Marra
    Genome Res. September 2009 19: 1639-1645; Published in Advance June 18, 2009, doi:10.1101/gr.092759.109

  • RazerS—fast read mapping with sensitivity control

    • David Weese,
    • Anne-Katrin Emde,
    • Tobias Rausch,
    • Andreas Döring,
    • and Knut Reinert
    Genome Res. September 2009 19: 1646-1654; Published in Advance July 10, 2009, doi:10.1101/gr.088823.108

  • Fast model-based estimation of ancestry in unrelated individuals

    • David H. Alexander,
    • John Novembre,
    • and Kenneth Lange
    Genome Res. September 2009 19: 1655-1664; Published in Advance July 31, 2009, doi:10.1101/gr.094052.109

  • The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine

    • Leslie G. Biesecker,
    • James C. Mullikin,
    • Flavia M. Facio,
    • Clesson Turner,
    • Praveen F. Cherukuri,
    • Robert W. Blakesley,
    • Gerard G. Bouffard,
    • Peter S. Chines,
    • Pedro Cruz,
    • Nancy F. Hansen,
    • Jamie K. Teer,
    • Baishali Maskeri,
    • Alice C. Young,
    • NISC Comparative Sequencing Program,
    • Teri A. Manolio,
    • Alexander F. Wilson,
    • Toren Finkel,
    • Paul Hwang,
    • Andrew Arai,
    • Alan T. Remaley,
    • Vandana Sachdev,
    • Robert Shamburek,
    • Richard O. Cannon,
    • and Eric D. Green
    Genome Res. September 2009 19: 1665-1674; Published in Advance July 14, 2009, doi:10.1101/gr.092841.109

  • Instrumenting the health care enterprise for discovery research in the genomic era

    • Shawn Murphy,
    • Susanne Churchill,
    • Lynn Bry,
    • Henry Chueh,
    • Scott Weiss,
    • Ross Lazarus,
    • Qing Zeng,
    • Anil Dubey,
    • Vivian Gainer,
    • Michael Mendis,
    • John Glaser,
    • and Isaac Kohane
    Genome Res. September 2009 19: 1675-1681; Published in Advance July 14, 2009, doi:10.1101/gr.094615.109
    OPEN ACCESS ARTICLE

  • High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications

    • Tamim H. Shaikh,
    • Xiaowu Gai,
    • Juan C. Perin,
    • Joseph T. Glessner,
    • Hongbo Xie,
    • Kevin Murphy,
    • Ryan O'Hara,
    • Tracy Casalunovo,
    • Laura K. Conlin,
    • Monica D'Arcy,
    • Edward C. Frackelton,
    • Elizabeth A. Geiger,
    • Chad Haldeman-Englert,
    • Marcin Imielinski,
    • Cecilia E. Kim,
    • Livija Medne,
    • Kiran Annaiah,
    • Jonathan P. Bradfield,
    • Elvira Dabaghyan,
    • Andrew Eckert,
    • Chioma C. Onyiah,
    • Svetlana Ostapenko,
    • F. George Otieno,
    • Erin Santa,
    • Julie L. Shaner,
    • Robert Skraban,
    • Ryan M. Smith,
    • Josephine Elia,
    • Elizabeth Goldmuntz,
    • Nancy B. Spinner,
    • Elaine H. Zackai,
    • Rosetta M. Chiavacci,
    • Robert Grundmeier,
    • Eric F. Rappaport,
    • Struan F.A. Grant,
    • Peter S. White,
    • and Hakon Hakonarson
    Genome Res. September 2009 19: 1682-1690; Published in Advance July 10, 2009, doi:10.1101/gr.083501.108

Erratum

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This Issue

September 2009; 19 (9)
Cover
  1. Letter
  2. Methods
  3. Resource
  4. Erratum

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