Table of Contents

May 2013; 23 (5)

Research

  • The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

    • Stephen B. Montgomery,
    • David L. Goode,
    • Erika Kvikstad,
    • Cornelis A. Albers,
    • Zhengdong D. Zhang,
    • Xinmeng Jasmine Mu,
    • Guruprasad Ananda,
    • Bryan Howie,
    • Konrad J. Karczewski,
    • Kevin S. Smith,
    • Vanessa Anaya,
    • Rhea Richardson,
    • Joe Davis,
    • The 1000 Genomes Project Consortium,
    • Daniel G. MacArthur,
    • Arend Sidow,
    • Laurent Duret,
    • Mark Gerstein,
    • Kateryna D. Makova,
    • Jonathan Marchini,
    • Gil McVean,
    • and Gerton Lunter
    Genome Res. May 2013 23: 749-761; Published in Advance March 11, 2013, doi:10.1101/gr.148718.112
    OPEN ACCESS ARTICLE

  • Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

    • Ankit Malhotra,
    • Michael Lindberg,
    • Gregory G. Faust,
    • Mitchell L. Leibowitz,
    • Royden A. Clark,
    • Ryan M. Layer,
    • Aaron R. Quinlan,
    • and Ira M. Hall
    Genome Res. May 2013 23: 762-776; Published in Advance February 14, 2013, doi:10.1101/gr.143677.112

  • Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

    • Nathan C. Sheffield,
    • Robert E. Thurman,
    • Lingyun Song,
    • Alexias Safi,
    • John A. Stamatoyannopoulos,
    • Boris Lenhard,
    • Gregory E. Crawford,
    • and Terrence S. Furey
    Genome Res. May 2013 23: 777-788; Published in Advance March 12, 2013, doi:10.1101/gr.152140.112
    OPEN ACCESS ARTICLE

  • DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure

    • Sahar Gelfman,
    • Noa Cohen,
    • Ahuvi Yearim,
    • and Gil Ast
    Genome Res. May 2013 23: 789-799; Published in Advance March 15, 2013, doi:10.1101/gr.143503.112

  • Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

    • Pouya Kheradpour,
    • Jason Ernst,
    • Alexandre Melnikov,
    • Peter Rogov,
    • Li Wang,
    • Xiaolan Zhang,
    • Jessica Alston,
    • Tarjei S. Mikkelsen,
    • and Manolis Kellis
    Genome Res. May 2013 23: 800-811; Published in Advance March 19, 2013, doi:10.1101/gr.144899.112
    OPEN ACCESS ARTICLE

  • Widespread and extensive lengthening of 3′ UTRs in the mammalian brain

    • Pedro Miura,
    • Sol Shenker,
    • Celia Andreu-Agullo,
    • Jakub O. Westholm,
    • and Eric C. Lai
    Genome Res. May 2013 23: 812-825; Published in Advance March 21, 2013, doi:10.1101/gr.146886.112

Methods

  • Sequencing of isolated sperm cells for direct haplotyping of a human genome

    • Ewen F. Kirkness,
    • Rashel V. Grindberg,
    • Joyclyn Yee-Greenbaum,
    • Christian R. Marshall,
    • Stephen W. Scherer,
    • Roger S. Lasken,
    • and J. Craig Venter
    Genome Res. May 2013 23: 826-832; Published in Advance January 2, 2013, doi:10.1101/gr.144600.112

  • An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

    • Yi Wang,
    • James Lu,
    • Jin Yu,
    • Richard A. Gibbs,
    • and Fuli Yu
    Genome Res. May 2013 23: 833-842; Published in Advance January 7, 2013, doi:10.1101/gr.146084.112

  • Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

    • Joseph B. Hiatt,
    • Colin C. Pritchard,
    • Stephen J. Salipante,
    • Brian J. O'Roak,
    • and Jay Shendure
    Genome Res. May 2013 23: 843-854; Published in Advance February 4, 2013, doi:10.1101/gr.147686.112

  • Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

    • Helena M.B. Seth-Smith,
    • Simon R. Harris,
    • Rachel J. Skilton,
    • Frans M. Radebe,
    • Daniel Golparian,
    • Elena Shipitsyna,
    • Pham Thanh Duy,
    • Paul Scott,
    • Lesley T. Cutcliffe,
    • Colette O’Neill,
    • Surendra Parmar,
    • Rachel Pitt,
    • Stephen Baker,
    • Catherine A. Ison,
    • Peter Marsh,
    • Hamid Jalal,
    • David A. Lewis,
    • Magnus Unemo,
    • Ian N. Clarke,
    • Julian Parkhill,
    • and Nicholas R. Thomson
    Genome Res. May 2013 23: 855-866; Published in Advance March 22, 2013, doi:10.1101/gr.150037.112

  • Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

    • Jeffrey S. McLean,
    • Mary-Jane Lombardo,
    • Michael G. Ziegler,
    • Mark Novotny,
    • Joyclyn Yee-Greenbaum,
    • Jonathan H. Badger,
    • Glenn Tesler,
    • Sergey Nurk,
    • Valery Lesin,
    • Daniel Brami,
    • Adam P. Hall,
    • Anna Edlund,
    • Lisa Z. Allen,
    • Scott Durkin,
    • Sharon Reed,
    • Francesca Torriani,
    • Kenneth H. Nealson,
    • Pavel A. Pevzner,
    • Robert Friedman,
    • J. Craig Venter,
    • and Roger S. Lasken
    Genome Res. May 2013 23: 867-877; Published in Advance April 5, 2013, doi:10.1101/gr.150433.112
    OPEN ACCESS ARTICLE

  • Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

    • Michael S. Fitzsimons,
    • Mark Novotny,
    • Chien-Chi Lo,
    • Armand E.K. Dichosa,
    • Joyclyn L. Yee-Greenbaum,
    • Jeremy P. Snook,
    • Wei Gu,
    • Olga Chertkov,
    • Karen W. Davenport,
    • Kim McMurry,
    • Krista G. Reitenga,
    • Ashlynn R. Daughton,
    • Jian He,
    • Shannon L. Johnson,
    • Cheryl D. Gleasner,
    • Patti L. Wills,
    • Beverly Parson-Quintana,
    • Patrick S. Chain,
    • John C. Detter,
    • Roger S. Lasken,
    • and Cliff S. Han
    Genome Res. May 2013 23: 878-888; Published in Advance March 14, 2013, doi:10.1101/gr.142208.112

Resource

  • PRISM offers a comprehensive genomic approach to transcription factor function prediction

    • Aaron M. Wenger,
    • Shoa L. Clarke,
    • Harendra Guturu,
    • Jenny Chen,
    • Bruce T. Schaar,
    • Cory Y. McLean,
    • and Gill Bejerano
    Genome Res. May 2013 23: 889-904; Published in Advance February 4, 2013, doi:10.1101/gr.139071.112
    OPEN ACCESS ARTICLE

Erratum

|

This Issue

May 2013; 23 (5)
Cover
  1. Research
  2. Methods
  3. Resource
  4. Erratum

Find articles in this issue containing these words:

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research