Table of Contents

July 2011; 21 (7)

Insight/Outlook

  • Ethical and practical challenges of sharing data from genome-wide association studies: The eMERGE Consortium experience

    • Amy L. McGuire,
    • Melissa Basford,
    • Lynn G. Dressler,
    • Stephanie M. Fullerton,
    • Barbara A. Koenig,
    • Rongling Li,
    • Cathy A. McCarty,
    • Erin Ramos,
    • Maureen E. Smith,
    • Carol P. Somkin,
    • Carol Waudby,
    • Wendy A. Wolf,
    • and Ellen Wright Clayton
    Genome Res. July 2011 21: 1001-1007; Published in Advance June 1, 2011, doi:10.1101/gr.120329.111

Research

  • A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort

    • Danielle M. Greenawalt,
    • Radu Dobrin,
    • Eugene Chudin,
    • Ida J. Hatoum,
    • Christine Suver,
    • John Beaulaurier,
    • Bin Zhang,
    • Victor Castro,
    • Jun Zhu,
    • Solveig K. Sieberts,
    • Susanna Wang,
    • Cliona Molony,
    • Steven B. Heymsfield,
    • Daniel M. Kemp,
    • Marc L. Reitman,
    • Pek Yee Lum,
    • Eric E. Schadt,
    • and Lee M. Kaplan
    Genome Res. July 2011 21: 1008-1016; Published in Advance May 20, 2011, doi:10.1101/gr.112821.110

  • DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer

    • Yuya Kobayashi,
    • Devin M. Absher,
    • Zulfiqar G. Gulzar,
    • Sarah R. Young,
    • Jesse K. McKenney,
    • Donna M. Peehl,
    • James D. Brooks,
    • Richard M. Myers,
    • and Gavin Sherlock
    Genome Res. July 2011 21: 1017-1027; Published in Advance April 26, 2011, doi:10.1101/gr.119487.110

  • Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

    • Jung H. Kim,
    • Saravana M. Dhanasekaran,
    • John R. Prensner,
    • Xuhong Cao,
    • Daniel Robinson,
    • Shanker Kalyana-Sundaram,
    • Christina Huang,
    • Sunita Shankar,
    • Xiaojun Jing,
    • Matthew Iyer,
    • Ming Hu,
    • Lee Sam,
    • Catherine Grasso,
    • Christopher A. Maher,
    • Nallasivam Palanisamy,
    • Rohit Mehra,
    • Hal D. Kominsky,
    • Javed Siddiqui,
    • Jindan Yu,
    • Zhaohui S. Qin,
    • and Arul M. Chinnaiyan
    Genome Res. July 2011 21: 1028-1041; doi:10.1101/gr.119347.110

  • Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex

    • Claire Vandiedonck,
    • Martin S. Taylor,
    • Helen E. Lockstone,
    • Katharine Plant,
    • Jennifer M. Taylor,
    • Caroline Durrant,
    • John Broxholme,
    • Benjamin P. Fairfax,
    • and Julian C. Knight
    Genome Res. July 2011 21: 1042-1054; Published in Advance May 31, 2011, doi:10.1101/gr.116681.110
    OPEN ACCESS ARTICLE

  • Combinatorial binding of transcription factors in the pluripotency control regions of the genome

    • Luciana Ferraris,
    • Allan P. Stewart,
    • Jinsuk Kang,
    • Alec M. DeSimone,
    • Matthew Gemberling,
    • Dean Tantin,
    • and William G. Fairbrother
    Genome Res. July 2011 21: 1055-1064; Published in Advance April 28, 2011, doi:10.1101/gr.115824.110

  • Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis

    • Soha N. Yazbek,
    • David A. Buchner,
    • Jonathan M. Geisinger,
    • Lindsay C. Burrage,
    • Sabrina H. Spiezio,
    • Gabriel E. Zentner,
    • Chang-Wen Hsieh,
    • Peter C. Scacheri,
    • Colleen M. Croniger,
    • and Joseph H. Nadeau
    Genome Res. July 2011 21: 1065-1073; Published in Advance April 19, 2011, doi:10.1101/gr.120741.111

  • Cell type–specific DNA methylation at intragenic CpG islands in the immune system

    • Aimée M. Deaton,
    • Shaun Webb,
    • Alastair R.W. Kerr,
    • Robert S. Illingworth,
    • Jacky Guy,
    • Robert Andrews,
    • and Adrian Bird
    Genome Res. July 2011 21: 1074-1086; Published in Advance May 31, 2011, doi:10.1101/gr.118703.110
    OPEN ACCESS ARTICLE

Methods

  • A reduced representation approach to population genetic analyses and applications to human evolution

    • Francesca Luca,
    • Richard R. Hudson,
    • David B. Witonsky,
    • and Anna Di Rienzo
    Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110

  • Association studies for next-generation sequencing

    • Li Luo,
    • Eric Boerwinkle,
    • and Momiao Xiong
    Genome Res. July 2011 21: 1099-1108; Published in Advance April 26, 2011, doi:10.1101/gr.115998.110

  • Prioritizing candidate disease genes by network-based boosting of genome-wide association data

    • Insuk Lee,
    • U. Martin Blom,
    • Peggy I. Wang,
    • Jung Eun Shim,
    • and Edward M. Marcotte
    Genome Res. July 2011 21: 1109-1121; Published in Advance May 2, 2011, doi:10.1101/gr.118992.110

  • Detection of common single nucleotide polymorphisms synthesizing quantitative trait association of rarer causal variants

    • Fumihiko Takeuchi,
    • Shotai Kobayashi,
    • Toshio Ogihara,
    • Akihiro Fujioka,
    • and Norihiro Kato
    Genome Res. July 2011 21: 1122-1130; Published in Advance March 25, 2011, doi:10.1101/gr.115832.110

  • Revealing the genetic structure of a trait by sequencing a population under selection

    • Leopold Parts,
    • Francisco A. Cubillos,
    • Jonas Warringer,
    • Kanika Jain,
    • Francisco Salinas,
    • Suzannah J. Bumpstead,
    • Mikael Molin,
    • Amin Zia,
    • Jared T. Simpson,
    • Michael A. Quail,
    • Alan Moses,
    • Edward J. Louis,
    • Richard Durbin,
    • and Gianni Liti
    Genome Res. July 2011 21: 1131-1138; Published in Advance March 21, 2011, doi:10.1101/gr.116731.110
    OPEN ACCESS ARTICLE

  • Genome-wide identification of conserved regulatory function in diverged sequences

    • Leila Taher,
    • David M. McGaughey,
    • Samantha Maragh,
    • Ivy Aneas,
    • Seneca L. Bessling,
    • Webb Miller,
    • Marcelo A. Nobrega,
    • Andrew S. McCallion,
    • and Ivan Ovcharenko
    Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
    OPEN ACCESS ARTICLE

  • Unamplified cap analysis of gene expression on a single-molecule sequencer

    • Mutsumi Kanamori-Katayama,
    • Masayoshi Itoh,
    • Hideya Kawaji,
    • Timo Lassmann,
    • Shintaro Katayama,
    • Miki Kojima,
    • Nicolas Bertin,
    • Ai Kaiho,
    • Noriko Ninomiya,
    • Carsten O. Daub,
    • Piero Carninci,
    • Alistair R.R. Forrest,
    • and Yoshihide Hayashizaki
    Genome Res. July 2011 21: 1150-1159; Published in Advance May 19, 2011, doi:10.1101/gr.115469.110

  • Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

    • Saiful Islam,
    • Una Kjällquist,
    • Annalena Moliner,
    • Pawel Zajac,
    • Jian-Bing Fan,
    • Peter Lönnerberg,
    • and Sten Linnarsson
    Genome Res. July 2011 21: 1160-1167; Published in Advance May 4, 2011, doi:10.1101/gr.110882.110

Resources

  • A method for detecting IBD regions simultaneously in multiple individuals—with applications to disease genetics

    • Ida Moltke,
    • Anders Albrechtsen,
    • Thomas v.O. Hansen,
    • Finn C. Nielsen,
    • and Rasmus Nielsen
    Genome Res. July 2011 21: 1168-1180; Published in Advance April 14, 2011, doi:10.1101/gr.115360.110

  • ECHO: A reference-free short-read error correction algorithm

    • Wei-Chun Kao,
    • Andrew H. Chan,
    • and Yun S. Song
    Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110

  • De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

    • Catherine Adamidi,
    • Yongbo Wang,
    • Dominic Gruen,
    • Guido Mastrobuoni,
    • Xintian You,
    • Dominic Tolle,
    • Matthias Dodt,
    • Sebastian D. Mackowiak,
    • Andreas Gogol-Doering,
    • Pinar Oenal,
    • Agnieszka Rybak,
    • Eric Ross,
    • Alejandro Sánchez Alvarado,
    • Stefan Kempa,
    • Christoph Dieterich,
    • Nikolaus Rajewsky,
    • and Wei Chen
    Genome Res. July 2011 21: 1193-1200; Published in Advance May 2, 2011, doi:10.1101/gr.113779.110

Erratum

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This Issue

July 2011; 21 (7)
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  1. Insight/Outlook
  2. Research
  3. Methods
  4. Resources
  5. Erratum

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