Table of Contents

April 2012; 22 (4)

Research

  • The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

    • Zhaoshi Jiang,
    • Suchit Jhunjhunwala,
    • Jinfeng Liu,
    • Peter M. Haverty,
    • Michael I. Kennemer,
    • Yinghui Guan,
    • William Lee,
    • Paolo Carnevali,
    • Jeremy Stinson,
    • Stephanie Johnson,
    • Jingyu Diao,
    • Stacy Yeung,
    • Adrian Jubb,
    • Weilan Ye,
    • Thomas D. Wu,
    • Sharookh B. Kapadia,
    • Frederic J. de Sauvage,
    • Robert C. Gentleman,
    • Howard M. Stern,
    • Somasekar Seshagiri,
    • Krishna P. Pant,
    • Zora Modrusan,
    • Dennis G. Ballinger,
    • and Zemin Zhang
    Genome Res. April 2012 22: 593-601; Published in Advance January 20, 2012, doi:10.1101/gr.133926.111
    OPEN ACCESS ARTICLE

  • Comparative RNA sequencing reveals substantial genetic variation in endangered primates

    • George H. Perry,
    • Páll Melsted,
    • John C. Marioni,
    • Ying Wang,
    • Russell Bainer,
    • Joseph K. Pickrell,
    • Katelyn Michelini,
    • Sarah Zehr,
    • Anne D. Yoder,
    • Matthew Stephens,
    • Jonathan K. Pritchard,
    • and Yoav Gilad
    Genome Res. April 2012 22: 602-610; Published in Advance December 29, 2011, doi:10.1101/gr.130468.111
    OPEN ACCESS ARTICLE

  • Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques

    • Xiling Liu,
    • Mehmet Somel,
    • Lin Tang,
    • Zheng Yan,
    • Xi Jiang,
    • Song Guo,
    • Yuan Yuan,
    • Liu He,
    • Anna Oleksiak,
    • Yan Zhang,
    • Na Li,
    • Yuhui Hu,
    • Wei Chen,
    • Zilong Qiu,
    • Svante Pääbo,
    • and Philipp Khaitovich
    Genome Res. April 2012 22: 611-622; Published in Advance February 2, 2012, doi:10.1101/gr.127324.111
    OPEN ACCESS ARTICLE

  • Age-associated DNA methylation in pediatric populations

    • Reid S. Alisch,
    • Benjamin G. Barwick,
    • Pankaj Chopra,
    • Leila K. Myrick,
    • Glen A. Satten,
    • Karen N. Conneely,
    • and Stephen T. Warren
    Genome Res. April 2012 22: 623-632; Published in Advance February 1, 2012, doi:10.1101/gr.125187.111
    OPEN ACCESS ARTICLE

  • Global profiling of DNA methylation erasure in mouse primordial germ cells

    • Sylvain Guibert,
    • Thierry Forné,
    • and Michael Weber
    Genome Res. April 2012 22: 633-641; Published in Advance February 22, 2012, doi:10.1101/gr.130997.111

  • An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

    • Ignacio Maeso,
    • Manuel Irimia,
    • Juan J. Tena,
    • Esther González-Pérez,
    • David Tran,
    • Vydianathan Ravi,
    • Byrappa Venkatesh,
    • Sonsoles Campuzano,
    • José Luis Gómez-Skarmeta,
    • and Jordi Garcia-Fernàndez
    Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111

  • The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

    • Rahul Satija and
    • Robert K. Bradley
    Genome Res. April 2012 22: 656-665; Published in Advance January 13, 2012, doi:10.1101/gr.130682.111
    OPEN ACCESS ARTICLE

  • A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

    • Donatella Canella,
    • David Bernasconi,
    • Federica Gilardi,
    • Gwendal LeMartelot,
    • Eugenia Migliavacca,
    • Viviane Praz,
    • Pascal Cousin,
    • Mauro Delorenzi,
    • Nouria Hernandez,
    • and The CycliX Consortium
    Genome Res. April 2012 22: 666-680; Published in Advance January 27, 2012, doi:10.1101/gr.130286.111
    OPEN ACCESS ARTICLE

  • Retrotransposon profiling of RNA polymerase III initiation sites

    • Xiaojie Qi,
    • Kenneth Daily,
    • Kim Nguyen,
    • Haoyi Wang,
    • David Mayhew,
    • Paul Rigor,
    • Sholeh Forouzan,
    • Mark Johnston,
    • Robi David Mitra,
    • Pierre Baldi,
    • and Suzanne Sandmeyer
    Genome Res. April 2012 22: 681-692; Published in Advance January 27, 2012, doi:10.1101/gr.131219.111

  • Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

    • Loris Mularoni,
    • Yulian Zhou,
    • Tyson Bowen,
    • Sunil Gangadharan,
    • Sarah J. Wheelan,
    • and Jef D. Boeke
    Genome Res. April 2012 22: 693-703; Published in Advance January 4, 2012, doi:10.1101/gr.129460.111

  • A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon

    • Joshua A. Baller,
    • Jiquan Gao,
    • Radostina Stamenova,
    • M. Joan Curcio,
    • and Daniel F. Voytas
    Genome Res. April 2012 22: 704-713; Published in Advance January 4, 2012, doi:10.1101/gr.129585.111

  • Evolutionary rate covariation reveals shared functionality and coexpression of genes

    • Nathan L. Clark,
    • Eric Alani,
    • and Charles F. Aquadro
    Genome Res. April 2012 22: 714-720; Published in Advance January 27, 2012, doi:10.1101/gr.132647.111

  • After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

    • Amine Namouchi,
    • Xavier Didelot,
    • Ulrike Schöck,
    • Brigitte Gicquel,
    • and Eduardo P.C. Rocha
    Genome Res. April 2012 22: 721-734; Published in Advance February 29, 2012, doi:10.1101/gr.129544.111

  • Microevolution of extensively drug-resistant tuberculosis in Russia

    • Nicola Casali,
    • Vladyslav Nikolayevskyy,
    • Yanina Balabanova,
    • Olga Ignatyeva,
    • Irina Kontsevaya,
    • Simon R. Harris,
    • Stephen D. Bentley,
    • Julian Parkhill,
    • Sergey Nejentsev,
    • Sven E. Hoffner,
    • Rolf D. Horstmann,
    • Timothy Brown,
    • and Francis Drobniewski
    Genome Res. April 2012 22: 735-745; Published in Advance January 31, 2012, doi:10.1101/gr.128678.111

Methods

  • Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

    • John E. McCormack,
    • Brant C. Faircloth,
    • Nicholas G. Crawford,
    • Patricia Adair Gowaty,
    • Robb T. Brumfield,
    • and Travis C. Glenn
    Genome Res. April 2012 22: 746-754; Published in Advance December 29, 2011, doi:10.1101/gr.125864.111

  • Unified modeling of gene duplication, loss, and coalescence using a locus tree

    • Matthew D. Rasmussen and
    • Manolis Kellis
    Genome Res. April 2012 22: 755-765; Published in Advance January 23, 2012, doi:10.1101/gr.123901.111
    OPEN ACCESS ARTICLE

  • Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

    • Florian A. Steiner,
    • Paul B. Talbert,
    • Sivakanthan Kasinathan,
    • Roger B. Deal,
    • and Steven Henikoff
    Genome Res. April 2012 22: 766-777; Published in Advance January 4, 2012, doi:10.1101/gr.131748.111
    OPEN ACCESS ARTICLE

Resources

  • Copy number variation of individual cattle genomes using next-generation sequencing

    • Derek M. Bickhart,
    • Yali Hou,
    • Steven G. Schroeder,
    • Can Alkan,
    • Maria Francesca Cardone,
    • Lakshmi K. Matukumalli,
    • Jiuzhou Song,
    • Robert D. Schnabel,
    • Mario Ventura,
    • Jeremy F. Taylor,
    • Jose Fernando Garcia,
    • Curtis P. Van Tassell,
    • Tad S. Sonstegard,
    • Evan E. Eichler,
    • and George E. Liu
    Genome Res. April 2012 22: 778-790; Published in Advance February 2, 2012, doi:10.1101/gr.133967.111

  • Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs

    • Sara Sharifpoor,
    • Dewald van Dyk,
    • Michael Costanzo,
    • Anastasia Baryshnikova,
    • Helena Friesen,
    • Alison C. Douglas,
    • Ji-Young Youn,
    • Benjamin VanderSluis,
    • Chad L. Myers,
    • Balázs Papp,
    • Charles Boone,
    • and Brenda J. Andrews
    Genome Res. April 2012 22: 791-801; Published in Advance January 26, 2012, doi:10.1101/gr.129213.111

  • A vast collection of microbial genes that are toxic to bacteria

    • Aya Kimelman,
    • Asaf Levy,
    • Hila Sberro,
    • Shahar Kidron,
    • Azita Leavitt,
    • Gil Amitai,
    • Deborah R. Yoder-Himes,
    • Omri Wurtzel,
    • Yiwen Zhu,
    • Edward M. Rubin,
    • and Rotem Sorek
    Genome Res. April 2012 22: 802-809; Published in Advance February 1, 2012, doi:10.1101/gr.133850.111

Erratum

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This Issue

April 2012; 22 (4)
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  1. Research
  2. Methods
  3. Resources
  4. Erratum

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