Table of Contents

December 2012; 22 (12)

Research

  • Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events

    • Jinfeng Liu,
    • William Lee,
    • Zhaoshi Jiang,
    • Zhongqiang Chen,
    • Suchit Jhunjhunwala,
    • Peter M. Haverty,
    • Florian Gnad,
    • Yinghui Guan,
    • Houston N. Gilbert,
    • Jeremy Stinson,
    • Christiaan Klijn,
    • Joseph Guillory,
    • Deepali Bhatt,
    • Steffan Vartanian,
    • Kimberly Walter,
    • Jocelyn Chan,
    • Thomas Holcomb,
    • Peter Dijkgraaf,
    • Stephanie Johnson,
    • Julie Koeman,
    • John D. Minna,
    • Adi F. Gazdar,
    • Howard M. Stern,
    • Klaus P. Hoeflich,
    • Thomas D. Wu,
    • Jeff Settleman,
    • Frederic J. de Sauvage,
    • Robert C. Gentleman,
    • Richard M. Neve,
    • David Stokoe,
    • Zora Modrusan,
    • Somasekar Seshagiri,
    • David S. Shames,
    • and Zemin Zhang
    Genome Res. December 2012 22: 2315-2327; Published in Advance October 2, 2012, doi:10.1101/gr.140988.112
    OPEN ACCESS ARTICLE

  • Extensive somatic L1 retrotransposition in colorectal tumors

    • Szilvia Solyom,
    • Adam D. Ewing,
    • Eric P. Rahrmann,
    • Tara Doucet,
    • Heather H. Nelson,
    • Michael B. Burns,
    • Reuben S. Harris,
    • David F. Sigmon,
    • Alex Casella,
    • Bracha Erlanger,
    • Sarah Wheelan,
    • Kyle R. Upton,
    • Ruchi Shukla,
    • Geoffrey J. Faulkner,
    • David A. Largaespada,
    • and Haig H. Kazazian, Jr.
    Genome Res. December 2012 22: 2328-2338; Published in Advance September 11, 2012, doi:10.1101/gr.145235.112

  • A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation

    • Christopher G. Duncan,
    • Benjamin G. Barwick,
    • Genglin Jin,
    • Carlo Rago,
    • Priya Kapoor-Vazirani,
    • Doris R. Powell,
    • Jen-Tsan Chi,
    • Darell D. Bigner,
    • Paula M. Vertino,
    • and Hai Yan
    Genome Res. December 2012 22: 2339-2355; Published in Advance August 16, 2012, doi:10.1101/gr.132738.111

  • Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

    • Manuel Irimia,
    • Juan J. Tena,
    • Maria S. Alexis,
    • Ana Fernandez-Miñan,
    • Ignacio Maeso,
    • Ozren Bogdanović,
    • Elisa de la Calle-Mustienes,
    • Scott W. Roy,
    • José L. Gómez-Skarmeta,
    • and Hunter B. Fraser
    Genome Res. December 2012 22: 2356-2367; Published in Advance June 21, 2012, doi:10.1101/gr.139725.112

  • Sex-biased genetic effects on gene regulation in humans

    • Antigone S. Dimas,
    • Alexandra C. Nica,
    • Stephen B. Montgomery,
    • Barbara E. Stranger,
    • Towfique Raj,
    • Alfonso Buil,
    • Thomas Giger,
    • Tuuli Lappalainen,
    • Maria Gutierrez-Arcelus,
    • MuTHER Consortium,
    • Mark I. McCarthy,
    • and Emmanouil T. Dermitzakis
    Genome Res. December 2012 22: 2368-2375; Published in Advance September 7, 2012, doi:10.1101/gr.134981.111
    OPEN ACCESS ARTICLE

  • Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

    • Angela Goncalves,
    • Sarah Leigh-Brown,
    • David Thybert,
    • Klara Stefflova,
    • Ernest Turro,
    • Paul Flicek,
    • Alvis Brazma,
    • Duncan T. Odom,
    • and John C. Marioni
    Genome Res. December 2012 22: 2376-2384; Published in Advance August 23, 2012, doi:10.1101/gr.142281.112
    OPEN ACCESS ARTICLE

  • Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq

    • Michael R. Tallack,
    • Graham W. Magor,
    • Benjamin Dartigues,
    • Lei Sun,
    • Stephen Huang,
    • Jessica M. Fittock,
    • Sally V. Fry,
    • Evgeny A. Glazov,
    • Timothy L. Bailey,
    • and Andrew C. Perkins
    Genome Res. December 2012 22: 2385-2398; Published in Advance July 26, 2012, doi:10.1101/gr.135707.111

  • CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

    • Romain Fenouil,
    • Pierre Cauchy,
    • Frederic Koch,
    • Nicolas Descostes,
    • Joaquin Zacarias Cabeza,
    • Charlène Innocenti,
    • Pierre Ferrier,
    • Salvatore Spicuglia,
    • Marta Gut,
    • Ivo Gut,
    • and Jean-Christophe Andrau
    Genome Res. December 2012 22: 2399-2408; Published in Advance October 25, 2012, doi:10.1101/gr.138776.112

  • Noise–mean relationship in mutated promoters

    • Gil Hornung,
    • Raz Bar-Ziv,
    • Dalia Rosin,
    • Nobuhiko Tokuriki,
    • Dan S. Tawfik,
    • Moshe Oren,
    • and Naama Barkai
    Genome Res. December 2012 22: 2409-2417; Published in Advance July 20, 2012, doi:10.1101/gr.139378.112
    OPEN ACCESS ARTICLE

  • Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets

    • Michael Stadler,
    • Karen Artiles,
    • Julia Pak,
    • and Andrew Fire
    Genome Res. December 2012 22: 2418-2426; Published in Advance August 1, 2012, doi:10.1101/gr.136515.111

  • Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant

    • Takashi Makino and
    • Aoife McLysaght
    Genome Res. December 2012 22: 2427-2435; Published in Advance July 26, 2012, doi:10.1101/gr.131953.111

  • Genic and nongenic contributions to natural variation of quantitative traits in maize

    • Xianran Li,
    • Chengsong Zhu,
    • Cheng-Ting Yeh,
    • Wei Wu,
    • Elizabeth M. Takacs,
    • Katherine A. Petsch,
    • Feng Tian,
    • Guihua Bai,
    • Edward S. Buckler,
    • Gary J. Muehlbauer,
    • Marja C.P. Timmermans,
    • Michael J. Scanlon,
    • Patrick S. Schnable,
    • and Jianming Yu
    Genome Res. December 2012 22: 2436-2444; Published in Advance June 14, 2012, doi:10.1101/gr.140277.112
    OPEN ACCESS ARTICLE

  • Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

    • Anja Paschold,
    • Yi Jia,
    • Caroline Marcon,
    • Steve Lund,
    • Nick B. Larson,
    • Cheng-Ting Yeh,
    • Stephan Ossowski,
    • Christa Lanz,
    • Dan Nettleton,
    • Patrick S. Schnable,
    • and Frank Hochholdinger
    Genome Res. December 2012 22: 2445-2454; Published in Advance October 19, 2012, doi:10.1101/gr.138461.112

  • Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes

    • Konstantinos Kritsas,
    • Samuel E. Wuest,
    • Daniel Hupalo,
    • Andrew D. Kern,
    • Thomas Wicker,
    • and Ueli Grossniklaus
    Genome Res. December 2012 22: 2455-2466; Published in Advance September 17, 2012, doi:10.1101/gr.129346.111
    OPEN ACCESS ARTICLE

  • Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis

    • Alistair C. Darby,
    • Stuart D. Armstrong,
    • Germanus S. Bah,
    • Gaganjot Kaur,
    • Margaret A. Hughes,
    • Suzanne M. Kay,
    • Pia Koldkjær,
    • Lucille Rainbow,
    • Alan D. Radford,
    • Mark L. Blaxter,
    • Vincent N. Tanya,
    • Alexander J. Trees,
    • Richard Cordaux,
    • Jonathan M. Wastling,
    • and Benjamin L. Makepeace
    Genome Res. December 2012 22: 2467-2477; Published in Advance August 23, 2012, doi:10.1101/gr.138420.112
    OPEN ACCESS ARTICLE

  • Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

    • Christina A. Cuomo,
    • Christopher A. Desjardins,
    • Malina A. Bakowski,
    • Jonathan Goldberg,
    • Amy T. Ma,
    • James J. Becnel,
    • Elizabeth S. Didier,
    • Lin Fan,
    • David I. Heiman,
    • Joshua Z. Levin,
    • Sarah Young,
    • Qiandong Zeng,
    • and Emily R. Troemel
    Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112

Methods

  • Copy-number-aware differential analysis of quantitative DNA sequencing data

    • Mark D. Robinson,
    • Dario Strbenac,
    • Clare Stirzaker,
    • Aaron L. Statham,
    • Jenny Song,
    • Terence P. Speed,
    • and Susan J. Clark
    Genome Res. December 2012 22: 2489-2496; Published in Advance August 9, 2012, doi:10.1101/gr.139055.112
    OPEN ACCESS ARTICLE

  • Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

    • Theresa K. Kelly,
    • Yaping Liu,
    • Fides D. Lay,
    • Gangning Liang,
    • Benjamin P. Berman,
    • and Peter A. Jones
    Genome Res. December 2012 22: 2497-2506; Published in Advance September 7, 2012, doi:10.1101/gr.143008.112

  • Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster

    • Bing He,
    • Amy Caudy,
    • Lance Parsons,
    • Adam Rosebrock,
    • Attilio Pane,
    • Sandeep Raj,
    • and Eric Wieschaus
    Genome Res. December 2012 22: 2507-2519; Published in Advance June 28, 2012, doi:10.1101/gr.137406.112
    OPEN ACCESS ARTICLE

Resources

  • A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

    • Oronzo Capozzi,
    • Lucia Carbone,
    • Roscoe R. Stanyon,
    • Annamaria Marra,
    • Fengtang Yang,
    • Christopher W. Whelan,
    • Pieter J. de Jong,
    • Mariano Rocchi,
    • and Nicoletta Archidiacono
    Genome Res. December 2012 22: 2520-2528; Published in Advance August 14, 2012, doi:10.1101/gr.138651.112

  • Long noncoding RNAs in C. elegans

    • Jin-Wu Nam and
    • David P. Bartel
    Genome Res. December 2012 22: 2529-2540; Published in Advance June 15, 2012, doi:10.1101/gr.140475.112
    OPEN ACCESS ARTICLE

  • A fine scale phenotype–genotype virulence map of a bacterial pathogen

    • Tim van Opijnen and
    • Andrew Camilli
    Genome Res. December 2012 22: 2541-2551; Published in Advance July 23, 2012, doi:10.1101/gr.137430.112

Author Index

Reviewer Index

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This Issue

December 2012; 22 (12)
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  1. Research
  2. Methods
  3. Resources
  4. Author Index
  5. Reviewer Index

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