Table of Contents

March 2009; 19 (3)

Article

  • MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

    • Hongjae Sunwoo,
    • Marcel E. Dinger,
    • Jeremy E. Wilusz,
    • Paulo P. Amaral,
    • John S. Mattick,
    • and David L. Spector
    Genome Res. March 2009 19: 347-359; Published in Advance December 22, 2008, doi:10.1101/gr.087775.108

  • A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome

    • Bryan J. Venters and
    • B. Franklin Pugh
    Genome Res. March 2009 19: 360-371; Published in Advance January 5, 2009, doi:10.1101/gr.084970.108

Letter

  • Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers

    • Jérôme Eeckhoute,
    • Mathieu Lupien,
    • Clifford A. Meyer,
    • Michael P. Verzi,
    • Ramesh A. Shivdasani,
    • X. Shirley Liu,
    • and Myles Brown
    Genome Res. March 2009 19: 372-380; Published in Advance January 7, 2009, doi:10.1101/gr.084582.108

  • Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

    • Jeremy R. Sanford,
    • Xin Wang,
    • Matthew Mort,
    • Natalia VanDuyn,
    • David N. Cooper,
    • Sean D. Mooney,
    • Howard J. Edenberg,
    • and Yunlong Liu
    Genome Res. March 2009 19: 381-394; Published in Advance December 30, 2008, doi:10.1101/gr.082503.108

  • HBEGF, SRA1, and IK: Three cosegregating genes as determinants of cardiomyopathy

    • Frauke Friedrichs,
    • Christian Zugck,
    • Gerd-Jörg Rauch,
    • Boris Ivandic,
    • Dieter Weichenhan,
    • Margit Müller-Bardorff,
    • Benjamin Meder,
    • Nour Eddine El Mokhtari,
    • Vera Regitz-Zagrosek,
    • Roland Hetzer,
    • Arne Schäfer,
    • Stefan Schreiber,
    • Jian Chen,
    • Isaac Neuhaus,
    • Ruiru Ji,
    • Nathan O. Siemers,
    • Norbert Frey,
    • Wolfgang Rottbauer,
    • Hugo A. Katus,
    • and Monika Stoll
    Genome Res. March 2009 19: 395-403; Published in Advance December 8, 2008, doi:10.1101/gr.076653.108

  • Histone H3.3 incorporation provides a unique and functionally essential telomeric chromatin in embryonic stem cells

    • Lee H. Wong,
    • Hua Ren,
    • Evan Williams,
    • James McGhie,
    • Soyeon Ahn,
    • Marcus Sim,
    • Angela Tam,
    • Elizabeth Earle,
    • Melissa A. Anderson,
    • Jeffrey Mann,
    • and K.H. Andy Choo
    Genome Res. March 2009 19: 404-414; Published in Advance February 5, 2009, doi:10.1101/gr.084947.108

  • Into the blue: Gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii

    • Wayne L. Davies,
    • Livia S. Carvalho,
    • Boon-Hui Tay,
    • Sydney Brenner,
    • David M. Hunt,
    • and Byrappa Venkatesh
    Genome Res. March 2009 19: 415-426; Published in Advance February 4, 2009, doi:10.1101/gr.084509.108

  • Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

    • Zachary A. Lewis,
    • Shinji Honda,
    • Tamir K. Khlafallah,
    • Jennifer K. Jeffress,
    • Michael Freitag,
    • Fabio Mohn,
    • Dirk Schübeler,
    • and Eric U. Selker
    Genome Res. March 2009 19: 427-437; Published in Advance December 17, 2008, doi:10.1101/gr.086231.108

  • The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer

    • Agustin F. Fernandez,
    • Cecilia Rosales,
    • Pilar Lopez-Nieva,
    • Osvaldo Graña,
    • Esteban Ballestar,
    • Santiago Ropero,
    • Jesus Espada,
    • Sonia A. Melo,
    • Amaia Lujambio,
    • Mario F. Fraga,
    • Irene Pino,
    • Biola Javierre,
    • Francisco J. Carmona,
    • Francesco Acquadro,
    • Renske D.M. Steenbergen,
    • Peter J.F. Snijders,
    • Chris J. Meijer,
    • Pascal Pineau,
    • Anne Dejean,
    • Belen Lloveras,
    • Gabriel Capella,
    • Josep Quer,
    • Maria Buti,
    • Juan-Ignacio Esteban,
    • Helena Allende,
    • Francisco Rodriguez-Frias,
    • Xavier Castellsague,
    • Janos Minarovits,
    • Jordi Ponce,
    • Daniela Capello,
    • Gianluca Gaidano,
    • Juan Cruz Cigudosa,
    • Gonzalo Gomez-Lopez,
    • David G. Pisano,
    • Alfonso Valencia,
    • Miguel Angel Piris,
    • Francesc X. Bosch,
    • Ellen Cahir-McFarland,
    • Elliott Kieff,
    • and Manel Esteller
    Genome Res. March 2009 19: 438-451; Published in Advance February 10, 2009, doi:10.1101/gr.083550.108
    OPEN ACCESS ARTICLE

  • Two duplicated P450 genes are associated with pyrethroid resistance in Anopheles funestus, a major malaria vector

    • Charles S. Wondji,
    • Helen Irving,
    • John Morgan,
    • Neil F. Lobo,
    • Frank H. Collins,
    • Richard H. Hunt,
    • Maureen Coetzee,
    • Janet Hemingway,
    • and Hilary Ranson
    Genome Res. March 2009 19: 452-459; Published in Advance February 5, 2009, doi:10.1101/gr.087916.108

Methods

  • Genome-wide profiling of salt fractions maps physical properties of chromatin

    • Steven Henikoff,
    • Jorja G. Henikoff,
    • Akiko Sakai,
    • Gabriel B. Loeb,
    • and Kami Ahmad
    Genome Res. March 2009 19: 460-469; Published in Advance December 16, 2008, doi:10.1101/gr.087619.108
    OPEN ACCESS ARTICLE

  • Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

    • Antoine Barrière,
    • Shiaw-Pyng Yang,
    • Elizabeth Pekarek,
    • Cristel G. Thomas,
    • Eric S. Haag,
    • and Ilya Ruvinsky
    Genome Res. March 2009 19: 470-480; Published in Advance February 9, 2009, doi:10.1101/gr.081851.108

Resource

  • MicroRNA target prediction by expression analysis of host genes

    • Vincenzo Alessandro Gennarino,
    • Marco Sardiello,
    • Raffaella Avellino,
    • Nicola Meola,
    • Vincenza Maselli,
    • Santosh Anand,
    • Luisa Cutillo,
    • Andrea Ballabio,
    • and Sandro Banfi
    Genome Res. March 2009 19: 481-490; Published in Advance December 16, 2008, doi:10.1101/gr.084129.108

  • The genomic architecture of segmental duplications and associated copy number variants in dogs

    • Thomas J. Nicholas,
    • Ze Cheng,
    • Mario Ventura,
    • Katrina Mealey,
    • Evan E. Eichler,
    • and Joshua M. Akey
    Genome Res. March 2009 19: 491-499; Published in Advance January 7, 2009, doi:10.1101/gr.084715.108

  • Mapping DNA structural variation in dogs

    • Wei-Kang Chen,
    • Joshua D. Swartz,
    • Laura J. Rush,
    • and Carlos E. Alvarez
    Genome Res. March 2009 19: 500-509; Published in Advance November 17, 2008, doi:10.1101/gr.083741.108

  • A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

    • Martien A.M. Groenen,
    • Per Wahlberg,
    • Mario Foglio,
    • Hans H. Cheng,
    • Hendrik-Jan Megens,
    • Richard P.M.A. Crooijmans,
    • Francois Besnier,
    • Mark Lathrop,
    • William M. Muir,
    • Gane Ka-Shu Wong,
    • Ivo Gut,
    • and Leif Andersson
    Genome Res. March 2009 19: 510-519; Published in Advance December 16, 2008, doi:10.1101/gr.086538.108

Erratum

  • Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy

    • Edward F. Attiyeh,
    • Sharon J. Diskin,
    • Marc A. Attiyeh,
    • Yaël P. Mossé,
    • Cuiping Hou,
    • Eric M. Jackson,
    • Cecilia Kim,
    • Joseph Glessner,
    • Hakon Hakonarson,
    • Jaclyn A. Biegel,
    • and John M. Maris
    Genome Res. March 2009 19: 520
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This Issue

March 2009; 19 (3)
Cover
  1. Article
  2. Letter
  3. Methods
  4. Resource
  5. Erratum

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