Table of Contents

February 2009; 19 (2)

LETTERS

  • A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

    • Oliver A. Hampton,
    • Petra Den Hollander,
    • Christopher A. Miller,
    • David A. Delgado,
    • Jian Li,
    • Cristian Coarfa,
    • Ronald A. Harris,
    • Stephen Richards,
    • Steven E. Scherer,
    • Donna M. Muzny,
    • Richard A. Gibbs,
    • Adrian V. Lee,
    • and Aleksandar Milosavljevic
    Genome Res. February 2009 19: 167-177; Published in Advance December 3, 2008, doi:10.1101/gr.080259.108
    OPEN ACCESS ARTICLE

  • Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

    • Santhosh Girirajan,
    • Lin Chen,
    • Tina Graves,
    • Tomas Marques-Bonet,
    • Mario Ventura,
    • Catrina Fronick,
    • Lucinda Fulton,
    • Mariano Rocchi,
    • Robert S. Fulton,
    • Richard K. Wilson,
    • Elaine R. Mardis,
    • and Evan E. Eichler
    Genome Res. February 2009 19: 178-190; Published in Advance November 24, 2008, doi:10.1101/gr.086041.108

  • Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans

    • Hidehito Inagaki,
    • Tamae Ohye,
    • Hiroshi Kogo,
    • Takema Kato,
    • Hasbaira Bolor,
    • Mariko Taniguchi,
    • Tamim H. Shaikh,
    • Beverly S. Emanuel,
    • and Hiroki Kurahashi
    Genome Res. February 2009 19: 191-198; Published in Advance November 7, 2008, doi:10.1101/gr.079244.108

  • Widespread balancing selection and pathogen-driven selection at blood group antigen genes

    • Matteo Fumagalli,
    • Rachele Cagliani,
    • Uberto Pozzoli,
    • Stefania Riva,
    • Giacomo P. Comi,
    • Giorgia Menozzi,
    • Nereo Bresolin,
    • and Manuela Sironi
    Genome Res. February 2009 19: 199-212; Published in Advance November 7, 2008, doi:10.1101/gr.082768.108

  • The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

    • Webb Miller,
    • Daniela I. Drautz,
    • Jan E. Janecka,
    • Arthur M. Lesk,
    • Aakrosh Ratan,
    • Lynn P. Tomsho,
    • Mike Packard,
    • Yeting Zhang,
    • Lindsay R. McClellan,
    • Ji Qi,
    • Fangqing Zhao,
    • M. Thomas P. Gilbert,
    • Love Dalén,
    • Juan Luis Arsuaga,
    • Per G.P. Ericson,
    • Daniel H. Huson,
    • Kristofer M. Helgen,
    • William J. Murphy,
    • Anders Götherström,
    • and Stephan C. Schuster
    Genome Res. February 2009 19: 213-220; Published in Advance January 12, 2009, doi:10.1101/gr.082628.108
    OPEN ACCESS ARTICLE

  • H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

    • Florian M. Pauler,
    • Mathew A. Sloane,
    • Ru Huang,
    • Kakkad Regha,
    • Martha V. Koerner,
    • Ido Tamir,
    • Andreas Sommer,
    • Andras Aszodi,
    • Thomas Jenuwein,
    • and Denise P. Barlow
    Genome Res. February 2009 19: 221-233; Published in Advance December 1, 2008, doi:10.1101/gr.080861.108

  • Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes

    • David Alvarez-Ponce,
    • Montserrat Aguadé,
    • and Julio Rozas
    Genome Res. February 2009 19: 234-242; Published in Advance January 13, 2009, doi:10.1101/gr.084038.108

  • Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

    • Regina S. Baucom,
    • James C. Estill,
    • Jim Leebens-Mack,
    • and Jeffrey L. Bennetzen
    Genome Res. February 2009 19: 243-254; Published in Advance November 24, 2008, doi:10.1101/gr.083360.108

Methods

  • Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

    • Eivind Valen,
    • Giovanni Pascarella,
    • Alistair Chalk,
    • Norihiro Maeda,
    • Miki Kojima,
    • Chika Kawazu,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Dejan Lazarevic,
    • Dario Motti,
    • Troels Torben Marstrand,
    • Man-Hung Eric Tang,
    • Xiaobei Zhao,
    • Anders Krogh,
    • Ole Winther,
    • Takahiro Arakawa,
    • Jun Kawai,
    • Christine Wells,
    • Carsten Daub,
    • Matthias Harbers,
    • Yoshihide Hayashizaki,
    • Stefano Gustincich,
    • Albin Sandelin,
    • and Piero Carninci
    Genome Res. February 2009 19: 255-265; Published in Advance December 11, 2008, doi:10.1101/gr.084541.108
    OPEN ACCESS ARTICLE

  • High-resolution human core-promoter prediction with CoreBoost_HM

    • Xiaowo Wang,
    • Zhenyu Xuan,
    • Xiaoyue Zhao,
    • Yanda Li,
    • and Michael Q. Zhang
    Genome Res. February 2009 19: 266-275; Published in Advance November 7, 2008, doi:10.1101/gr.081638.108

  • 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. February 2009 19: 276-283; Published in Advance January 13, 2009, doi:10.1101/gr.075671.107

  • A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements

    • Gerhard Mittler,
    • Falk Butter,
    • and Matthias Mann
    Genome Res. February 2009 19: 284-293; Published in Advance November 17, 2008, doi:10.1101/gr.081711.108

  • De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

    • Josephine A. Reinhardt,
    • David A. Baltrus,
    • Marc T. Nishimura,
    • William R. Jeck,
    • Corbin D. Jones,
    • and Jeffery L. Dangl
    Genome Res. February 2009 19: 294-305; Published in Advance November 17, 2008, doi:10.1101/gr.083311.108
    OPEN ACCESS ARTICLE

  • Inferring genomic flux in bacteria

    • Xavier Didelot,
    • Aaron Darling,
    • and Daniel Falush
    Genome Res. February 2009 19: 306-317; Published in Advance November 17, 2008, doi:10.1101/gr.082263.108

RESOURCES

  • Whole population, genome-wide mapping of hidden relatedness

    • Alexander Gusev,
    • Jennifer K. Lowe,
    • Markus Stoffel,
    • Mark J. Daly,
    • David Altshuler,
    • Jan L. Breslow,
    • Jeffrey M. Friedman,
    • and Itsik Pe'er
    Genome Res. February 2009 19: 318-326; Published in Advance October 29, 2008, doi:10.1101/gr.081398.108

  • EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

    • Albert J. Vilella,
    • Jessica Severin,
    • Abel Ureta-Vidal,
    • Li Heng,
    • Richard Durbin,
    • and Ewan Birney
    Genome Res. February 2009 19: 327-335; Published in Advance November 24, 2008, doi:10.1101/gr.073585.107
    OPEN ACCESS ARTICLE

  • De novo fragment assembly with short mate-paired reads: Does the read length matter?

    • Mark J. Chaisson,
    • Dumitru Brinza,
    • and Pavel A. Pevzner
    Genome Res. February 2009 19: 336-346; Published in Advance December 3, 2008, doi:10.1101/gr.079053.108
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This Issue

February 2009; 19 (2)
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  1. LETTERS
  2. Methods
  3. RESOURCES

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