Table of Contents

April 2009; 19 (4)

Next-Generation DNA Sequencing/Review

  • Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

    • Melissa J. Fullwood,
    • Chia-Lin Wei,
    • Edison T. Liu,
    • and Yijun Ruan
    Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
    OPEN ACCESS ARTICLE

Article

  • Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing

    • Jung-Hyun Kim,
    • Thomas Ebersole,
    • Natalay Kouprina,
    • Vladimir N. Noskov,
    • Jun-Ichirou Ohzeki,
    • Hiroshi Masumoto,
    • Brankica Mravinac,
    • Beth A. Sullivan,
    • Adam Pavlicek,
    • Sinisa Dovat,
    • Svetlana D. Pack,
    • Yoo-Wook Kwon,
    • Patrick T. Flanagan,
    • Dmitri Loukinov,
    • Victor Lobanenkov,
    • and Vladimir Larionov
    Genome Res. April 2009 19: 533-544; Published in Advance January 13, 2009, doi:10.1101/gr.086496.108

  • Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?

    • Matthew S. Comeaux,
    • Astrid M. Roy-Engel,
    • Dale J. Hedges,
    • and Prescott L. Deininger
    Genome Res. April 2009 19: 545-555; Published in Advance March 9, 2009, doi:10.1101/gr.089789.108
    OPEN ACCESS ARTICLE

  • High-resolution DNA-binding specificity analysis of yeast transcription factors

    • Cong Zhu,
    • Kelsey J.R.P. Byers,
    • Rachel Patton McCord,
    • Zhenwei Shi,
    • Michael F. Berger,
    • Daniel E. Newburger,
    • Katrina Saulrieta,
    • Zachary Smith,
    • Mita V. Shah,
    • Mathangi Radhakrishnan,
    • Anthony A. Philippakis,
    • Yanhui Hu,
    • Federico De Masi,
    • Marcin Pacek,
    • Andreas Rolfs,
    • Tal Murthy,
    • Joshua LaBaer,
    • and Martha L. Bulyk
    Genome Res. April 2009 19: 556-566; Published in Advance January 21, 2009, doi:10.1101/gr.090233.108
    OPEN ACCESS ARTICLE

Letter

  • Common polymorphic transcript variation in human disease

    • Hunter B. Fraser and
    • Xiaohui Xie
    Genome Res. April 2009 19: 567-575; Published in Advance February 2, 2009, doi:10.1101/gr.083477.108

  • mtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints

    • Ilia Zhidkov,
    • Erez A. Livneh,
    • Eitan Rubin,
    • and Dan Mishmar
    Genome Res. April 2009 19: 576-580; Published in Advance February 10, 2009, doi:10.1101/gr.086462.108

  • HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination

    • Martin I. Sigurdsson,
    • Albert V. Smith,
    • Hans T. Bjornsson,
    • and Jon J. Jonsson
    Genome Res. April 2009 19: 581-589; Published in Advance January 21, 2009, doi:10.1101/gr.086181.108

  • Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns

    • Michael P. Schnetz,
    • Cynthia F. Bartels,
    • Kuntal Shastri,
    • Dheepa Balasubramanian,
    • Gabriel E. Zentner,
    • Ravishankar Balaji,
    • Xiaodong Zhang,
    • Lingyun Song,
    • Zhenghe Wang,
    • Thomas LaFramboise,
    • Gregory E. Crawford,
    • and Peter C. Scacheri
    Genome Res. April 2009 19: 590-601; Published in Advance February 27, 2009, doi:10.1101/gr.086983.108

  • Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard

    • Nicolas Di-Poï,
    • Juan I. Montoya-Burgos,
    • and Denis Duboule
    Genome Res. April 2009 19: 602-610; Published in Advance February 18, 2009, doi:10.1101/gr.087932.108
    OPEN ACCESS ARTICLE

  • The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion

    • Angela Taddei,
    • Griet Van Houwe,
    • Shigeki Nagai,
    • Ionas Erb,
    • Erik van Nimwegen,
    • and Susan M. Gasser
    Genome Res. April 2009 19: 611-625; Published in Advance January 29, 2009, doi:10.1101/gr.083881.108

  • Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

    • Stephen A. James,
    • Michael J.T. O'Kelly,
    • David M. Carter,
    • Robert P. Davey,
    • Alexander van Oudenaarden,
    • and Ian N. Roberts
    Genome Res. April 2009 19: 626-635; Published in Advance January 13, 2009, doi:10.1101/gr.084517.108

  • Global diversity in the human salivary microbiome

    • Ivan Nasidze,
    • Jing Li,
    • Dominique Quinque,
    • Kun Tang,
    • and Mark Stoneking
    Genome Res. April 2009 19: 636-643; Published in Advance February 27, 2009, doi:10.1101/gr.084616.108

Methods

  • A transcription factor affinity-based code for mammalian transcription initiation

    • Molly Megraw,
    • Fernando Pereira,
    • Shane T. Jensen,
    • Uwe Ohler,
    • and Artemis G. Hatzigeorgiou
    Genome Res. April 2009 19: 644-656; Published in Advance January 13, 2009, doi:10.1101/gr.085449.108

Resource

  • Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

    • LaDeana W. Hillier,
    • Valerie Reinke,
    • Philip Green,
    • Martin Hirst,
    • Marco A. Marra,
    • and Robert H. Waterston
    Genome Res. April 2009 19: 657-666; Published in Advance January 30, 2009, doi:10.1101/gr.088112.108

  • A piggyBac transposon-based genome-wide library of insertionally mutated Blm-deficient murine ES cells

    • Wei Wang,
    • Allan Bradley,
    • and Yue Huang
    Genome Res. April 2009 19: 667-673; Published in Advance February 20, 2009, doi:10.1101/gr.085621.108
    OPEN ACCESS ARTICLE

  • HistoneHits: A database for histone mutations and their phenotypes

    • Hailiang Huang,
    • Alexandra M. Maertens,
    • Edel M. Hyland,
    • Junbiao Dai,
    • Anne Norris,
    • Jef D. Boeke,
    • and Joel S. Bader
    Genome Res. April 2009 19: 674-681; Published in Advance February 13, 2009, doi:10.1101/gr.083402.108
    OPEN ACCESS ARTICLE

  • Multiple whole-genome alignments without a reference organism

    • Inna Dubchak,
    • Alexander Poliakov,
    • Andrey Kislyuk,
    • and Michael Brudno
    Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108

Errata

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This Issue

April 2009; 19 (4)
Cover
  1. Next-Generation DNA Sequencing/Review
  2. Article
  3. Letter
  4. Methods
  5. Resource
  6. Errata

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