Table of Contents

November 2011; 21 (11)

Review

  • What fraction of the human genome is functional?

    • Chris P. Ponting and
    • Ross C. Hardison
    Genome Res. November 2011 21: 1769-1776; Published in Advance August 29, 2011, doi:10.1101/gr.116814.110
    OPEN ACCESS ARTICLE

Research

  • Widespread signatures of recent selection linked to nucleosome positioning in the human lineage

    • James G.D. Prendergast and
    • Colin A.M. Semple
    Genome Res. November 2011 21: 1777-1787; Published in Advance September 8, 2011, doi:10.1101/gr.122275.111

  • Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant

    • Haya H. Al-Balool,
    • David Weber,
    • Yilei Liu,
    • Mark Wade,
    • Kamlesh Guleria,
    • Pitsien Lang Ping Nam,
    • Jake Clayton,
    • William Rowe,
    • Jonathan Coxhead,
    • Julie Irving,
    • David J. Elliott,
    • Andrew G. Hall,
    • Mauro Santibanez-Koref,
    • and Michael S. Jackson
    Genome Res. November 2011 21: 1788-1799; Published in Advance September 23, 2011, doi:10.1101/gr.116442.110
    OPEN ACCESS ARTICLE

  • Coevolution of retroelements and tandem zinc finger genes

    • James H. Thomas and
    • Sean Schneider
    Genome Res. November 2011 21: 1800-1812; Published in Advance July 22, 2011, doi:10.1101/gr.121749.111

  • Extensive variation and low heritability of DNA methylation identified in a twin study

    • Kristina Gervin,
    • Martin Hammerø,
    • Hanne E. Akselsen,
    • Rune Moe,
    • Heidi Nygård,
    • Ingunn Brandt,
    • Håkon K. Gjessing,
    • Jennifer R. Harris,
    • Dag E. Undlien,
    • and Robert Lyle
    Genome Res. November 2011 21: 1813-1821; Published in Advance September 26, 2011, doi:10.1101/gr.119685.110

  • Genome-wide depletion of replication initiation events in highly transcribed regions

    • Melvenia M. Martin,
    • Michael Ryan,
    • RyangGuk Kim,
    • Anna L. Zakas,
    • Haiqing Fu,
    • Chii Mei Lin,
    • William C. Reinhold,
    • Sean R. Davis,
    • Sven Bilke,
    • Hongfang Liu,
    • James H. Doroshow,
    • Mark A. Reimers,
    • Manuel S. Valenzuela,
    • Yves Pommier,
    • Paul S. Meltzer,
    • and Mirit I. Aladjem
    Genome Res. November 2011 21: 1822-1832; Published in Advance August 3, 2011, doi:10.1101/gr.124644.111

  • Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome

    • Masako Suzuki,
    • Mayumi Oda,
    • María-Paz Ramos,
    • Marién Pascual,
    • Kevin Lau,
    • Edyta Stasiek,
    • Frederick Agyiri,
    • Reid F. Thompson,
    • Jacob L. Glass,
    • Qiang Jing,
    • Richard Sandstrom,
    • Melissa J. Fazzari,
    • R. Scott Hansen,
    • John A. Stamatoyannopoulos,
    • Andrew S. McLellan,
    • and John M. Greally
    Genome Res. November 2011 21: 1833-1840; Published in Advance September 28, 2011, doi:10.1101/gr.116509.110

  • Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates

    • Lisa Nanty,
    • Guillermo Carbajosa,
    • Graham A. Heap,
    • Francis Ratnieks,
    • David A. van Heel,
    • Thomas A. Down,
    • and Vardhman K. Rakyan
    Genome Res. November 2011 21: 1841-1850; Published in Advance September 22, 2011, doi:10.1101/gr.121640.111

  • Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

    • Alex Tsankov,
    • Yoshimi Yanagisawa,
    • Nicholas Rhind,
    • Aviv Regev,
    • and Oliver J. Rando
    Genome Res. November 2011 21: 1851-1862; Published in Advance September 13, 2011, doi:10.1101/gr.122267.111
    OPEN ACCESS ARTICLE

  • Variety of genomic DNA patterns for nucleosome positioning

    • Ilya Ioshikhes,
    • Sergey Hosid,
    • and B. Franklin Pugh
    Genome Res. November 2011 21: 1863-1871; Published in Advance July 12, 2011, doi:10.1101/gr.116228.110

  • A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

    • Raghothama Chaerkady,
    • Dhanashree S. Kelkar,
    • Babylakshmi Muthusamy,
    • Kumaran Kandasamy,
    • Sutopa B. Dwivedi,
    • Nandini A. Sahasrabuddhe,
    • Min-Sik Kim,
    • Santosh Renuse,
    • Sneha M. Pinto,
    • Rakesh Sharma,
    • Harsh Pawar,
    • Nirujogi Raja Sekhar,
    • Ajeet Kumar Mohanty,
    • Derese Getnet,
    • Yi Yang,
    • Jun Zhong,
    • Aditya P. Dash,
    • Robert M. MacCallum,
    • Bernard Delanghe,
    • Godfree Mlambo,
    • Ashwani Kumar,
    • T.S. Keshava Prasad,
    • Mobolaji Okulate,
    • Nirbhay Kumar,
    • and Akhilesh Pandey
    Genome Res. November 2011 21: 1872-1881; Published in Advance July 27, 2011, doi:10.1101/gr.127951.111

  • Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

    • Andrew J. Heidel,
    • Hajara M. Lawal,
    • Marius Felder,
    • Christina Schilde,
    • Nicholas R. Helps,
    • Budi Tunggal,
    • Francisco Rivero,
    • Uwe John,
    • Michael Schleicher,
    • Ludwig Eichinger,
    • Matthias Platzer,
    • Angelika A. Noegel,
    • Pauline Schaap,
    • and Gernot Glöckner
    Genome Res. November 2011 21: 1882-1891; Published in Advance July 14, 2011, doi:10.1101/gr.121137.111
    OPEN ACCESS ARTICLE

  • Parallel evolution of transcriptome architecture during genome reorganization

    • Sung Ho Yoon,
    • David J. Reiss,
    • J. Christopher Bare,
    • Dan Tenenbaum,
    • Min Pan,
    • Joseph Slagel,
    • Robert L. Moritz,
    • Sujung Lim,
    • Murray Hackett,
    • Angeli Lal Menon,
    • Michael W.W. Adams,
    • Adam Barnebey,
    • Steven M. Yannone,
    • John A. Leigh,
    • and Nitin S. Baliga
    Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111

Methods

  • Digital gene expression for non-model organisms

    • Lewis Z. Hong,
    • Jun Li,
    • Anne Schmidt-Küntzel,
    • Wesley C. Warren,
    • and Gregory S. Barsh
    Genome Res. November 2011 21: 1905-1915; Published in Advance August 15, 2011, doi:10.1101/gr.122135.111

  • Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

    • Michael F. Lin,
    • Pouya Kheradpour,
    • Stefan Washietl,
    • Brian J. Parker,
    • Jakob S. Pedersen,
    • and Manolis Kellis
    Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
    OPEN ACCESS ARTICLE

  • New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

    • Brian J. Parker,
    • Ida Moltke,
    • Adam Roth,
    • Stefan Washietl,
    • Jiayu Wen,
    • Manolis Kellis,
    • Ronald Breaker,
    • and Jakob Skou Pedersen
    Genome Res. November 2011 21: 1929-1943; Published in Advance October 12, 2011, doi:10.1101/gr.112516.110

  • Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases

    • Tony Gutschner,
    • Marion Baas,
    • and Sven Diederichs
    Genome Res. November 2011 21: 1944-1954; Published in Advance August 15, 2011, doi:10.1101/gr.122358.111

  • Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of SRC kinases

    • Julia Ritzerfeld,
    • Steffen Remmele,
    • Tao Wang,
    • Koen Temmerman,
    • Britta Brügger,
    • Sabine Wegehingel,
    • Stella Tournaviti,
    • Jeroen R.P.M. Strating,
    • Felix T. Wieland,
    • Beate Neumann,
    • Jan Ellenberg,
    • Chris Lawerenz,
    • Jürgen Hesser,
    • Holger Erfle,
    • Rainer Pepperkok,
    • and Walter Nickel
    Genome Res. November 2011 21: 1955-1968; Published in Advance July 27, 2011, doi:10.1101/gr.116087.110

Resources

  • Genome-scale phylogenetic function annotation of large and diverse protein families

    • Barbara E. Engelhardt,
    • Michael I. Jordan,
    • John R. Srouji,
    • and Steven E. Brenner
    Genome Res. November 2011 21: 1969-1980; Published in Advance July 22, 2011, doi:10.1101/gr.104687.109
    OPEN ACCESS ARTICLE

  • The Proteome Folding Project: Proteome-scale prediction of structure and function

    • Kevin Drew,
    • Patrick Winters,
    • Glenn L. Butterfoss,
    • Viktors Berstis,
    • Keith Uplinger,
    • Jonathan Armstrong,
    • Michael Riffle,
    • Erik Schweighofer,
    • Bill Bovermann,
    • David R. Goodlett,
    • Trisha N. Davis,
    • Dennis Shasha,
    • Lars Malmström,
    • and Richard Bonneau
    Genome Res. November 2011 21: 1981-1994; Published in Advance August 8, 2011, doi:10.1101/gr.121475.111
    OPEN ACCESS ARTICLE
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This Issue

November 2011; 21 (11)
Cover
  1. Review
  2. Research
  3. Methods
  4. Resources

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