Table of Contents

September 2012; 22 (9)

Commentary

  • Decoding the human genome

    • Kelly A. Frazer
    Genome Res. September 2012 22: 1599-1601; doi:10.1101/gr.146175.112
    OPEN ACCESS ARTICLE

Perspectives

  • What does our genome encode?

    • John A. Stamatoyannopoulos
    Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
    OPEN ACCESS ARTICLE

  • Toward mapping the biology of the genome

    • Stephen Chanock
    Genome Res. September 2012 22: 1612-1615; doi:10.1101/gr.144980.112
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Research

  • Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

    • Hagen Tilgner,
    • David G. Knowles,
    • Rory Johnson,
    • Carrie A. Davis,
    • Sudipto Chakrabortty,
    • Sarah Djebali,
    • João Curado,
    • Michael Snyder,
    • Thomas R. Gingeras,
    • and Roderic Guigó
    Genome Res. September 2012 22: 1616-1625; doi:10.1101/gr.134445.111
    OPEN ACCESS ARTICLE

  • RNA editing in the human ENCODE RNA-seq data

    • Eddie Park,
    • Brian Williams,
    • Barbara J. Wold,
    • and Ali Mortazavi
    Genome Res. September 2012 22: 1626-1633; doi:10.1101/gr.134957.111
    OPEN ACCESS ARTICLE

  • Discovery of hundreds of mirtrons in mouse and human small RNA data

    • Erik Ladewig,
    • Katsutomo Okamura,
    • Alex S. Flynt,
    • Jakub O. Westholm,
    • and Eric C. Lai
    Genome Res. September 2012 22: 1634-1645; doi:10.1101/gr.133553.111
    OPEN ACCESS ARTICLE

  • Long noncoding RNAs are rarely translated in two human cell lines

    • Balázs Bánfai,
    • Hui Jia,
    • Jainab Khatun,
    • Emily Wood,
    • Brian Risk,
    • William E. Gundling, Jr.,
    • Anshul Kundaje,
    • Harsha P. Gunawardena,
    • Yanbao Yu,
    • Ling Xie,
    • Krzysztof Krajewski,
    • Brian D. Strahl,
    • Xian Chen,
    • Peter Bickel,
    • Morgan C. Giddings,
    • James B. Brown,
    • and Leonard Lipovich
    Genome Res. September 2012 22: 1646-1657; doi:10.1101/gr.134767.111
    OPEN ACCESS ARTICLE

  • Understanding transcriptional regulation by integrative analysis of transcription factor binding data

    • Chao Cheng,
    • Roger Alexander,
    • Renqiang Min,
    • Jing Leng,
    • Kevin Y. Yip,
    • Joel Rozowsky,
    • Koon-Kiu Yan,
    • Xianjun Dong,
    • Sarah Djebali,
    • Yijun Ruan,
    • Carrie A. Davis,
    • Piero Carninci,
    • Timo Lassman,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Ewan Birney,
    • Zhiping Weng,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. September 2012 22: 1658-1667; doi:10.1101/gr.136838.111
    OPEN ACCESS ARTICLE

  • A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells

    • Alexandra E. Charos,
    • Brian D. Reed,
    • Debasish Raha,
    • Anna M. Szekely,
    • Sherman M. Weissman,
    • and Michael Snyder
    Genome Res. September 2012 22: 1668-1679; doi:10.1101/gr.127761.111
    OPEN ACCESS ARTICLE

  • Widespread plasticity in CTCF occupancy linked to DNA methylation

    • Hao Wang,
    • Matthew T. Maurano,
    • Hongzhu Qu,
    • Katherine E. Varley,
    • Jason Gertz,
    • Florencia Pauli,
    • Kristen Lee,
    • Theresa Canfield,
    • Molly Weaver,
    • Richard Sandstrom,
    • Robert E. Thurman,
    • Rajinder Kaul,
    • Richard M. Myers,
    • and John A. Stamatoyannopoulos
    Genome Res. September 2012 22: 1680-1688; doi:10.1101/gr.136101.111
    OPEN ACCESS ARTICLE

  • Personal and population genomics of human regulatory variation

    • Benjamin Vernot,
    • Andrew B. Stergachis,
    • Matthew T. Maurano,
    • Jeff Vierstra,
    • Shane Neph,
    • Robert E. Thurman,
    • John A. Stamatoyannopoulos,
    • and Joshua M. Akey
    Genome Res. September 2012 22: 1689-1697; doi:10.1101/gr.134890.111
    OPEN ACCESS ARTICLE

Methods

  • Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

    • Cédric Howald,
    • Andrea Tanzer,
    • Jacqueline Chrast,
    • Felix Kokocinski,
    • Thomas Derrien,
    • Nathalie Walters,
    • Jose M. Gonzalez,
    • Adam Frankish,
    • Bronwen L. Aken,
    • Thibaut Hourlier,
    • Jan-Hinnerk Vogel,
    • Simon White,
    • Stephen Searle,
    • Jennifer Harrow,
    • Tim J. Hubbard,
    • Roderic Guigó,
    • and Alexandre Reymond
    Genome Res. September 2012 22: 1698-1710; doi:10.1101/gr.134478.111
    OPEN ACCESS ARTICLE

  • Predicting cell-type–specific gene expression from regions of open chromatin

    • Anirudh Natarajan,
    • Galip Gürkan Yardımcı,
    • Nathan C. Sheffield,
    • Gregory E. Crawford,
    • and Uwe Ohler
    Genome Res. September 2012 22: 1711-1722; doi:10.1101/gr.135129.111
    OPEN ACCESS ARTICLE

  • Sequence and chromatin determinants of cell-type–specific transcription factor binding

    • Aaron Arvey,
    • Phaedra Agius,
    • William Stafford Noble,
    • and Christina Leslie
    Genome Res. September 2012 22: 1723-1734; doi:10.1101/gr.127712.111
    OPEN ACCESS ARTICLE

  • Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

    • Anshul Kundaje,
    • Sofia Kyriazopoulou-Panagiotopoulou,
    • Max Libbrecht,
    • Cheryl L. Smith,
    • Debasish Raha,
    • Elliott E. Winters,
    • Steven M. Johnson,
    • Michael Snyder,
    • Serafim Batzoglou,
    • and Arend Sidow
    Genome Res. September 2012 22: 1735-1747; doi:10.1101/gr.136366.111
    OPEN ACCESS ARTICLE

  • Linking disease associations with regulatory information in the human genome

    • Marc A. Schaub,
    • Alan P. Boyle,
    • Anshul Kundaje,
    • Serafim Batzoglou,
    • and Michael Snyder
    Genome Res. September 2012 22: 1748-1759; doi:10.1101/gr.136127.111
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Resources

  • GENCODE: The reference human genome annotation for The ENCODE Project

    • Jennifer Harrow,
    • Adam Frankish,
    • Jose M. Gonzalez,
    • Electra Tapanari,
    • Mark Diekhans,
    • Felix Kokocinski,
    • Bronwen L. Aken,
    • Daniel Barrell,
    • Amonida Zadissa,
    • Stephen Searle,
    • If Barnes,
    • Alexandra Bignell,
    • Veronika Boychenko,
    • Toby Hunt,
    • Mike Kay,
    • Gaurab Mukherjee,
    • Jeena Rajan,
    • Gloria Despacio-Reyes,
    • Gary Saunders,
    • Charles Steward,
    • Rachel Harte,
    • Michael Lin,
    • Cédric Howald,
    • Andrea Tanzer,
    • Thomas Derrien,
    • Jacqueline Chrast,
    • Nathalie Walters,
    • Suganthi Balasubramanian,
    • Baikang Pei,
    • Michael Tress,
    • Jose Manuel Rodriguez,
    • Iakes Ezkurdia,
    • Jeltje van Baren,
    • Michael Brent,
    • David Haussler,
    • Manolis Kellis,
    • Alfonso Valencia,
    • Alexandre Reymond,
    • Mark Gerstein,
    • Roderic Guigó,
    • and Tim J. Hubbard
    Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111
    OPEN ACCESS ARTICLE

  • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

    • Thomas Derrien,
    • Rory Johnson,
    • Giovanni Bussotti,
    • Andrea Tanzer,
    • Sarah Djebali,
    • Hagen Tilgner,
    • Gregory Guernec,
    • David Martin,
    • Angelika Merkel,
    • David G. Knowles,
    • Julien Lagarde,
    • Lavanya Veeravalli,
    • Xiaoan Ruan,
    • Yijun Ruan,
    • Timo Lassmann,
    • Piero Carninci,
    • James B. Brown,
    • Leonard Lipovich,
    • Jose M. Gonzalez,
    • Mark Thomas,
    • Carrie A. Davis,
    • Ramin Shiekhattar,
    • Thomas R. Gingeras,
    • Tim J. Hubbard,
    • Cedric Notredame,
    • Jennifer Harrow,
    • and Roderic Guigó
    Genome Res. September 2012 22: 1775-1789; doi:10.1101/gr.132159.111
    OPEN ACCESS ARTICLE

  • Annotation of functional variation in personal genomes using RegulomeDB

    • Alan P. Boyle,
    • Eurie L. Hong,
    • Manoj Hariharan,
    • Yong Cheng,
    • Marc A. Schaub,
    • Maya Kasowski,
    • Konrad J. Karczewski,
    • Julie Park,
    • Benjamin C. Hitz,
    • Shuai Weng,
    • J. Michael Cherry,
    • and Michael Snyder
    Genome Res. September 2012 22: 1790-1797; doi:10.1101/gr.137323.112
    OPEN ACCESS ARTICLE

  • Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

    • Jie Wang,
    • Jiali Zhuang,
    • Sowmya Iyer,
    • XinYing Lin,
    • Troy W. Whitfield,
    • Melissa C. Greven,
    • Brian G. Pierce,
    • Xianjun Dong,
    • Anshul Kundaje,
    • Yong Cheng,
    • Oliver J. Rando,
    • Ewan Birney,
    • Richard M. Myers,
    • William S. Noble,
    • Michael Snyder,
    • and Zhiping Weng
    Genome Res. September 2012 22: 1798-1812; doi:10.1101/gr.139105.112
    OPEN ACCESS ARTICLE

  • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

    • Stephen G. Landt,
    • Georgi K. Marinov,
    • Anshul Kundaje,
    • Pouya Kheradpour,
    • Florencia Pauli,
    • Serafim Batzoglou,
    • Bradley E. Bernstein,
    • Peter Bickel,
    • James B. Brown,
    • Philip Cayting,
    • Yiwen Chen,
    • Gilberto DeSalvo,
    • Charles Epstein,
    • Katherine I. Fisher-Aylor,
    • Ghia Euskirchen,
    • Mark Gerstein,
    • Jason Gertz,
    • Alexander J. Hartemink,
    • Michael M. Hoffman,
    • Vishwanath R. Iyer,
    • Youngsook L. Jung,
    • Subhradip Karmakar,
    • Manolis Kellis,
    • Peter V. Kharchenko,
    • Qunhua Li,
    • Tao Liu,
    • X. Shirley Liu,
    • Lijia Ma,
    • Aleksandar Milosavljevic,
    • Richard M. Myers,
    • Peter J. Park,
    • Michael J. Pazin,
    • Marc D. Perry,
    • Debasish Raha,
    • Timothy E. Reddy,
    • Joel Rozowsky,
    • Noam Shoresh,
    • Arend Sidow,
    • Matthew Slattery,
    • John A. Stamatoyannopoulos,
    • Michael Y. Tolstorukov,
    • Kevin P. White,
    • Simon Xi,
    • Peggy J. Farnham,
    • Jason D. Lieb,
    • Barbara J. Wold,
    • and Michael Snyder
    Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
    OPEN ACCESS ARTICLE
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This Issue

September 2012; 22 (9)
Cover
  1. Commentary
  2. Perspectives
  3. Research
  4. Methods
  5. Resources

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