Table of Contents

June 2007; 17 (6)

COMMENTARY

  • ENCODE: More genomic empowerment

    • George M. Weinstock
    Genome Res. June 2007 17: 667-668; doi:10.1101/gr.6534207
    OPEN ACCESS ARTICLE

PERSPECTIVES

  • What is a gene, post-ENCODE? History and updated definition

    • Mark B. Gerstein,
    • Can Bruce,
    • Joel S. Rozowsky,
    • Deyou Zheng,
    • Jiang Du,
    • Jan O. Korbel,
    • Olof Emanuelsson,
    • Zhengdong D. Zhang,
    • Sherman Weissman,
    • and Michael Snyder
    Genome Res. June 2007 17: 669-681; doi:10.1101/gr.6339607
    OPEN ACCESS ARTICLE

  • Origin of phenotypes: Genes and transcripts

    • Thomas R. Gingeras
    Genome Res. June 2007 17: 682-690; doi:10.1101/gr.6525007
    OPEN ACCESS ARTICLE

ARTICLES

  • The landscape of histone modifications across 1% of the human genome in five human cell lines

    • Christoph M. Koch,
    • Robert M. Andrews,
    • Paul Flicek,
    • Shane C. Dillon,
    • Ulaş Karaöz,
    • Gayle K. Clelland,
    • Sarah Wilcox,
    • David M. Beare,
    • Joanna C. Fowler,
    • Phillippe Couttet,
    • Keith D. James,
    • Gregory C. Lefebvre,
    • Alexander W. Bruce,
    • Oliver M. Dovey,
    • Peter D. Ellis,
    • Pawandeep Dhami,
    • Cordelia F. Langford,
    • Zhiping Weng,
    • Ewan Birney,
    • Nigel P. Carter,
    • David Vetrie,
    • and Ian Dunham
    Genome Res. June 2007 17: 691-707; doi:10.1101/gr.5704207
    OPEN ACCESS ARTICLE

  • Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

    • Alvaro Rada-Iglesias,
    • Stefan Enroth,
    • Adam Ameur,
    • Christoph M. Koch,
    • Gayle K. Clelland,
    • Patricia Respuela-Alonso,
    • Sarah Wilcox,
    • Oliver M. Dovey,
    • Peter D. Ellis,
    • Cordelia F. Langford,
    • Ian Dunham,
    • Jan Komorowski,
    • and Claes Wadelius
    Genome Res. June 2007 17: 708-719; doi:10.1101/gr.5540007
    OPEN ACCESS ARTICLE

  • Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

    • Nathan D. Trinklein,
    • Ulaş Karaöz,
    • Jiaqian Wu,
    • Anason Halees,
    • Shelley Force Aldred,
    • Patrick J. Collins,
    • Deyou Zheng,
    • Zhengdong D. Zhang,
    • Mark B. Gerstein,
    • Michael Snyder,
    • Richard M. Myers,
    • and Zhiping Weng
    Genome Res. June 2007 17: 720-731; doi:10.1101/gr.5716607
    OPEN ACCESS ARTICLE

  • The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

    • Joel S. Rozowsky,
    • Daniel Newburger,
    • Fred Sayward,
    • Jiaqian Wu,
    • Greg Jordan,
    • Jan O. Korbel,
    • Ugrappa Nagalakshmi,
    • Jin Yang,
    • Deyou Zheng,
    • Roderic Guigó,
    • Thomas R. Gingeras,
    • Sherman Weissman,
    • Perry Miller,
    • Michael Snyder,
    • and Mark B. Gerstein
    Genome Res. June 2007 17: 732-745; doi:10.1101/gr.5696007
    OPEN ACCESS ARTICLE

  • Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions

    • France Denoeud,
    • Philipp Kapranov,
    • Catherine Ucla,
    • Adam Frankish,
    • Robert Castelo,
    • Jorg Drenkow,
    • Julien Lagarde,
    • Tyler Alioto,
    • Caroline Manzano,
    • Jacqueline Chrast,
    • Sujit Dike,
    • Carine Wyss,
    • Charlotte N. Henrichsen,
    • Nancy Holroyd,
    • Mark C. Dickson,
    • Ruth Taylor,
    • Zahra Hance,
    • Sylvain Foissac,
    • Richard M. Myers,
    • Jane Rogers,
    • Tim Hubbard,
    • Jennifer Harrow,
    • Roderic Guigó,
    • Thomas R. Gingeras,
    • Stylianos E. Antonarakis,
    • and Alexandre Reymond
    Genome Res. June 2007 17: 746-759; doi:10.1101/gr.5660607
    OPEN ACCESS ARTICLE

  • Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

    • Elliott H. Margulies,
    • Gregory M. Cooper,
    • George Asimenos,
    • Daryl J. Thomas,
    • Colin N. Dewey,
    • Adam Siepel,
    • Ewan Birney,
    • Damian Keefe,
    • Ariel S. Schwartz,
    • Minmei Hou,
    • James Taylor,
    • Sergey Nikolaev,
    • Juan I. Montoya-Burgos,
    • Ari Löytynoja,
    • Simon Whelan,
    • Fabio Pardi,
    • Tim Massingham,
    • James B. Brown,
    • Peter Bickel,
    • Ian Holmes,
    • James C. Mullikin,
    • Abel Ureta-Vidal,
    • Benedict Paten,
    • Eric A. Stone,
    • Kate R. Rosenbloom,
    • W. James Kent,
    • Gerard G. Bouffard,
    • Xiaobin Guan,
    • Nancy F. Hansen,
    • Jacquelyn R. Idol,
    • Valerie V.B. Maduro,
    • Baishali Maskeri,
    • Jennifer C. McDowell,
    • Morgan Park,
    • Pamela J. Thomas,
    • Alice C. Young,
    • Robert W. Blakesley,
    • Donna M. Muzny,
    • Erica Sodergren,
    • David A. Wheeler,
    • Kim C. Worley,
    • Huaiyang Jiang,
    • George M. Weinstock,
    • Richard A. Gibbs,
    • Tina Graves,
    • Robert Fulton,
    • Elaine R. Mardis,
    • Richard K. Wilson,
    • Michele Clamp,
    • James Cuff,
    • Sante Gnerre,
    • David B. Jaffe,
    • Jean L. Chang,
    • Kerstin Lindblad-Toh,
    • Eric S. Lander,
    • Angie Hinrichs,
    • Heather Trumbower,
    • Hiram Clawson,
    • Ann Zweig,
    • Robert M. Kuhn,
    • Galt Barber,
    • Rachel Harte,
    • Donna Karolchik,
    • Matthew A. Field,
    • Richard A. Moore,
    • Carrie A. Matthewson,
    • Jacqueline E. Schein,
    • Marco A. Marra,
    • Stylianos E. Antonarakis,
    • Serafim Batzoglou,
    • Nick Goldman,
    • Ross Hardison,
    • David Haussler,
    • Webb Miller,
    • Lior Pachter,
    • Eric D. Green,
    • and Arend Sidow
    Genome Res. June 2007 17: 760-774; doi:10.1101/gr.6034307
    OPEN ACCESS ARTICLE

LETTERS

  • Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

    • David C. King,
    • James Taylor,
    • Ying Zhang,
    • Yong Cheng,
    • Heather A. Lawson,
    • Joel Martin,
    • ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
    • Francesca Chiaromonte,
    • Webb Miller,
    • and Ross C. Hardison
    Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
    OPEN ACCESS ARTICLE

  • Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

    • Zhengdong D. Zhang,
    • Alberto Paccanaro,
    • Yutao Fu,
    • Sherman Weissman,
    • Zhiping Weng,
    • Joseph Chang,
    • Michael Snyder,
    • and Mark B. Gerstein
    Genome Res. June 2007 17: 787-797; doi:10.1101/gr.5573107
    OPEN ACCESS ARTICLE

  • Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1

    • Hualin Xi,
    • Yong Yu,
    • Yutao Fu,
    • Jonathan Foley,
    • Anason Halees,
    • and Zhiping Weng
    Genome Res. June 2007 17: 798-806; doi:10.1101/gr.5754707
    OPEN ACCESS ARTICLE

  • Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

    • Victor X. Jin,
    • Henriette O’Geen,
    • Sushma Iyengar,
    • Roland Green,
    • and Peggy J. Farnham
    Genome Res. June 2007 17: 807-817; doi:10.1101/gr.6006107
    OPEN ACCESS ARTICLE

  • Transcription factor binding and modified histones in human bidirectional promoters

    • Jane M. Lin,
    • Patrick J. Collins,
    • Nathan D. Trinklein,
    • Yutao Fu,
    • Hualin Xi,
    • Richard M. Myers,
    • and Zhiping Weng
    Genome Res. June 2007 17: 818-827; doi:10.1101/gr.5623407
    OPEN ACCESS ARTICLE

  • Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

    • Yijun Ruan,
    • Hong Sain Ooi,
    • Siew Woh Choo,
    • Kuo Ping Chiu,
    • Xiao Dong Zhao,
    • K.G. Srinivasan,
    • Fei Yao,
    • Chiou Yu Choo,
    • Jun Liu,
    • Pramila Ariyaratne,
    • Wilson G.W. Bin,
    • Vladimir A. Kuznetsov,
    • Atif Shahab,
    • Wing-Kin Sung,
    • Guillaume Bourque,
    • Nallasivam Palanisamy,
    • and Chia-Lin Wei
    Genome Res. June 2007 17: 828-838; doi:10.1101/gr.6018607
    OPEN ACCESS ARTICLE

  • Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

    • Deyou Zheng,
    • Adam Frankish,
    • Robert Baertsch,
    • Philipp Kapranov,
    • Alexandre Reymond,
    • Siew Woh Choo,
    • Yontao Lu,
    • France Denoeud,
    • Stylianos E. Antonarakis,
    • Michael Snyder,
    • Yijun Ruan,
    • Chia-Lin Wei,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Jennifer Harrow,
    • and Mark B. Gerstein
    Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
    OPEN ACCESS ARTICLE

  • Structured RNAs in the ENCODE selected regions of the human genome

    • Stefan Washietl,
    • Jakob S. Pedersen,
    • Jan O. Korbel,
    • Claudia Stocsits,
    • Andreas R. Gruber,
    • Jörg Hackermüller,
    • Jana Hertel,
    • Manja Lindemeyer,
    • Kristin Reiche,
    • Andrea Tanzer,
    • Catherine Ucla,
    • Carine Wyss,
    • Stylianos E. Antonarakis,
    • France Denoeud,
    • Julien Lagarde,
    • Jorg Drenkow,
    • Philipp Kapranov,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Michael Snyder,
    • Mark B. Gerstein,
    • Alexandre Reymond,
    • Ivo L. Hofacker,
    • and Peter F. Stadler
    Genome Res. June 2007 17: 852-864; doi:10.1101/gr.5650707
    OPEN ACCESS ARTICLE

  • Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas

    • Neerja Karnani,
    • Christopher Taylor,
    • Ankit Malhotra,
    • and Anindya Dutta
    Genome Res. June 2007 17: 865-876; doi:10.1101/gr.5427007
    OPEN ACCESS ARTICLE

Methods

  • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

    • Paul G. Giresi,
    • Jonghwan Kim,
    • Ryan M. McDaniell,
    • Vishwanath R. Iyer,
    • and Jason D. Lieb
    Genome Res. June 2007 17: 877-885; Published in Advance December 19, 2006, doi:10.1101/gr.5533506
    OPEN ACCESS ARTICLE

  • Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

    • Olof Emanuelsson,
    • Ugrappa Nagalakshmi,
    • Deyou Zheng,
    • Joel S. Rozowsky,
    • Alexander E. Urban,
    • Jiang Du,
    • Zheng Lian,
    • Viktor Stolc,
    • Sherman Weissman,
    • Michael Snyder,
    • and Mark B. Gerstein
    Genome Res. June 2007 17: 886-897; Published in Advance November 21, 2006, doi:10.1101/gr.5014606
    OPEN ACCESS ARTICLE

  • Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

    • Ghia M. Euskirchen,
    • Joel S. Rozowsky,
    • Chia-Lin Wei,
    • Wah Heng Lee,
    • Zhengdong D. Zhang,
    • Stephen Hartman,
    • Olof Emanuelsson,
    • Viktor Stolc,
    • Sherman Weissman,
    • Mark B. Gerstein,
    • Yijun Ruan,
    • and Michael Snyder
    Genome Res. June 2007 17: 898-909; doi:10.1101/gr.5583007
    OPEN ACCESS ARTICLE

  • Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)

    • Akshay A. Bhinge,
    • Jonghwan Kim,
    • Ghia M. Euskirchen,
    • Michael Snyder,
    • and Vishwanath R. Iyer
    Genome Res. June 2007 17: 910-916; doi:10.1101/gr.5574907
    OPEN ACCESS ARTICLE

  • Identification of higher-order functional domains in the human ENCODE regions

    • Robert E. Thurman,
    • Nathan Day,
    • William S. Noble,
    • and John A. Stamatoyannopoulos
    Genome Res. June 2007 17: 917-927; doi:10.1101/gr.6081407
    OPEN ACCESS ARTICLE

  • Independent and complementary methods for large-scale structural analysis of mammalian chromatin

    • Jonathan H. Dennis,
    • Hua-Ying Fan,
    • Sheila M. Reynolds,
    • Guocheng Yuan,
    • James C. Meldrim,
    • Daniel J. Richter,
    • Daniel G. Peterson,
    • Oliver J. Rando,
    • William S. Noble,
    • and Robert E. Kingston
    Genome Res. June 2007 17: 928-939; doi:10.1101/gr.5636607
    OPEN ACCESS ARTICLE

  • Detection of DNA structural motifs in functional genomic elements

    • Jason A. Greenbaum,
    • Stephen C.J. Parker,
    • and Thomas D. Tullius
    Genome Res. June 2007 17: 940-946; doi:10.1101/gr.5602807
    OPEN ACCESS ARTICLE

RESOURCES

  • Construction of a genome-scale structural map at single-nucleotide resolution

    • Jason A. Greenbaum,
    • Bo Pang,
    • and Thomas D. Tullius
    Genome Res. June 2007 17: 947-953; doi:10.1101/gr.6073107
    OPEN ACCESS ARTICLE

  • The ENCODEdb portal: Simplified access to ENCODE Consortium data

    • Laura L. Elnitski,
    • Prachi Shah,
    • R. Travis Moreland,
    • Lowell Umayam,
    • Tyra G. Wolfsberg,
    • and Andreas D. Baxevanis
    Genome Res. June 2007 17: 954-959; doi:10.1101/gr.5582207
    OPEN ACCESS ARTICLE

  • A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

    • Daniel Blankenberg,
    • James Taylor,
    • Ian Schenck,
    • Jianbin He,
    • Yi Zhang,
    • Matthew Ghent,
    • Narayanan Veeraraghavan,
    • Istvan Albert,
    • Webb Miller,
    • Kateryna D. Makova,
    • Ross C. Hardison,
    • and Anton Nekrutenko
    Genome Res. June 2007 17: 960-964; doi:10.1101/gr.5578007
    OPEN ACCESS ARTICLE
|

This Issue

June 2007; 17 (6)
Cover
  1. COMMENTARY
  2. PERSPECTIVES
  3. ARTICLES
  4. LETTERS
  5. Methods
  6. RESOURCES

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