COMMENTARY:

George M. Weinstock

ENCODE: More genomic empowerment
Genome Res. 2007 17: 667-668. [Full Text] [PDF] OPEN ACCESS ARTICLE  

PERSPECTIVE:

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

What is a gene, post-ENCODE? History and updated definition
Genome Res. 2007 17: 669-681. [Abstract] [Full Text] [PDF] [Fig._1_Timeline_Poster.pdf] OPEN ACCESS ARTICLE  

Thomas R. Gingeras

Origin of phenotypes: Genes and transcripts
Genome Res. 2007 17: 682-690. [Abstract] [Full Text] [PDF] OPEN ACCESS ARTICLE  

ARTICLES:

Christoph M. Koch, Robert M. Andrews, Paul Flicek, Shane C. Dillon, Ulas 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

The landscape of histone modifications across 1% of the human genome in five human cell lines
Genome Res. 2007 17: 691-707. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

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

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes
Genome Res. 2007 17: 708-719. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

Nathan D. Trinklein, Ulas 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

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
Genome Res. 2007 17: 720-731. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

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

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
Genome Res. 2007 17: 732-745. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

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

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
Genome Res. 2007 17: 746-759. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

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

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Genome Res. 2007 17: 760-774. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

LETTERS:

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

Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
Genome Res. 2007 17: 775-786. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

Zhengdong D. Zhang, Alberto Paccanaro, Yutao Fu, Sherman Weissman, Zhiping Weng, Joseph Chang, Michael Snyder, and Mark B. Gerstein

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
Genome Res. 2007 17: 787-797. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Hualin Xi, Yong Yu, Yutao Fu, Jonathan Foley, Anason Halees, and Zhiping Weng

Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1
Genome Res. 2007 17: 798-806. [Abstract] [Full Text] [PDF] [Supplemental Reseach Data] OPEN ACCESS ARTICLE  

Victor X. Jin, Henriette O’Geen, Sushma Iyengar, Roland Green, and Peggy J. Farnham

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
Genome Res. 2007 17: 807-817. [Abstract] [Full Text] [PDF] [Supplementary Research Data] OPEN ACCESS ARTICLE  

Jane M. Lin, Patrick J. Collins, Nathan D. Trinklein, Yutao Fu, Hualin Xi, Richard M. Myers, and Zhiping Weng

Transcription factor binding and modified histones in human bidirectional promoters
Genome Res. 2007 17: 818-827. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
Genome Res. 2007 17: 828-838. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
Genome Res. 2007 17: 839-851. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Structured RNAs in the ENCODE selected regions of the human genome
Genome Res. 2007 17: 852-864. [Abstract] [Full Text] [PDF] OPEN ACCESS ARTICLE  

Neerja Karnani, Christopher Taylor, Ankit Malhotra, and Anindya Dutta

Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
Genome Res. 2007 17: 865-876. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

METHODS:

Paul G. Giresi, Jonghwan Kim, Ryan M. McDaniell, Vishwanath R. Iyer, and Jason D. Lieb

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
Genome Res. 2007 17: 877-885. Published in Advance December 19, 2006, 10.1101/gr.5533506 [Abstract] [Full Text] [PDF] OPEN ACCESS ARTICLE  

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

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
Genome Res. 2007 17: 886-897. Published in Advance November 21, 2006, 10.1101/gr.5014606 [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
Genome Res. 2007 17: 898-909. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Akshay A. Bhinge, Jonghwan Kim, Ghia M. Euskirchen, Michael Snyder, and Vishwanath R. Iyer

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
Genome Res. 2007 17: 910-916. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Robert E. Thurman, Nathan Day, William S. Noble, and John A. Stamatoyannopoulos

Identification of higher-order functional domains in the human ENCODE regions
Genome Res. 2007 17: 917-927. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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

Independent and complementary methods for large-scale structural analysis of mammalian chromatin
Genome Res. 2007 17: 928-939. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Jason A. Greenbaum, Stephen C.J. Parker, and Thomas D. Tullius

Detection of DNA structural motifs in functional genomic elements
Genome Res. 2007 17: 940-946. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

RESOURCES:

Jason A. Greenbaum, Bo Pang, and Thomas D. Tullius

Construction of a genome-scale structural map at single-nucleotide resolution
Genome Res. 2007 17: 947-953. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

Laura L. Elnitski, Prachi Shah, R. Travis Moreland, Lowell Umayam, Tyra G. Wolfsberg, and Andreas D. Baxevanis

The ENCODEdb portal: Simplified access to ENCODE Consortium data
Genome Res. 2007 17: 954-959. [Abstract] [Full Text] [PDF] OPEN ACCESS ARTICLE  

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

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
Genome Res. 2007 17: 960-964. [Abstract] [Full Text] [PDF] [Supplemental Research Data] OPEN ACCESS ARTICLE  

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