Volume 22, Issue 9 | September 2012

Commentary
- - Decoding the human genome
    Kelly A. Frazer
    First Published September 5, 2012
Perspectives
- - What does our genome encode?
    John A. Stamatoyannopoulos
    First Published September 5, 2012
  - Toward mapping the biology of the genome
    Stephen Chanock
    First Published September 5, 2012
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
    ...[+1 authors]...,
    João Curado
    Michael Snyder
    Thomas R. Gingeras
    Roderic Guigó
    First Published September 5, 2012
  - RNA editing in the human ENCODE RNA-seq data
    Eddie Park
    Brian Williams
    Barbara J. Wold
    Ali Mortazavi
    First Published September 5, 2012
  - Discovery of hundreds of mirtrons in mouse and human small RNA data
    Erik Ladewig
    Katsutomo Okamura
    Alex S. Flynt
    Jakub O. Westholm
    Eric C. Lai
    First Published September 5, 2012
  - Long noncoding RNAs are rarely translated in two human cell lines
    Balázs Bánfai
    Hui Jia
    Jainab Khatun
    Emily Wood
    Brian Risk
    William E. Gundling Anshul Kundaje Harsha P. Gunawardena Yanbao Yu Ling Xie Krzysztof Krajewski Brian D. Strahl Xian Chen
    ...[+8 authors]...,
    Peter Bickel
    Morgan C. Giddings
    James B. Brown
    Leonard Lipovich
    First Published September 5, 2012
  - 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
    ...[+10 authors]...,
    Ewan Birney
    Zhiping Weng
    Michael Snyder
    Mark Gerstein
    First Published September 5, 2012
  - 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
    First Published September 5, 2012
  - 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
    ...[+5 authors]...,
    Robert E. Thurman
    Rajinder Kaul
    Richard M. Myers
    John A. Stamatoyannopoulos
    First Published September 5, 2012
  - Personal and population genomics of human regulatory variation
    Benjamin Vernot
    Andrew B. Stergachis
    Matthew T. Maurano
    Jeff Vierstra
    Shane Neph
    First Published September 5, 2012
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
    ...[+8 authors]...,
    Jennifer Harrow
    Tim J. Hubbard
    Roderic Guigó
    Alexandre Reymond
    First Published September 5, 2012
  - Predicting cell-type–specific gene expression from regions of open chromatin
    Anirudh Natarajan
    Galip Gürkan Yardımcı
    Nathan C. Sheffield
    Gregory E. Crawford
    Uwe Ohler
    First Published September 5, 2012
  - Sequence and chromatin determinants of cell-type–specific transcription factor binding
    Aaron Arvey
    Phaedra Agius
    William Stafford Noble
    Christina Leslie
    First Published September 5, 2012
  - 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
    ...[+1 authors]...,
    Steven M. Johnson
    Michael Snyder
    Serafim Batzoglou
    Arend Sidow
    First Published September 5, 2012
  - Linking disease associations with regulatory information in the human genome
    Marc A. Schaub
    Alan P. Boyle
    Anshul Kundaje
    Serafim Batzoglou
    Michael Snyder
    First Published September 5, 2012
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
    ...[+32 authors]...,
    Alexandre Reymond
    Mark Gerstein
    Roderic Guigó
    Tim J. Hubbard
    First Published September 5, 2012
  - 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
    ...[+18 authors]...,
    Tim J. Hubbard
    Cedric Notredame
    Jennifer Harrow
    Roderic Guigó
    First Published September 5, 2012
  - 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
    ...[+3 authors]...,
    Benjamin C. Hitz
    Shuai Weng
    J. Michael Cherry
    Michael Snyder
    First Published September 5, 2012
  - 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
    ...[+7 authors]...,
    Richard M. Myers
    William S. Noble
    Michael Snyder
    Zhiping Weng
    First Published September 5, 2012
  - 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
    ...[+38 authors]...,
    Peggy J. Farnham
    Jason D. Lieb
    Barbara J. Wold
    Michael Snyder
    First Published September 5, 2012

Table of Contents

Volume 22, Issue 9 | September 2012

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Commentary

Perspectives

Research

Methods

Resources