Search | Genome Research

A limited set of transcriptional programs define major cell types

Alessandra Breschi
Manuel Muñoz-Aguirre
Valentin Wucher
Carrie A. Davis
Diego Garrido-Martín
Sarah Djebali Jesse Gillis Dmitri D. Pervouchine Anna Vlasova Alexander Dobin Chris Zaleski Jorg Drenkow Cassidy Danyko Alexandra Scavelli
... [+9 authors] ...,
Ferran Reverter
Michael P. Snyder
Thomas R. Gingeras
Roderic Guigó

First Published July 29, 2020

Dynamics of microRNA expression during mouse prenatal development

Sorena Rahmanian
Rabi Murad
Alessandra Breschi
Weihua Zeng
Mark Mackiewicz
Brian Williams Carrie A. Davis Brian Roberts Sarah Meadows Dianna Moore Diane Trout Chris Zaleski Alex Dobin Lei-Hoon Sei Jorg Drenkow Alex Scavelli Thomas R. Gingeras
... [+12 authors] ...,
Barbara J. Wold
Richard M. Myers
Roderic Guigó
Ali Mortazavi

First Published October 23, 2019

Alu elements suggests cell-type–specific enhancer function" > Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

Xiao-Ou Zhang
Thomas R. Gingeras
Zhiping Weng

First Published August 14, 2019

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target

Myungjin Jo
Ah Young Chung
Nozomu Yachie
Minchul Seo
Hyejin Jeon
Youngpyo Nam Yeojin Seo Eunmi Kim Quan Zhong
... [+4 authors] ...,
Marc Vidal
Hae Chul Park
Frederick P. Roth
Kyoungho Suk

First Published June 8, 2017

An extended set of yeast-based functional assays accurately identifies human disease mutations

Song Sun
Fan Yang
Guihong Tan
Michael Costanzo
Rose Oughtred
Jodi Hirschman Chandra L. Theesfeld Pritpal Bansal Nidhi Sahni Song Yi Analyn Yu Tanya Tyagi Cathy Tie David E. Hill Marc Vidal
... [+10 authors] ...,
Brenda J. Andrews
Charles Boone
Kara Dolinski
Frederick P. Roth

First Published March 14, 2016

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

Felix Schlesinger
Andrew D. Smith
Thomas R. Gingeras
Gregory J. Hannon
Emily Hodges

First Published June 28, 2013

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

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

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

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

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

Philippe Batut
Alexander Dobin
Charles Plessy
Piero Carninci
Thomas R. Gingeras

First Published August 30, 2012

Synthetic spike-in standards for RNA-seq experiments

Lichun Jiang
Felix Schlesinger
Carrie A. Davis
Yu Zhang
Renhua Li
Marc Salit
Thomas R. Gingeras
Brian Oliver

First Published August 4, 2011

Drosophila cell lines" > The transcriptional diversity of 25 Drosophila cell lines

Lucy Cherbas
Aarron Willingham
Dayu Zhang
Li Yang
Yi Zou
Brian D. Eads Joseph W. Carlson Jane M. Landolin Philipp Kapranov Jacqueline Dumais Anastasia Samsonova Jeong-Hyeon Choi Johnny Roberts Carrie A. Davis Haixu Tang Marijke J. van Baren Srinka Ghosh Alexander Dobin Kim Bell Wei Lin Laura Langton Michael O. Duff Aaron E. Tenney Chris Zaleski Michael R. Brent Roger A. Hoskins Thomas C. Kaufman Justen Andrews Brenton R. Graveley
... [+24 authors] ...,
Norbert Perrimon
Susan E. Celniker
Thomas R. Gingeras
Peter Cherbas

First Published December 22, 2010

C. elegans ORFeome" > Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome

Kourosh Salehi-Ashtiani
Chenwei Lin
Tong Hao
Yun Shen
David Szeto
Xinping Yang Lila Ghamsari HanJoo Lee Changyu Fan Ryan R. Murray Stuart Milstein Nenad Svrzikapa
... [+7 authors] ...,
Michael E. Cusick
Frederick P. Roth
David E. Hill
Marc Vidal

First Published October 2, 2009

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network

Gabriel Markson
Christina Kiel
Russell Hyde
Stephanie Brown
Panagoula Charalabous
Anja Bremm Jennifer Semple Jonathan Woodsmith Simon Duley Kourosh Salehi-Ashtiani Marc Vidal
... [+6 authors] ...,
David Komander
Luis Serrano
Paul Lehner
Christopher M. Sanderson

First Published June 23, 2009

Shifted Transversal Design smart-pooling for high coverage interactome mapping

Xiaofeng Xin
Jean-François Rual
Tomoko Hirozane-Kishikawa
David E. Hill
Marc Vidal
Charles Boone
Nicolas Thierry-Mieg

First Published May 15, 2009

Saccharomyces cerevisiae predicted ORFeome" > Revisiting the Saccharomyces cerevisiae predicted ORFeome

Qian-Ru Li
Anne-Ruxandra Carvunis
Haiyuan Yu
Jing-Dong J. Han
Quan Zhong
Nicolas Simonis Stanley Tam Tong Hao Niels J. Klitgord Denis Dupuy Danny Mou Ilan Wapinski
... [+7 authors] ...,
Aviv Regev
David E. Hill
Michael E. Cusick
Marc Vidal

First Published May 23, 2008

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

David S. Johnson
Wei Li
D. Benjamin Gordon
Arindam Bhattacharjee
Bo Curry
Jayati Ghosh Leonardo Brizuela Jason S. Carroll Myles Brown Paul Flicek Christoph M. Koch Ian Dunham Mark Bieda Xiaoqin Xu Peggy J. Farnham Philipp Kapranov David A. Nix Thomas R. Gingeras Xinmin Zhang Heather Holster Nan Jiang Roland D. Green Jun S. Song Scott A. McCuine Elizabeth Anton Loan Nguyen Nathan D. Trinklein Zhen Ye Keith Ching David Hawkins Bing Ren Peter C. Scacheri Joel Rozowsky Alexander Karpikov Ghia Euskirchen Sherman Weissman Mark Gerstein Michael Snyder Annie Yang Zarmik Moqtaderi Heather Hirsch Hennady P. Shulha Yutao Fu Zhiping Weng
... [+39 authors] ...,
Kevin Struhl
Richard M. Myers
Jason D. Lieb
X. Shirley Liu

First Published February 7, 2008

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

Alvaro Rada-Iglesias
Adam Ameur
Philipp Kapranov
Stefan Enroth
Jan Komorowski
Thomas R. Gingeras
Claes Wadelius

First Published January 29, 2008

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
... [+6 authors] ...,
Sherman Weissman
Perry Miller
Michael Snyder
Mark B. Gerstein

First Published June 13, 2007

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
... [+17 authors] ...,
Roderic Guigó
Thomas R. Gingeras
Stylianos E. Antonarakis
Alexandre Reymond

First Published June 13, 2007

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
... [+7 authors] ...,
Thomas R. Gingeras
Roderic Guigó
Jennifer Harrow
Mark B. Gerstein

First Published June 13, 2007

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
... [+15 authors] ...,
Mark B. Gerstein
Alexandre Reymond
Ivo L. Hofacker
Peter F. Stadler

First Published June 13, 2007

Origin of phenotypes: Genes and transcripts

Thomas R. Gingeras

First Published June 13, 2007

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

Philipp Kapranov
Jorg Drenkow
Jill Cheng
Jeffrey Long
Gregg Helt
Sujit Dike
Thomas R. Gingeras

First Published July 5, 2005

C. elegans ORFeome by cloning TWINSCAN predictions" > Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions

Chaochun Wei
Philippe Lamesch
Manimozhiyan Arumugam
Jennifer Rosenberg
Ping Hu
Marc Vidal
Michael R. Brent

First Published April 1, 2005

C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones" > New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones

Anita G. Fernandez
Kristin C. Gunsalus
Jerry Huang
Ling-Shiang Chuang
Nancy Ying
Hsiao-lan Liang Caroline Tang Aaron J. Schetter Charles Zegar Jean-François Rual
... [+5 authors] ...,
David E. Hill
Valerie Reinke
Marc Vidal
Fabio Piano

First Published February 1, 2005

ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List

Michael A. Brasch
James L. Hartley
Marc Vidal

First Published October 15, 2004

Academia-Industry Collaboration: An Integral Element for Building “Omic” Resources

David E. Hill
Michael A. Brasch
Anthony A. del Campo
Lynn Doucette-Stamm
James I. Garrels
Judith Glaven
... [+1 authors] ...,
James L. Hartley
James R. Hudson
Troy Moore
Marc Vidal

First Published October 15, 2004

C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions" > C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions

Philippe Lamesch
Stuart Milstein
Tong Hao
Jennifer Rosenberg
Ning Li
Reynaldo Sequerra Stephanie Bosak
... [+2 authors] ...,
Lynn Doucette-Stamm
Jean Vandenhaute
David E. Hill
Marc Vidal

First Published October 15, 2004

Caenorhabditis elegans Using a MultiSite Gateway Recombination System" > Feasibility of Genome-Scale Construction of Promoter::Reporter Gene Fusions for Expression in Caenorhabditis elegans Using a MultiSite Gateway Recombination System

Ian A. Hope
Jonathan Stevens
Anna Garner
Josie Hayes
David L. Cheo
Michael A. Brasch
Marc Vidal

First Published October 15, 2004

A Gateway-Compatible Yeast One-Hybrid System

Bart Deplancke
Denis Dupuy
Marc Vidal
Albertha J.M. Walhout

First Published October 15, 2004

C. elegans Proteins" > High-Throughput Expression of C. elegans Proteins

Chi-Hao Luan
Shihong Qiu
James B. Finley
Mike Carson
Rita J. Gray
Wenying Huang David Johnson Jun Tsao Jérôme Reboul Philippe Vaglio
... [+5 authors] ...,
David E. Hill
Marc Vidal
Lawrence J. DeLucas
Ming Luo

First Published October 15, 2004

Human ORFeome Version 1.1: A Platform for Reverse Proteomics

Jean-François Rual
Tomoko Hirozane-Kishikawa
Tong Hao
Nicolas Bertin
Siming Li
Amélie Dricot Ning Li Jennifer Rosenberg Philippe Lamesch Pierre-Olivier Vidalain Tracey R. Clingingsmith James L. Hartley Dominic Esposito David Cheo Troy Moore Blake Simmons Reynaldo Sequerra Stephanie Bosak Lynn Doucette-Stamm Christian Le Peuch Jean Vandenhaute
... [+16 authors] ...,
Michael E. Cusick
Joanna S. Albala
David E. Hill
Marc Vidal

First Published October 15, 2004

Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library" > Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library

Jean-François Rual
Julian Ceron
John Koreth
Tong Hao
Anne-Sophie Nicot
Tomoko Hirozane-Kishikawa Jean Vandenhaute
... [+2 authors] ...,
Stuart H. Orkin
David E. Hill
Sander van den Heuvel
Marc Vidal

First Published October 15, 2004

Caenorhabditis elegans Promoterome" > A First Version of the Caenorhabditis elegans Promoterome

Denis Dupuy
Qian-Ru Li
Bart Deplancke
Mike Boxem
Tong Hao
Philippe Lamesch Reynaldo Sequerra Stephanie Bosak Lynn Doucette-Stamm
... [+4 authors] ...,
Ian A. Hope
David E. Hill
Albertha J.M. Walhout
Marc Vidal

First Published October 15, 2004

Brucella melitensis ORFeome Version 1.1" > Generation of the Brucella melitensis ORFeome Version 1.1

Amélie Dricot
Jean-François Rual
Philippe Lamesch
Nicolas Bertin
Denis Dupuy
Tong Hao Christophe Lambert Régis Hallez Jean-Marc Delroisse Jean Vandenhaute Ignacio Lopez-Goñi Ignacio Moriyon Juan M. Garcia-Lobo Félix J. Sangari Alastair P. MacMillan Sally J. Cutler Adrian M. Whatmore Stephanie Bozak Reynaldo Sequerra Lynn Doucette-Stamm
... [+15 authors] ...,
Marc Vidal
David E. Hill
Jean-Jacques Letesson
Xavier De Bolle