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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

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs

Severin Berger
Mikhail Pachkov
Phil Arnold
Saeed Omidi
Nicholas Kelley
Silvia Salatino
Erik van Nimwegen

First Published May 28, 2019

Drosophila wing development" > A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

Claus Schertel
Monica Albarca
Claudia Rockel-Bauer
Nicholas W. Kelley
Johannes Bischof
Korneel Hens
Erik van Nimwegen
Konrad Basler
Bart Deplancke

First Published January 7, 2015

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

Piotr J. Balwierz
Mikhail Pachkov
Phil Arnold
Andreas J. Gruber
Mihaela Zavolan
Erik van Nimwegen

First Published February 10, 2014

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

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

Phil Arnold
Anne Schöler
Mikhail Pachkov
Piotr J. Balwierz
Helle Jørgensen
Michael B. Stadler
Erik van Nimwegen
Dirk Schübeler

First Published September 10, 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

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

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