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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

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

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events

  • Jinfeng Liu
  • William Lee
  • Zhaoshi Jiang
  • Zhongqiang Chen
  • Suchit Jhunjhunwala
  • Peter M. Haverty Florian Gnad Yinghui Guan Houston N. Gilbert Jeremy Stinson Christiaan Klijn Joseph Guillory Deepali Bhatt Steffan Vartanian Kimberly Walter Jocelyn Chan Thomas Holcomb Peter Dijkgraaf Stephanie Johnson Julie Koeman John D. Minna Adi F. Gazdar Howard M. Stern Klaus P. Hoeflich Thomas D. Wu Jeff Settleman Frederic J. de Sauvage Robert C. Gentleman Richard M. Neve David Stokoe
  • ... [+25 authors] ...,
  • Zora Modrusan
  • Somasekar Seshagiri
  • David S. Shames
  • Zemin Zhang
  • First Published October 2, 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

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

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

  • Zhaoshi Jiang
  • Suchit Jhunjhunwala
  • Jinfeng Liu
  • Peter M. Haverty
  • Michael I. Kennemer
  • Yinghui Guan William Lee Paolo Carnevali Jeremy Stinson Stephanie Johnson Jingyu Diao Stacy Yeung Adrian Jubb Weilan Ye Thomas D. Wu Sharookh B. Kapadia Frederic J. de Sauvage Robert C. Gentleman Howard M. Stern Somasekar Seshagiri
  • ... [+15 authors] ...,
  • Krishna P. Pant
  • Zora Modrusan
  • Dennis G. Ballinger
  • Zemin Zhang
  • First Published January 20, 2012
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