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Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements

Hosiana Abewe
Alexandra Richey
Jeffery M. Vahrenkamp
Matthew Ginley-Hidinger
Craig M. Rush
Noel Kitchen
Xiaoyang Zhang
Jason Gertz

First Published March 3, 2025

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

FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples

Jeffery M. Vahrenkamp
Kathryn Szczotka
Mark K. Dodson
Elke A. Jarboe
Andrew P. Soisson
Jason Gertz

First Published October 24, 2019

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

Estrogen-independent molecular actions of mutant estrogen receptor 1 in endometrial cancer

Zannel Blanchard
Jeffery M. Vahrenkamp
Kristofer C. Berrett
Spencer Arnesen
Jason Gertz

First Published July 30, 2019

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

Daniel Savic
Brian S. Roberts
Julia B. Carleton
E. Christopher Partridge
Michael A. White
Barak A. Cohen
Gregory M. Cooper
Jason Gertz
Richard M. Myers

First Published October 20, 2015

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

Georgi K. Marinov
Brian A. Williams
Ken McCue
Gary P. Schroth
Jason Gertz
Richard M. Myers
Barbara J. Wold

First Published December 3, 2013

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

Dynamic DNA methylation across diverse human cell lines and tissues

Katherine E. Varley
Jason Gertz
Kevin M. Bowling
Stephanie L. Parker
Timothy E. Reddy
Florencia Pauli-Behn Marie K. Cross Brian A. Williams John A. Stamatoyannopoulos
... [+4 authors] ...,
Gregory E. Crawford
Devin M. Absher
Barbara J. Wold
Richard M. Myers

First Published January 16, 2013

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