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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Thomas R. Gingeras

First Published June 17, 2026

Resource

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

Resource

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

Research

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

Corrigendum

Corrigendum: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

PingHsun Hsieh
August E. Woerner
Jeffrey D. Wall
Joseph Lachance
Sarah A. Tishkoff
Ryan N. Gutenkunst
Michael F. Hammer

First Published May 2, 2016

Research

Callithrix jacchus genome" > Discovery of a new repeat family in the Callithrix jacchus genome

Miriam K. Konkel
Brygg Ullmer
Erika L. Arceneaux
Sreeja Sanampudi
Sarah A. Brantley
Robert Hubley
Arian F.A. Smit
Mark A. Batzer

First Published February 25, 2016

Research

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

PingHsun Hsieh
Krishna R. Veeramah
Joseph Lachance
Sarah A. Tishkoff
Jeffrey D. Wall
Michael F. Hammer
Ryan N. Gutenkunst

First Published February 17, 2016

Research

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

PingHsun Hsieh
August E. Woerner
Jeffrey D. Wall
Joseph Lachance
Sarah A. Tishkoff
Ryan N. Gutenkunst
Michael F. Hammer

First Published February 17, 2016

Research

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

Method

Alu insertions in diverse human populations" > Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations

David J. Witherspoon
Yuhua Zhang
Jinchuan Xing
W. Scott Watkins
Hongseok Ha
Mark A. Batzer
Lynn B. Jorde

First Published April 18, 2013

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