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The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Thomas R. Gingeras

First Published June 17, 2026

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Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals" > The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

Christine E. Schnitzler
E. Sally Chang
Justin Waletich
Gonzalo Quiroga-Artigas
Wai Yee Wong
Anh-Dao Nguyen Sofia N. Barreira Liam B. Doonan Paul Gonzalez Sergey Koren James M. Gahan Steven M. Sanders Brian Bradshaw Timothy Q. DuBuc Febrimarsa Danielle de Jong Eric P. Nawrocki Alexandra Larson Samantha Klasfeld Sebastian G. Gornik R. Travis Moreland Tyra G. Wolfsberg Adam M. Phillippy James C. Mullikin Oleg Simakov
... [+20 authors] ...,
Paulyn Cartwright
Matthew Nicotra
Uri Frank
Andreas D. Baxevanis

First Published March 20, 2024

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Hydra genome reveals conserved regulators of cell state" > A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

Jack F. Cazet
Stefan Siebert
Hannah Morris Little
Philip Bertemes
Abby S. Primack
Peter Ladurner Matthias Achrainer Mark T. Fredriksen R. Travis Moreland Sumeeta Singh Suiyuan Zhang Tyra G. Wolfsberg Christine E. Schnitzler
... [+8 authors] ...,
Andreas D. Baxevanis
Oleg Simakov
Bert Hobmayer
Celina E. Juliano

First Published January 13, 2023

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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

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

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

Research

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

Resource

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

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

Research

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

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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Resource

Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals" > The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

Resource

Hydra genome reveals conserved regulators of cell state" > A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

Resource

A limited set of transcriptional programs define major cell types

Resource

Dynamics of microRNA expression during mouse prenatal development

Research

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

Research

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

Research

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Resource

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

Research

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

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