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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Thomas R. Gingeras

First Published June 17, 2026

Research

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

Chris Papadopoulos
Isabelle Callebaut
Jean-Christophe Gelly
Isabelle Hatin
Olivier Namy
Maxime Renard
Olivier Lespinet
Anne Lopes

First Published November 22, 2021

Research

Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Jennifer F. Hughes
Helen Skaletsky
Tatyana Pyntikova
Natalia Koutseva
Terje Raudsepp
Laura G. Brown Daniel W. Bellott Ting-Jan Cho Shannon Dugan-Rocha Ziad Khan Colin Kremitzki Catrina Fronick Tina A. Graves-Lindsay Lucinda Fulton Wesley C. Warren Richard K. Wilson Elaine Owens James E. Womack William J. Murphy Donna M. Muzny
... [+15 authors] ...,
Kim C. Worley
Bhanu P. Chowdhary
Richard A. Gibbs
David C. Page

First Published November 18, 2020

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

Research

Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Éléonore Durand
Isabelle Gagnon-Arsenault
Johan Hallin
Isabelle Hatin
Alexandre K. Dubé
Lou Nielly-Thibault
Olivier Namy
Christian R. Landry

First Published May 31, 2019

Corrigendum

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data

John Huddleston
Mark J.P. Chaisson
Karyn Meltz Steinberg
Wes Warren
Kendra Hoekzema
David Gordon Tina A. Graves-Lindsay Katherine M. Munson Zev N. Kronenberg Laura Vives Paul Peluso Matthew Boitano
... [+7 authors] ...,
Chen-Shin Chin
Jonas Korlach
Richard K. Wilson
Evan E. Eichler

First Published January 2, 2018

Corrigendum

Corrigendum: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Mario Ventura
Claudia R. Catacchio
Saba Sajjadian
Laura Vives
Peter H. Sudmant
Tomas Marques-Bonet
Tina A. Graves
Richard K. Wilson
Evan E. Eichler

First Published September 1, 2017

Resource

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Valerie A. Schneider
Tina Graves-Lindsay
Kerstin Howe
Nathan Bouk
Hsiu-Chuan Chen
Paul A. Kitts Terence D. Murphy Kim D. Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S. Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T. Simpson Glen Threadgold James Torrance Jonathan M. Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M. Phillippy Richard Durbin
... [+29 authors] ...,
Richard K. Wilson
Paul Flicek
Evan E. Eichler
Deanna M. Church

First Published April 10, 2017

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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Research

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

Research

Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

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

Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Corrigendum

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data

Corrigendum

Corrigendum: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Resource

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

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