Search | Genome Research

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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Thomas R. Gingeras

First Published June 17, 2026

Research

Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development

Patricia Gerdes
Dorothy Chan
Mischa Lundberg
Francisco J. Sanchez-Luque
Gabriela O. Bodea
Adam D. Ewing
Geoffrey J. Faulkner
Sandra R. Richardson

First Published October 5, 2023

Method

Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs

Michiel de Hoon
Alessandro Bonetti
Charles Plessy
Yoshinari Ando
Chung-Chau Hon
Yuri Ishizu Masayoshi Itoh Sachi Kato Dongyan Lin Sho Maekawa Mitsuyoshi Murata Hiromi Nishiyori Jay W. Shin Jens Stolte Ana Maria Suzuki Michihira Tagami Hazuki Takahashi Supat Thongjuea
... [+13 authors] ...,
Alistair R.R. Forrest
Yoshihide Hayashizaki
Juha Kere
Piero Carninci

First Published August 12, 2022

Research

Somatic retrotransposition in the developing rhesus macaque brain

Victor Billon
Francisco J. Sanchez-Luque
Jay Rasmussen
Gabriela O. Bodea
Daniel J. Gerhardt
Patricia Gerdes Seth W. Cheetham Stephanie N. Schauer Prabha Ajjikuttira Thomas J. Meyer Cora E. Layman Kimberly A. Nevonen Natasha Jansz Jose L. Garcia-Perez
... [+9 authors] ...,
Sandra R. Richardson
Adam D. Ewing
Lucia Carbone
Geoffrey J. Faulkner

First Published June 21, 2022

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

Research

Comparative transcriptomics of primary cells in vertebrates

Tanvir Alam
Saumya Agrawal
Jessica Severin
Robert S. Young
Robin Andersson
Erik Arner Akira Hasegawa Marina Lizio Jordan A. Ramilowski Imad Abugessaisa Yuri Ishizu Shohei Noma Hiroshi Tarui Martin S. Taylor Timo Lassmann Masayoshi Itoh Takeya Kasukawa Hideya Kawaji Luigi Marchionni Guojun Sheng Alistair R.R. Forrest
... [+16 authors] ...,
Levon M. Khachigian
Yoshihide Hayashizaki
Piero Carninci
Michiel J.L. de Hoon

First Published July 27, 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

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

Stephanie N. Schauer
Patricia E. Carreira
Ruchi Shukla
Daniel J. Gerhardt
Patricia Gerdes
Francisco J. Sanchez-Luque Paola Nicoli Michaela Kindlova Serena Ghisletti Alexandre Dos Santos Delphine Rapoud Didier Samuel
... [+7 authors] ...,
Jamila Faivre
Adam D. Ewing
Sandra R. Richardson
Geoffrey J. Faulkner

First Published April 11, 2018

Research

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

Sandra R. Richardson
Patricia Gerdes
Daniel J. Gerhardt
Francisco J. Sanchez-Luque
Gabriela-Oana Bodea
Martin Muñoz-Lopez J. Samuel Jesuadian Marie-Jeanne H.C. Kempen Patricia E. Carreira Jeffrey A. Jeddeloh
... [+5 authors] ...,
Jose L. Garcia-Perez
Haig H. Kazazian
Adam D. Ewing
Geoffrey J. Faulkner

First Published May 8, 2017

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