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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Thomas R. Gingeras

First Published June 17, 2026

Research

Inference of selective forces on house mouse genomes during secondary contact in East Asia

Kazumichi Fujiwara
Shunpei Kubo
Toshinori Endo
Toyoyuki Takada
Toshihiko Shiroishi
Hitoshi Suzuki
Naoki Osada

First Published March 20, 2024

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

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target

Myungjin Jo
Ah Young Chung
Nozomu Yachie
Minchul Seo
Hyejin Jeon
Youngpyo Nam Yeojin Seo Eunmi Kim Quan Zhong
... [+4 authors] ...,
Marc Vidal
Hae Chul Park
Frederick P. Roth
Kyoungho Suk

First Published June 8, 2017

Method

An extended set of yeast-based functional assays accurately identifies human disease mutations

Song Sun
Fan Yang
Guihong Tan
Michael Costanzo
Rose Oughtred
Jodi Hirschman Chandra L. Theesfeld Pritpal Bansal Nidhi Sahni Song Yi Analyn Yu Tanya Tyagi Cathy Tie David E. Hill Marc Vidal
... [+10 authors] ...,
Brenda J. Andrews
Charles Boone
Kara Dolinski
Frederick P. Roth

First Published March 14, 2016

Resource

Coelacanth genomes reveal signatures for evolutionary transition from water to land

Masato Nikaido
Hideki Noguchi
Hidenori Nishihara
Atsushi Toyoda
Yutaka Suzuki
Rei Kajitani Hikoyu Suzuki Miki Okuno Mitsuto Aibara Benjamin P. Ngatunga Semvua I. Mzighani Hassan W.J. Kalombo Kawilarang W.A. Masengi Josef Tuda Sadao Nogami Ryuichiro Maeda Masamitsu Iwata Yoshitaka Abe Koji Fujimura Masataka Okabe Takanori Amano Akiteru Maeno Toshihiko Shiroishi Takehiko Itoh
... [+19 authors] ...,
Sumio Sugano
Yuji Kohara
Asao Fujiyama
Norihiro Okada

First Published July 22, 2013

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

Resource

The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains

Toyoyuki Takada
Toshinobu Ebata
Hideki Noguchi
Thomas M. Keane
David J. Adams
Takanori Narita Tadasu Shin-I Hironori Fujisawa Atsushi Toyoda Kuniya Abe Yuichi Obata Yoshiyuki Sakaki
... [+7 authors] ...,
Kazuo Moriwaki
Asao Fujiyama
Yuji Kohara
Toshihiko Shiroishi

First Published April 19, 2013

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