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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

  • Thomas R. Gingeras
  • First Published June 17, 2026
Research

CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain" > Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

  • James L. Shepherdson
  • David M. Granas
  • Jie Li
  • Zara Shariff
  • Stephen P. Plassmeyer
  • Alex S. Holehouse
  • Michael A. White
  • Barak A. Cohen
  • First Published September 25, 2024
Research

CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors" > Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

  • James L. Shepherdson
  • Ryan Z. Friedman
  • Yiqiao Zheng
  • Chi Sun
  • Inez Y. Oh
  • David M. Granas
  • Barak A. Cohen
  • Shiming Chen
  • Michael A. White
  • First Published February 14, 2024
Research

Functional characterization of enhancer activity during a long terminal repeat's evolution

  • Alan Y. Du
  • Xiaoyu Zhuo
  • Vasavi Sundaram
  • Nicholas O. Jensen
  • Hemangi G. Chaudhari
  • Nancy L. Saccone
  • Barak A. Cohen
  • Ting Wang
  • First Published October 3, 2022
Research

Genomic environments scale the activities of diverse core promoters

  • Clarice K.Y. Hong
  • Barak A. Cohen
  • First Published December 27, 2021
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

cis-regulatory activity" > Local sequence features that influence AP-1 cis-regulatory activity

  • Hemangi G. Chaudhari
  • Barak A. Cohen
  • First Published January 5, 2018
Research

cis-regulation in embryonic stem cells" > Interactions between pluripotency factors specify cis-regulation in embryonic stem cells

  • Chris Fiore
  • Barak A. Cohen
  • First Published April 15, 2016
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