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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

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

Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation

  • Marlies E. Oomen
  • A. Nicole Fox
  • Inma Gonzalez
  • Amandine Molliex
  • Thaleia Papadopoulou
  • Pablo Navarro
  • Job Dekker
  • First Published June 6, 2025
Research

Revisiting chromatin packaging in mouse sperm

  • Qiangzong Yin
  • Chih-Hsiang Yang
  • Olga S. Strelkova
  • Jingyi Wu
  • Yu Sun
  • Sneha Gopalan Liyan Yang Job Dekker
  • ... [+3 authors] ...,
  • Thomas G. Fazzio
  • Xin Zhiguo Li
  • Johan Gibcus
  • Oliver J. Rando
  • First Published December 21, 2023
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

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

  • Marlies E. Oomen
  • Anders S. Hansen
  • Yu Liu
  • Xavier Darzacq
  • Job Dekker
  • First Published January 17, 2019
Research

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

  • A. Rasim Barutcu
  • Bryan R. Lajoie
  • Andrew J. Fritz
  • Rachel P. McCord
  • Jeffrey A. Nickerson
  • Andre J. van Wijnen Jane B. Lian
  • ... [+2 authors] ...,
  • Janet L. Stein
  • Job Dekker
  • Gary S. Stein
  • Anthony N. Imbalzano
  • First Published July 19, 2016
Research

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

  • Elizabeth Ing-Simmons
  • Vlad C. Seitan
  • Andre J. Faure
  • Paul Flicek
  • Thomas Carroll
  • Job Dekker
  • Amanda G. Fisher
  • Boris Lenhard
  • Matthias Merkenschlager
  • First Published February 12, 2015
Research

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

  • Vlad C. Seitan
  • Andre J. Faure
  • Ye Zhan
  • Rachel Patton McCord
  • Bryan R. Lajoie
  • Elizabeth Ing-Simmons Boris Lenhard Luca Giorgetti Edith Heard
  • ... [+4 authors] ...,
  • Amanda G. Fisher
  • Paul Flicek
  • Job Dekker
  • Matthias Merkenschlager
  • First Published September 3, 2013
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