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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

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

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

  • Byron J. Smith
  • Chunyu Zhao
  • Veronika Dubinkina
  • Xiaofan Jin
  • Liron Zahavi
  • Saar Shoer
  • Jacqueline Moltzau-Anderson
  • Eran Segal
  • Katherine S. Pollard
  • First Published April 10, 2025
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

Sequence determinants of polyadenylation-mediated regulation

  • Ilya Vainberg Slutskin
  • Adina Weinberger
  • Eran Segal
  • First Published September 17, 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

Systematic interrogation of human promoters

  • Shira Weingarten-Gabbay
  • Ronit Nir
  • Shai Lubliner
  • Eilon Sharon
  • Yael Kalma
  • Adina Weinberger
  • Eran Segal
  • First Published January 8, 2019
Research

Arabidopsis thaliana transposons and gene regulatory regions" > Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions

  • Kyuha Choi
  • Xiaohui Zhao
  • Andrew J. Tock
  • Christophe Lambing
  • Charles J. Underwood
  • Thomas J. Hardcastle Heïdi Serra Juhyun Kim Hyun Seob Cho Jaeil Kim Piotr A. Ziolkowski
  • ... [+6 authors] ...,
  • Nataliya E. Yelina
  • Ildoo Hwang
  • Robert A. Martienssen
  • Ian R. Henderson
  • First Published March 12, 2018
Research

Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation" > Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation

  • Charles J. Underwood
  • Kyuha Choi
  • Christophe Lambing
  • Xiaohui Zhao
  • Heïdi Serra
  • Filipe Borges Joe Simorowski
  • ... [+2 authors] ...,
  • Evan Ernst
  • Yannick Jacob
  • Ian R. Henderson
  • Robert A. Martienssen
  • First Published March 12, 2018
Corrigendum

Corrigendum: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators

  • David van Dijk
  • Eilon Sharon
  • Maya Lotan-Pompan
  • Adina Weinberger
  • Eran Segal
  • Lucas B. Carey
  • First Published March 1, 2017
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