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Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

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

Tetrahymena" > A systems view on DNA damage response kinetics in Tetrahymena

  • Emily Nischwitz
  • Vivien A.C. Schoonenberg
  • Rachel Mullner
  • Albert Fradera-Sola
  • Susanne Zimbelmann
  • Joshua J. Smith
  • Falk Butter
  • First Published January 28, 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
Research

Paramecium" > ISWI1 complex proteins facilitate developmental genome editing in Paramecium

  • Aditi Singh
  • Lilia Häußermann
  • Christiane Emmerich
  • Emily Nischwitz
  • Brandon K.B. Seah
  • Falk Butter
  • Mariusz Nowacki
  • Estienne C. Swart
  • First Published November 14, 2024
Research

TERT promoter" > E4F1 and ZNF148 are transcriptional activators of the −57A > C and wild-type TERT promoter

  • Boon Haow Chua
  • Nurkaiyisah Zaal Anuar
  • Laure Ferry
  • Cecilia Domrane
  • Anna Wittek
  • Vineeth T. Mukundan Sudhakar Jha
  • ... [+2 authors] ...,
  • Falk Butter
  • Daniel G. Tenen
  • Pierre-Antoine Defossez
  • Dennis Kappei
  • First Published November 2, 2023
Method

Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis

  • Alejandro Ceron-Noriega
  • Miguel V. Almeida
  • Michal Levin
  • Falk Butter
  • First Published January 18, 2023
Research

Rhizophagus irregularis" > Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

  • Alexandra Dallaire
  • Bethan F. Manley
  • Maya Wilkens
  • Iliana Bista
  • Clement Quan
  • Edouard Evangelisti Charles R. Bradshaw Navin B. Ramakrishna
  • ... [+3 authors] ...,
  • Sebastian Schornack
  • Falk Butter
  • Uta Paszkowski
  • Eric A. Miska
  • First Published November 12, 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

Sequence determinants of polyadenylation-mediated regulation

  • Ilya Vainberg Slutskin
  • Adina Weinberger
  • Eran Segal
  • First Published September 17, 2019
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