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Research

Epigenetic characterization of pseudogenes across human tissues

  • Yunzhe Jiang
  • Beatrice Borsari
  • Mark Gerstein
  • First Published April 15, 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
Resource

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

  • Michelle Kudron
  • Louis Gevirtzman
  • Alec Victorsen
  • Bridget C. Lear
  • Jiahao Gao
  • Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
  • ... [+16 authors] ...,
  • LaDeana Hillier
  • Susan E. Celniker
  • Valerie Reinke
  • Robert H. Waterston
  • First Published October 22, 2024
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
Method

Ancestry-agnostic estimation of DNA sample contamination from sequence reads

  • Fan Zhang
  • Matthew Flickinger
  • Sarah A. Gagliano Taliun
  • Gonçalo R. Abecasis
  • Laura J. Scott
  • Steven A. McCaroll
  • Carlos N. Pato
  • Michael Boehnke
  • Hyun Min Kang
  • First Published January 24, 2020
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

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

  • David Thybert
  • Maša Roller
  • Fábio C.P. Navarro
  • Ian Fiddes
  • Ian Streeter
  • Christine Feig David Martin-Galvez Mikhail Kolmogorov Václav Janoušek Wasiu Akanni Bronwen Aken Sarah Aldridge Varshith Chakrapani William Chow Laura Clarke Carla Cummins Anthony Doran Matthew Dunn Leo Goodstadt Kerstin Howe Matthew Howell Ambre-Aurore Josselin Robert C. Karn Christina M. Laukaitis Lilue Jingtao Fergal Martin Matthieu Muffato Stefanie Nachtweide Michael A. Quail Cristina Sisu Mario Stanke Klara Stefflova Cock Van Oosterhout Frederic Veyrunes Ben Ward Fengtang Yang Golbahar Yazdanifar Amonida Zadissa David J. Adams Alvis Brazma Mark Gerstein Benedict Paten
  • ... [+37 authors] ...,
  • Son Pham
  • Thomas M. Keane
  • Duncan T. Odom
  • Paul Flicek
  • First Published March 21, 2018
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
Method

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data

  • Goo Jun
  • Mary Kate Wing
  • Gonçalo R. Abecasis
  • Hyun Min Kang
  • First Published April 16, 2015
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
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