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Method

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie

  • Krzysztof H. Banecki
  • Haoxi Chai
  • Yijun Ruan
  • Dariusz Plewczynski
  • First Published April 8, 2026
Resource

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > 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
Resource

Caenorhabditis elegans nematodes" > Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

  • Timothy J. Durham
  • Riza M. Daza
  • Louis Gevirtzman
  • Darren A. Cusanovich
  • Olubusayo Bolonduro
  • William Stafford Noble
  • Jay Shendure
  • Robert H. Waterston
  • First Published April 22, 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
Resource

C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution" > The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

  • Adam D. Warner
  • Louis Gevirtzman
  • LaDeana W. Hillier
  • Brent Ewing
  • Robert H. Waterston
  • First Published May 23, 2019
Research

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

  • Zhizhuo Zhang
  • Kern Rei Chng
  • Shreyas Lingadahalli
  • Zikai Chen
  • Mei Hui Liu
  • Huy Hoang Do Shaojiang Cai Nicola Rinaldi Huay Mei Poh Guoliang Li Ying Ying Sung Charlie L. Heng Leighton J. Core Si Kee Tan Xiaoan Ruan John T. Lis
  • ... [+11 authors] ...,
  • Manolis Kellis
  • Yijun Ruan
  • Wing-Kin Sung
  • Edwin Cheung
  • First Published January 3, 2019
In memoriam

John Sulston (1942–2018)

  • Robert H. Waterston
  • First Published June 1, 2018
Method

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

  • Przemysław Szałaj
  • Zhonghui Tang
  • Paul Michalski
  • Michal J. Pietal
  • Oscar J. Luo
  • Michał Sadowski
  • ... [+1 authors] ...,
  • Xingwang Li
  • Kamen Radew
  • Yijun Ruan
  • Dariusz Plewczynski
  • First Published October 27, 2016
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