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Research

Epigenetic characterization of pseudogenes across human tissues

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

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

  • Guanjue Xiang
  • Xi He
  • Belinda M. Giardine
  • Kathryn J. Isaac
  • Dylan J. Taylor
  • Rajiv C. McCoy Camden Jansen Cheryl A. Keller Alexander Q. Wixom April Cockburn Amber Miller Qian Qi Yanghua He Yichao Li Jens Lichtenberg Elisabeth F. Heuston Stacie M. Anderson Jing Luan Marit W. Vermunt Feng Yue Michael E.G. Sauria Michael C. Schatz James Taylor Berthold Göttgens Jim R. Hughes Douglas R. Higgs Mitchell J. Weiss Yong Cheng Gerd A. Blobel David M. Bodine
  • ... [+25 authors] ...,
  • Yu Zhang
  • Qunhua Li
  • Shaun Mahony
  • Ross C. Hardison
  • First Published July 1, 2024
Method

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

  • Kelly Cochran
  • Divyanshi Srivastava
  • Avanti Shrikumar
  • Akshay Balsubramani
  • Ross C. Hardison
  • Anshul Kundaje
  • Shaun Mahony
  • First Published January 18, 2022
Research

Alu insertion variants alter gene transcript levels" > Alu insertion variants alter gene transcript levels

  • Lindsay M. Payer
  • Jared P. Steranka
  • Maria S. Kryatova
  • Giacomo Grillo
  • Mathieu Lupien
  • Pedro P. Rocha
  • Kathleen H. Burns
  • First Published November 19, 2021
Resource

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

  • Guanjue Xiang
  • Cheryl A. Keller
  • Elisabeth Heuston
  • Belinda M. Giardine
  • Lin An
  • Alexander Q. Wixom Amber Miller April Cockburn Michael E.G. Sauria Kathryn Weaver Jens Lichtenberg Berthold Göttgens Qunhua Li David Bodine Shaun Mahony James Taylor Gerd A. Blobel Mitchell J. Weiss Yong Cheng Feng Yue
  • ... [+15 authors] ...,
  • Jim Hughes
  • Douglas R. Higgs
  • Yu Zhang
  • Ross C. Hardison
  • First Published March 4, 2020
Method

cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks" > Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks

  • Seyed Ali Madani Tonekaboni
  • Parisa Mazrooei
  • Victor Kofia
  • Benjamin Haibe-Kains
  • Mathieu Lupien
  • First Published September 18, 2019
Research

High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma

  • Michael J. Johnston
  • Ana Nikolic
  • Nicoletta Ninkovic
  • Paul Guilhamon
  • Florence M.G. Cavalli
  • Steven Seaman Franz J. Zemp John Lee Aly Abdelkareem Katrina Ellestad Alex Murison Michelle M. Kushida Fiona J. Coutinho Yussanne Ma Andrew J. Mungall Richard Moore Marco A. Marra Michael D. Taylor Peter B. Dirks Trevor J. Pugh Sorana Morrissy
  • ... [+16 authors] ...,
  • Bradley St Croix
  • Douglas J. Mahoney
  • Mathieu Lupien
  • Marco Gallo
  • First Published June 27, 2019
Research

Mus caroli and Mus pahari genomes" > 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
Method

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

  • Tao Yang
  • Feipeng Zhang
  • Galip Gürkan Yardımcı
  • Fan Song
  • Ross C. Hardison
  • William Stafford Noble
  • Feng Yue
  • Qunhua Li
  • First Published August 30, 2017
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