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Research

Epigenetic characterization of pseudogenes across human tissues

  • Yunzhe Jiang
  • Beatrice Borsari
  • Mark Gerstein
  • First Published April 15, 2026
Resource

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

  • Sophia C. Gaynor-Gillett
  • Lijun Cheng
  • Manman Shi
  • Jason Liu
  • Gaoyuan Wang
  • Megan Spector Qiuyu Guo Le Qi Mary Flaherty Martha Wall Ahyeon Hwang Mengting Gu Zhanlin Chen Yuhang Chen Jennifer R. Moran Jing Zhang
  • ... [+11 authors] ...,
  • Donghoon Lee
  • Mark Gerstein
  • Daniel Geschwind
  • Kevin P. White
  • First Published July 11, 2025
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
In memoriam

C. Thomas Caskey (1938–2022)

  • Richard A. Gibbs
  • Aravinda Chakravarti
  • Evan E. Eichler
  • Eric D. Green
  • Richard M. Myers
  • Anne C. Ferguson-Smith
  • Kateryna D. Makova
  • Hillary E. Sussman
  • First Published February 17, 2022
In memoriam

Deborah A. Nickerson (1954 –2021)

  • Aravinda Chakravarti
  • Evan E. Eichler
  • Richard A. Gibbs
  • Eric D. Green
  • Richard M. Myers
  • Hillary E. Sussman
  • First Published January 24, 2022
Research

Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

  • Jennifer F. Hughes
  • Helen Skaletsky
  • Tatyana Pyntikova
  • Natalia Koutseva
  • Terje Raudsepp
  • Laura G. Brown Daniel W. Bellott Ting-Jan Cho Shannon Dugan-Rocha Ziad Khan Colin Kremitzki Catrina Fronick Tina A. Graves-Lindsay Lucinda Fulton Wesley C. Warren Richard K. Wilson Elaine Owens James E. Womack William J. Murphy Donna M. Muzny
  • ... [+15 authors] ...,
  • Kim C. Worley
  • Bhanu P. Chowdhary
  • Richard A. Gibbs
  • David C. Page
  • First Published November 18, 2020
Method

Accurate reconstruction of bacterial pan- and core genomes with PEPPAN

  • Zhemin Zhou
  • Jane Charlesworth
  • Mark Achtman
  • First Published October 14, 2020
Resource

Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity" > The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

  • Zhemin Zhou
  • Nabil-Fareed Alikhan
  • Khaled Mohamed
  • Yulei Fan
  • Mark Achtman
  • Derek Brown Marie Chattaway Tim Dallman Richard Delahay Christian Kornschober Ariane Pietzka Burkhard Malorny Liljana Petrovska Rob Davies Andy Robertson
  • ... [+10 authors] ...,
  • William Tyne
  • François-Xavier Weill
  • Marie Accou-Demartin
  • Nicola Williams
  • First Published December 6, 2019
Method

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

  • Zhemin Zhou
  • Nabil-Fareed Alikhan
  • Martin J. Sergeant
  • Nina Luhmann
  • Cátia Vaz
  • Alexandre P. Francisco
  • João André Carriço
  • Mark Achtman
  • First Published July 26, 2018
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
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