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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
Research

PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination

  • Petros Kolovos
  • Koutarou Nishimura
  • Aditya Sankar
  • Simone Sidoli
  • Paul A. Cloos
  • Kristian Helin
  • Jesper Christensen
  • First Published August 3, 2020
Method

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing

  • Laura M. Agosto
  • Matthew R. Gazzara
  • Caleb M. Radens
  • Simone Sidoli
  • Josue Baeza
  • Benjamin A. Garcia
  • Kristen W. Lynch
  • First Published November 14, 2019
Method

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry

  • Simone Sidoli
  • Yekaterina Kori
  • Mariana Lopes
  • Zuo-Fei Yuan
  • Hee Jong Kim
  • Katarzyna Kulej Kevin A. Janssen
  • ... [+2 authors] ...,
  • Laura M. Agosto
  • Julia Pinheiro Chagas da Cunha
  • Andrew J. Andrews
  • Benjamin A. Garcia
  • First Published May 23, 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
Research

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

  • Kirsty Jamieson
  • Elizabeth T. Wiles
  • Kevin J. McNaught
  • Simone Sidoli
  • Neena Leggett
  • Yanchun Shao
  • Benjamin A. Garcia
  • Eric U. Selker
  • First Published November 4, 2015
Research

C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2" > Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2

  • Jacob M. Garrigues
  • Simone Sidoli
  • Benjamin A. Garcia
  • Susan Strome
  • First Published December 2, 2014
Research

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

  • Alexej Abyzov
  • Rebecca Iskow
  • Omer Gokcumen
  • David W. Radke
  • Suganthi Balasubramanian
  • Baikang Pei
  • Lukas Habegger
  • Charles Lee
  • Mark Gerstein
  • First Published September 11, 2013
Research

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

  • Stephen B. Montgomery
  • David L. Goode
  • Erika Kvikstad
  • Cornelis A. Albers
  • Zhengdong D. Zhang
  • Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
  • ... [+12 authors] ...,
  • Kateryna D. Makova
  • Jonathan Marchini
  • Gil McVean
  • Gerton Lunter
  • First Published March 11, 2013
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