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Research

Epigenetic characterization of pseudogenes across human tissues

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

Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End

  • Lucinda C. Xiao
  • Ayush Semwal
  • Brianna St John
  • Kathleen Zeglinski
  • Shian Su
  • James Lancaster Shifeng Xue Bruno Reversade
  • ... [+3 authors] ...,
  • Matthew E. Ritchie
  • Frédérique Magdinier
  • Marnie E. Blewitt
  • Quentin Gouil
  • First Published March 23, 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
Method

Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes

  • Hongke Peng
  • Jafar S. Jabbari
  • Luyi Tian
  • Changqing Wang
  • Yupei You
  • Chong Chyn Chua Natasha S. Anstee Noorul Amin Andrew H. Wei Nadia M. Davidson
  • ... [+5 authors] ...,
  • Andrew W. Roberts
  • David C.S. Huang
  • Matthew E. Ritchie
  • Rachel Thijssen
  • First Published January 10, 2025
Method

An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing

  • Kathleen Zeglinski
  • Christian Montellese
  • Matthew E. Ritchie
  • Monther Alhamdoosh
  • Cédric Vonarburg
  • Rory Bowden
  • ... [+1 authors] ...,
  • Monika Jordi
  • Quentin Gouil
  • Florian Aeschimann
  • Arthur Hsu
  • First Published October 28, 2024
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
Method

Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing

  • Sena A. Gocuk
  • James Lancaster
  • Shian Su
  • Jasleen K. Jolly
  • Thomas L. Edwards
  • Doron G. Hickey
  • ... [+1 authors] ...,
  • Matthew E. Ritchie
  • Marnie E. Blewitt
  • Lauren N. Ayton
  • Quentin Gouil
  • First Published September 16, 2024
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

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin

  • Alexej Abyzov
  • Livia Tomasini
  • Bo Zhou
  • Nikolaos Vasmatzis
  • Gianfilippo Coppola
  • Mariangela Amenduni Reenal Pattni Michael Wilson
  • ... [+3 authors] ...,
  • Mark Gerstein
  • Sherman Weissman
  • Alexander E. Urban
  • Flora M. Vaccarino
  • First Published February 24, 2017
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
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