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Research

Epigenetic characterization of pseudogenes across human tissues

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

Long-read reconstruction of many diverse haplotypes with devider

  • Jim Shaw
  • Christina Boucher
  • Yun William Yu
  • Noelle Noyes
  • Heng Li
  • First Published September 23, 2025
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
Erratum

O(m log n) time through an average-case analysis of the seed-chain-extend heuristic" > Erratum: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

  • Jim Shaw
  • Yun William Yu
  • First Published June 25, 2024
Method

O(m log n) time through an average-case analysis of the seed-chain-extend heuristic" > Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

  • Jim Shaw
  • Yun William Yu
  • First Published March 29, 2023
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
Erratum

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles" > Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

  • Tannistha Nandi
  • Matthew T.G. Holden
  • Xavier Didelot
  • Kurosh Mehershahi
  • Justin A. Boddey
  • Ifor Beacham Ian Peak John Harting Primo Baybayan Yan Guo Susana Wang Lee Chee How Bernice Sim Angela Essex-Lopresti Mitali Sarkar-Tyson Michelle Nelson Sophie Smither Catherine Ong Lay Tin Aw Chua Hui Hoon Stephen Michell David J. Studholme
  • ... [+17 authors] ...,
  • Richard Titball
  • Swaine L. Chen
  • Julian Parkhill
  • Patrick Tan
  • First Published April 1, 2015
Research

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles" > Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

  • Tannistha Nandi
  • Matthew T.G. Holden
  • Xavier Didelot
  • Kurosh Mehershahi
  • Justin A. Boddey
  • Ifor Beacham Ian Peak John Harting Primo Baybayan Yan Guo Susana Wang Lee Chee How Bernice Sim Angela Essex-Lopresti Mitali Sarkar-Tyson Michelle Nelson Sophie Smither Catherine Ong Lay Tin Aw Chua Hui Hoon Stephen Michell David J. Studholme
  • ... [+17 authors] ...,
  • Richard Titball
  • Swaine L. Chen
  • Julian Parkhill
  • Patrick Tan
  • First Published September 18, 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
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