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Research

Epigenetic characterization of pseudogenes across human tissues

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

RECOMB 2025 Special Issue

  • Sriram Sankararaman
  • Bonnie Berger
  • First Published December 3, 2025
Method

Graph-based deep reinforcement learning for haplotype assembly with Ralphi

  • Enzo Battistella
  • Anant Maheshwari
  • Barış Ekim
  • Bonnie Berger
  • Victoria Popic
  • First Published November 14, 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
Editorial

Innovations in computational biology: RECOMB 2024 Special Issue

  • Jian Ma
  • Bonnie Berger
  • First Published October 11, 2024
Method

Secure discovery of genetic relatives across large-scale and distributed genomic data sets

  • Matthew M. Hong
  • David Froelicher
  • Ricky Magner
  • Victoria Popic
  • Bonnie Berger
  • Hyunghoon Cho
  • First Published August 7, 2024
Method

k using minimum decycling sets" > Efficient minimizer orders for large values of k using minimum decycling sets

  • David Pellow
  • Lianrong Pu
  • Bariş Ekim
  • Lior Kotlar
  • Bonnie Berger
  • Ron Shamir
  • Yaron Orenstein
  • First Published August 9, 2023
Method

Assessing transcriptomic reidentification risks using discriminative sequence models

  • Shuvom Sadhuka
  • Daniel Fridman
  • Bonnie Berger
  • Hyunghoon Cho
  • First Published August 4, 2023
Method

Efficient mapping of accurate long reads in minimizer space with mapquik

  • Bariş Ekim
  • Kristoffer Sahlin
  • Paul Medvedev
  • Bonnie Berger
  • Rayan Chikhi
  • First Published June 30, 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
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