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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

Drosophila melanogaster ovary" > Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

  • Satyam P. Srivastav
  • Cédric Feschotte
  • Andrew G. Clark
  • First Published May 15, 2024
Method

Semisupervised adversarial neural networks for single-cell classification

  • Jacob C. Kimmel
  • David R. Kelley
  • First Published February 24, 2021
Corrigendum

Corrigendum: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

  • Jacob C. Kimmel
  • Lolita Penland
  • Nimrod D. Rubinstein
  • David G. Hendrickson
  • David R. Kelley
  • Adam Z. Rosenthal
  • First Published January 9, 2020
Resource

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

  • Jacob C. Kimmel
  • Lolita Penland
  • Nimrod D. Rubinstein
  • David G. Hendrickson
  • David R. Kelley
  • Adam Z. Rosenthal
  • First Published November 21, 2019
Method

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

  • David R. Kelley
  • Yakir A. Reshef
  • Maxwell Bileschi
  • David Belanger
  • Cory Y. McLean
  • Jasper Snoek
  • First Published March 27, 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
Method

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

  • David R. Kelley
  • Jasper Snoek
  • John L. Rinn
  • First Published May 3, 2016
Research

Drosophila" > Evidence for the fixation of gene duplications by positive selection in Drosophila

  • Margarida Cardoso-Moreira
  • J. Roman Arguello
  • Srikanth Gottipati
  • L.G. Harshman
  • Jennifer K. Grenier
  • Andrew G. Clark
  • First Published April 12, 2016
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