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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
Method

Bombyx mori" > High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori

  • Sanyuan Ma
  • Tong Zhang
  • Ruolin Wang
  • Pan Wang
  • Yue Liu
  • Jiasong Chang Aoming Wang Xinhui Lan Le Sun Hao Sun Run Shi Wei Lu Dan Liu Na Zhang Wenbo Hu
  • ... [+10 authors] ...,
  • Xiaogang Wang
  • Weiqing Xing
  • Ling Jia
  • Qingyou Xia
  • First Published January 8, 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
Method

Read clouds uncover variation in complex regions of the human genome

  • Alex Bishara
  • Yuling Liu
  • Ziming Weng
  • Dorna Kashef-Haghighi
  • Daniel E. Newburger
  • Robert West
  • Arend Sidow
  • Serafim Batzoglou
  • First Published August 18, 2015
Method

Discovery of recurrent structural variants in nasopharyngeal carcinoma

  • Anton Valouev
  • Ziming Weng
  • Robert T. Sweeney
  • Sushama Varma
  • Quynh-Thu Le
  • Christina Kong
  • Arend Sidow
  • Robert B. West
  • First Published November 8, 2013
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

Genome evolution during progression to breast cancer

  • Daniel E. Newburger
  • Dorna Kashef-Haghighi
  • Ziming Weng
  • Raheleh Salari
  • Robert T. Sweeney
  • Alayne L. Brunner Shirley X. Zhu Xiangqian Guo Sushama Varma
  • ... [+4 authors] ...,
  • Megan L. Troxell
  • Robert B. West
  • Serafim Batzoglou
  • Arend Sidow
  • First Published April 8, 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
Method

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

  • Anshul Kundaje
  • Sofia Kyriazopoulou-Panagiotopoulou
  • Max Libbrecht
  • Cheryl L. Smith
  • Debasish Raha
  • Elliott E. Winters
  • ... [+1 authors] ...,
  • Steven M. Johnson
  • Michael Snyder
  • Serafim Batzoglou
  • Arend Sidow
  • First Published September 5, 2012
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