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Research

Epigenetic characterization of pseudogenes across human tissues

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

Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing

  • Kristine Bilgrav Saether
  • Angelo Salazar Mantero
  • Marlene Ek
  • Maria Pettersson
  • Elisabeth Syk Lundberg
  • Christopher M. Grochowski
  • Claudia M.B. Carvalho
  • Jesper Eisfeldt
  • Anna Lindstrand
  • First Published March 25, 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

Highly accurate assembly polishing with DeepPolisher

  • Mira Mastoras
  • Mobin Asri
  • Lucas Brambrink
  • Prajna Hebbar
  • Alexey Kolesnikov
  • Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Richard Durbin Jana Ebler Evan E Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa' A. Garrison John Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
  • ... [+196 authors] ...,
  • Wenjin Zhang
  • Ying Zhou
  • Ivo Violich
  • Giulia Zunino
  • First Published May 19, 2025
Research

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

  • Fu Xiang Quah
  • Miguel Vasconcelos Almeida
  • Moritz Blumer
  • Chengwei Ulrika Yuan
  • Bettina Fischer
  • Kirsten See Ben Jackson Richard Zatha Bosco Rusuwa George F. Turner M. Emília Santos
  • ... [+6 authors] ...,
  • Hannes Svardal
  • Martin Hemberg
  • Richard Durbin
  • Eric Miska
  • First Published April 10, 2025
Method

MCHelper automatically curates transposable element libraries across eukaryotic species

  • Simon Orozco-Arias
  • Pío Sierra
  • Richard Durbin
  • Josefa González
  • First Published December 9, 2024
Research

Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps

  • Kristine Bilgrav Saether
  • Jesper Eisfeldt
  • Jesse D. Bengtsson
  • Ming Yin Lun
  • Christopher M. Grochowski
  • Medhat Mahmoud Hsiao-Tuan Chao Jill A. Rosenfeld Pengfei Liu Marlene Ek Jakob Schuy Adam Ameur Hongzheng Dai James Paul Hwang Fritz J. Sedlazeck Weimin Bi Ronit Marom
  • ... [+12 authors] ...,
  • Josephine Wincent
  • Ann Nordgren
  • Claudia M.B. Carvalho
  • Anna Lindstrand
  • First Published November 1, 2024
Research

Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing

  • Jesper Eisfeldt
  • Edward J. Higginbotham
  • Felix Lenner
  • Jennifer Howe
  • Bridget A. Fernandez
  • Anna Lindstrand
  • Stephen W. Scherer
  • Lars Feuk
  • First Published October 29, 2024
Research

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities

  • Jesper Eisfeldt
  • Adam Ameur
  • Felix Lenner
  • Esmee Ten Berk de Boer
  • Marlene Ek
  • Josephine Wincent Raquel Vaz Jesper Ottosson Tord Jonson Sofie Ivarsson Sofia Thunström Alexandra Topa Simon Stenberg Anna Rohlin Anna Sandestig Margareta Nordling Pia Palmebäck Magnus Burstedt Frida Nordin Eva-Lena Stattin Maria Sobol Panagiotis Baliakas Marie-Louise Bondeson Ida Höijer Kristine Bilgrav Saether Lovisa Lovmar
  • ... [+21 authors] ...,
  • Hans Ehrencrona
  • Malin Melin
  • Lars Feuk
  • Anna Lindstrand
  • First Published October 29, 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
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