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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

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

MCHelper automatically curates transposable element libraries across eukaryotic species

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

The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome

  • Young-Lim Lee
  • Aniek C. Bouwman
  • Chad Harland
  • Mirte Bosse
  • Gabriel Costa Monteiro Moreira
  • Roel F. Veerkamp Erik Mullaart Nadine Cambisano Martien A.M. Groenen
  • ... [+4 authors] ...,
  • Latifa Karim
  • Wouter Coppieters
  • Michel Georges
  • Carole Charlier
  • First Published October 4, 2023

An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants

  • Can Yuan
  • Lijing Tang
  • Thomas Lopdell
  • Vyacheslav A. Petrov
  • Claire Oget-Ebrad
  • Gabriel Costa Monteiro Moreira José Luis Gualdrón Duarte Arnaud Sartelet Zhangrui Cheng Mazdak Salavati D. Claire Wathes Mark A. Crowe Wouter Coppieters Mathew Littlejohn Carole Charlier Tom Druet Michel Georges Haruko Takeda Mark Crowe Niamh McLoughlin Alan Fahey Elizabeth Matthews Andreia Santoro Colin Byrne Pauline Rudd Roisin O'Flaherty Sinead Hallinan Claire Wathes Zhangrui Cheng Ali Fouladi Geoff Pollott Dirk Werling Beatriz Sanz Bernardo Mazdak Salavati Laura Buggiotti Alistair Wylie Matt Bell Conrad Ferris Mieke Vaneetvelde Kristof Hermans Geert Opsomer Sander Moerman Jenne De Koster Hannes Bogaert Jan Vandepitte Leila Vandevelde Bonny Vanranst Johanna Hoglund Susanne Dahl Klaus Ingvartsen Martin Sørensen Leslie Foldager Soren Ostergaard Janne Rothmann Mogens Krogh Else Meyer Charlotte Gaillard Jehan Ettema Tine Rousing Federica Signorelli Francesco Napolitano Bianca Moioli Alessandra Crisa Luca Buttazzoni Jennifer McClure Daragh Matthews Francis Kearney Andrew Cromie Matt McClure Shujun Zhang Xing Chen Huanchun Chen Junlong Zhao Liguo Yang Guohua Hua Chen Tan Guiqiang Wang Michel Bonneau Andrea Pompozzi Armin Pearn Arnold Evertson Linda Kosten Anders Fogh Thomas Andersen Matthew Lucy Chris Elsik Gavin Conant Jerry Taylor Nicolas Gengler Michel Georges Frederic Colinet Marilou Ramos Pamplona Hedi Hammami Catherine Bastin Haruko Takeda Aurelie Laine
  • ... [+91 authors] ...,
  • Lijing Tang
  • Martin Schulze
  • Cinzia Marchitelli
  • Sergio Palma-Vera
  • First Published September 26, 2023

Ultrafast genome-wide inference of pairwise coalescence times

  • Regev Schweiger
  • Richard Durbin
  • First Published August 10, 2023

Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera

  • Peter O. Mulhair
  • Liam Crowley
  • Douglas H. Boyes
  • Amber Harper
  • Owen T. Lewis
  • Peter W.H. Holland Mark Blaxter Nova Mieszkowska Federica Di Palma Peter Holland Richard Durbin Thomas Richards Matthew Berriman Paul Kersey Peter Hollingsworth Willie Wilson Alex Twyford Ester Gaya Mara Lawniczak Owen Lewis Gavin Broad
  • ... [+16 authors] ...,
  • Kevin Howe
  • Michelle Hart
  • Paul Flicek
  • Ian Barnes
  • First Published December 8, 2022

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

  • Valerie A. Schneider
  • Tina Graves-Lindsay
  • Kerstin Howe
  • Nathan Bouk
  • Hsiu-Chuan Chen
  • Paul A. Kitts Terence D. Murphy Kim D. Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S. Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T. Simpson Glen Threadgold James Torrance Jonathan M. Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M. Phillippy Richard Durbin
  • ... [+29 authors] ...,
  • Richard K. Wilson
  • Paul Flicek
  • Evan E. Eichler
  • Deanna M. Church
  • First Published April 10, 2017

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

  • Dirk D. Dolle
  • Zhicheng Liu
  • Matthew Cotten
  • Jared T. Simpson
  • Zamin Iqbal
  • Richard Durbin
  • Shane A. McCarthy
  • Thomas M. Keane
  • First Published December 16, 2016

NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock

  • Carole Charlier
  • Wanbo Li
  • Chad Harland
  • Mathew Littlejohn
  • Wouter Coppieters
  • Frances Creagh Steve Davis Tom Druet Pierre Faux François Guillaume Latifa Karim Mike Keehan
  • ... [+7 authors] ...,
  • Naveen Kumar Kadri
  • Nico Tamma
  • Richard Spelman
  • Michel Georges
  • First Published September 19, 2016
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