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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

A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

  • Shuai Guo
  • Xiaoqian Liu
  • Xuesen Cheng
  • Yujie Jiang
  • Shuangxi Ji
  • Qingnan Liang Andrew Koval Yumei Li Leah A. Owen Ivana K. Kim Ana Aparicio Sanghoon Lee Anil K. Sood Scott Kopetz John Paul Shen
  • ... [+10 authors] ...,
  • John N. Weinstein
  • Margaret M. DeAngelis
  • Rui Chen
  • Wenyi Wang
  • First Published November 25, 2024

Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples

  • Shuangxi Ji
  • Tong Zhu
  • Ankit Sethia
  • Wenyi Wang
  • First Published April 8, 2024

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

Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data

  • Kaixuan Luo
  • Jianling Zhong
  • Alexias Safi
  • Linda K. Hong
  • Alok K. Tewari
  • Lingyun Song
  • ... [+1 authors] ...,
  • Timothy E. Reddy
  • Li Ma
  • Gregory E. Crawford
  • Alexander J. Hartemink
  • First Published May 24, 2022

cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants" > Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants

  • Dongwon Lee
  • Ashish Kapoor
  • Alexias Safi
  • Lingyun Song
  • Marc K. Halushka
  • Gregory E. Crawford
  • Aravinda Chakravarti
  • First Published August 23, 2018

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

  • Ian C. McDowell
  • Alejandro Barrera
  • Anthony M. D'Ippolito
  • Christopher M. Vockley
  • Linda K. Hong
  • Sarah M. Leichter Luke C. Bartelt William H. Majoros Lingyun Song Alexias Safi D. Dewran Koçak Charles A. Gersbach
  • ... [+7 authors] ...,
  • Alexander J. Hartemink
  • Gregory E. Crawford
  • Barbara E. Engelhardt
  • Timothy E. Reddy
  • First Published August 10, 2018
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