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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
Method

De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies

  • John Beaulaurier
  • Lynn Ly
  • J. Andrew Duty
  • Carly Tyer
  • Christian Stevens
  • Chuan-Tien Hung Akash Sookdeo Alex W. Drong Shreyas Kowdle Axel Guzman-Solis Domenico Tortorella
  • ... [+6 authors] ...,
  • Daniel J. Turner
  • Sissel Juul
  • Scott Hickey
  • Benhur Lee
  • First Published March 21, 2025
Method

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

  • Tanner D. Jensen
  • Bohan Ni
  • Chloe M. Reuter
  • John E. Gorzynski
  • Sarah Fazal
  • Devon Bonner Rachel A. Ungar Pagé C. Goddard Archana Raja Euan A. Ashley Jonathan A. Bernstein Stephan Zuchner Michael D. Greicius
  • ... [+8 authors] ...,
  • Stephen B. Montgomery
  • Michael C. Schatz
  • Matthew T. Wheeler
  • Alexis Battle
  • First Published March 20, 2025
Method

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

  • Sergey Koren
  • Zhigui Bao
  • Andrea Guarracino
  • Shujun Ou
  • Sara Goodwin
  • Katharine M. Jenike Julian Lucas Brandy McNulty Jimin Park Mikko Rautiainen Arang Rhie Dick Roelofs Harrie Schneiders Ilse Vrijenhoek Koen Nijbroek Olle Nordesjo Sergey Nurk Mike Vella Katherine R. Lawrence Doreen Ware Michael C. Schatz Erik Garrison Sanwen Huang
  • ... [+18 authors] ...,
  • William Richard McCombie
  • Karen H. Miga
  • Alexander H.J. Wittenberg
  • Adam M. Phillippy
  • First Published November 6, 2024
Method

Optimized sample selection for cost-efficient long-read population sequencing

  • T. Rhyker Ranallo-Benavidez
  • Zachary Lemmon
  • Sebastian Soyk
  • Sergey Aganezov
  • William J. Salerno
  • Rajiv C. McCoy
  • Zachary B. Lippman
  • Michael C. Schatz
  • Fritz J. Sedlazeck
  • First Published April 2, 2021
Method

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

  • John Beaulaurier
  • Elaine Luo
  • John M. Eppley
  • Paul Den Uyl
  • Xiaoguang Dai
  • Andrew Burger Daniel J. Turner
  • ... [+2 authors] ...,
  • Matthew Pendelton
  • Sissel Juul
  • Eoghan Harrington
  • Edward F. DeLong
  • First Published February 19, 2020
Method

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing

  • Shijia Zhu
  • John Beaulaurier
  • Gintaras Deikus
  • Tao P. Wu
  • Maya Strahl
  • Ziyang Hao Guanzheng Luo James A. Gregory Andrew Chess Chuan He
  • ... [+5 authors] ...,
  • Andrew Xiao
  • Robert Sebra
  • Eric E. Schadt
  • Gang Fang
  • First Published May 15, 2018
Method

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

  • Sara Goodwin
  • James Gurtowski
  • Scott Ethe-Sayers
  • Panchajanya Deshpande
  • Michael C. Schatz
  • W. Richard McCombie
  • First Published October 7, 2015
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