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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

TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance

  • Muhammad Yasir
  • A. Keith Turner
  • Sarah Bastkowski
  • David Baker
  • Andrew J. Page
  • Andrea Telatin Minh-Duy Phan Leigh Monahan
  • ... [+3 authors] ...,
  • George M. Savva
  • Aaron Darling
  • Mark A. Webber
  • Ian G. Charles
  • First Published February 12, 2020
Resource

A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection

  • Mats E. Pettersson
  • Christina M. Rochus
  • Fan Han
  • Junfeng Chen
  • Jason Hill
  • Ola Wallerman Guangyi Fan Xiaoning Hong Qiwu Xu He Zhang Shanshan Liu Xin Liu Leanne Haggerty Toby Hunt Fergal J. Martin
  • ... [+10 authors] ...,
  • Paul Flicek
  • Ignas Bunikis
  • Arild Folkvord
  • Leif Andersson
  • First Published October 24, 2019
Resource

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

  • Jonathan M. Mudge
  • Irwin Jungreis
  • Toby Hunt
  • Jose Manuel Gonzalez
  • James C. Wright
  • Mike Kay Claire Davidson Stephen Fitzgerald Ruth Seal Susan Tweedie Liang He Robert M. Waterhouse Yue Li
  • ... [+8 authors] ...,
  • Elspeth Bruford
  • Jyoti S. Choudhary
  • Adam Frankish
  • Manolis Kellis
  • First Published September 19, 2019
Resource

The pig X and Y Chromosomes: structure, sequence, and evolution

  • Benjamin M. Skinner
  • Carole A. Sargent
  • Carol Churcher
  • Toby Hunt
  • Javier Herrero
  • Jane E. Loveland Matt Dunn Sandra Louzada Beiyuan Fu William Chow James Gilbert Siobhan Austin-Guest Kathryn Beal Denise Carvalho-Silva William Cheng Daria Gordon Darren Grafham Matt Hardy Jo Harley Heidi Hauser Philip Howden Kerstin Howe Kim Lachani Peter J.I. Ellis Daniel Kelly Giselle Kerry James Kerwin Bee Ling Ng Glen Threadgold Thomas Wileman Jonathan M.D. Wood
  • ... [+26 authors] ...,
  • Fengtang Yang
  • Jen Harrow
  • Nabeel A. Affara
  • Chris Tyler-Smith
  • First Published November 11, 2015
Resource

GENCODE: The reference human genome annotation for The ENCODE Project

  • Jennifer Harrow
  • Adam Frankish
  • Jose M. Gonzalez
  • Electra Tapanari
  • Mark Diekhans
  • Felix Kokocinski Bronwen L. Aken Daniel Barrell Amonida Zadissa Stephen Searle If Barnes Alexandra Bignell Veronika Boychenko Toby Hunt Mike Kay Gaurab Mukherjee Jeena Rajan Gloria Despacio-Reyes Gary Saunders Charles Steward Rachel Harte Michael Lin Cédric Howald Andrea Tanzer Thomas Derrien Jacqueline Chrast Nathalie Walters Suganthi Balasubramanian Baikang Pei Michael Tress Jose Manuel Rodriguez Iakes Ezkurdia Jeltje van Baren Michael Brent David Haussler Manolis Kellis Alfonso Valencia
  • ... [+32 authors] ...,
  • Alexandre Reymond
  • Mark Gerstein
  • Roderic Guigó
  • Tim J. Hubbard
  • First Published September 5, 2012
Resource

Assemblathon 1: A competitive assessment of de novo short read assembly methods

  • Dent Earl
  • Keith Bradnam
  • John St. John
  • Aaron Darling
  • Dawei Lin
  • Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
  • ... [+62 authors] ...,
  • Richard E. Green
  • David Haussler
  • Ian Korf
  • Benedict Paten
  • First Published September 16, 2011
Methods

Inferring genomic flux in bacteria

  • Xavier Didelot
  • Aaron Darling
  • Daniel Falush
  • First Published November 17, 2008
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