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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
Resource

Charting the regulatory landscape of TP53 on transposable elements in cancer

  • Xuan Qu
  • Yonghao Liang
  • Colin McCornack
  • Xiaoyun Xing
  • Heather Schmidt
  • Chad Tomlinson
  • ... [+1 authors] ...,
  • Catrina Fronick
  • Edward A. Belter
  • Juan F. Macias-Velasco
  • Ting Wang
  • First Published May 13, 2025
Method

Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm

  • Samuel T. Horsfield
  • Basil C.T. Fok
  • Yuhan Fu
  • Paul Turner
  • John A. Lees
  • Nicholas J. Croucher
  • First Published March 4, 2025
Resource

Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

  • Jiawei Shen
  • Siyuan Cheng
  • Deepak Purushotham
  • Xiaoyu Zhuo
  • Alan Y Du
  • Wenjin Zhang
  • Daofeng Li
  • Ting Wang
  • First Published February 21, 2025
Resource

Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution

  • Yujie Chen
  • Yiran Hou
  • Qinglin Zeng
  • Irene Wang
  • Meiru Shang
  • Kwangdeok Shin Christopher Hemauer
  • ... [+2 authors] ...,
  • Xiaoyun Xing
  • Junsu Kang
  • Guoyan Zhao
  • Ting Wang
  • First Published January 14, 2025
Method

k-mer analysis" > Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

  • Romain Derelle
  • Johanna von Wachsmann
  • Tommi Mäklin
  • Joel Hellewell
  • Timothy Russell
  • Ajit Lalvani
  • ... [+1 authors] ...,
  • Leonid Chindelevitch
  • Nicholas J. Croucher
  • Simon R. Harris
  • John A. Lees
  • First Published October 15, 2024
Method

Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs

  • Juri Kuronen
  • Samuel T. Horsfield
  • Anna K. Pöntinen
  • Sudaraka Mallawaarachchi
  • Sergio Arredondo-Alonso
  • Harry Thorpe Rebecca A. Gladstone Rob J.L. Willems Stephen D. Bentley Nicholas J. Croucher
  • ... [+5 authors] ...,
  • Johan Pensar
  • John A. Lees
  • Gerry Tonkin-Hill
  • Jukka Corander
  • First Published August 12, 2024
Method

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

  • Ju Heon Maeng
  • H. Josh Jang
  • Alan Y. Du
  • Shin-Cheng Tzeng
  • Ting Wang
  • First Published December 8, 2023
Method

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

  • Samuel T. Horsfield
  • Gerry Tonkin-Hill
  • Nicholas J. Croucher
  • John A. Lees
  • First Published August 24, 2023
Method

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK

  • Bin Zhao
  • John A. Lees
  • Hongjin Wu
  • Chao Yang
  • Daniel Falush
  • First Published May 30, 2023
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