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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
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

Bombyx mori" > High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism, Bombyx mori

  • Sanyuan Ma
  • Tong Zhang
  • Ruolin Wang
  • Pan Wang
  • Yue Liu
  • Jiasong Chang Aoming Wang Xinhui Lan Le Sun Hao Sun Run Shi Wei Lu Dan Liu Na Zhang Wenbo Hu
  • ... [+10 authors] ...,
  • Xiaogang Wang
  • Weiqing Xing
  • Ling Jia
  • Qingyou Xia
  • First Published January 8, 2024
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

Bombyx mori" > Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori

  • Jiasong Chang
  • Ruolin Wang
  • Kai Yu
  • Tong Zhang
  • Xiaoxu Chen
  • Yue Liu
  • ... [+1 authors] ...,
  • Run Shi
  • Xiaogang Wang
  • Qingyou Xia
  • Sanyuan Ma
  • First Published May 18, 2020
Method

Fast and flexible bacterial genomic epidemiology with PopPUNK

  • John A. Lees
  • Simon R. Harris
  • Gerry Tonkin-Hill
  • Rebecca A. Gladstone
  • Stephanie W. Lo
  • Jeffrey N. Weiser
  • Jukka Corander
  • Stephen D. Bentley
  • Nicholas J. Croucher
  • First Published January 24, 2019
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