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John A. Lees
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Displaying results 1-7 of
7
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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
,
and
Nicholas J. Croucher
Genome Res.
April 2025
35
:
1025
-
1040
;
Published in Advance
March 4, 2025
,
doi:
10.1101/gr.279435.124
Abstract
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Method
:
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
,
Leonid Chindelevitch
,
Nicholas J. Croucher
,
Simon R. Harris
,
and
John A. Lees
Genome Res.
October 2024
34
:
1661
-
1673
;
Published in Advance
October 15, 2024
,
doi:
10.1101/gr.279449.124
Abstract
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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
,
Johan Pensar
,
John A. Lees
,
Gerry Tonkin-Hill
,
and
Jukka Corander
Genome Res.
July 2024
34
:
1081
-
1088
;
Published in Advance
August 12, 2024
,
doi:
10.1101/gr.278485.123
Abstract
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Method
:
Accurate and fast graph-based pangenome annotation and clustering with ggCaller
Samuel T. Horsfield
,
Gerry Tonkin-Hill
,
Nicholas J. Croucher
,
and
John A. Lees
Genome Res.
September 2023
33
:
1622
-
1637
;
Published in Advance
August 24, 2023
,
doi:
10.1101/gr.277733.123
Abstract
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Method
:
Genealogical inference and more flexible sequence clustering using iterative PopPUNK
Bin Zhao
,
John A. Lees
,
Hongjin Wu
,
Chao Yang
,
and
Daniel Falush
Genome Res.
May 30, 2023
gr.277395.122
;
Published in Advance
May 30, 2023
,
doi:
10.1101/gr.277395.122
Abstract
Full Text (PDF)
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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
,
and
Nicholas J. Croucher
Genome Res.
February 2019
29
:
304
-
316
;
Published in Advance
January 24, 2019
,
doi:
10.1101/gr.241455.118
Abstract
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Research
:
Multiple major disease-associated clones of
Legionella pneumophila
have emerged recently and independently
Sophia David
,
Christophe Rusniok
,
Massimo Mentasti
,
Laura Gomez-Valero
,
Simon R. Harris
,
Pierre Lechat
,
John Lees
,
Christophe Ginevra
,
Philippe Glaser
,
Laurence Ma
,
Christiane Bouchier
,
Anthony Underwood
,
Sophie Jarraud
,
Timothy G. Harrison
,
Julian Parkhill
,
and
Carmen Buchrieser
Genome Res.
November 2016
26
:
1555
-
1564
;
Published in Advance
September 23, 2016
,
doi:
10.1101/gr.209536.116
Abstract
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