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R. Alan Harris
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22
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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
:
Accurate sequencing of DNA motifs able to form alternative (non-B) structures
Matthias H. Weissensteiner
,
Marzia A. Cremona
,
Wilfried M. Guiblet
,
Nicholas Stoler
,
Robert S. Harris
,
Monika Cechova
,
Kristin A. Eckert
,
Francesca Chiaromonte
,
Yi-Fei Huang
,
and
Kateryna D. Makova
Genome Res.
July 11, 2023
;
Published in Advance
July 11, 2023
,
doi:
10.1101/gr.277490.122
Abstract
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Research
:
Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability
Richard J. Wang
,
Gregg W.C. Thomas
,
Muthuswamy Raveendran
,
R. Alan Harris
,
Harshavardhan Doddapaneni
,
Donna M. Muzny
,
John P. Capitanio
,
Predrag Radivojac
,
Jeffrey Rogers
,
and
Matthew W. Hahn
Genome Res.
June 2020
30
:
826
-
834
;
Published in Advance
May 27, 2020
,
doi:
10.1101/gr.255174.119
Abstract
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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
:
Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
Wilfried M. Guiblet
,
Marzia A. Cremona
,
Monika Cechova
,
Robert S. Harris
,
Iva Kejnovská
,
Eduard Kejnovsky
,
Kristin Eckert
,
Francesca Chiaromonte
,
and
Kateryna D. Makova
Genome Res.
December 2018
28
:
1767
-
1778
;
Published in Advance
November 6, 2018
,
doi:
10.1101/gr.241257.118
Abstract
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Research
:
Systematic longitudinal survey of invasive
Escherichia coli
in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
Teemu Kallonen
,
Hayley J. Brodrick
,
Simon R. Harris
,
Jukka Corander
,
Nicholas M. Brown
,
Veronique Martin
,
Sharon J. Peacock
,
and
Julian Parkhill
Genome Res.
August 2017
27
:
1437
-
1449
;
Published in Advance
July 18, 2017
,
doi:
10.1101/gr.216606.116
Abstract
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Research
:
Comprehensive global genome dynamics of
Chlamydia trachomatis
show ancient diversification followed by contemporary mixing and recent lineage expansion
James Hadfield
,
Simon R. Harris
,
Helena M.B. Seth-Smith
,
Surendra Parmar
,
Patiyan Andersson
,
Philip M. Giffard
,
Julius Schachter
,
Jeanne Moncada
,
Louise Ellison
,
María Lucía Gallo Vaulet
,
Marcelo Rodríguez Fermepin
,
Frans Radebe
,
Suyapa Mendoza
,
Sander Ouburg
,
Servaas A. Morré
,
Konrad Sachse
,
Mirja Puolakkainen
,
Suvi J. Korhonen
,
Chris Sonnex
,
Rebecca Wiggins
,
Hamid Jalal
,
Tamara Brunelli
,
Patrizia Casprini
,
Rachel Pitt
,
Cathy Ison
,
Alevtina Savicheva
,
Elena Shipitsyna
,
Ronza Hadad
,
Laszlo Kari
,
Matthew J. Burton
,
David Mabey
,
Anthony W. Solomon
,
David Lewis
,
Peter Marsh
,
Magnus Unemo
,
Ian N. Clarke
,
Julian Parkhill
,
and
Nicholas R. Thomson
Genome Res.
July 2017
27
:
1220
-
1229
;
Published in Advance
June 6, 2017
,
doi:
10.1101/gr.212647.116
Abstract
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Research
:
The population genomics of rhesus macaques (
Macaca mulatta
) based on whole-genome sequences
Cheng Xue
,
Muthuswamy Raveendran
,
R. Alan Harris
,
Gloria L. Fawcett
,
Xiaoming Liu
,
Simon White
,
Mahmoud Dahdouli
,
David Rio Deiros
,
Jennifer E. Below
,
William Salerno
,
Laura Cox
,
Guoping Fan
,
Betsy Ferguson
,
Julie Horvath
,
Zach Johnson
,
Sree Kanthaswamy
,
H. Michael Kubisch
,
Dahai Liu
,
Michael Platt
,
David G. Smith
,
Binghua Sun
,
Eric J. Vallender
,
Feng Wang
,
Roger W. Wiseman
,
Rui Chen
,
Donna M. Muzny
,
Richard A. Gibbs
,
Fuli Yu
,
and
Jeffrey Rogers
Genome Res.
December 2016
26
:
1651
-
1662
;
Published in Advance
October 17, 2016
,
doi:
10.1101/gr.204255.116
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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Method
:
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
Marta Tomaszkiewicz
,
Samarth Rangavittal
,
Monika Cechova
,
Rebeca Campos Sanchez
,
Howard W. Fescemyer
,
Robert Harris
,
Danling Ye
,
Patricia C.M. O'Brien
,
Rayan Chikhi
,
Oliver A. Ryder
,
Malcolm A. Ferguson-Smith
,
Paul Medvedev
,
and
Kateryna D. Makova
Genome Res.
April 2016
26
:
530
-
540
;
Published in Advance
March 2, 2016
,
doi:
10.1101/gr.199448.115
Abstract
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Cross-modality translation in single-cell multiomics
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