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SCOTTI: Efficient reconstruction of transmission within outbreaks with the structured coalescent

Abstract:

Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients. Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that ...

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Publication status:
Published
Peer review status:
Peer reviewed

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Publisher copy:
10.1371/journal.pcbi.1005130

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Institution:
University of Oxford
Division:
MSD
Department:
NDM
Sub department:
NDM Experimental Medicine
Role:
Author
More by this author
Institution:
University of Oxford
Division:
MSD
Department:
NDM
Sub department:
NDM Experimental Medicine
Role:
Author
More by this author
Institution:
University of Oxford
Division:
MSD
Department:
NDM
Sub department:
NDM Experimental Medicine
Role:
Author
More from this funder
Funding agency for:
Wu, C
Grant:
101237/Z/13/Z
More from this funder
Funding agency for:
Wu, C
Grant:
101237/Z/13/Z
More from this funder
Funding agency for:
Wilson, D
Grant:
101237/Z/13/Z
More from this funder
Funding agency for:
De Maio, N
More from this funder
Funding agency for:
Wilson, D
Grant:
101237/Z/13/Z
Publisher:
Public Library of Science Publisher's website
Journal:
PLoS Computational Biology Journal website
Volume:
12
Issue:
9
Article number:
e1005130
Publication date:
2016-09-28
Acceptance date:
2016-09-05
DOI:
ISSN:
1553-7358
Source identifiers:
646560
Pubs id:
pubs:646560
UUID:
uuid:a71787b2-b4d4-4a55-8991-14288ab22ff4
Local pid:
pubs:646560
Deposit date:
2016-09-29

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