Imperial College London
Alternate

DrOliverRatmann

Faculty of Natural Sciences, Department of Mathematics

Reader in Statistics and Machine Learning for Public Good
 
 
 
//

Contact

 

oliver.ratmann05 Website

 
 
//

Location

 

525Huxley BuildingSouth Kensington Campus

//

Summary

 

Publications

Citation

BibTex format

@article{Wymant:2018:molbev/msx304,
author = {Wymant, C and Hall, M and Ratmann, O and Bonsall, D and Golubchik, T and de, Cesare M and Gall, A and Cornelissen, M and Fraser, C and STOP-HCV, Consortium and The, Maela Pneumococcal Collaboration and and, The BEEHIVE Collaboration},
doi = {molbev/msx304},
journal = {Mol Biol Evol},
pages = {719--733},
title = {PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.},
url = {http://dx.doi.org/10.1093/molbev/msx304},
volume = {35},
year = {2018}
}
Download

RIS format (EndNote, RefMan)

TY  - JOUR
AB  - A central feature of pathogen genomics is that different infectious particles (virions and bacterial cells) within an infected individual may be genetically distinct, with patterns of relatedness among infectious particles being the result of both within-host evolution and transmission from one host to the next. Here, we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. Multiply infected individuals are also identified, as they harbor subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contamination is flagged and removed. We illustrate phyloscanner on both viral and bacterial pathogens, namely HIV-1 sequenced on Illumina and Roche 454 platforms, HCV sequenced with the Oxford Nanopore MinION platform, and Streptococcus pneumoniae with sequences from multiple colonies per individual. phyloscanner is available from https://github.com/BDI-pathogens/phyloscanner.
AU  - Wymant,C
AU  - Hall,M
AU  - Ratmann,O
AU  - Bonsall,D
AU  - Golubchik,T
AU  - de,Cesare M
AU  - Gall,A
AU  - Cornelissen,M
AU  - Fraser,C
AU  - STOP-HCV,Consortium
AU  - The,Maela Pneumococcal Collaboration
AU  - and,The BEEHIVE Collaboration
DO  - molbev/msx304
EP  - 733
PY  - 2018///
SP  - 719
TI  - PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
T2  - Mol Biol Evol
UR  - http://dx.doi.org/10.1093/molbev/msx304
UR  - https://www.ncbi.nlm.nih.gov/pubmed/29186559
UR  - http://hdl.handle.net/10044/1/54593
VL  - 35
ER  -
Download