Imperial College London
Alternate

ProfessorPeterWhite

Faculty of Medicine, School of Public Health

Professor of Public Health Modelling
 
 
 
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Contact

 

p.white Website

 
 
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Location

 

Praed StreetSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Didelot:2021:10.1002/cpz1.60,
author = {Didelot, X and Kendall, M and Xu, Y and White, PJ and McCarthy, N},
doi = {10.1002/cpz1.60},
journal = {Current Protocols},
pages = {1--23},
title = {Genomic epidemiology analysis of infectious disease outbreaks using TransPhylo.},
url = {http://dx.doi.org/10.1002/cpz1.60},
volume = {1},
year = {2021}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo. © 2021 The Authors. Basic Protocol 1: First steps with TransPhylo Basic Protocol 2: Simulation of outbreak data Basic Protocol 3: Inference of transmission Basic Protocol 4: Exploring the results of inference.
AU  - Didelot,X
AU  - Kendall,M
AU  - Xu,Y
AU  - White,PJ
AU  - McCarthy,N
DO  - 10.1002/cpz1.60
EP  - 23
PY  - 2021///
SN  - 2691-1299
SP  - 1
TI  - Genomic epidemiology analysis of infectious disease outbreaks using TransPhylo.
T2  - Current Protocols
UR  - http://dx.doi.org/10.1002/cpz1.60
UR  - https://www.ncbi.nlm.nih.gov/pubmed/33617114
UR  - https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.60
UR  - http://hdl.handle.net/10044/1/87169
VL  - 1
ER  -
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