Imperial College London
Alternate

DrXavierDidelot

Faculty of Medicine, School of Public Health

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 3622x.didelot

 
 
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Location

 

G30Medical SchoolSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{O'Brien:2014,
author = {O'Brien, J and Didelot, X and Iqbal, Z and LucasAmenga-Etego and Ahiska, B and Falush, D},
title = {A Bayesian approach to inferring the phylogenetic structure of  communities from metagenomic data},
url = {http://arxiv.org/abs/1306.6313v1},
year = {2014}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Metagenomics provides a powerful new tool set for investigating evolutionaryinteractions with the environment. However, an absence of model-basedstatistical methods means that researchers are often not able to make full useof this complex information. We present a Bayesian method for inferring thephylogenetic relationship among related organisms found within metagenomicsamples. Our approach exploits variation in the frequency of taxa among samplesto simultaneously infer each lineage haplotype, the phylogenetic treeconnecting them, and their frequency within each sample. Applications of thealgorithm to simulated data show that our method can recover a substantialfraction of the phylogenetic structure even in the presence of strong mixingamong samples. We provide examples of the method applied to data from greensulfur bacteria recovered from an Antarctic lake, plastids from mixedPlasmodium falciparum infections, and virulent Neisseria meningitidis samples.
AU  - O'Brien,J
AU  - Didelot,X
AU  - Iqbal,Z
AU  - LucasAmenga-Etego
AU  - Ahiska,B
AU  - Falush,D
PY  - 2014///
TI  - A Bayesian approach to inferring the phylogenetic structure of  communities from metagenomic data
UR  - http://arxiv.org/abs/1306.6313v1
ER  -
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