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SUMMARY:Study of the dynamics of bacterial communities in the Human Microb
iome - Susan Holmes (Stanford University)
DTSTART:20161213T134500Z
DTEND:20161213T144500Z
UID:TALK69472@talks.cam.ac.uk
CONTACT:INI IT
DESCRIPTION: Co-authors: Kris Sankaran (Stanford)\, Julia
Fukuyama (Stanford)\, Lan Nguyen (Stanford)\, Diana Proctor (Stanfor
d)\, David Relman (Stanford)\, Sergio Bacallado (Cambridge)\, Boyu Ren
(Stanford)\, Pratheepa Jeganathan (Stanford)
\
;
The human microbiome is a complex assembly of bacteria that are sens
itive to many perturbations. In several longitudinal analyses we study pe
rturbations of bacterial community networks over time. For this\, we have
developed specific tools for modeling the vaginal\, intestinal and oral
microbiomes under these different perturbations (pregnancy\, hypo-saliva
tion inducing medications and antibiotics are some examples).
&nbs
p\;
A suite of statistical tools written in R based on a Bioconductor
package (phyloseq) allows for easy normalization\, visualization and sta
tistical testing of the longitudinal multi-table data composed of 16sRNA
reads combined with clinical data\, transcriptomic and metabolomic profi
les. Challenges we have had to address include information leaks\, the h
eterogeneity of the data\, multiplicity of choices during the analyses an
d validation of results.
\;
Each different body site require
s a different modeling strategy as some sites form tight communities easi
ly modeled with Stochastic Block Models whereas others show more diverse
assemblies that require complex latent variable models.
R
elated Links
LOCATION:Seminar Room 1\, Newton Institute
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