Predicting preterm birth from the vaginal microbiome: a case study in reproducible research.

Oct 2

Friday, October 2, 2015

12:00 pm - 1:00 pm
Gross Hall 330


Susan Holmes, Stanford University

LUNCH SEMINAR only today! Abstract: This talk will show an of reproducible research we performed to predict preterm birth using data from a longitudinal analysis of vaginal microbiome. A multiplicity of choices and lack of consistent documentation at each stage of the sequential processing pipeline for the microbiome can lead to spurious results. We propose its replacement with reproducible and documented iterations using R packages knitr, phyloseq, ggplot2, ade4 and lme4. We were able to find specific microbial biomarkers of preterm birth which were validated on a separate set of patients. This is joint work with Ben J Callahan, PJ McMurdie and David Relman's lab. to meet with Professor Holmes, contact