Sep - Katherine Pollard¶
Speaker: Katherine Pollard
PIMS-sponsored speaker
Talk Title: Quantifying taxonomic and functional diversity of metagenomes from next-generation sequencing data
Date/Time:
Thursday, September 13th, 2012, 6:00 pm
Affiliation: Associate Investigator – Gladstone Institutes
Associate Professor – Department of Epidemiology & Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences
University of California, San Francisco
URL: Pollard Group
Abstract:
Analysis of shotgun sequenced environmental DNA, known as metagenomics, promises insight into the taxonomic and functional composition of microbial communities. To overcome challenges associated with the fragmentary, non-overlapping nature of metagenomic sequence data, we developed novel statistical phylogenetic methods for de novo identification of operational taxonomic units (OTUs) and operational protein families (OPFs). To test the performance of these and other metagenomics analysis tools, we developed read-based error detection methods and a simulation pipeline. Two key features of our approach are the use of probabilistic models of gene family evolution (e.g., profile hidden Markov models and stochastic context free grammars) and the generation of phylogenetic trees in which each leaf is a metagenomic sequencing read from a particular gene family. We applied our analysis tools to identify novel bacteria and to quantify the diversity of microbial communities from the world’s oceans and the human gut.
Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC
Recommended Readings
Microbial community profiling for human microbiome projects
Environmental Shotgun Sequencing
Introductory Speaker: Luisa Chan, MSc candidate, Brinkman Lab, Simon Fraser University
Title: Whole-genome transcriptome analysis of 5’-triphosphate and 5’-monophosphate RNAs in Pseudomonas aeruginosa strain PAO1