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Vancouver Bioinformatics User Group (VanBUG) » archive for September, 2012

 Katherine Pollard

PIMS-sponsored speaker

Download Seminar Poster PDF

Talk Title:
Quantifying taxonomic and functional diversity of metagenomes from next-generation sequencing data

Thursday, September 13th, 2012, 6:00 pm

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

Pollard Group

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

Whole-genome transcriptome analysis of 5’-triphosphate and 5’-monophosphate RNAs in Pseudomonas aeruginosa strain PAO1