PIMS-VanBUG Seminar: Dr. Katherine Pollard
Topic
Quantifying taxonomic and functional diversity of metagenomes from next-generation sequencing data
Speakers
Details
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.
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.
Additional Information
The seminar will be held at the Gordon and Leslie Diamond Family Theatre at the BC Cancer Agency Research Center, 600 W 10th Ave., Vancouver.
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
Dr. Katherine Pollard
(UC San Francisco, http://docpollard.com/katie.html)
