Biological Applications of High-Performance Computing in Metagenomics and Metaproteomics
Dr. Chongle Pan
Time: Friday, Nov. 13rd, 2015
Location: Conference Room #755
Human microbiomes and environmental microbial communities drive many important biological processes in their ecosystems. The taxonomic composition and genetic potential of a microbial community can be measured by metagenomics. We developed the Sigma algorithm to identify different strains of microorganisms in a microbial community and find their genomic variations from metagenomic sequencing. A nonlinear programming method was used to solve a maximum likelihood estimation problem in the Sigma probabilistic model. This allowed rigorous assignment of ambiguous reads that can be aligned to multiple genomes. Sigma can be used for metagenomic biosurveillance as demonstrated by the identification of a pathogenic E. coli strain from a fecal sample. We addressed the computational challenge of PTM identification in metaproteomes by using a scalable database searching algorithm, Sipros, and the Titan supercomputer. We found extensive PTMs on enzymes involved in central metabolisms, chemotaxis, and other cellular functions in a model microbial community and uncovered dynamic regulation of these PTMs between two growth stages of this community.
About the Speaker: Dr. Chongle Pan is a staff scientist in the Computer Science and Mathematics Division of Oak Ridge National Laboratory and a joint associate professor in the Department of Microbiology of the University of Tennessee. He is interested in the characterization of microbial communities using integrated omics analyses. His computational research is focused on analysis of big data from metagenomics and metaproteomics measurements with scalable distributed computing. Omics results provide the foundation for studying microbial ecology and evolutionary biology in ecosystems of relevance to global carbon cycling and human health.
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