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 Steven Hallam

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Talk Title:
Metabolic Interaction Networks for the Whole Community

Date/Time:
Thursday, October 14, 2010, 6:00 pm

Affiliation:
Department of Microbiology and Immunology , University of British Columbia

URL:
Steven Hallam

Abstract:
Environmental genomics captures the diversity and dynamics of naturally occurring microbial communities. The metabolic potential of an organism or community can be inferred from primary sequence information with the aid of computational methods that assemble or cluster contiguous reads, search for patterns or motifs representing genes, and reconstruct metabolic pathways based on known biochemical rules. One of the emerging concepts in environmental genomic data analysis is the distributed nature of metabolic transformations mediated by diverse microbial partners linked together in syntrophic or substrate dependency relationships. Understanding how distributed metabolic networks link microbial activity with biogeochemical cycles has emerged as a fundamental scientific problem guiding the peer efforts of scientists and engineers around the world. Although, new sequencing technologies are rapidly expanding our capacity to explore the microcosm, there are a number of computational and analytical challenges that limit full data utilization and interpretation. Here we explore the development of a novel analytic pipeline that adopts Pathway Tools (http://bioinformatics.ai.sri.com/ptools/ptools-overview.html) to metabolic reconstruction of microbial community interaction networks. Pathway Tools is a reusable, production-quality software environment for creating and managing pathway/genome databases (PGDBs) and predicting metabolic pathway interaction networks for these PGDBs using a highly curated database of metabolic pathways and components representing all domains of life (MetaCyc). Unlike the Kyoto Encyclopedia of Genes and Genomes (KEGG), MetaCyc emphasizes core microbial metabolism including biogeochemically relevant pathways.

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

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Introductory Speaker:
Denil Wickrama, MSc Candidate, Jones Lab, Genome Science Centre, BCCA

Title:
Mapping putative regulatory regions in breast cancer using histone H3K4 mono-methylation in multiple breast cancer cell lines

Presentation:
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