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Abstract
For over 3.5 billion years microorganisms have evolved to solve complex metabolic problems at the individual, population and community levels of biological organization, innovating distributed solutions to nutrient and energy conversion processes that have fundamentally transformed the surface chemistry of the earth and generated a deep reservoir of genomic diversity. Over the past decade, high-throughput sequencing and mass spectrometry platforms have transformed our perception of this microcosmos, illuminating microbial dark matter and conceptually linking microbial interactions to a wide range of ecosystem functions and services. Here, I explore problems and solutions in microbial sequence analysis spanning different levels of biological organization along defined redox gradients in the ocean. I highlight emerging open source tools for integrating and visualizing multi-omic (DNA, RNA, protein and metabolite) and environmental parameter data and consider the future of data intensive computation and environmental sensing as it relates to pathway reconstruction, predictive modeling and synthetic ecology in a time of climate change.
Bio
Dr. Steven Hallam is a University of California Santa Cruz and MIT trained molecular biologist, microbial ecologist, entrepreneur, and innovator with over 20 years of experience in field and laboratory research. He is a Professor in the Department of Microbiology and Immunology and a Leopold Leadership Fellow. He is also a program faculty member in the Bioinformatics and Genome Sciences and Technology training programs at UBC. Dr. Hallam co-directs the ECOSCOPE innovation ecosystem consisting of an NSERC CREATE training program, a research network, the Biofactorial core facility for high-throughput screening and a curriculum development initiative in data science (EDUCE) based on four research and training pillars: i) microbial ecology, ii) biological engineering, iii) data platforms, and iv) networking and entrepreneurship. His research intersects these program pillars with specific emphasis on the creation of functional screens and computational tools that reveal hidden metabolic powers of uncultivated microbial communities. His laboratory has developed MetaPathways, a modular annotation and analysis pipeline to predict metabolic interactions from microbial sequence information. Other research areas include single-cell genome sequencing and biosensor development for environmental monitoring and high-throughput enzyme discovery. He is the co-founder of Koonkie Inc., a bioinformatics consulting company that designs and provides scalable algorithmic and data analytics solutions in the cloud.
For more information visit:
URL: http://hallam.microbiology.ubc.ca/
URL: http://ecoscope.ubc.ca
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