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Vancouver Bioinformatics User Group (VanBUG) » archive for October, 2017

 Laura Parfrey

Talk Title:
“Microbial community assembly on seaweeds and seagrasses”

Date/Time:
Thursday, Nov. 9, 2017 6:00pm

Affiliation:
Assistant Professor, University of British Columbia

Web-site: Laura Parfrey

Abstract:
Multicellular marine organisms host diverse collections of microbes (bacteria, protists, and others) on their surface and within their tissues. These microbes are integral to the biology of the host, playing key roles in defense, development, and nutrient acquisition. Yet, we do not understand basic parameters of community assembly and dynamics on marine hosts. For example, is there a core microbiota for each species that performs essential functions? Are microbial taxa species-specific, or are they broadly shared across seaweed species? We surveyed the epibiotic communities of bacteria and protists living on 35 sympatric species of seagrass and seaweed in the nearshore environment along the central coast of British Columbia. By sampling multiple replicates for each species and the environmental pool of microbes from the water column and biofilms we are able determine which microbes are 1) characteristic of host species, 2) broadly distributed across seaweeds and seagrass, and 3) transients from the environment. We show that bacteria are much more likely to be specific to a host species, while protists are broadly distributed across seaweeds and seagrasses. These results suggest that community assembly and co-evolutionary history differ for protists and bacteria on marine hosts.

Bio:
Dr. Laura Parfrey is an Assistant Professor in Botany and Zoology at the University of British Columbia. Research in the Parfrey lab focuses on the microbial ecology of eukaryotic microbes (protists) and their interaction with bacteria. We work in two distinct ecosystems: the mammalian gut and coastal ecosystems. Along coastal British Columbia we are investigating how water column and biofilm microbes colonize marine hosts (invertebrates, seaweed, and sea grass), and how these host-associated microbes impact host and ecosystem health. Laura is fascinated by microbial diversity and enjoys exploring many facets of our microbial world. She got her scientific start investigating the eukaryotic tree of life and carries this phylogenetic perspective into all aspects of research.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 5:00-5:45pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings

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Introductory Speaker:
Jasleen Grewal (PhD Student, Dr. Steven Jones’ lab, BC Cancer Agency’s Genome Sciences Centre)

Title:
“Using machine learning to identify the site of origin of metastatic cancers”

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Webcast Link:
http://vidyoreplay.computecanada.ca/replay/webcastShow.html?key=TAKdbjoDvIqKdLn
(This technology is brought to you by Compute Canada and WestGrid with support from PHSA Telehealth)






 Lior Pachter

Talk Title:
“What do we mean by differential expression?”

Date/Time:
Thursday, Oct. 12, 2017 6:00pm

Affiliation:
Professor of Computational Biology and Computing and Mathematical Sciences, Caltech

Web-site: Lior Pachter
Twitter: @lpachter

Bio:
Lior Pachter received a B.S. in Mathematics from Caltech in 1994, then went to MIT where he was awarded a PhD in applied mathematics in 1999. He then moved to the University of California at Berkeley where he was a postdoctoral researcher (1999-2001), assistant professor (2001-2005), associate professor (2005-2009), and until 2017 the Raymond and Beverly Sackler professor of computational biology and professor of mathematics and molecular and cellular biology with a joint appointment in computer science. Since January 2017 he has been the Bren professor of computational biology at Caltech.
His research interests span the mathematical and biological sciences, and he has authored over 100 research articles in the areas of algorithms, combinatorics, comparative genomics, algebraic statistics, molecular biology and evolution. He has taught a wide range of courses in mathematics, computational biology and genomics. He has also been awarded a National Science Foundation CAREER award, a Sloan Research Fellowship, the Miller Professorship, and a Federal Laboratory Consortium award for the successful technology transfer of widely used sequence alignment software developed in his group.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 5:00-5:45pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings

——————————

Introductory Speaker:
Shaun Jackman (PhD Candidate, BC Cancer Agency Genome Sciences Centre, Inanc Birol’s Lab)

Title:
“Assembling genomes using 10x Genomics linked reads”

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Webcast Link:
http://vidyoreplay.computecanada.ca/replay/webcastShow.html?key=TAKdbjoDvIqKdLn
(This technology is brought to you by Compute Canada and WestGrid with support from PHSA Telehealth)