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Vancouver Bioinformatics User Group (VanBUG) » archive for February, 2013

 Art Poon

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Presentation:
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Talk Title:
Reconstructing the evolution of HIV within a patient

Date/Time:
Thursday, March 7th, 2013, 6:00 pm

Affiliation:
Assistant Professor (Partner) – UBC Department of Medicine
Associate Research Scientist, British Columbia Centre for Excellence in HIV/AIDS
Adjunct Assistant Professor – Simon Fraser University, Faculty of Health Sciences

URL:
Art Poon

Abstract:
HIV evolves very rapidly because it makes frequent errors as it copies its genome to produce new viruses. For this reason, it has been difficult to develop an effective anti-HIV vaccine, as the incoming HIV genome can look very different from one infection to another. The rapid mutation of HIV genomes also causes an infection to proliferate into a highly diverse population within a single patient, and enables the virus to escape the immune system. Recent innovations in genome sequencing technology (known as “next-generation sequencing”) are providing us with the tools necessary to grapple with the extensive variation of HIV. However, the massive size and complexity of these sequence data presents a new bioinformatic challenge to HIV biologists. In my research, I am developing new software tools to extract key information from next-generation sequencing data to address critical problems in HIV treatment and prevention. I will show how these data can be used to determine when a patient became infected by HIV, what the initial HIV genome looked like, and how we can reconstruct a detailed history of how an infection has evolved over time.

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

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Introductory Speaker:
Matthew Whiteside, PhD candidate, Brinkman Lab, Simon Fraser University

Title:
Improving the Performance of Computational Ortholog Prediction






 Bonnie Kirkpatrick

Download Seminar Poster PDF

Presentation:
Download PresentationPDF

Talk Title:
Biological Models with Combinatorial Spaces

Date/Time:
Thursday, February 7th, 2013, 6:00 pm

Affiliation:
Postdoctoral Researcher at University of British Columbia

URL:
Bonnie Kirkpatrick

Abstract:
Probabilistic models are common in biology. Many of the successful models have been readily tractable, leaving calculations on models with a combinatorial-sized state space as an open problem. This talk examines two kinds of models with combinatorial state spaces: continuous-time and discrete-time Markov chains. These models are applied to two problems: RNA folding pathways and family genetics. While the applications are disparate topics in biology, they are related via their models, the statistical quantities of interest, and in some cases the computational techniques used to calculate those quantities.

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

——————————

Introductory Speaker:
Gavin Ha, PhD candidate, Shah Lab, BC Cancer Research Centre

Title:
Probabilistic approach to detect subclonal copy number and LOH from heterogeneous cell populations in whole genome sequencing of tumour biopsies