Date	Speaker	Title and Abstract
April 5th	Bonnie Kirkpatrick Computer Science University of British Columbia	TBA
February 2nd	Wyeth Wasserman Centre for Molecular Medicine and Theraputics Child and Family Research Institute University of British Columbia	MeSH Over-representation Profiles (MeSHOPs): Generation and applications of quantitative annotation vectors for biological entities Abstract: A key challenge in computational biology is the transfer of literature-based knowledge into formats suitable for large-scale computation. Challenges range from the implementation of controlled vocabularies and ontologies to expert curation of knowledge repositories. While domain-focused efforts offer the greatest resolution, annotation providing broad coverage across biomedical research could facilitate the creation of algorithms of wide utility. In this lecture I will introduce MeSH Overrepresentation Profiles, which build on decades of curator-assigned keywords attached to biomedical abstracts in the Medline database. Given a set of articles sharing reference to a common entity, one can generate an annotation vector describing the curator keyword assignments over-represented within the set. An entity may be any object or concept for which a group of articles can be defined, such as a disease, gene, drug or author. Metrics are explored for the quantitative comparison of any two MeSHOPs, and the methods are extended for the prediction of entity-entity relationships. The computational challenges of comparing vast numbers of MeSHOPs are discussed. The research to be described was performed with Warren Cheung and B.F. Francis Ouellette.
December 1st	Paul Pavlidis Centre for High-Throughput Biology (CHiBi) University of British Columbia	The challenge of interpreting gene lists in the face of multifunctionality Abstract: In functional genomics, prior knowledge of gene function is used in numerous contexts, both in 'manual' analyses and in computational approaches. This includes "guilt-by-association" approaches to predicting function and "set enrichment" analyses used to interpret gene lists. I will describe recent investigations into the effect gene multifunctionality plays in such analyses, concluding that many analyses are dominated by its impact. I will first define multifunctionality and explain its general importance. I will then briefly review published and unpublished work on the correlation between network node degree and multifunctionality. Finally, I will describe unpublished findings on the the impact of highly multifunctional genes on "enrichment" analyses.
October 6th	Nicolas Lartillot Department of Biochemistry, University of Montreal	Reconstructing rates, traits and dates. Towards integrated models of macroevolution. Abstract: Estimating divergence times, understanding molecular evolutionary mechanisms, or testing macroevolutionary hypotheses about patterns of diversification and morphological evolution, are usually considered as separate research questions, addressed by distinct, although overlapping, scientific communities. Yet, many connections would deserve to be made between these various topics in evolutionary sciences. As a first step towards integrated macroevolutionary modeling, we recently introduced a method for jointly estimating divergence times, substitution rates, life-history traits, and correlations between them, along phylogenies. The framework is a fusion between classical codon models, relaxed molecular clocks, and comparative independent-contrast methods, and works by conditioning a probabilistic model simultaneously on a codon sequence alignment and on a matrix of quantitative characters such as morphological data or life-history traits.As an application of the method, we will present a reconstruction of body size, substitution rate, dN/dS and GC content at the scale of placental mammals. Our analysis confirms classical predictions of the nearly neutral theory concerning generation time and population size, while supporting the hypothesis of small and fast-reproducing ancestors with large populations for most mammalian orders, and suggesting the existence of systematic trends in body-size evolution. Reference: Lartillot N and Poujol R, 2011. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Molecular Biology and Evolution, 28:729. Software Download Work in collaboration with Frédéric Delsuc, Raphael Poujol and Nicole Uwimana.