Colloquium Details
Boosting biological discovery through phylogenomics
| Author: | Kimmen Sjölander University of California, Berkeley |
|---|---|
| Date: | February 05, 2009 |
| Time: | 15:30 |
| Location: | 220 Deschutes Hall, University of Oregon |
| Host: | John Conery |
Abstract
Phylogenomic methods - integrating genome information and phylogenetic reconstruction -- are used for both the inference of species phylogenies and for the prediction of gene function. In this talk, I will discuss the explicit use of evolution as a fundamental principle in bioinformatics, using machine learning methods in combination with evolutionary models to improve the power and specificity of a number of bioinformatics tasks. I will present new methods from my group for multiple sequence alignment, phylogenetic tree construction, ortholog identification, protein structure prediction and prediction of protein active site and specificity residues. I will also present our PhyloFacts Phylogenomic Encyclopedias that we provide as a resource to the scientific community. PhyloFacts includes pre-calculated phylogenies for over 56K protein families and structural domains, with over 1.4M hidden Markov models for classification of new sequences to functional families and subfamilies. PhyloFacts is available at http://phylogenomics.berkeley.edu/phylofacts/.
Biography
Dr. Kimmen Sjölander is an Associate Professor at UC Berkeley, where she is a faculty member in the Department of Bioengineering and the Department of Plant and Microbial Biology. She received her B.A. and Ph.D. in Computer Science from UC Santa Cruz. She is known for her work with David Haussler and others as pioneers in the use of Hidden Markov Models for sequence alignment and the analysis of protein structure. Her current interests in bioinformatics include methods for phylogenetic tree reconstruction, remote homolog recognition, protein structure prediction, subfamily classification, prediction of critical positions in molecules, multiple sequence alignment, protein-protein interaction, pathway inference, computational prediction of protein domain structure, and other aspects of protein function and structure. She is the head of the Berkeley Phylogenomics Group http://phylogenomics.berkeley.edu/