Oscar Westesson

Name: Oscar Westesson Email: oscar.westesson Failed to parse (unknown function "\begin"): \begin{picture}(10,10)\put(5,5){\circle{10}}\put(2,3){$\alpha$}\end{picture} gmail dottt com Berkeley Office: 381D Stanley Hall UCSF: I can usually be found in the Andino wet lab or the Derisi computational room, both at UCSFMissionBay About Oscar I am a bioengineering graduate student interested in computational sequence analysis. I studied mathematics at Univeristy of Rochester and UC Berkeley. Besides computational biology I like climbing, bicycling, harassing my lab-mates, recovering bread, and drinking tea. I used to mostly drink green tea, but in recent years I have shifted towards black tea, especially Chinese teas. Lars Barquist and I keep an impressive selection in the lab, feel free to come by and talk transducers over a cup of Golden Monkey . Though Lars has left, his tea selection remains! I am also a big fan of acronyms, especially inventing and propagating them. If you have any to contribute, please feel free: Acronym List Interests Originally I studied math, and became interested in computational biology during a class with Bernd Sturmfels. I am broadly interested in applying mathematical/statistical/algorithmic tools to analyze biological sequence data, particularly from an evolutionary perspective. I find viruses to be an especially interesting venue for this sort of analysis: their small, absurdly complex/sophisticated genomes demand sophisticated modeling, and they evolve so fast that we can watch their genomes evolve in a laboratory setting. During graduate school I worked on various aspects of viral genomics, modeling recombination, structured RNA, and population mutation distributions. I also worked on more general algorithms for multiple sequence alignment/evolutionary reconstruction and prediction of deleterious SNPs in proteins. My Ph D research is summarized in my dissertation (25MB PDF).

Papers Westesson & Holmes: Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput. Biol. 2009;5:e1000318. Westesson et al.: HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinformatics 2012;28:1170-1. Westesson et al.: Visualizing next-generation sequencing data with JBrowse. Brief. Bioinformatics 2013;14:172-7. Westesson et al.: Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS ONE 2012;7:e34572. Westesson & Holmes: Developing and applying heterogeneous phylogenetic models with XRate. PLoS ONE 2012;7:e36898. Westesson O, Lunter G, Paten B, Holmes I. Phylogenetic automata, pruning, and multiple alignment. arXiv preprint Runckel C, Derisi J, Westesson O. Molecular determinants influencing poliovirus recombination revealed by high resolution mapping. In review at PLoS Pathogens Burrill C, Westesson O, Andino R. Identification of a novel functional structured element in poliovirus using SHAPE. In prep. Westesson O, Holmes I. Accurate prediction of mutational tolerance in proteins. In prep. Ovaskainen et al. A probabilistic heirachical taxonomic classifier with applications to fungus in decaying logs. In prep