A photo of Victor jumping into the air above Spencer's Butte in the town of Eugene, Oregon.

Victor Hanson-Smith, Ph.D.

EMAIL: victor 'dot' hanson 'hyphen' smith 'at' ucsf 'dot' edu

How do genomes evolve?

My research investigates how genomes evolve, using a computational approach and interdisciplenary collaboration with several molecular biology labs around the world. Specifically, I use mathematical models and simulations to study multiple evolutionary phenomenen, including gene duplication, the evolution of gene regulatory circuits, and the role of natural selection. I have an ongoing interest in the theory and practice of phylogenetic ancestral sequence reconstruction as a means to generate and test hypotheses about specific genetic mechanisms that caused historic changes in cellular function. Overall, my research uses comptuer science to address basic questions in biology, while incorporating aspects of applied mathematics, statistics, and high-performance computing.

Selected Peer-Reviewed Publications



Active Open-Source Software Projects

PhyloBot is a web portal for automated phylogenetics and ancestral protein sequence reconstruction.

M3L is an extended version of PhyML. M3L implements maximum likelihood phylogenetic inference using multidimensional parameter optimization, and supports complex branch length mixture models.

Lazarus is a set of Python scripts wrapping PAML, useful for reconstructing maximum likelihood ancestral state sequences with posterior probability support values. Lazarus extends PAML with an easier-to-use software interface, better support for computational job batching, and implements several post-analysis data analysis tasks.