Victor Hanson-Smith :: Science
I am a postdoctoral scholar in Alexander Johnson's lab at UCSF. I recently completed my PhD from the Department of Computer and Information Science at the University of Oregon. My PhD work was primarily conducted in Joe Thornton's lab, in the Center for Ecology and Evolutionary Biology. I have recently been funded through an NSF IGERT grant for interdisciplinary studies in evolution, development, and genomics.
Understanding how living systems evolve is necessary to solve many of the grandest challenges confronting humans. Although contemporary problems -- including retroviruses and global climate change -- may seem unrelated, they in fact share many similar causes: in both cases, genomic systems evolved -- and continue to evolve -- as a consequence of evolutionary drift and changing selective pressures. We can learn how these systems function (and how they malfunction) by studying their evolution.
I am specifically interested in how the genomic architectures are sculpted by evolution, in the context of overall cellular systems, populations, and environments. How do transcription regulatory re-wiring events constrain or enable the evolution of new physiological forms? How do complex molecular machines evolve from simpler ancestral forms? What evolutionary steps are neccessary to create new modes of DNA-binding and ligand-binding specificity? How do populations of genomes evolve in response to new environmental constraints?
PhyESTA is an extended version of PhyML. PhyESTA 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.
I co-author the blog titled "Evolution, Development, and Genomics."
CONTACT :: mail at VictorHansonSmith dot com