Victor Hanson-Smith, Ph.D.
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
- V. Hanson-Smith, A.D. Johnson. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories. PLoS Computational Biology, 2016 Jul 29; 12(7).
- D.P. Anderson, D.S. Whitney, V. Hanson-Smith, A. Woznica, W. Campodonico-Burnett, B.F. Volkman, N. King, J.W. Thornton, K.E. Prehoda. Evolution of an ancient protein function involved in organized multicellularity in animals. eLife, 2016 Jan 7; 5:e10147
- C.J. Howard, V. Hanson-Smith, K.J. Kennedy, C.J. Miller, H.J. Lou, A.D. Johnson, B.E. Turk, L.J. Holt. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. eLife, 2014 Oct 13;3. doi: 10.7554/eLife.0412
- Perez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD. How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes. Genes Dev., 2014 Jun 15;28(12)
- C.R. Baker, V. Hanson-Smith, and A.D. Johnson. Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science, October 2013.
- A.H. Yona, Z. Bloom-Ackermann, I. Frumkin, V. Hanson-Smith, Y. Charpak-Amikam, Q.H. Feng, J.D. Boeke, O. Dahan and Y. Pilpel. tRNA genes rapidly change in evolution to meet novel translational demands. eLife, e01339 (2013).
- C. Merz, J.M. Catchen, V. Hanson-Smith, K.J. Emerson, W.E. Bradshaw, C.M. Holzapfel. Replicate Phylogenies and Post-Glacial Range Expansion of the Pitcher-Plant Mosquito, Wyeomyia smithii, in North America PLos One, September, 2013.
- M.B. Lohse, A.D. Hernday, P.M. Fordyce, L. Noiman, T.R. Sorrells, V. Hanson-Smith, C.J. Nobile, J.L. Derisi, A.D. Johnson. Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. Proceedings of the National Academy of Sciences, May, 2013.
- G.C. Finnigan, V. Hanson-Smith, T.H. Stevens, and J.W. Thornton. Evolution of increased complexity in a molecular machine. Nature, January 2012.
- G.C. Finnigan, V. Hanson-Smith, B.D. Houser, H.J. Park, and T.H. Stevens. The reconstructed ancestral subunit a functions as both V-ATPase isoforms vph1p and stv1p in S. Cerevisiae. Molecular Biology of the Cell, July 2011.
- V. Hanson-Smith, B. Kolaczkowski, and J.W. Thornton. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Molecular Biology and Evolution, April 2010.
- V. Hanson-Smith. Error and Uncertainty in Computational Phylogenetics. University of Oregon, 2011.
- Ph.D. Computer and Information Science, University of Oregon, 2011
- M.S. Computer and Information Science, University of Oregon, 2007
- B.S. Computer Science, Seattle University, 2003
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.