Ph.D. UC Davis 2004
My primary research involves phylogenomics, which is the combination of two major fields in life sciences: Genomics, i.e. the function and structure of genes and genomes; and Molecular Phylogenetics, i.e., the hierarchical evolutionary relationships among organisms or genes. My work involves a synergy of large-scale computational and statistical problems, due to the sheer size and nature of genomic data.
Computational Biology, Discrete Optimization, Algebraic Statistics
- "Normalizing kernels in the Billera-Holmes-Vogtmann treespace." IEEE/ACM transactions on computational biology and bioinformatics (2016): Details. Full text
- "Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes." Molecular biology and evolution 33, 6 (2016): 1618-24. Details. Full text
- "kdetrees: Non-parametric estimation of phylogenetic tree distributions." Bioinformatics (Oxford, England) 30, 16 (2014): 2280-7. Details. Full text
- "Late removal of titanium hardware from the elbow is problematic." ISRN orthopedics 2012, (2012): 256239. Details.
- "Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope." Bulletin of mathematical biology 73, 11 (2011): 2627-48. Details. Full text
- "Experiments with the site frequency spectrum." Bulletin of mathematical biology 73, 4 (2011): 829-72. Details. Full text
- "Statistical phylogenetic tree analysis using differences of means." Frontiers in neuroscience 4, (2010): Details. Full text
- "Statistical Analysis on Detecting Recombination Sites in DNA-β Satellites Associated with Old World Geminiviruses." Frontiers in psychiatry 1, (2010): 138. Details. Full text
- "On the optimality of the neighbor-joining algorithm." Algorithms for molecular biology : AMB 3, (2008): 5. Details. Full text
- "Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates." Molecular biology and evolution 23, 3 (2006): 491-8. Details. Full text
- "Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci." PLoS genetics 9, 2 (0): e1003323. Details. Full text