Research Statement

I work on evolutionary history methodology and algorithms in Biology and Historical Linguistics. See my lab webpage for additional information about the biological research, and the Computational phylogenetics in historical linguistics project for the more details about the work in historical linguistics.

My recent work focuses on five major issues, all related to evolutionary history reconstruction:

• New algorithms for simultaneous reconstruction of a phylogeny and multiple sequence alignment. This work is funded by an ATOL (Assembling the Tree of Life) grant from the National Science Foundation, and includes collaborations with the University of Georgia, The University of Kansas, and The University of Nebraska. See this page for more on this approach.
• Fast techniques for NP-hard optimization problems, such as maximum likelihood and maximum parsimony. Our research project has produced a very powerful technique called "Rec-I-DCM3" for dramatically speeding up even the best of the current heuristics for maximum parsimony on large dataset analyses.
• The inference of complex evolutionary histories. In this area, I have focused on the inference of evolution from whole genomes, and the detection and inference of reticulate evolution (i.e., horizontal gene transfer and/or hybridizing speciation). In the contet of whole genome evolution, I work with Bernard Moret of EPFL. For reticulate evolution, I work with Luay Nakhleh of Rice University.
• The analytical study of the sequence length requirements (also known as convergence rates) of different phylogenetic estimation methods, and the development of provably fast converging methods.
• Computational phylogenetics in historical linguistics. This work was funded by an ITR grants from the National Science Foundation, and is a collaboration with Donald Ringe at the University of Pennsylvania. We are developing mathematical models for how languages evolve, software for estimating trees and networks from data (lexical, morphological, and phonological) gathered for the languages. See also this write-up at NSF, and this page.