Research Statement

I work on evolutionary history methodology and algorithms in Biology and 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 (see this page for some discussion about our 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).
• The analytical study of convergence rates of different methods, and the development of provably fast converging methods.
• Computational phylogenetics in historical linguistics (see also this write-up at NSF, and this page). (On March 21, 2005, Harvard University sponsored a workshop on this topic, which Jay Jasanoff and I co-organized; see this page for more information, and click here for a poster of the workshop.)