Computational Biology and Computational Historical Linguistics Research: If you are interested in exploring research in computational biology or historical linguistics, please get in touch with me; there is space in my lab for one or two more students at this time. To join the group, you should take my graduate class CS 394C, but you are also encouraged to attend my weekly research group (time to be determined).

My research focuses on the development of mathematical models and algorithms for estimating evolutionary history in Biology and Historical Linguistics. The main objective is to develop methods that produce much more accurate estimations of evolutionary history than can be obtained using existing tools. Our group is distinguished from many other groups in computational biology due to our focus on ultra-large datasets (anywhere from 10,000 to 1,000,000 sequences). We use real data and perform simulations to evaluate the performance of methods that we develop. This research area inolves mathematics, probability, statistics, computer science, and intensive collaborations with domain specialists. My current research is funded by the National Science Foundation (DEB 0733029 and DBI-1062335). I also recently benefited from support of the John P. Simon Guggenheim Foundation.

"Plus de détails, plus de détails, disait-il à son fils, il n'y a d'originalité et de vérité que dans les détails..." -- Stendhal, Lucien Leuwen (a quote much loved by my stepfather, Martin J. Klein, and an essential guide for all scholarship).

I am one of the organizers of a programme on Mathematical, Statistical and Computational Aspects of the new science of Metagenomics, to be held from 24 March to 17 April, 2014, at the Sir Isaac Newton Institute for Mathematical Sciences at Cambridge University, UK.

My research project has held annual Symposia and Software Tutorials on computational phylogenetics and phylogenomics, and expects to hold one more in 2014 (probably co-located with the Evolution 2014 meeting in Raleigh, North Carolina). For the most recent symposium and workshop, please see the webpages for the Symposium and Workshop on New Methods for Phylogenomics and Metagenomics, that was held at UT-Austin on Feb 16 and 17, 2013.

Click here for Google Scholar Citations (i10-index 95 and h-index 43).

The CIPRES Project is finally over, but the CIPRES Portal is still available through the TeraGrid. For an abridged version of our final report, see this. The CIPRES Science Gateway, story. I am on leave for the 2012-2013 academic year, and will return in August 2013. My (tentative) schedule for the Fall 2013 semester will be:

Siavash Mirarab, my PhD student, has been awarded a fellowship by the Howard Hughes Medical Institute.

Collaborations

My students and I are actively working on developing new methods for estimating alignments and trees (both gene trees and species trees), as well as for taxon identification of metagenomic data. We are currently working with three international research projects, two involved with estimating the Avian phylogeny, and also the Thousand Transcriptome Project (1KP), using our methods to estimate alignments and trees on individual genes, and to estimate species trees from these multi-marker datasets. We welcome collaborations with biologists who have data that are difficult to analyze, either because the datasets are too large for current methods, or because current methods fail to have sufficiently high accuracy.

Teaching (Fall 2013) 


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