Tandy Warnow Founder Professor of Computer Science, and Associate Head of CS Area Chair, Bioinformatics and Computational Biology Group Member, Institute for Genomic Biology, Biocomplexity Theme National Center for Supercomputing Applications Affiliate in the departments of Electrical and Computer Engineering, Mathematics, Statistics, Animal Biology, Entomology, and Plant Biology PhD (Mathematics) University of California at Berkeley, 1991 B.S. (Mathematics) University of California at Berkeley, 1984

Brief Biosketch

Fellow of the ISCB (International Society for Computational Biology), 2017
Fellow of the ACM (Association for Computing Machinery), 2015: For contributions to mathematical theory, algorithms, and software for large-scale molecular phylogenetics and historical linguistics

Teaching awards: I am on the 2017 list and 2018 list of teachers ranked as excellent by their students for CS 581 (2017 and 2018) and CS 466 (2017).

Phylogenomics Software Symposium 2018: We will hold a symposium on new computational methods in phylogenomics on August 17, 2018, in Montpellier, France. Please see this page for more information. Travel awards will be available.

Research Overview: My research combines mathematics, computer science, probability, and statistics, in order to develop algorithms with improved accuracy for large-scale and complex estimation problems in phylogenomics (genome-scale phylogeny estimation), multiple sequence alignment, metagenomics, and historical linguistics. I am a big fan of Blue Waters, and have benefitted from two allocations. Click here for the 2017 annual report for my Blue Waters allocation on algorithms for big data phylogenomics, proteomics, and metagenomics. Click here or here for more about my research and the students I work with, and here for a brief biosketch.

Computational Phylogenetics: An introduction to designing methods for phylogeny estimation, published by Cambridge University Press (and available for purchase at Amazon and as an E-book at Google Play). Errata are posted as I find them. The image of the Monterey Cypress is there because of the NSF-funded CIPRES project, whose purpose was to develop the methods and computational infrastructure to improve large-scale phylogeny estimation. Why I wrote this book.

Fall 2018, CS 581: Algorithmic Computational Genomics

CS 581 is a course on applied algorithms, focusing on the use of discrete mathematics, graph theory, probability theory, statistics, machine learning, and simulations, to design and analyze algorithms for phylogeny (evolutionary tree) estimation, multiple sequence alignment, genome-scale phylogenetics, genome assembly and annotation, and metagenomics. Each of these biological problems is important and unsolved, so that new methods are needed. Hence, this course will provide opportunities for computer scientists, mathematicians, and statisticians, to do original and important research that can have an impact on biology. Every year, two or more students from this course have done final projects that were subsequently published in major scientific journals; you can be one of them! For more about the course, see the course website for Spring 2018; Fall 2018 will be similar.

Research Positions Available: If you are an undergraduate seeking a research position, please see this page. I have openings in my group for graduate students (PhD or MS) to work on developing computational methods for large-scale multiple sequence alignment, phylogeny estimation, metagenomics, and even historical linguistics. Strong programming skills, mathematical intuition, and interest in collaboration are necessary. If you are already a graduate student at UIUC, please contact me directly. If you are interested in applying to UIUC for graduate school and would like to work with me, please read this first and then contact me. Unfortunately, I do not have any funding available for postdoctoral researchers. However, if you have your own source of funds and have published papers directly related to my research, I'll be glad to talk with you about working together.

Current NSF Funding: My research in currently funded by three grants from the National Science Foundation.

• Multiple sequence alignment, funded by NSF grant ABI-1458652, beginning August 2015. This project will develop new methods for multiple sequence alignment, building on our SATé, PASTA, and UPP methods.
• Metagenomics, funded by NSF grant III:AF:1513629. This is a collaborative grant with the University of Maryland, for new methods for metagenomic dataset analysis, building on our TIPP method for taxon identification of reads in a metagenomic sample.
• Graph-Theoretic Algorithms to Improve Phylogenomic Analyses, funded by NSF grant CCF-1535977. I am the overall PI, and this project is collaborative with Satish Rao (UC Berkeley PI) and Chandra Chekuri (UIUC). We are developing new theoretical computer science and discrete algorithms for improving the estimation of large species and gene trees, and specifically enabling statistical methods to scale to ultra-large datasets.

A day in the life of an SRO at NIH (not by me)

"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).

Click here for Google Scholar Citations (i10-index 142 and h-index 58).

For prospective students and postdocs Current and former students and postdocs Teaching Recent Symposia and Software Schools CIPRES Personal Conference Calendar News Articles

Downloadable papers Complete vita and publication list Software Research data from UT-Austin Guidelines for writing scholarly papers Seminar Talks (2015-present) My F1000 recommendations

Contact info

My favorite Kimonos!