Tandy Warnow

Associate Head, Department of Computer Science
Special advisor to the Head of Computer Science
Founder Professor of Computer Science
Area Chair, Bioinformatics and Computational Biology Group
Member, Carl R. Woese Institute for Genomic Biology
Affiliate, National Center for Supercomputing Applications
Affiliate, Coordinated Sciences Laboratory
Affiliate, Unit for Criticism and Literary Theory
Affiliate, departments of Electrical and Computer Engineering, Bioengineering, 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

Research Overview: I am a computer scientist, data scientist, and applied mathematician (in equal measures). 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.

I am looking to hire 2 postoctoral researchers! If you are a strong researcher with prior experience in algorithm design and analysis, please see this page.

Brief Biosketch and Full CV

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

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.

I dedicated the book to my PhD advisor Gene Lawler, who died in 1994; see this memorium (published in the Journal of Computational Biology, 10 Jun 2009) that I co-authored with Dan Gusfield, David Shmoys, and Jan Karel Lenstra about Gene.

Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, published by Springer. This book is a Festschrift for Bernard Moret, who retired from EPFL in December 2016. The book contains a collection of self-contained chapters that can be used for an advanced course in computational biology and bioinformatics.

Research Positions Available: I have openings in my group for graduate students (PhD or MS) and postdocs 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 a graduate student, please read this first and then contact me.
If you are an undergraduate, please see this page.
If you are looking for a postdoc position, see this.

Current Funding:

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 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.

Recent NSF funding has supported work in phylogenomics, described here. This is still an area of very active research in my group. I also recently benefited from support of the John P. Simon Guggenheim Foundation, and earlier support from the David and Lucile Packard Foundation, the Radcliffe Institute for Advanced Study at Harvard University, the Program for Evolutionary Dynamics at Harvard University, and Microsoft Research, New England. The Founder Professorship is funded through the Grainger Engineering Breakthroughs Initiative, which is supporting development of research in Big Data and Bioengineering at UIUC. I am grateful to the National Science Foundation for its continuous support since 1994. See this page for completed projects funded by NSF, starting in 2001.

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 149 and h-index 62).

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

Publications Complete vita and publication list Software and research data Guidelines for reading and writing scholarly papers Seminar Talks (2015-present) My F1000 recommendations Ethics in science Academic Integrity REU in Computational Phylogenetics

Contact info

Elegant swimwear and other clothing (from Amaio) and my favorite kimonos!