Tandy Warnow Associate Head, Department of Computer Science Special advisor to the Head of Computer Science Founder Professor of Computer Science Member, 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; Evolution, Ecology, and Behavior; Entomology; and Plant Biology. Fellow of the ISCB (International Society for Computational Biology), 2017 Fellow of the ACM (Association for Computing Machinery), 2015 PhD (Mathematics) University of California at Berkeley, 1991 B.S. (Mathematics) University of California at Berkeley, 1984 biosketch Wikipedia page Google Scholar page

News:

• I contributed to a paper about 1 Billion Years of Green Plant Evolution, published in Nature by the One Thousand Plant Transcriptomes Initiative. (PDF)
• I published a bibliometrics paper in Quantitative Science Studies, published by MIT press, in which we identify model misspecification as a problem for a prior publication published in Science.
• I will hold a 2020 Phylogenomics Software Symposium, January 3, 2020, at the SSB Standalone Meeting, Systematics in the Swamp.

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 several allocations.

I am seeking new grad students available: 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 interested in working with me, you should take my graduate course CS 581: Algorithmic Genomic Biology which I will teach in Spring 2020.

Interested in working with me?

• 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.

Postdoc positions at UIUC Computer Science. These are flexible postdocs that can be used with anyone in the CS department. If you want to teach, then these positions will be funded 50% by the department and 50% by the research faculty mentor. In exchange for departmental funding, these postdocs will teach 1 course per year, based on department needs and the candidate's interest; if the candidate wants to teach more, they will have the opportunity to do so.

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.

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.

"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).

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 Postdoc opportunities

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 Data Science Institutes

Contact info

Elegant swimwear and other clothing (from Amaio)