News:

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?

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:

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.

"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).




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REU in Computational Phylogenetics

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