Associate Head, Department of Computer Science
Fellow of the ISCB (International Society for Computational Biology), 2017
I am a computer scientist, data scientist,
and applied mathematician (in equal measures).
My research combines
mathematics, computer science,
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,
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
who died in 1994; see
(published in the Journal of Computational Biology,
10 Jun 2009)
that I co-authored
with Dan Gusfield, David Shmoys, and Jan Karel Lenstra
Bioinformatics and Phylogenetics:
Seminal Contributions of Bernard Moret, published by
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.
"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).
Elegant swimwear and other clothing (from Amaio)