Special advisor to the Head of Computer Science, 2016-present
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
Fall 2019 course, CS 581: Algorithmic Computational Genomics: Please consider taking this class if you are a graduate student with strong mathematical training and are interested in potentially doing research in algorithm design and implementation, with an application to biology or linguistics. No background in biology or linguistics is needed -- seriously! This 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, at least one student in the course has done a project that was subsequently published in scientific conferences and journals; you can be one of these students! For examples of these papers, see Mirarab et al., Bioinformatics 2014, Zimmermann et al., BMC Genomics 2014, Davidson et al., BMC Genomics 2015, Chou et al., BMC Genomics 2015, Vachaspati and Warnow, BMC Genomics 2015, Nute and Warnow, BMC Genomics 2016, Christensen et al., Algorithms for Molecular Biology 2018, and Pattabiraman and Warnow, ACM-BCB 2018.
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 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
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.
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.
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.
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 146 and h-index 61).