Fall 2021, 9:30 AM to 10:45 AM, 1131 Siebel Center.
Course description: 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. 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!
Who should take this class: The course is designed for graduate students in CS, ECE, Math, and Statistics; no background in biology is required.
Undergraduate students: If you are an advanced undergraduate student (in CS, ECE, Mathematics, Physics, or Statistics) and interested in taking the course, please email me to discuss your qualifications. I generally do not let undergraduate students into the class because this is a research-focused advanced course requiring many different skills (including theorem proving, implementation, analysis of algorithms, scientific literature reviews, etc.). However, if you are sufficiently advanced (preferably a senior with substantial coursework already completed that shows these multitude of skills), serious about the commitment necessary to do this course, and planning to apply for PhD programs, then I may allow you into the class.
Course Textbook: Computational Phylogenetics: An introduction to designing methods for phylogeny estimation, published by Cambridge University Press.