Special Topics in Data Science

Algorithms for Computational Biology

Spring 2021

Instructor Dan DeBlasio Time TR 15:00-16:30
Email dfdeblasio _at_ utep.edu Location Online (Zoom, contact instructor for password)
OfficeCCSB 3.1008
online until further notice:
Office Hours:M 2-3pm, R 1-2pm
or by appointment (calendly.deblasiolab.org).
Syllabus updated: January 18 2021

This course will cover the algorithms that make modern computational biology and bioinformatics possible. The plan is to cover both foundational algorithms such as sequence alignment, as well as their modern applications in solving problems such a genome assembly. The focus of this course is on how computer scientists apply their knowledge to frame a computational problem inspired by a specific real-world problem and to solve such computational problems. In addition to standard algorithm development, the course will cover the influence of convex optimization (mainly integer linear programming) and machine learning on computational biology. The course assumes no previous knowledge in biology or genetics. The course will build on and enhance students’ basic understanding of the principle of algorithm design and analysis by applying such principles in the context of bioinformatics.

The topics discussed are likely to include:

CS 2302 is a pre-requisite, please contact the instructor with any questions.

We will use "Algorithms in Bioinformatics" by Wing-Kin Sung[1] as our primary text, but this will be supplemented with other literature soruces that will be provided.

[1] CRC Press, ISBN 9781420070330(Hardcover)/9780367659318(Paperback)

Date Slides Homework Other
19 January 2021 (W1T) Introduction Slides
Algorithm Refresher
21 January 2021 (W1R) Linear Programming Welcome Survey