Special Topics in Data Science

Algorithms in Computational Biology

Spring 2022

CS 4364/CS 5364 (CRNs 27123/28040)
Instructor Dan DeBlasio Time TR 16:30-17:50
Email dfdeblasio _at_ utep.edu Location Chemistry and Computer Science Building 1.0202
OfficeCCSB 3.1008 and teamsChat.deblasiolab.org Office Hours:TBD
or by appointment (calendly.deblasiolab.org).
Syllabus updated: January 20 2022
Source code for the syllabus and all homework assignments can be found on github and are licensed under Creative Commons (CC-BY-SA-4.0).

We will through the duration of the semester examine common algorithmic solutions to domain specific data science problems, and how to distill computational problems from questions asked in other domains (i.e. computational biology). While the specific applications we will use as examples are in biology, the approaches discussed are applicable to many interdisciplinary fields. That said, this course is self contained and no previous knowledge of biology is needed. The solution techniques include dynamic programming, computational optimization/integer linear programming, and machine learning to name a few.

Some of the specific biological problems to be discussed are:

While these are some of the topics we will discuss they are in no way exhaustive of the field; as with previous versions of the course I am open to suggestions of topics of interest to the students enrolled. The only prerequisite is CS 3 (CS 2302), only the minimum amount of biology will be included to understand the underlying question and the extraction of the computational problem, but it will be self contained and none is expected ahead of time.

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
18 January 2021 (W1T) Introduction Slides
Algorithm Refresher
20 January 2021 (W1R) Linear Programming Welcome Survey
25 January 2021 (W2T) Biology Primer

Useful External Links

Slides:

Homework