| Instructor | Dan DeBlasio | Time | TR 15:00-16:30 |
| dfdeblasio _at_ utep.edu | Location | Online (Zoom, contact instructor for password) | |
| Office | CCSB 3.1008 online until further notice: teamsChat.deblasiolab.org |
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 |
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| 21 January 2021 (W1R) | Linear Programming | Welcome Survey | |
| 26 January 2021 (W2T) | Biology Primer | ||
| 28 January 2021 (W2R) | Sequence Similarity | ||
| 2 February 2021 (W3T) | Sequence Similarity Continued | Homework 1 | Example Homework Solution |
| 4 February 2021 (W3R) | Sequence Similarity Continued | ||
| 9 February 2021 (W4T) | Parametric Alignment | Alignment exercise (solution) | |
| 11 February 2021 (W4R) | Parametric Alignment | ||
| 16 February 2021 (W5T) | Suffix Trees | Homework 2 | |
| 18 February 2021 (W5R) | Suffix Arrays | ||
| 23 February 2021 (W6T) | BWT & FM-Index | ||
| 25 February 2021 (W6R) | Longest Common Subsequence | Homework 2 Deadline Extended 2 March | Group Activities |
| 2 March 2021 (W7T) | Longest Common Subsequence | Homework 3 | |
| 4 March 2021 (W7R) | Multiple Sequence Alignment |
Extra office hours on 5 March 1:30-2:30pm No office hours 8 March 2021 Alignment Review |
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| 9 March 2021 (W8T) | Multiple Sequence Alignment | Extra office hours on 10 March 11am-12pm | |
| 11 March 2021 (W8R) | Midterm Exam | Practice Midterm (Solution) | |
| 23 March 2021 (W9T) | Genome Alignment | ||
| 25 March 2021 (W9R) | Genome Alignment | Final Project Info | |
| 30 March 2021 (W10T) | Database Search | ||
| 1 April 2021 (W10R) | Database Search (Continued) | Homework 4 (Due 12 April 2021) | |
| 6 April 2021 (W11T) | Hashing and Sketching | ||
| 8 April 2021 (W11R) | Hashing and Sketching (continued) | ||
| 12 April 2021 (W12T) | Phylogenetics | Homework 2 Solution Posted | |
| 20 April 2021 (W13T) | Read Alignment (Reference-based Alignment) | Homework 5 | Thursday Office Hours: 12:30p-1:30p |
| 22 April 2021 (W13R) | RNA-Seq | ||
| 27 April 2021 (W14T) | Guest "Lecture" on de novo assembly Feel free to watch the videos in a group on zoom |
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| 29 April 2021 (W14R) | de novo Assembly | Final Project Due on May 11! (Hard deadline) | |
| 4 May 2021 (W15T) | Alignment Free Genomics |
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| 6 May 2021 (W15R) | Review |