| Instructor | Dan DeBlasio | Time | TR 16:30-17:50 |
| dfdeblasio _at_ utep.edu | Location | Chemistry and Computer Science Building 1.0202 | |
| Office | CCSB 3.1008 and teamsChat.deblasiolab.org | Office Hours: | 2-3pm Monday and Tuesday or by appointment (calendly.deblasiolab.org). |
| Syllabus | updated: February 08 2022 |
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 2022 (W1T) | Introduction Slides Algorithm Refresher |
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| 20 January 2022 (W1R) | Linear Programming | Welcome Survey | |
| 25 January 2022 (W2T) | Biology Primer | Homework 1 (due 31 January 2022) Example Solution |
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| 27 January 2022 (W2R) | Sequence Similarity | ||
| 1 February 2022 (W3T) | Sequence Similarity (continued) | Homework 2 (due 14 |
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| 3 February 2022 (W3R) | weather day |
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| 8 February 2022 (W4T) | Sequence Similarity (continued) | updated syllabus to include late homework policy |
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| 10 February 2022 (W4R) | Parametric Alignment | Gusfield Chapter 13 posted on Teams | |
| 15 February 2022 (W5T) | Suffix Trees | in class: activity No office hours 21 Feb 2022 |
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| 17 February 2022 (W5R) | Suffix Trees | Homework 3 (due 23 February 2022) |
Replacement Office Hours: Monday 21 Feb @ 3pm |
| 22 February 2022 (W6T) | Suffix Trees BWT/FM |
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| 24 February 2022 (W6R) | BWT/FM LCS |
Homework 4 (due 7 March 2022) |
Midterm Exam: 10 March 2022 |
| 1 March 2022 (W7T) | Multiple Sequence Alignment | ||
| 3 March 2022 (W7R) | Multiple Sequence Alignment | Spring 2021 Midterm (with solution) |
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| 8 March 2022 (W8T) | Review | ||
| 10 March 2022 (W8R) | Midterm Exam (Solutions) | No Office Hours 21 March 2022 (Monday after SB) |
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| 15&17 March 2022: Spring Break | |||
| 22 March 2022 (W9T) | Project Description | ||
| 24 March 2022 (W9R) | Genome Alignment | Homework 5 (due 30 March 2022) |
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| 29 March 2022 (W10T) | Database Search Hashing |
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| 31 March 2022 (W10R) | Database Search Hashing |
Homework 6 (due |
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| 5 April 2022 (W11T) | Hashing | ||
| 7 April 2022 (W10R) | Phylogenetics | ||
| 12 April 2022 (W11T) | Phylogenetics | Homework 7 (due 18 April 2022) |
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| 14 April 2022 (W11R) | Read Alignment | ||
| 19 April 2022 (W12T) | RNA-Seq Assembly | ||
| 21 April 2022 (W12T) | de novo Assembly | Homework 8 (due 27 April 2022) |
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| 26 April 2022 (W13T) | Biological Networks | Homework 9 (due 9 May 2022) |
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| 28 April 2022 (W13R) | Alignment-Free Genomics | ||
| 3 May 2022 (W14T) | Final Review | updated HW9 with typo: runngin time is O(m^2n) not O(mn^2) | |
| 5 May 2022 (W14R) | Term Paper Presentations | ||