Instructor: Shaojie Zhang
Lectures: T/Th 4:30-5:45 pm ENGR 286
Office hours: T/Th 3:00 - 4:00 pm, HEC 311
Syllabus: The course will concentrate on computer science aspects of computational molecular biology and will emphasize the recent advances and open problems in the area.
The computational techniques will include algorithms, graph theory, combinatorics, machine learning, etc. Many important bioinformatics topics will be used as examples to illustrate how the formulation and solution of a computer science problem can help to answer a biological question.
This course is designed for computer science graduate students. No biology knowledge is required.
Graduate students with either biology or physical/computer science backgrounds who have taken a fundamental bioinformatics course are also welcome to take this course.
Preliminary topics to be covered:
1. Introduction to algorithms
2. Exact string matching, Data structure: Suffix tree
3. Suffix tree: applications
4. Mismatch tree and the motif finding problem
5. Breaking problems down: dynamic programming
6. Combinatorial search: intractable problems
7. Integer programming; Reductions
8. Graph algorithms: trees
9. Haplotyping via perfect phylogeny
10. Comparing trees
11. De Bruijn graph; Eulerian graphs
12. Minimum Spanning trees; Shortest paths
13. Matching problems; Network flow
14. Breakpoint graph
15. Set cover and set packing
16. Graph-based clustering
17. Heuristic algorithms
Assignments: We will have 4 take-home assignments.
Grading: Assignments (40%), Midterm exam (25%), Final exam (25%), Attendance (10%).
Topics and Tentative Agenda:
|1||08/21||Introduction to algorithm|
|08/23||Exact string matching||Dan 2.3, Dan 1.4 KMP|
|2||08/28, 08/30||Z-value|| PDF |
Assignment #1 (Due 09/11)
|3||09/04,09/06||Suffix trees|| Dan 6
|4||09/11||Dynamic Programming|| CMB CMB 6.2 and 6.3
|09/13||DP Applications: RNA folding, complicated parameters|| mfold
|5||09/18||DP Applications: RNA alignments with guiding tree|| PDF |
Assignment 2 (Due 10/04)
|09/20||DP Applications: Pseudoknotted RNA alignments||pseudoknot|
|6||09/25||DP Applications: RNA folding, a different formulation||RNAscf|
|09/27||DP Applications: Spliced sequence alignment||CMB 9.4|
|7||10/02||NP-hard problem and multiple sequence alignment|
| 10/04 |
We are always looking for motivated students. If you are looking for research projects, please get in touch.