Fall 2011, CAP 6515: Algorithms in Computational Biology


Instructor: Shaojie Zhang

Lectures: T/Th 4:30-5:45 pm ENGR 286

Office hours: T/Th 10:30 am -11:30 pm and 3:30 - 4:30 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

Reference Textbooks:

  • P.A. Pevzner, Computational Molecular Biology: An Algorithmic Approach. The MIT Press, 2000 (CMB)
  • D. Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press. 1997 (Dan)
  • Assignments: We will have 4 take-home assignments.

    Grading: Assignments (40%), Midterm exam (25%), Final exam (25%), Attendance (10%).

    Topics and Tentative Agenda:

    Week Date Topic Slides Notes
    1 08/23, 08/25 Introduction to algorithm PDF
    08/25, 08/30 Exact string matching PDF Dan 2.3, Dan 1.4 KMP
    2 08/30, 09/01 Z-value, Suffix trees PDF
    Assignment 1 (Due 09/15)
    Dan 1.4, Dan 6
    Circular Pattern Matching (suggested by Arup)
    3 09/06,09/08 Suffix trees PDF Dan 6
    Suffix
    4 09/13 Dynamic Programming PDF CMB CMB 6.2 and 6.3
    Myers-Miller algorithm
    09/15 DP Applications: RNA folding, complicated parameters PDF mfold
    Zuker-Sankoff(1984)
    5 09/20 DP Applications: RNA alignments with guiding tree PDF
    Assignment 2 (Due 10/04)
    Paper_1
    Paper_2
    09/22 DP Applications: Pseudoknotted RNA alignments PDF pseudoknot
    6 09/27 DP Applications: RNA folding, a different formulation PDF RNAscf
    09/29 DP Applications: Spliced sequence alignment PDF CMB 9.4
    7 10/04 NP-hard problem and multiple sequence alignment PDF
    10/06 Algorithmic problems related to phylogenetic trees-1 PDF
    8 10/11 Algorithmic problems related to phylogenetic trees-2 (Fitch Algorithm) See above
    10/13 Mid-term Exam (take-home)
    9 10/18 Algorithmic problems related to phylogenetic trees-4 (perfect phylogeny) See above
    10/20 Algorithmic problems related to phylogenetic trees-5 (SNP) See above PPH
    10 10/25 Algorithmic problems related to phylogenetic trees-5 (SNP and Haplotyping) See above
    Assignment #3 (Due 11/08)
    PPH
    10/27 De Bruijn graph and Eulerian graph-1 PDF CMB 5
    11 11/01
    No class on 11/03
    De Bruijn graph and Eulerian graph-2 (fragment assembly) See above CMB 5
    12 11/08 Genome rearrangements and breakpoint graph-1 PDF CMB 10
    11/10 Genome rearrangements and breakpoint graph-2 See above
    Assignment 4 (Due 11/29)
    CMB 10
    13 11/15 Genome rearrangements and cancer genomics
    Linear Programming and Interger Programming
    PDF
    PDF (LP and ILP)
    11/17 Computational Proteomics (Spectrum Graphs and Spectral Alignment)-1 PDF CMB 11
    14 11/22 Computational Proteomics (Spectrum Graphs and Spectral Alignment)-2 PDF CMB 11
    11/24 No Class (Thanksgiving Day)
    15 11/29 Computational Proteomics (Spectrum Graphs and Spectral Alignment)-3 See above CMB 11
    12/01 Computational Proteomics (Spectrum Graphs and Spectral Alignment)-4 See above CMB 11
    16 12/06 Take-home Final Exam Due

    Research:
    We are always looking for motivated students. If you are looking for research projects, please get in touch.