Wi07: CSE280a: Advanced Topics in Computational Molecular Biology

Instructors:
Vineet Bafna

Lectures: TR 5:00-6:20pm. CENTR220

Office hours:
Vineet Bafna CSE 4218: by appointment

Course Information:
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Course Outline (pdf)

Background

The course should be self-contained. However, a concise introduction to Biology can be found at the Bioinformatics Algorithms web-site (chapter 3).
Also, the text of Mol. Biol. of the Cell can be searched online.
There is no required text for the course. We will use the following as optional texts:
  • D. Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press. 1997
  • P.A. Pevzner. Computational Molecular Biology: An Algorithmic Approach. The MIT Press, 2000
  • N.C, Jones and P.A. Pevzner. Introduction to Bioinformatics Algorithms. The MIT Press, 2004.
  • Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison. Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1999.

    • Projects

    Final (due March 22)

    Lectures

    Lecture Topic Slides Suggested Reading
    1/9/2007 Course outline
    ncRNA     		L1
    1/11/2007 ncRNA
    de novo structure prediction
    handling pseudo-knots     		L2 Wexler et al.
    Akutsu
    1/16/2007 ncRNA
    Stochastic Context Free Grammars
    Comparative methods QRNA     		L3 RNA structure chapter in Durbin's book
    Rivas Eddy
    1/18/2007 ncRNA
    project description     		L4 Projects
    1/23/2007 ncRNA prediction from multiple alignments
    QRNA
    comparative structure prediction     		L5
    QRNA
    RNAz
    1/25/2007 RNA structure prediction L6 RNAscf
    1/30/2007 ncRNA based homology search
    filtering for ncRNA     		L7 Sequence based filtering
    Structure based filtering
    2/1/2007 Filtering for sequence homology L8 preview Blast
    Dictionary Search Notes
    Patternhunter (spaced seeds)
    2/6/2007 Student L9
    2/8/2007 L10
    2/13/2007 L11
    2/15/2007 Keyword search in Blast
    Gapped Seeds Selection    		 L12 Blast
    Dictionary Search Notes
    Patternhunter (spaced seeds)
    2/20/2007 Spaced Seed Design
    Seed Design using DFAs     		(D.p. for seed design)
    Mandala
    NP-hardness of seed design
    2/22/2007 Buehler's algorithm for spaced seed design
    Regular Expression Matching
    Population Genetics basics
    L14     		Regular Expression Search Notes
    2/27/2007 Sources of variation
    HW equilibrium
    Linkage (dis)-equilibrium
    Coalescent theory     		L15 Read
    3/1/2007 Coalescent theory L16 Nordborg's review of coalescent theory
    Coalescent Applications
    3/6/2007 Population sub-structure L17 Structure
    3/8/2007 Recombination L18 Myers Griffiths
    3/13/2007 L19
    3/15/2007 L20

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