Wi04: CSE206B: Algorithms in Computational Molecular Biology

Instructors: Vineet Bafna and Pavel A. Pevzner

Lectures: TR 12:30-1:50pm. York4060B

Office hours:
Vineet Bafna APM3832: by appointment
Pavel A. Pevzner APM4802: by appointment

Course Information:

Course Outline (pdf)


Project Descriptions (updated 1/22/05)
This is an incomplete list. If you would like to explore further, please send email to the instructors for alternative projects.


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.
  • Lectures

    Lecture Topic Slides Suggested Reading
    1/4/05 Genome rearrangements
    Breakpoint Reuse
    Nadeau-Taylor hypothesis
    L1 (pdf)
    1/6/05 Whole Genome Duplication in
    S. cerevisae and Tetraodon
    L2 (pdf) ) yeast WGD (Wolfe) (1997)
    Wong Wolfe (2002)
    Kellis et al. (2004)
    Tetraodon WGD (2004)
    1/11/05 Genome rearrangements L3 (pdf) )
    1/13/05 Mass spectrometry L4 (pdf) )
    1/18/05 Repeats
    1/20/05 Repeats
    non-coding RNA

    L6 (ncRNA) (pdf) )
    1/25/05 RNA structure
    Akutsu's formulation
    Locating ncRNA using structure
    Sequence Structure alignment

    L7 (ncRNA) (pdf) )
    ncRNA prediction using structure
    RSEARCH (This paper has details on the paramter computation, and some real examples)
    FastR (see this paper (page 16, 17) for sequence structure alignment).
    1/27/05 QRNA
    SCFGs for RNA structure

    L8 (ncRNA) (pdf) )
    2/1/05 Covariance models
    RNA multiple alignment

    See chapter 10 of "Biological Sequence Analysis"
    2/1/05 RNA multiple alignment

    L9 (ncRNA) (pdf) )
    2/1/05 Covariance models
    RNA multiple alignment

    See chapter 10 of "Biological Sequence Analysis"

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