Computer Science 648 - Computational Biology
Fall 2000

Instructor: Steven Skiena

Office: 1411 Computer Science Building

Phone: 631-632-9026

Email: skiena@cs.sunysb.edu

Office Hours: 11:15AM-12:45PM Tuesday-Thursday, and by appointment.

Course Time: 12:50-2:10PM Tuesday-Thursday Place: 237 Humanities

Textbook: There is no textbook for this course. Much of the material we will cover appears in the following books:

• Gusfield, Algorithms on Strings, Trees, and Sequences, Cambridge Univ. Press, 1997.

• Durbin, Eddy, Krogh, and Mitchison, Biological Sequence Analysis, Cambridge Univ. Press, 1998.

• Setabal and Meidanis, Introduction to Computational Molecular Biology, PWS, 1997.

• Bishop and Rawlins, DNA and Protein Sequence Analysis Oxford University Press, 1997.

• Baxevanis and Ouellette, Bioinformatics, Wiley, 1998

• Sankoff and Kruskal Time Warps, String Edits, and Macromolecules, CSLI Publications 1999 (reprint).

• Watson, Gilman, Witkowski, and Zoller, Recombinant DNA, Scientific American Press, 1992.

• Grading: Grades will be assigned based on the following formula, with cut-offs determined by my opinion of students on the boundary.

  Presentation - 30%

  Semester Project - 70%

• Material: This is an advanced course in computational biology, focusing current problems in genomics. Our emphasis will be algorithmic, on discovering appropriate combinatorial algorithm problems and the techniques to solve these problems. Primary topics will include DNA sequence assembly, DNA/protein sequence comparison, hybridization array analysis, RNA and protein folding, and phylogenic trees.

• Presentation: I will be lecturing on foundational material in computational biology and algorithms. To augment this theoretical material, each student (presumably in a group) will required to make a presentation on the software tools currently available for some class of problems. This presentation will emphasize both what the software does via demonstration, and a discussion of what the associated algorithmic issues are. Each presentation must leave behind a WWW page with links to appropriate systems and resources, as well as the slides used in the presentation.

• Graduate Student Project: This is your opportunity to study some aspect of computational biology in depth. Suitable projects will be term papers, original research or implementations. A list of possible topics will be distributed early in the semester, although you are encouraged to devise your own. A brief proposal of what you intend to do must be submitted after the first month of classes.

Rules of the Game:

1.

This is intended as an advanced course in algorithms, targeted to PhD students and advanced masters students. You should not take this course if you have not had (or done badly in) the equivalent of CSE 373/548, unless you can prove to me you have a strong biology background.

2.

I strongly encourage interest from students with a life sciences background. My vision is to pair up computational and life scientists for presentations and projects, so as to help each other get a more balanced view.

3.

The WWW page for the course is http://www.cs.sunysb.edu/ skiena/648/. All course handouts and notes are available there, along with the latest announcements. Please check it out.

4.

Because a primary goal of the course is to teach professionalism, any academic dishonesty will be viewed as evidence that this goal has not been achieved, and will be grounded for receiving a grade of F. (See CEAS Procedures and Guideline Governing Academic Dishonesty, 1/81.)

5.

If you have a physical, psychological, medical or learning disability that may impact on your ability to carry out assigned course work, I would urge that you contact the staff in the Disabled Student Services office (DSS), Room 133 Humanities, 632-6748/TDD. DSS will review your concerns and determine, with you, what accommodations are necessary and appropriate. All information and documentation of disability is confidential.