Computer Science 549 - Computational Biology
Fall 2007

Instructor: Steven Skiena

Office: 1417 Computer Science Building

Phone: 631-632-9026

Email: skiena@cs.sunysb.edu

Office Hours: 5:15PM-6PM Tuesday-Thursday, and by appointment.

Course Time: 3:50-5:10PM Tuesday-Thursday Place: E4315 Melville Library

Textbook: The textbook for the course will be:

• Jones and Pevzner, An Introduction to Bioinformatics Algorithms, MIT Press, 2004

Other books which I recommend as supplements are:

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

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

• Claverie and Notredame, Bioinfomatics for Dummies, For Dummies Press, 2003.

• Dwyer, Genomic Perl, Cambridge Univ. Press, 2003

• 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.

  Semester Project - Proposal 10%

  Semester Project - Progress Report 15%

  Semester Project - Final Report 25%

  Midterm Exam - 20%

  Final Exam - 30%

• Material: This is an 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.

• Homework Assignments: In past years, there has been three group homeworks over the course of the semester. Part will be algorithmic in nature and part biological. Some might involve light programming and/or web search. These will not be collected or graded this year, but related questions are likely to appear on the midterm and final exams.

• Graduate Student Project: This is your opportunity to study some aspect of computational biology in depth. Suitable projects will be course presentations, original research or implementations. A list of possible topics will be distributed about a month into the semester, although you are encouraged to devise your own.

  A project proposal with progress report will be be due about a month later. A second progress report will be due at Thanksgiving. Both will be graded, to provide motivation not to leave the project to the last week of the semester.

  I intend to schedule brief discussions with each group to make sure I understand the progress and final reports.

• Midterm and Final Exams: There will be midterm and final exams to encourage students to review the material during and at the end of the course. These account for half the course grade between them. Last year's midterm will be made available as a study aid.

Rules of the Game:

1. The basic structure of the lectures will mirror the CSE 549 course I taught in Fall 2004. My full lecture notes (with audio!) from that year are available on the web.

2. This course reflects a bias toward the algorithmic aspects of computational biology. CS students should not take this course if you have not had the equivalent of CSE 373/548, unless you can prove to me you have a strong biology background.

3. I will not sign proficiency for CSE 373/548 based on the results of this class, so do not ask me.

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

5. Life science students with an interest in obtaining M.S. degrees in Computer Science are advised to take more ``hard-core'' Computer Science courses instead of this one.

6. The WWW page for the course is http://www.cs.sunysb.edu/ skiena/549/. All course handouts and notes are available there, along with the latest announcements. Please check it out.

7. Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Any suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/

8. 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), ECC Building, 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.