Topics in Computational Biology: Genomes, Networks, and Cancer (CS296-5)

Spring 2007

Tuesday/Thursday 2:30-3:50pm [CIT 345]

Professor: Ben Raphael

This course will investigate active and emerging areas of research in computational methods for biological problems. The format of the course will be a mixture of lectures and student presentations of recent papers.





CS 181 or equivalent; or permission of the instructor.

Course Credits (tentative)


Participation (10%)

A critial reading of the literature requires engagement in the discussions of papers. Students are expected to contribute to class discussions by asking questions, making observations, identifying strengths and weaknesses, etc.

Written reports (30%)

You will critically analyze the papers in the reading list. Critical reading of technical papers is a must-have skill in research. You will write a review summarizing the contributions of the paper, assess its weaknesses, and suggest further research areas or alternative approaches. Reports for three papers (approximately 2 pages each) and must be distributed between the three major topics of the course. Each review will be worth 10% of your grade.

Presentations (20%)

Each student will be make one or two presentations from the reading list (the number depends on class size). A week before the presentation, the participant will email the instructor a detailed outline of the presentation. Similarly, the talk slides will be submitted at least two days before the presentation. The outline and slides should be modified on the basis of feedback before the presentation. After the presentation, a page summary (html) will be made for the benefit of future students.

Class Project (40%)

Based on the background and interests of the student, the project can be theory, practice, or a combination of the two. Examples include:

  1. An implementation of one of the algorithms discussed in class with testing on new biological data.
  2. Development of a new approach for a problem in computational biology.
During the term, students will turn in a written project proposal which will count towards part of the project grade. Further details to come.

Extra Credit (up to 10%)

Up to 5% extra credit can be earned twice for attending a computational biology seminar and writing a one page summary of the talk. Such credit MUST be approved by the instructor BEFORE the seminar.