Topics in Computational Biology: Genomes, Networks, and Cancer (CSCI2950-C)

Tuesday/Thursday 2:30-3:20pm [CIT 506]

Professor: Ben Raphael

The Cancer Genome Atlas, a new genome project for cancer, presents numerous algorithmic, machine learning, and modeling challenges. We will examine in this context new and classic problems in computational biology including: genome assembly, genome rearrangements, phylogeny, and cellular interaction networks.


  • 12/4/08 -- Final papers for presentation posted.
  • 11/17/08 -- More papers for presentation posted.
  • 11/10/08 -- Suggested readings and papers for presentation posted.
  • Course Organization

    The course will be organized in seminar style where students will present recent papers on the topics listed below. Each topic will be introduced with background lectures. Students will undertake either two half-semester or one full semester (with a midterm report) project(s) to further study one of the class topics. The project could range from theoretical (e.g. designing a new algorithm and proving its correctness), to the practical (a software implementation) depending on the interest of the student.


    Paper Reviews

    Paper reviews are due BEFORE the class when the paper is presented. Email your review to me using this review form.

    Course Credits (tentative)

    Previous versions of this course are available here:
  • Spring 2007.
  • Fall 2007.