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.
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.