Announcements:

• Documents outlining project "milestones" have been sent to students registered for any of the suggested projects. Students who have chosen their own project idea may not have received such an email.
• Home assignment 1 posted on the "Readings" page.
• Reading assignment 2 posted on the "Readings" page.
• Lecture 4 powerpoint slides have been posted on the Schedule page.
• Class mailing list cs598ss (At cs DOT uiuc DOT edu) created. If you didnt receive an email from this list already, please subscribe yourself at http://lists.cs.uiuc.edu/mailman/listinfo/cs598ss
• Please also check out the companion course on bioinformatics CS498-CXZ Algorithms in Bioinformatics.

The emergent field of bioinformatics will play a crucial role in the upcoming biotech revolution, by providing the computational framework to extract knowledge from the terabytes of raw data available. This course will present some of the important research topics pertaining to the computational processing of genomic sequences, focusing on probabilistic approaches to the problem.

We will discuss, among other topics,

• probabilistic techniques such as Expectation-Maximization, Hidden Markov Models, Bayesian inference, Monte carlo sampling, with applications in bioinformatics.
• computational assessment of sequence statistics (such as alignment scores and word frequencies),
• mathematical models of evolution, algorithms for infering evolutionary relationships, etc.

Computational techniques will be discussed in the context of the important biological process of gene regulation, and problems such as sequence alignment, motif finding, and module detection, will be studied in detail. A recurrent theme of the course will be comparative genomics -- the paradigm of examining data from multiple species for improving the extracted signal.

The course will be partly lecture-based, and partly student presentations. A research project will be a major component of the course.

Prerequisites include programming skills, and basic probability and statistics.
No background in biology is required.