1. CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical Engineering)

2. Goal & Design Provide an introduction to bioinformatics from a computer science perspective (as opposed to a biology perspective) Prepare students for doing research/development in bioinformatics Targeted at students with sufficient programming skills and basic knowledge of probability and statistics

3. Format Lecture-based 6~8 Assignments –Coding –Experimenting with data –Analyzing results –Open explorations Midterm & Final Extra 0.25 unit project (literature review or mini research project)

4. Grading Assignments: 45% Midterm: 25% Final: 30% Project: 25% Total scores will be scaled appropriately for students who take the course for 3- hour or 0.75 unit credit

5. Schedule Part I: Background (molecular biology + math) Part II: Sequence alignment Part III: Hidden Markov Models (HMMs) Part IV: Microarray data analysis Part V: Sequence pattern mining Part VI: Protein sequence analysis Midterm : March 10 Office hours: 8:00am-9:30am Tuesday & 2:00-3:00pm Friday 2116 Siebel Center

6. Textbooks 2. Computational Molecular Biology: An Algorithmic Approach by Pavel A. Pevzner 1.Probabilistic Models of Proteins and Nucleic Acids by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison Additional readings will be assigned for some topics

7. Questions? http://sifaka.cs.uiuc.edu/course/397cxz04s Newsgroup: uiuc.class.cs397cxz Mailing list: cs397cxz@cs.uiuc.edu