CS397-CXZ

Algorithms in Bioinformatics

ChengXiang (“Cheng”) Zhai, Robert Skeel

(Department of Computer Science)

Nick Sahinidis

(Department of Chemical Engineering)

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

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)

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

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 10Office hours: 8:00am-9:30am Tuesday & 2:00-3:00pm Friday

2116 Siebel Center

Textbooks2. 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

Questions?

http://sifaka.cs.uiuc.edu/course/397cxz04s

Newsgroup: uiuc.class.cs397cxz

Mailing list: cs397cxz@cs.uiuc.edu