CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of...
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Transcript of CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of...
![Page 1: CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical.](https://reader035.fdocuments.us/reader035/viewer/2022080917/56649ec85503460f94bd5a38/html5/thumbnails/1.jpg)
CS397-CXZ
Algorithms in Bioinformatics
ChengXiang (“Cheng”) Zhai, Robert Skeel
(Department of Computer Science)
Nick Sahinidis
(Department of Chemical Engineering)
![Page 2: CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical.](https://reader035.fdocuments.us/reader035/viewer/2022080917/56649ec85503460f94bd5a38/html5/thumbnails/2.jpg)
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
![Page 3: CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical.](https://reader035.fdocuments.us/reader035/viewer/2022080917/56649ec85503460f94bd5a38/html5/thumbnails/3.jpg)
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)
![Page 4: CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical.](https://reader035.fdocuments.us/reader035/viewer/2022080917/56649ec85503460f94bd5a38/html5/thumbnails/4.jpg)
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
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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
![Page 6: CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical.](https://reader035.fdocuments.us/reader035/viewer/2022080917/56649ec85503460f94bd5a38/html5/thumbnails/6.jpg)
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
![Page 7: CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical.](https://reader035.fdocuments.us/reader035/viewer/2022080917/56649ec85503460f94bd5a38/html5/thumbnails/7.jpg)
Questions?
http://sifaka.cs.uiuc.edu/course/397cxz04s
Newsgroup: uiuc.class.cs397cxz
Mailing list: [email protected]