| Lectures: | Monday / Wednesday 12:30-1:30pm |
| EBU3B (CSE building) 2154 | |
| Discussion section: | Wednesday 10:00-10:50am |
| HSS 2321 |
Instructor: Pavel Pevzner, Dept Computer Science and Engineering, http://www-cse.ucsd.edu/users/ppevzner
Teaching Assistants:
Textbook: An introduction to bioinformatics algorithms
Neil Jones and Pavel Pevzner, ISBN 978-0262101066
Book website
Syllabus
| Date | Topic (subject to change) | Slides | ||
|---|---|---|---|---|
| Mon Jan 9, 2012 | Transforming mice to men Part 1 | Lecture 1/2 | ||
| Wed Jan 11, 2012 | Transforming mice to men Part 2 | |||
| Mon Jan 16, 2012 | MLK Holiday | |||
| Wed Jan 18, 2012 | Edit Distance | Lecture 3 - Part1 | ||
| Alignment algorithms | Lecture 3 - Part2 | |||
| Mon Jan 23, 2012 | Alignment algorithms / Divide and Conquer | Lecture 4 | ||
| Wed Jan 25, 2012 | Multiple Alignment | Lecture 5 - Part 1 | ||
| HMM | Lecture 5 - Part 2 | |||
| Mon Jan 30, 2012 | HMM - Part 2 | Pattern matching | Gene prediction - stat | Gene prediction - sim |
| Wed Feb 1, 2012 | Mass spectrometry and graphs | Lecture 7 | ||
| Mon Feb 6, 2012 | Mass spectrometry and motif finding | Motif lecture | ||
| Wed Feb 8, 2012 | Mass spectrometry algorithms | Lecture 9 | ||
| Mon Feb 13, 2012 | --- Midterm --- | |||
| Wed Feb 15 | Pattern Matching | |||
| Mon Feb 20 | Graphs | GraphsDNAseq | A-Bruijn | |
| Wed Feb 22 | Graphs | NGS assembly | ||
| Mon Feb 27 | Clustering | Clustering | ||
| Wed Feb 29 | Antibiotics | Antibiotics | ||
| Mon March 5 | Molecular evolution | Mol evolution | ||
| Wed March 7 | Molecular Evolution I (neighbor joining, parsimony) | Lecture 16 | ||
| Molecular Evolution (maximum likelihood) | Lecture 17 | |||
| Molecular signatures of natural selection | Lecture 18 | |||
| Applications to pathogen evolution | ||||
| --- Final --- |