UCSF Jain Laboratory

BMI-203: Biocomputing Algorithms, Spring 2008 - 3 units
Class: Tuesdays and Thursdays 3-5pm
Room: Genentech Hall S271 (Mission Bay campus)

Week Date Topic Lecturer Assignment

1 April 1 Course overview
Complexity theory and Sorting Jain 1

1 April 3 Paper presentation Student -

2 April 8 Graph theory and Searching Jain -

2 April 10 Paper presentation Student -

3 April 15 Clustering Pegg 2

3 April 17 Paper presentation Student -

4 April 22 Dynamic Programming Jain -

4 April 24 Paper presentation Student -

5 April 29 Optimization I: Overview and Global Methods Jain 3

5 May 1 Paper presentation Student -

6 May 6 Optimization II: Local Methods Jain -

6 May 8 Paper presentation Student -

7 May 13 Parameter Estimation and Machine Learning Jain Final Project

7 May 15 Paper presentation Student -

8 May 20 Probabilistic models I: Hidden Markov Models Pegg 4

8 May 22 Paper presentation Student -

9 May 27 Probabilistic models II: Phylogenetic Trees and Matrices Pegg -

9 May 29 Paper presentation Student -

10 June 3 Final Topic TBD Pegg -

Final projects are due on Friday, June 6.
Homework assignments represent 40% of final course grade. They are due two weeks after being assigned (by midnight according to email timestamp).
Classroom participation represents 30%.
The final project represents 30%.