| Aug 29,2006 | Lecture 1 | Introduction to BME380 | Simon | Lecture 2 | Review of Probability | Simon | Lecture 3 | Biology Review - Genetics | Simon |
| Sept 5,2006 | Lecture 4 | Biology Review - Proteins | Simon | Lecture 5 | Problems and Solutions,Complexity | Simon |
| Lecture 6 | Computer Models, Formal Languages | Simon | |
| Sept 12,2006 | Lecture 7 | Approaches to Hard Problems | Mandiou |
| Lecture 8 | String Matching and Alignment | Simon | |
| Lecture 9 | Tools: Expectation Maximization, Simulated Annealing | Simon | |
| Sept 19,2006 | Lecture 10 | Cloning, DNA Amplification and DNA Sequencing | Gunzl |
| Lecture 11 | Physical Mapping, Fragment Assembly | Simon | |
| Sept 26,2006 | Lectures 12,13 | Motif Finding,Artificial Neural Nets | Rajasekaran |
| Oct 3,2006 | Lecture 14 | Gene Finding, HMMs | Simon |
| Oct 10,2006 | Lecture 15 | HMMs Revisited | Simon |
| Lecture 16 | Mutation, Homology, Forensics | Simon | |
| Lecture 17 | Molecular Evolution, Mutation Rates, Molecular Clocks | Simon | |
| Lecture 18 | Character Phylogeny | Simon | |
| Lecture 19 | Distance Phylogeny | Simon | |
| Oct 17,2006 | Lecture 20 | Gene Chips and Large Data Array Analysis | Krueger |
| Lecture 21 | Principal and Independent Components Analysis | Simon | |
| Oct 24,2006 | Lecture 22 | Clusters, Self-organizing Maps | Simon |
| Lecture 23 | Homology, Blocks, Substitution Matrices, BLAST | Simon | |
| Oct 31,2006 | Lecture 24 | BLAST: Database searching, Statistics, Variations | Simon |
| Lecture 25 | FASTA | Simon | |
| Nov 7,2004 | Lecture 26 | Bioenergetics, StructurePrediction | Hoch |
| Lecture 27 | 3-D Structure Database Searching, DALI | Maciejewski | |
| Nov 14,2006 | Lecture 28 | EM in Motif Discovery | Simon |
| Lecture 29 | Review | Simon | |
| Nov 22,2006 | Thanksgiving Holiday | ||
| Nov 28,2006 | STUDENT FINAL PROJECTS |