| 1 | Introduction/Sequence Comparison and Dynamic Programming | |
| 2 | Multiple Sequence Alignments I | |
| 3 | Multiple Sequence Alignments II | Homework 1 handed out |
| 4 | Phylogenetic Analysis | |
| 5 | Literature Discussion | |
| 6 | Genome Sequencing and DNA Sequence Analysis | Homework 1 due |
| 7 | DNA Sequence Comparison and Alignment | |
| 8 | DNA Motif Modeling and Discovery | Homework 2 handed out |
| 9 | Markov and Hidden Markov Models for DNA Sequences | |
| 10 | DNA Sequence Evolution | |
| 11 | RNA Secondary Structure Prediction | Homework 2 due |
| 12 | Literature Discussion on Predicting the Functions of DNA/RNA Sequences | |
| 13 | Midterm Exam – in class – Protein and DNA Sequence Analysis | |
| 14 | Protein Secondary Structure Prediction | |
| 15 | Introduction to Protein Structure and Classification | |
| 16 | Comparing Protein Structures
Molecular Modeling: Methods and Applications | |
| 17 | Using Computational Methods to Analyze, Predict, and Design Protein Sequences and Structures
Solving Structures using X-ray Crystallographpy and NMR | |
| 18 | Solving Structures using X-ray Crystallographpy and NMR (cont.)
Homology Modeling | Homework 3 handed out |
| 19 | Methods for Protein Structure Prediction: Homology Modeling and Fold Recognition | |
| 20 | Threading and ab initio Structure Prediction
Computational Protein Design | Homework 3 due |
| 21 | Introduction to Systems Biology | Homework 4 handed out |
| 22 | Feedback Systems and Coupled Differential Equations | |
| 23 | DNA Microarrays and Clustering | |
| 24 | Literature Discussion on DNA Microarrays and Clustering | Homework 4 due
(a day after Lec #24) |
| 25 | Computational Annotation of the Proteome | |
| 26 | Literature Discussion on Computational Annotation of the Proteome | |