| 1 | Course Introduction: History of Computational Biology; Overview of the Course; Course Policies and Mechanics; DNA Sequencing Technologies (PDF - 5.0MB) | CB, DG, EF |
| Genomic Analysis |
| 2 | Local Alignment (BLAST) and Statistics (PDF - 2.0MB) | CB |
| 3 | Global Alignment of Protein Sequences (NW, SW, PAM, BLOSUM) (PDF) | CB |
| 4 | Comparative Genomic Analysis of Gene Regulation (PDF - 2.9MB) | CB |
| Genomic Analysis—Next Gen Sequencing |
| 5 | Library Complexity and Short Read Alignment (Mapping) (PDF - 1.4MB) | DG |
| 6 | Genome Assembly (PDF) | DG |
| 7 | ChIP-seq Analysis; DNA-protein Interactions (PDF - 2.0MB) | DG |
| 8 |
 RNA-sequence Analysis: Expression, Isoforms (PDF - 2.9MB)
| DG |
| Modeling Biological Function |
| 9 | Modeling and Discovery of Sequence Motifs (Gibbs Sampler, Alternatives) (PDF) | CB |
| 10 | Markov and Hidden Markov Models of Genomic and Protein Features (PDF) | CB |
| 11 | RNA Secondary Structure–Biological Functions and Prediction (PDF - 1.6MB) | CB |
| Proteomics |
| 12 | Introduction to Protein Structure; Structure Comparison and Classification (PDF - 3.1MB) | EF |
| 13 | Predicting Protein Structure (PDF - 3.4MB) | EF |
| 14 | Predicting Protein Interactions (PDF - 4.7MB) | EF |
| Regulatory Networks |
| 15 | Gene Regulatory Networks (PDF - 6.1MB) | EF |
| 16 | Protein Interaction Networks (PDF - 7.6MB) | EF |
| 17 |
Logic Modeling of Cell Signaling Networks (PDF - 3.1MB) Guest Lecture: Doug Lauffenburger
| GL |
| 18 | Analysis of Chromatin Structure (PDF - 3.8MB) | DG |
| Computational Genetics |
| 19 | Discovering Quantitative Trait Loci (QTLs) (PDF - 2.8MB) | DG |
| 20 | Human Genetics, SNPs, and Genome Wide Associate Studies (PDF - 3.3MB) | DG |
| 21 |
Synthetic Biology: From Parts to Modules to Therapeutic Systems. Guest Lecture: Ron Weiss Slides of this guest lecture are not available.
| GL |
| 22 |
Causality, Natural Computing, and Engineering Genomes. Guest Lecture: George Church Slides of this guest lecture are not available.
| GL |
