| LEC # | Topics |
|---|---|
| 1 | Intro 1: Course overview and introduction to the computational side of computational biology. Why use Perl & Mathematica? Write and run simple scripts. We will also assign sections addressing Biology, computing, and advanced topics. Questionaires due. |
| 2 | Intro 2: Biological Side of Computational Biology; Central Dogma; Comparative Genomics; Models & Real World Applications. Note: Please take your initial observations about Problem Set#1 to you first section meetings (i.e. check that you actually have access to Perl & Mathematica). |
| 3 | DNA 1: Genome Sequencing, Polymorphisms, Populations, Statistics, Pharmacogenomics; Databases. Note: Problem Set #1 is due at the start of class. (Answers will be posted 48 hrs later.) |
| 4 | DNA 2: Dynamic Programming, Blast, Multi-alignment, HiddenMarkovModels. |
| 5 | RNA 1: Microarrays, Library Sequencing and Quantitation Concepts. Note: Problem Set #2 is due. |
| 6 | RNA 2: Clustering by Gene or Condition and Other Regulon Data Sources Nucleic Acid Motifs; The Nature of Biological "proofs." |
| 7 | Proteins 1: 3D Structural Genomics, Homology, Catalytic and Regulatory Dynamics, Function & Drug Design. |
| 8 | Proteins 2: Mass Spectrometry, Post-synthetic Modifications, Quantitation of Proteins, Metabolites, & Interactions. |
| 9 | Networks 1: Systems Biology, Metabolic Kinetic & Flux Balance Optimization Methods. Note: Problem Set #4 is due. (#5 will be available but not due until lecture 14.) |
| 10 | Networks 2: Molecular Computing, Self-assembly, Genetic Algorithms, Neural Networks. |
| 11 | Networks 3: The Future of Computational Biology: Cellular, Developmental, Social, Ecological & Commercial Models. |
| 12 | Project Presentations; All written project reports and overhead slides (for presentations) due. |
| 13 | Project Presentations. |
| 14 | Project Presentations; Problem Set #5 due. |
