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.