Sep 16

Integrate 1: Minimal BioSystems: Course overview and introduction to the computational side of computational biology. Why use Perl & Excel? Write and run simple scripts. We will also assign sections addressing Biology, computing, and advanced topics. Questionaires due.
Readings: Mount Chapter 1. Gibas & Jambeck (G&J) Chapters 1,2,12 (Those running Unix may find G&J Chaps. 3-5 useful). Students familiar with the above topics should look ahead to next week's readings.

Sep 23

Integrate 2: Optimal BioSystems: 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).
Readings: (for non-biologists) Primer on molecular biology and Molecular Biology for Computer Scientists

Sep 30

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.)
Readings: Mount Chap. 2 & 7. G&J Chap. 6, 11 pp. 294-303.
Advanced: Pritchard JK Are rare variants responsible for susceptibility to complex diseases?   Am. J. Hum Gen. 69:124

Oct 7

DNA 2: Dynamic programming, Blast, Multi-alignment, HiddenMarkovModels.
Related Readings:Mount Chap. 3. Durbin Chap. 3-5, G&J Chap. 7, 8 (pp.191-9). Smith TF, Waterman MS, Identification of common molecular subsequences. J Mol Biol 1981 147:195-7.

Oct 14

RNA 1: Microarrays, library sequencing and quantitation concepts
Note: Problem Set #2 is due.
Readings: Mount Chap. 10. G&J pp. 311-317, Lockhart & Winzeler Genomics, gene expression and DNA arrays. Nature 2000 405:827-36.

Oct 21

RNA 2: Clustering by gene or condition and other regulon data sources Nucleic acid motifs; the nature of biological "proofs".
Readings:G&J pp. 205-214; Tavazoie et al, 1999 Systematic determination of genetic network architecture. Nature Genetics 22:281-5.

Oct 28

Proteins 1: 3D structural genomics, homology, catalytic and regulatory dynamics, function & drug design.
Note: Problem Set #3 is due.
Readings:G&J Chap. 9 pp. 215-29 and Chap. 10. Advanced: Thompson J, et al. Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit. PNAS 2001 Jul 31;98(16):9002-9007

Nov 4

Proteins 2: Mass spectrometry, post-synthetic modifications,  Quantitation of proteins, metabolites, & interactions.
Readings:G&J Chap. 11 pp. 321-328. Ideker et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929 (2001)

Nov 11

Networks 1: Systems Biology, Metabolic kinetic & flux balance optimization methods
Note: Problem Set #4 is due (#5 will be available but not due until Dec 11).
Readings: Edwards & Palsson Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 2000;1(1):1
Jamshidi N, et al. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 2001 Mar;17(3):286-287

Nov 18

Networks 2: Molecular computing, self-assembly, genetic algorithms, neural networks
Readings:Hopfield JJ. Odor space and olfactory processing: collective algorithms and neural implementation. PNAS 96(22):12506-12511 (1999)

Nov 25

Networks 3: The future of computational biology: Cellular, developmental, social, ecological & commercial models.
Readings: Bagowski CP, Ferrell JE. Bistability in the JNK cascade. Curr Biol 2001 Aug 7;11(15):1176-1182

Dec 2

Project Presentations; All written project reports and overhead slides (for presentations) due.

Dec 9

Project Presentations; Problem Set #5 due.

Dec 16

Project Presentations.