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Lecture Notes for
2003
The PPT files are subject to significant change up to 4 PM the day of the lecture (Tue). The lecture videos
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Sep 16
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Integrate 1: Minimal Biosystems: BioComplexity;
Replication; Exponential growth; Logistic equations; Statistics of single
DNAs.
MS-PPT | PDF
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Sep 23
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Integrate 2: Optimal BioSystems: Comparative
genomics; metabolic, structural, & regulatory network optimization
concepts.
MS-PPT | PDF
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Section 1 notes | Biology Section Video | CS
Section Audio (The first 7.5 minutes of the audio are inaudible)
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Sep 30
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DNA 1: Genotyping: What sequencing tells us about
populations, polymorphisms, pharmacogenomics; statistics & databases.
MS-PPT | PDF
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Section 2 notes | Biology Section Video | Bio
Section notes
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Oct 7
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DNA 2: Biome sequencing: What it tells us about
conserved functions. Dynamic programming, Blast, Multi-alignment,
HiddenMarkovModels.
MS-PPT | PDF
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Section 3 notes | Biology Section Video | CS
Section Audio (covering material from sections 2 and 3) | Bio Section notes
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Oct 14
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RNA 1: Quantitation concepts; Microarrays,
library sequencing
MS-PPT | PDF
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Section 4 notes | Biology Section Video
Using
Microarrays (in-lab photos, PDF)
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Oct 21
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RNA 2: Clustering by gene or condition and other regulon
data sources Nucleic acid motifs; the nature of biological
"proofs".
MS-PPT | PDF
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Section notes | Notes w/answers | Biology Section Video
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Oct 28
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Protein 1: 3D structural genomics, homology, catalytic
and regulatory dynamics, function & drug design.
MS-PPT | PDF
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Section notes | Biology Section Video
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Nov 4
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Protein 2: Mass spectrometry, post-synthetic
modifications, quantitation of proteins, metabolites, & interactions.
MS-PPT | PDF
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Section notes | Biology Section Video
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Nov 11
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Networks 1: Systems Biology, Metabolic kinetic &
flux balance optimization methods
MS-PPT | PDF
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Section notes | Biology Section Video
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Nov 18
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Networks 2: Molecular computing, self-assembly, genetic
algorithms, neural networks
MS-PPT | PDF
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Section notes | Biology Section Video
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Nov 25
Dec 9
Dec 16
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Networks 3: The future of computational biology: Cellular,
developmental, social, ecological & commercial models.
MS-PPT | PDF
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Section notes | Biology Section Video
Student presentations: final project
Video
Student presentations: final project
Video
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Lectures for 2000-1,2001-2,
2002-3.
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