| SES # | TOPICS | |
|---|---|---|
| L0 | Introduction - Prof. Leonid Mirny ( PDF - 1.8 MB) |
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| Module 1: Evolutionary and Population Genetics - Lectures by Prof. Robert Berwick | ||
| L1 | The Basic Forces of Evolution: Mutation, Recombination and Mating, Migration, Neutral Evolution and Drift, Effective Population Size (PDF) | |
| L2 | Selection, Fitness, Probability of Fixation, Coalescent Theory (PDF - 3.3 MB) Parameter Estimation |
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| R1 | The Basic Forces of Evolution: Mutation, Recombination and Mating, Migration, Neutral Evolution and Drift, Effective Population Size Selection, Fitness, Probability of Fixation, Coalescent Theory Parameter Estimation |
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| L3 | Selection, Fitness, and Diffusion Models (PDF - 3.4 MB) Molecular Evolution, Jukes-Cantor Model, Kimura Model |
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| L4 | Human/Mouse/Rat Examples Measuring Selection: From 'Classical' Methods to Maximum Likelihood (With Applications to Disease Evolution, HIV and Influenza) McDonald-Kreitman Test |
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| R2 | Discussion of Problem Set 1 | |
| L5 | Medical Lecture: Genetic Diversity and Evolution of Hepatitis C Virus - Prof. Isaac Kohane | |
| L6 | Guest Lecture - Prof. Richard Lewontin | |
| Module 2: Comparative Genomics - Lectures by Prof. Shamil Sunyaev | ||
| L7 | Domain Structure of Proteins, Sequence-Structure-Function Relationships Orthologs, Paralogs, In/Out-Paralogs Pairwise Sequence Comparison - Substitution Matrices (PAM, BLOSUM, Gonnet) - Alignment Methods - Alignment Statistics |
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| L8 | Structure of the Genome Genome Comparison and Genome Evolution: Duplication, Recombination, Insertions, Repeats Finding Genome Elements: Genes, Regulatory Regions Motif Searching Conserved Non-coding |
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| R3 | Infinite Site Model: Nucleotide Diversity, Allele Frequency | |
| L9 | Multiple Alignments, Profiles and PSSM, HMMs, Domain Databases Prediction of Gene Function Using: Homology, Context, Structure |
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| L10 | SNPs: Microevolution, Inference of Population History LD, Haplotypes, Medical Applications Effect of SNPs on Function |
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| R4 | Recitation: SNPs | |
| L11 | Medical Lecture: Human Variations Genes, Genotypes and Generations - Dr. Marco Ramoni (PDF) (Courtesy of Dr. Marco Ramoni. Used with permission.) |
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| Module 3: Structural Genomics and Proteomics - Lectures by Prof. Leonid Mirny | ||
| L12 | Overview of Protein Structures, Domain Architecture (PDF - 1.2 MB) Sequence-structure Mapping, Protein Folding, Forces and Interactions |
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| L13 | Structure-based Substitution Matrices (PDF - 1.1 MB) Protein Structure Prediction Threading Protein Function: Binding and Kinetics, Michaelis-Menthen Kinetics, Inhibition Protein-DNA Recognition: Models and Algorithms |
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| L14 | Proteomics: Networks of Protein-protein Interactions, Complexes, Modules Power-law Distributions, Clustering Coefficient |
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| L15 | Proteomics: Evolution of Protein and Regulatory Networks, Function and Misfunction of Genes in Networks | |
| R5 | Recitation | |
| L16 | Medical Lecture: Hemoglobin and the Anemias - Prof. Isaac Kohane | |
| L17 | Guest Lecture | |
| Module 4: Functional Genomics and Networks - Lectures by Prof. Alvin Kho | ||
| L18 | Gene Regulation and Function, Conservation, Detecting Regulatory Elements (PDF - 2.0 MB)
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| L19 | RNA Expression: Clustering and Classification (PDF - 5.0 MB) |
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| L20 | RNA Expression: Classification, 2-way Clustering, Regulatory Modules (PDF) Integration of Expression and Proteomic Data |
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| R6 | Recitation | |
| L21 | Dynamics of Biological Networks Metabolic, Regulatory FBA, Signaling, Regulation of Gene Expression |
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| L22 | Medical Lectures - Prof. Isaac Kohane Two Examples: Phenylketonuria (monogenic) and Diabetes Type 2 (multigenic+) "Disease" Genes vs. "Susceptibility" Genes "Environmental" vs. "Developmental" Regulation of Gene Expression |
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| L23 | Guest Lecture | |
| L24 | Final Presentations | |