| SES # | TOPICS | KEY DATES |
|---|---|---|
| L0 | Introduction - Prof. Leonid Mirny | |
| 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 | |
| L2 | Selection, Fitness, Probability of Fixation, Coalescent Theory Parameter Estimation | |
| 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 | |
| L3 | Selection, Fitness, and Diffusion Models Molecular Evolution, Jukes-Cantor Model, Kimura Model | |
| L4 | Human/Mouse/Rat Examples Measuring Selection: From 'Classical' Methods to Maximum Likelihood (With Applications to Disease Evolution, HIV and Influenza) McDonald-Kreitman Test | Problem set 1 out |
| 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 | Final projects discussed with class faculty after the lecture |
| 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 | Problem set 1 due |
| 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 | |
| R3 | Infinite Site Model: Nucleotide Diversity, Allele Frequency | Problem set 2 out |
| L9 | Multiple Alignments, Profiles and PSSM, HMMs, Domain Databases Prediction of Gene Function Using: Homology, Context, Structure | |
| L10 | SNPs: Microevolution, Inference of Population History LD, Haplotypes, Medical Applications Effect of SNPs on Function | |
| R4 | Recitation: SNPs | |
| L11 | Medical Lecture: Human Variations Genes, Genotypes and Generations - Dr. Marco Ramoni | Summary of final projects due |
| Module 3: Structural Genomics and Proteomics - Lectures by Prof. Leonid Mirny | ||
| L12 | Overview of Protein Structures, Domain Architecture Sequence-structure Mapping, Protein Folding, Forces and Interactions | Problem set 2 due |
| L13 | Structure-based Substitution Matrices Protein Structure Prediction Threading Protein Function: Binding and Kinetics, Michaelis-Menthen Kinetics, Inhibition Protein-DNA Recognition: Models and Algorithms | |
| L14 | Proteomics: Networks of Protein-protein Interactions, Complexes, Modules Power-law Distributions, Clustering Coefficient | |
| 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 | Problem set 3 out |
| L17 | Guest Lecture | Final projects progress report due |
| Module 4: Functional Genomics and Networks - Lectures by Prof. Alvin Kho | ||
| L18 | Gene Regulation and Function, Conservation, Detecting Regulatory Elements | |
| L19 | RNA Expression: Clustering and Classification | Problem Set 3 due |
| L20 | RNA Expression: Classification, 2-way Clustering, Regulatory Modules Integration of Expression and Proteomic Data | Problem set 4 out |
| R6 | Recitation | |
| L21 | Dynamics of Biological Networks Metabolic, Regulatory FBA, Signaling, Regulation of Gene Expression | |
| 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 | |
| L23 | Guest Lecture | Problem set 4 due |
| L24 | Final Presentations | |