| L0 |
Introduction - Prof. Leonid Mirny |
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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 |
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| 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 |
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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 |
Problem set 1 out |
| R2 |
Discussion of Problem Set 1 |
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| L5 |
Medical Lecture: Genetic Diversity and Evolution of Hepatitis C Virus - Prof. Isaac Kohane |
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| 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 |
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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 |
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| 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 |
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| L15 |
Proteomics: Evolution of Protein and Regulatory Networks, Function and Misfunction of Genes in Networks |
|
| R5 |
Recitation |
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| 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 |
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| 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 |
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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 |
Problem set 4 due |
| L24 |
Final Presentations |
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