Quantitative Genomics

Lecture Notes

SES #	TOPICS
L0	Introduction - Prof. Leonid Mirny (PDF - 1.8 MB)
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
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 (PDF - 3.4 MB) 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
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
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
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 (PDF) (Courtesy of Dr. Marco Ramoni. Used with permission.)
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
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
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
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)
L19	RNA Expression: Clustering and Classification (PDF - 5.0 MB)
L20	RNA Expression: Classification, 2-way Clustering, Regulatory Modules (PDF) Integration of Expression and Proteomic Data
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
L24	Final Presentations