Quantitative Genomics

Calendar

The calendar below provides information on the course’s lecture (L) and recitation (R) sessions.

Except where indicated in the Topic specific fields, lectures are given by the faculty members listed next to the module names in the table below.

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