Homework

Note: Homework dates are tentative but should give you a good idea for how assignments will be scheduled.

Title Assigned Date Due Date Assignment

Linkage Disequilibrium

2/14

2/28

HW 1

Required Readings:

Patterns of Linkage Disequilibrium in the Human Genome

Linkage Disequilibrium -- understanding the evolutionary past and mapping the medical future

Linkage Disequilibrium in Humans: Models and Data

SNP selection, Informativeness, Phasing

3/5

3/19

HW 2

Dataset: dataset1

Readings:

Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium (Optional, depending on how much you are able to answer the first and third reading questions, might not need to read )

Efficient selection of tagging single-nucleotide polymorphisms in multiple populations

Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies

Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection

Finding Haplotype Tagging SNPs by Use of Principal Components Analysis

More Phasing

3/21

4/11

HW 3

Datasets: Data folder

Readings:

Haplotype phasing: Existing methods and new developments

A New Statistical Method for Haplotype Reconstruction from Population Data

Islands of Tractability for Parsimony Haplotyping

Maximum-Likelihood Estimation of Molecular Haplotype Frequencies in a Diploid Population

GWAS, ARG reconstruction and Minichiello-Durbin

4/11

4/26

HW4

Genomic Privacy + Causality and Prediction

4/26

5/2

HW5

Final Project Presentation Activities

5/7

5/14