CSCI2950-L: Medical Bioinformatics: Disease Associations, Protein Folding and Immunogenomics

Homework

Note: Some documents are only accessible from within the campus network.

Date Assigned Due Homework
September 9 September 16 Homework 1
Write a summary and two critical questions you would have asked for the sweatbox session for the Jonathan Yewdell and Sam Broder lectures. The 2 summaries and 4 questions should total about 2 pages. You are free to use whatever software you'd like but we'd recommend LaTeX (see notes or email Derek for help with LaTeX).
September 23 September 30

This homework will investigate GWAS caveats and utilize Mathematica for support. No previous programming experience is required, but, if you are unfamiliar with Mathematica, it would help to run through this quick tutorial. If you don't have access to Mathematica you can download it from the CIS software website (it can only be used while on campus). Alternatively, you can email Sorin and he can request a CS account for you. The PDF contains just the questions and the hw2.nb notebook file (NB) contains the Mathematica notebook you are required to complete.

Homework 2 [PDF] [NB] Population Genetics Hardy-Weinberg notebook

Homework 2 Answer [NB]

September 30 October 7

Homework 3 [PDF]
LD-Interpretation.nb [NB]
LD-Interpretation_math6.nb (if you are using Mathematica 6 and cannot open the notebook above) [NB]

Required Readings

Efficiency and power in genetic association studies

Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium

Data for the extra credit part
dataset1.txt dataset2.txt dataset3.txt

HapMap data to use for comparison for the extra credit part.
In Haploview, use the Haps Format
Data files:
haplotypes_dataset1.txt
haplotypes_dataset2.txt
haplotypes_dataset3.txt
Locus Information Files:
snps_info1.txt
snps_info2.txt
snps_info3.txt

Homework 3 Answer [PDF]
October 7 October 14

Homework 4 [PDF]

Homework 4 Answer [PDF]
October 14 October 21

Homework 5 [PDF]

Reading: Comparative immunopeptidomics of humans and their pathogens [PDF]

Data
dataset1_genotypes.txt
dataset2_genotypes.txt
dataset3_genotypes.txt

(Solutions) Sample Phasing Programs
EM Phasing [Mathematica]
Clark Phaser [Java Exec Jar]
Clark Phaser [Java src]
October 28 November 2

Midterm [PDF]

A genome-wide linkage and association scan reveals novel loci for autism [PDF]

Supplementary 1 [PDF]

Supplementary 2 [PDF]

Data
midterm_haplotypes_pop.txt
November 13 November 18

Homework 6

Final project preparation [PDF]

Homework 6 will be graded as part of the final project.
November 18 November 25

Homework 7 [PDF]

Homework 7 Solution [PDF]