Gonçalo's Lecture Notes

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The following lecture notes are available:

BIOSTAT 615/815 -- Statistical Computing

Lecture Notes

New Notes -- These were updated in the Fall of 2006
Lecture 01 -- The Connectivity Problem
Lecture 02 -- Programming in C
Lecture 03 -- Programming Tools
Lecture 04 -- Algorithm Analysis
Lecture 05 -- Dynamic Programming
Lecture 06 -- Basic Sorting
Lecture 07 -- Shell's Sort
Lecture 08 -- Quick Sort
Lecture 09 -- Merge Sort
Lecture 10 -- Introduction to Hashing
Lecture 11 -- Hashing (Part II)
Lecture 12 -- Mid-Term Review
Lecture 13 -- Mid-Term Evaluation
Lecture 14 -- Random Numbers
Lecture 15 -- Numerical Optimization
Lecture 16 -- Optimization with Parabolas, Mixture Distributions
Lecture 17 -- Nelder Mead Simplex Optimization
Lecture 18 -- The E-M Algorithm
Lecture 19 -- Simulated Annealing
Lecture 20 -- Gibbs Sampling
Lecture 21 -- Introduction to Numerical Integration
Lecture 22 -- Monte Carlo Integration
Lecture 23 -- Introduction to R

Data for Worksheet 8 is available here.

Old Notes -- These were updated in the Fall of 2004
Lecture 04 -- Introduction to R
Lecture 05 -- Graphics in R
Lecture 24 -- Half-Term Review II
Lecture 25 -- Half-Term Evaluation II

Problem Sets

These were last updated in the Fall of 2004

Worksheet 01 -- Introductory Questionnaire
Worksheet 02 -- Union Find Algorithms
Worksheet 03 -- Floating Point Precision
Worksheet 04 -- Dynamic Programming
Worksheet 05 -- Sorting (Part I)
Worksheet 06 -- Sorting (Part II)
Worksheet 07 -- Hashing
Worksheet 08 -- Random Numbers, Integration
Worksheet 09 -- Numerical Optimization
Worksheet 10 -- The Nelder Mead Simplex Method
Worksheet 11 -- Multidimensional Optimization

Data for Worksheet 11 is available here.

Textbooks

Robert Sedgewick. Algorithms in C. (3rd ed., 1998). Published by Adison Wesley Professional.
Press, Teukolsky, Vetterling, Flannery. Numerical Recipes in C. (2nd ed., 1998). Published by Cambridge University Press.

2004 lecture notes are available here.

BIOSTAT 666 -- Models in Human Genetics

Lecture Notes

New Notes -- These were updated in the Winter of 2006
Lecture 01 -- Review Class
Lecture 02 -- Hardy Weinberg Equilibrium
Lecture 03 -- Linkage Disequilibrium
Lecture 04 -- The Coalescent
Lecture 05 -- Allele Frequency Distributions
Lecture 06 -- Coalescent with Recombination
Lecture 07 -- Allele Frequency Estimation
Lecture 08 -- The E-M Algorithm
Lecture 09 -- Haplotyping
Lecture 10 -- Haplotype Association Tests
Guest Lecture -- Advanced Haplotype Inference (Steve Qin)
Lecture 11 -- Modeling Population Structure
Lecture 12 -- Review for the Midterm
Lecture 13 -- Midterm Assessment
Lecture 14 -- Linkage Analysis using Identity-by-State
Lecture 15 -- The MLS Method
Lecture 16 -- Discussion of Midterm Results
Lecture 17 -- Relative Recurrence Risks and the Possible Triangle
Lecture 18 -- Introduction to Multipoint Analysis
Lecture 19 -- Relationship Inference
Lecture 20 -- Lander Green Algorithm I
Lecture 21 -- Lander Green Algorithm II

Old Notes -- These were updated in the Winter of 2005
Lecture 24 -- Elston Stewart Algorithm
Lecture 25 -- Parametric Linkage Analysis
Lecture 26 -- No class, Polio Symposium
Lecture 27 -- Variance Components
Lecture 28 -- Review

Problem Sets

New Assignments -- These were updated in the Winter of 2006
Worksheet 01 -- Introductory Questionnaire
Worksheet 02 -- Genes in Populations
Worksheet 03 -- The Coalescent
Worksheet 04 -- Coalescent; E-M Algorithm
Worksheet 05 -- Haplotyping and Association Tests
Worksheet 06 -- Affected Sibpair Analysis
Worksheet 07 -- Multipoint Analysis
Worksheet 08 -- Inheritance Vector Based Linkage Analysis

Old Assignments -- These were updated in the Winter of 2005
   [Files: example.dat example.ped example-map.txt ]
Worksheet 09 -- Basics of the Elston Stewart and Lander Green Algorithms

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