Here is the running class notes for Spring 2019. For your reference, we left the notes from previous semesters below.
Lecture/Date  Topic  Slides and Notes  Suggested Readings 

9/10  Variation and the human genome 
Denotes seminal work Denotes review article 

9/12  Variation and the human genome; causality  
9/17  Linkage disequilibrium  
9/19  LD, Haplotype phasing, data 


9/24  Haplotype Phasing by EM  
9/26  Haplotype Phasing by EM 


10/1  Haplotype Phasing by EM 


10/3  Haplotype Phasing by Identity by Descent 


10/8  Tagging SNPs selection algorithm based on r^2: The LDselect Algorithm 


10/10  SNP Tagging, LDselect, Informativeness; The LDSelect algorithm (cont); Tagging SNPs selection algorithm based on "Informativeness": Set Cover based Algorithm 


10/15  Informativeness  
10/17  Urn Models, Wright Fisher, Ewens Sampling Lemma 


10/22  Markov Chains, adding mutations to urn models, GWAS 


10/24  Population Genetics and the HardyWeinberg model 


10/29  Haplotype assembly  
10/31  Spooky haplotype assembly 


11/5  polyploid haplotype assembly; recombination in listephens model 


11/7  Introduction to the Coalescent  1. The Basic Coalescent (without recombination) 


11/12  Calculating probabilities of ancestral events (e.g. coalescence) in the basic coalescent using the WrightFisher model. 


11/14  The Coalescent with recombination, the Ancestral Recombination Graphs (ARGs) and the MinicielloDurbin Algorithm  Part I 


11/19  MinichielloDurbin algorithm II; ancestral recombination graphs 


12/17 at 2pm  Final Project Presentations 


12/21  ALL final project materials due 