Class Notes

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
  • Haplotype phasing by EM old lecture class notes [pdf]
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 LD-select Algorithm
  • Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium [PDF]
10/10 SNP Tagging, LD-select, Informativeness; The LD-Select algorithm (cont); Tagging SNPs selection algorithm based on "Informativeness": Set Cover based Algorithm
10/15 Informativeness
  • Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies [PDF]
  • Optimal Haplotype Block-Free ... Supplemental Proof[PDF]
  • Optimal Haplotype Block-Free ... Supplemental Informativeness[PDF]
10/17 Urn Models, Wright Fisher, Ewens Sampling Lemma
  • Urn Models, Wright Fisher, Ewens Sampling Lemma [pdf]
10/22 Markov Chains, adding mutations to urn models, GWAS
  • Computational Workflows for Genome-Wide Association Studies I [pdf] and II [pdf]
  • Markov chains intro [pdf]
  • URN MODELS in GENETICS: Wright-Fisher Models and the Ewens Sampling Lemma [pdf]
  • A tutorial on hidden Markov models [pdf]
10/24 Population Genetics and the Hardy-Weinberg model
  • Population Genetics: The Hardy-Weinberg Model [pdf]
  • Population Genetics: The Hardy-Weinberg Model for Two Loci [pdf]
10/29 Haplotype assembly
  • Theory and algorithms for the haplotype assembly problem (Schwartz survey) [PDF]
  • The diploid genome sequence of an individual human (Levy et al. algorithm) [PDF]
  • HapCUT: an efficient and accurate algorithm for the haplotype assembly problem (HapCUT algorithm) [PDF]
10/31 Spooky haplotype assembly
  • HapCompass: A fast cycle basis algorithm for accurate haplotype assembly of sequence data (HapCompass algorithm) [PDF]
11/5 polyploid haplotype assembly; recombination in li-stephens model

Midterm prep. class summary

  • Haplotype assembly in polyploid genomes and identical by descent shared tracts [PDF]
11/7 Introduction to the Coalescent - 1. The Basic Coalescent (without recombination)
  • In-class notes
11/12 Calculating probabilities of ancestral events (e.g. coalescence) in the basic coalescent using the Wright-Fisher model.
  • In-class notes
11/14 The Coalescent with recombination, the Ancestral Recombination Graphs (ARGs) and the Miniciello-Durbin Algorithm - Part I
  • In-class notes
  • Mapping trait loci by use of inferred ancestral recombination graphs [HTML]
11/19 Minichiello-Durbin algorithm II; ancestral recombination graphs
  • Minichiello-durbin algorithm [pdf]
  • Mapping trait loci by use of inferred ancestral recombination graphs [HTML]
12/17 at 2pm Final Project Presentations
  • Please note the presentations will be due on the 17th but the final project may be handed in anytime up until the 21st at noon.
12/21 ALL final project materials due