Tu: Student presentation
|Papers presented: inference
of demographic history;
||Th: Student presentation
Tu: review and more applications and extensions
|Papers presented: Estimating
heterozygosity from sequences; inference
of population structure from haplotypes; analyze
incomplete lineage sorting and hybridization; MCMC
for coalescent likelihood computation; haplotype
||Th: Inference of population demographic
Tu: Recombination: the SMC model.
|The paper by Li
and Durbin, 2011.
The paper on SMC by McVean and Cardin.
||Th: Algorithms for building ARGs.
Tu: Recombination: galled tree. Heuristics.
on self-derivability and counting of minARGs.
Two galled tree papers: paper 1 and paper 2.
The heuristics on constructing ARGs is from: the paper by Song, Wu and Gusfield.
||Th: Discussion of projects.
Tu: Recombination: ancestral recombination graph and History bound.
|History bound was from the paper by Myers and Griffiths, and improved by Bafna and Bansal.|
||Th: PPH: perfect phylogeny haplotyping
Tu: Haplotype inference.
|The original PPH
paper by Gusfield.
The PHASE paper.
||Th: Lower bound on the minimum number of
Tu: Coalescent with recombination.
bound paper talked about in class by
Myers and Griffiths.
The paper on improved haplotype bound by Song, Wu and Gusfield.
Here is a chapter written by Gusfield about recombination. This provides some more accessible introduction to recombination to non-biologists
Here is a paper on coalescent ancestral configurations in recombination analysis.
Assignment: HW3 is out. Due: 3/27 in HuskyCT.
||Th: Markov chain Monte Carlo. Gusfield's
algorithm on perfect phylogeny.
Tu: Monte Carlo methods
paper on perfect phylogeny.
Wakeley's book: Ch. 8.4. Here is a paper on importance sampling.
||Th: The Griffiths-Tavare method.
Tu: Infinite sites model. The Griffiths-Tavare method.
|Wakeley's book, Ch. 8.4.
Importance sampling is a large topic in Monte Carlo methods. See, for example, this book chapter.
||Th: Ewens sampling formula (ESF)
Tu: Probability on coalescent: expected SFS; number of allele types on infinite alleles model.
|Wakeley's book, Ch. 4.1 and 4.2.
The paper on proof of ESF
Assignment: HW2 is out. Due: 3/3 in HuskyCT.
||Th: no class (snow day)
Tu: Coalescent and statistic for polymorphisms
|Wakeley's book, Ch. 4.1. Also, see
Wakeley's book Chapter
||Th: Basic probability for coalescent.
Tu: Varying population size.
|Variable population size is covered in Tavare's
book: up to page 24.
Basic probability: Chapter 2 of Wakeley's book (on reserve in the library). You really should read this chapter if you are not confident about probability.
||Th: Basic coalescent; properties .
Tu: Diffusion approximation on Wright-Fisher model.
book: up to page 24.
It does not cover much of diffusion process. So refer to this book chapter on diffusion on Wright-Fisher model. I feel it is more accessible than several other alternatives. Not surprisingly, it is mathematical, but if you can read it you will understand more.
Assignment: HW1 is out. Due: 2/13 in HuskyCT.
Wright-Fisher model. Probability
Tu: Introduction to population genetics.
Basic concepts and models.
book is now on reserve in the library.
Prof. Holsinger at UConn has lecture notes on population genetics.