Statistics 246 Statistical Genetics Spring 2006

Lectures: TueThu 11:00 a.m.-12:30 p.m., 330 Evans Hall;

Lab: Fri 11:00-1:00, 330 Evans Hall.


Outline
The course will have four parts, each taking roughly one quarter of the semester.
The order of topics given below will not necessarily be that of the lectures.
Some biological background will be given in class, but in general students will
be expected to obtain this through independent reading.

A. Statistical genetic analysis

B. Molecular evolution

C Analysis of GeneChip data

D Finding cis-regulatory modules and motifs


Assessment
Homeworks and labs will contribute 50% to the grade.
The remaining 50% will be for a project to be decided upon  after discussion          
with the instructor. All homeworks, labs and projects are to be handed in before
the last day of instruction.  There will be no final.

Instructor: Terry Speed, 327 Evans Hall, terry@stat.berkeley.edu
Office hours: MF 9-10.

NOTES

Week 1:  The statistics of DNA identification. Lecture 1: Basic notions and Hardy-Weinberg Equilibrium (.pdf)
Lecture 2: Linkage and Linkage Equilibrium (LE) (.pdf)    

Week 2:  Lecture 1: LE for 3 loci. Errors. (.pdf)                                                                                                                                                                 Lecture 2: J M Butler's slides illustrating forensic DNA typing using STRs. (.pdf)

Week 3: Lecture 1: Meiosis and recombination (.pdf)                                                                                                                                                        Lecture 2: Genetical interference (.pdf)

Week 4:  Lecture 1: The Chi-squared model for recombination, and its extensions (.pdf)                                                                                                  Lecture 2: Introduction to genetic mapping in inbred strains (.pdf) using HMMs (rabiner.pdf)

Week 5: Lecture 1: Mapping mouse coat color genes (.pdf)                                                                                                                                               Lecture 2: Introduction to molecular evolution (.pdf)    

Week 6: Lecture 1: More on molecular evolution (.pdf)                                                                                                                                                     Lecture 2: Inferring trees and estimating rate matrices (.pdf)  Neighbour-joining proof (.pdf)

Week 7:  Lecture 1: Gene and species tree reconciliation - beta-globin and SERA genes (.pdf)                                                                               Lecture 2: The SERA genes completed (.pdf)
    
Week 8:  Lecture 2: Oligonucleotide microarrays for quantifying mRNA abundance (.pdf)

Week 9: Lecture 1: Low level analysis of Affymetrix microarray expression data (.pdf)                                                                                          Lecture 2: Summarizing many probe intensities (.pdf)

Week 10: Lecture 1: Background models and GCRMA (.pdf)                                                                                                                               Lecture 2: Moderated t-statistics (.pdf)

Week 11: Spring break

Week 12: Lecture 1: Transcriptional regulation, by Greg Hather (.pdf)                                                                                                                  Lecture 2: Tiling arrays, ChIP and localizing protein-DNA interaction, by Richard Bourgon (.pdf)

Week 13: Lecture 1:  Introduction to motif representation and detection (.pdf)                                                                                                          Lecture 2: Methods for the discovery of cis-regulatory modules. Introduction (.pdf)

Week 14: Lecture 1: Methods for the discovery of cis-regulatory modules, 2. The Liu-Neuwald-Lawrence Gibbs sampler (.pdf)                         Lecture 2: Methods for the discovery of cis-regulatory modules, 3. The Wu-Xie Gibbs sampler (.pdf)  

Week 15:  Lecture 1: Methods for the discovery of cis-regulatory modules, 4. Comparative genomics (.pdf)
Lecture 2: Finding and validating a cis-regulatory module in humans (.pdf) to be posted when the accompanying ms is accespted.

Week 16: Lecture 1: Linear models to discover cis-regulatory modules (.pdf)                                                                                                        Lecture 2: Joint modelling of promoter elements  and expression data, by Nancy Zhang (.pdf)

Week 17: Some results on transcriptional regulation in mammalian systems, with assistance from Sam Wormald (.pdf)
to be posted when the accompanying ms is accepted.