Statistical Methods in Molecular Biology

UW Madison Statistics 992-2 (877) Spring 2008


 

Class overview  

Homework

Lectures

 

1

Jan 23/08

Newton

Background molecular biology

ppt

What is a gene, post-ENCODE? History and updated definition, by Gerstein et al. 2007

History of `gene’

2

Jan 28/08

Newton

Statistics of base calling

notes (pdf)

R scripts

Animation of Sanger sequencing

Li and Speed (2002) Ann. Statist.

Haan and Godsil (2000) IEEE.

Andrade-Cetto et al (2005) IEEE.pdf

3

Jan 30, 08

Newton

Statistics of alignment

notes (pdf)

R scripts

Arratia et al. (1990) Statist. Sci.pdf

 

4

Feb 4, 08

Larget

Introduction to phylogenetics and molecular evolution

pdf

 

5

Feb 6, 08

Larget

Models of molecular evolution; maximum likelihood estimation

pdf

 

6

Feb 11, 08

Ane

Bootstrapping phylogenies

 

 

7

Feb 13, 08

Larget

Bayesian phylogenetics

pdf

 

 

 

8

Feb 18, 08

Keles

Motif finding I

pdf [full set]

Lawrence et al (1993)

9

Feb 20, 08

Keles

Motif finding II

 

 

10

Feb 25, 08

Keles

 

 

 

11

Feb 27, 08

Keles

ChIP chip

 

 

 

 

12

Mar 3, 08

Splinter

Microarray technology

 

 

13

Mar 5, 08

Kendziorski

Preprocessing

ppt

 

14

Mar 10, 08

Kendziorski

Differential expression I (EBarrays)

 

 

15

Mar 12, 08

Newton

Differential expression II (multtest,locfdr,FDR,BH)

 

 

16

Mar 24, 08

Newton

Differential expression III (qvalue,cFDR,limma)

 

 

 

 

 

Spring break

 

 

17

Mar 26, 08

Newton

Gene set analysis

pdf

 

18

Mar 31, 08

Newton

Gene networks (graphical models; Gaussians; estimating large covariance matrices)

 

Schafer and Strimmer (2005a; 2005b)

Ledoit and Wolf (2001)

 

 

19

April 2, 08

Broman

B1 Meiosis and recombination

pdf (notes)

McPeek and Speed (1995)  (interference)

McPeek (1996)  (intro)

Speed (1997)  (map functions)

20

April 7, 08

Broman

B2 QTL mapping 1

 

 

21

April 9, 08

Broman

B3 QTL mapping continued

pdf (notes)

Broman (2002) (model selection)

Zeng et al (1999) (genetic architecture)

22

April 14, 08

Broman

Yandell

…part I concluded

Bayesian QTL

 

 

pdf

Reversible  jump details

 

Satagopan et al. (1996)

Sillanpaa (1998)

Yandell et al (2007)

Yi et al (2005)

Wang et al. (2005)

Sen and Churchill (2001)

23

April 16

Yandell

Bayesian QTL continued

 

 

24

April 21

Broman

B4 Linkage in humans

pdf (notes)

papers

25

April 23

Broman

B5 Allele sharing methods

pdf (notes)

papers

27

April 30

Broman

B6 QTL in humans

pdf (notes)

papers



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