Statistical Methods in Molecular Biology

UW Madison Statistics 992-2 (877) Spring 2008

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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