Statistics 166/366

Statistical Models in Biology

Spring 2010 ● Mon, Wed 11:00AM - 12:15PM ● McCullough 122

Professor Nancy Zhang

Announcements

Final project presentations will be Friday, June 4, 3-6 pm. Click here for the schedule of presentations. The location is Sequoia Hall 200.

Contacts

		Office / Office hours
Instructors	Nancy Zhang (nzhang)	Sequoia 141, 1:30-2:30 PM Mondays

TA	Hao Chen (haochen)	Sequoia 231, 4-5 PM Wednesdays

Pre-requisite

Basic probability and statistics at the level of Stats 116 and Stat 200.

Tentative Syallabus (Links will work after the lecture)

Week		Date	Topic	Reading	Slides / code
1
	1	29-Mar	Introduction, course logistics	Stat & Prob primer [by Woolfe et al.]	Slides, notes
	2	31-Mar	EM	Dempster et al. JRSSB, 1977.	Slides \| R code

	3	5-Apr	Estimating isoform expression. Guest lecturer: Hui Jiang, Stanford Univ.	Jiang and Wong, Bioinformatics, 2009.	Slides
	4	7-Apr	Hidden Markov Models	HMM tutorial by Rabiner	Slides
3
	6	14-Apr	HMM example I: DNA copy number estimation	Fridlyand et al., JMV, 2004. Lai, Xing and Zhang, Biostatistics, 2007.	Slides

	5	12-Apr	HMM example II: fastPHASE	Scheet & Stephens, AJHG, 2006.	Slides
4
	7	19-Apr	Monte Carlo integration, rejection method		Slides \| R code
	8	21-Apr	Rejection method example: coalescent	Tavare et al. Genetics, 1997.	Slides
5
	9	26-Apr	Metropolis-Hastings algorithm	Chib & Greenberg, American Statistician, 1995.	Slides
	10	28-Apr	Gibbs sampling	Casella & George, American Statistician, 1992.	Slides, R code
6
	11	3-May	Metropolis-Hastings example	Pritchard et al., Genetics, 2000.	Slides, movie
	12	5-May	Gibbs sampling example	Liu et al., JASA, 1995.	Slides, notes
7
	13	10-May	Network models in biology Guest lecturer: Jie Peng, UC Davis	Peng et al., AOAS, 2009.	Slides, notes
	14	12-May	Network models in biology. Guest lecturer: Haiyan Huang, UC Berkeley	Huang et al., PNAS, 2010	Slides
8	13	17-May	Bootstrap	Efron & Tibshirani. Stat. Sci, 1986.	Slides, R code, mammal.txt
	14	19-May	Bootstrap example: phylogenetic analysis	Felsenstein, Evolution, 1985.	Slides
9
	15	24-May	Scan statistics for genome-wide profiling.	Zhang, 2010, Frontiers in Computational and Systems Biology	Slides
	16	26-May	Multi-sample scan statistics and data integration.	Zhang et al., Bioinformatics 2010.	Slides
10
	19	31-May	Project presentations
	20	02-June	Project presentations

Textbook

There are no required texts for this class. Reading materials to complement the lectures will be posted here or distributed in class. Below is a partial list of books that covers some of the topics at a more advanced level.

· Statistical Analysis with Missing Data by Little & Rubin

· Computational Statistics by Givens & Hoeting

· An Introduction to the Bootstrap by Efron & Tibshirani

· Monte Carlo Strategies in Scientific Computing by Jun Liu

Course requirements

There will be three assignments, and one final projects. All will require some programming with R.

Homework 1. (Due April 26) Solutions

Homework 2. (Due May 10)

Homework 3. (Due May 26) X.txt, XY.txt

Final Project Guidelines (Due June 4, 3 pm)

Grading