02-711 Computational Molecular Biology and Genomics

1/12/09	- The first class will be held on Monday, 10:30-12:50 in Mellon Institute 409. See you there!
1/14/09	- Sign up for scribing here. Click Here - Quiz on Wednesday! - No class on Monday 1/19/09 (MLK)
1/19/09	- Supplemental readings for last Wednesday (1/14/09) is available for pick up in front of 411L
1/30/09	- Website is back in our control again - Handouts for the lecture 1-5 is out - Recitation slides is up on the syllabus section - Solution for quiz #1 is up
2/8/09	- Handouts (6,7, and 8) and scribe (6-7) is out.
2/9/09	- Handout 8 is updated to reflect new content added in the lecture - Project proposal is due 2/16/09
2/27/09	- Handouts and readings are now posted online - Practice midterm and solution is available - Midterm on Monday 3/2/09
4/2/09	- Updated scribing schedule. Click Here

This course provides an advanced introduction to computational molecular biology and genomics. The course particularly focuses on computational methods relevant to: (1) sequencing - DNA sequencing and genome assembly; (2) genetic variation - coalescent theory, haplotype inference, allele frequency estimation; (3) phenotypic variation - linkage analysis, association studies; and (4) evolution - multiple sequence alignment, comparative genomics, phylogeny reconstruction.

Students are expected to have the following background:

• Knowledge in basic principles and skills in computer science (15-211, 15-451) and in biology (03-121)
• Familiarity with basic probability theory and linear algebra.

Lecture: Mon Wed 10:30-11:50am, Mellon Institute 409.
Discussion section: to be announced.

Professor: Su-In Lee
Office: Mellon Institute 411L
Office hours: Tuesday 9-10am
Phone: (412) 268-4659
Email: 4123silee@cs.stanford.edu3214 (remove numbers)

Teaching Assistant: Ming-Chi Tsai
Office: Mellon Institute 654F
Office hours: Wednesday, 3:30-4:30pm
Phone: (412) 368-9733
Email: 5129mingchit@andrew.cmu.edu9215 (remove numbers)

There are four course requirements:

1. Miderm. The midterm will cover the material of the first part of the course.
2. Project. The term project may be done with 1-2 partners. Students should submit proposal (due 2/9), milestone (due 3/23) and final report (in the final week). Projects will be presented to the class during the final 1-2 days of the course.
3. Quiz. Each Wednesday (except in exam weeks), there will be a 10-15 minutes quiz over the material covered in the previous week.
4. Scribing. Each class will be scribed by a student. The scribed notes are due end of the week in which the lecture is given. Please sign up to scribe a particular lecture beforehand and email the scribed note to TA as an attachment.

Grades will be determined: 20% midterm, 60% project, 10% quiz and 10% scribing.

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	Date	Material Covered	Reading	Scribe	Handouts
1	1/12/09	Introduction
		0. Mathematical tools
2	1/14/09	Probability theory review and probabilistic models	Koller and Friedman (Ch. 2, pg. 29-62)
3	1/21/09	Probabilistic models	Koller and Friedman	Class3	Quiz 1; Solution
4	1/26/09	Maximum likelihood estimation	Koller and Friedman	Class4
5	1/28/09	Expectation maximization	Prof Andrew Ng's CS229 lecture note		Recitation Quiz 2
		1. Retrieving DNA sequence information
6	2/2/09	DNA sequencing and genome assembly		Class6
7	2/4/09	Genome assembly		Class7; Class 6-7 (v2)	Quiz 3
8	2/9/09	Whole-genome shotgun sequencing	ARACHNE (Batzoglou et al, 2002) Arachne 2 (Jaffe et al, 2003)	Class8
		2. Understanding genetic variation
9	2/11/09	Hardy-Weinberg equilibrium	Hartl and Clark (Ch. 2)		Quiz 4
10	2/16/09	Linkage disequilibrium I	Hartl and Clark (Ch. 2)	Class10
11	2/18/09	Linkage disequilibrium II	Hartl and Clark (Ch. 2)	Class11	Quiz 5; Solution
12	2/23/09	Introduction to coalescent models	Hudson et al, 1990	Class12; Class12 (v2); Class12 (v3)
13	2/25/09	Allele frequency distributions	Hudson et al, 1990	Class13	Quiz 6
	3/2/09	Midterm			Practice Midterm; Solution
14	3/4/09	Coalescent models with recombination	Hudson et al, 1990	Class14
15	3/16/09	Maximum Likelihood Estimate for Allele Frequencies		Class15
16	3/18/09	Expectation-Maximization	Stephens et al. AJHG 2001
17	3/23/09	Haplotype inference -- EM based algorithm	Excoffier and Slatkin. Mol Biol Evol 1995	Class17
18	3/25/09	Haplotype Inference	Clark. Mol Biol Evol 1990
		3. Genotype to phenotype
19	3/30/09	Association studies	Zaykin et al. Hum Hered 2002
20	4/1/09	Haplotype based association tests	Zaykin et al. Hum Hered 2002	Class20 Class20 (V2)
21	4/6/09	Indirect association; genotype imputation	Marchini et al. Nat Gen 2007	Class21 Class21a
		4. Evolution
22	4/8/09	Linkage Study		Class22
23	4/13/09	Linkage Study II		Class23
24	4/15/09
25	4/20/09	Multiple sequence alignment		Class25
26	4/22/09	Multiple sequence alignment
		5. Final project
	4/27/09	Final presentation I
	4/29/09	Final presentation II