Computational Genomics

Computational Genomics MSCBIO2070/02-710 (cross-listed as 10-810), Spring 2011

Ziv Bar-Joseph (8006 Gates Hillman Complex, Machine Learning Department, Carnegie-Mellon University)

Bino John (3080 BST-3, Department of Computational Biology, University of Pittsburgh)

Starting date: January 10, 2011
Class lectures: Mondays & Wednesdays from 1:30-2:50 pm
Location: From 1/10 to 2/21, lectures will be at BST3 3073. Starting from 2/23, lectures will be at CMU (Location: GHC 6501)
Teaching Assistants:
Aparna Kumar, aparnaku[AT]andrew.cmu.edu, 7407 Gates Hillman Complex, CMU; Office hours: Tue 11am-noon
Selen Uguroglu, sugurogl@cs.cmu.edu, 5501 Gates Hillman Complex, CMU; Office hours: Wed 5-6pm
Minli Xu minlix[AT]andrew.cmu.edu, 650 Mellon Institute, CMU; Office hours: Mon 4:15-5:15pm
Textbooks (suggested but not required): Durbin et al, Biological Sequence Analysis & Deonier et al, Computational Genome Analysis.
Course Summary and grading policies are listed here
Starting from 2/23, lectures will be at GHC 6501, CMU
Course Project page
Course Google Group, join this !

Date	Lecture Topics	Slides Download	Homeworks and Recitations
	Lectures will be at Pitt (BST3 3073)
1/10	Introduction to molecular biology	Lecture 1
1/12	DNA sequencing 1	Lecture 2
1/17	(Martin Luther King's Day, no class)
1/19	DNA sequencing 2 (Shot gun genome sequencing and assembly, sequencing by hybridization, BLAST analysis)	Lecture 3
1/24	Molecular evolution ( Molecular clock, selection tests, Evolutionary distance calculation using Jukes cantor & Kimura models)	Lecture 4
1/26 -> (1/30)	Phylogeny – Parsimony, Sankoff algorithm, Least square estimates for distances, Tree construction (UPGMA, and NJ)	Lecture 5
1/31	Scoring matrices, Pair wise Sequence alignment using DP (global, local, affine gap)	Lecture 6
2/2	Genomic features and their analysis: Fourier analysis for cyclic patterns (genes, nucleosome binding), Review of sensitivity/specificity concepts, Homolog search BLAST	Lecture 7
2/7	HMMs and their applications (Review of HMMs:Viterbi, Forward/Backward, and Baum, application to CpG islands)	Lecture 8
2/9	Applications of HMM (gene prediction, Higher order markov for DNA, Duration modeling, pair HMMs for alignment)	Lecture 9
2/14 (GHC 4405)	Applications of HMM 2 (pair HMMs – cont’d, profile HMMs, multiple sequence alignment)	Lecture 10
2/16	RNAs: structure prediction, microRNA, ncRNA	Lecture 11
2/21	motif discovery (Motif representation, Gibbs, EM)	Lecture 12
	From 2/23, lectures will be at CMU (Location: GHC 6501) [google map]
2/23	Microarrays (chip seq etc)	Lecture 13
2/28	Normalization, differentially expressed genes	Lecture 14
3/2	Differentially expressed genes	Lecture 15
3/7	(Spring Break, no class)
3/9	(Spring Break, no class)
3/14	Clustering	Lecture 16
3/16	Classification	Lecture 17	PS4 due
3/21	Classification II		Project proposals due
3/23	Mid-Term Exam (TA in charge: Selen)
3/28	Time series analysis	Lecture 18
3/30	RNA-Seq	Lecture 19	PS5 out (TA in charge: Selen)
4/4	Guest Speaker: Elodie Ghedin	Lecture notes
4/6	Regulatory networks	Lecture 20
4/11	Regulatory Modules	Lecture 21
4/13	Protein interactions	Lecture 22	PS5 due (Submission is extended to 4/14)
4/18	Genome variation
4/20	Project poster session, Location: TBD
5/3			Project report due at noon

Last Updated: 4/21/2011 1:13 PM