CSE 549 - Computational Biology 
		Tentative Lecture Schedule - Fall 2011
		Tuesday-Thursday 9:50-11:10PM -- SB Union 236

date	subject		lecture topic				reading	  deadline
----	-------		-------------				-------   --------
8/30	Preliminaries	Biology for Computer Scientists		57-79
9/1	"		Computer Science for Biologists		1-54

9/6*	"		Genbank and Bio-perl tools 		web-notes
9/8*	Systems Biology (David Green)

9/13	Assembly	Data structures for sequences		318-324   
9/15 	"		Shortest common superstring		247-265

9/20	"		Phrap, Drosophila assembly		275-287
9/22	Projects Out

9/27	Homology search Exact string matching 			311-318
9/29	Rosh Hashanah (no class)

10/4	"		Pairwise global alignment 		147-177   
10/6	"		Pairwise local alignment		177-184   

10/11	"		BLAST, FASTA, GCG			324-337   
10/13	MIDTERM EXAM

10/18	Gene prediction	Statistical/homological approaches	193-211
10/20	"		Hidden Markov Models			387-397	

10/25	"		Genmark, Grail				397-407	  Proposal in
10/27	Array analysis	Affymetrics/Microarrays			339-343   

11/1*	"		Sequencing by Hybridization		265-275
11/3	"		Clustering and time series analysis	343-354   

11/8	"		Microarray analysis software		web-notes
11/10	"		Tour of DNA Microarray Facility		Progress in

11/15	Proteins	Protein motifs, Swiss Prot, PDB		91-116
11/17	"		De novo and threading approaches	web-note  

11/22   Synthetic Biology (!)
11/24	Thanksgiving (class cancelled)

11/29	Phylogenies	Distance metrics			354-368
12/1	"		parsimony methods			368-384

12/6	"		reversal sorting			125-142
12/8	"		student presentations / review 		1-417     Project in

12/14	Final Exam (11:15AM-1:45PM) 

(*) Possible substitute lecturer
(+) Outside of normal class time
(!) New lecture