CSE 549 - Computational Biology 
		Tentative Lecture Schedule - Fall 2007
		Tuesday-Thursday 3:50-5:10PM -- E4315 Melville Library

date	subject		lecture topic				reading	  deadline
----	-------		-------------				-------   --------
9/4	Preliminaries	Biology for Computer Scientists		57-79
9/6	"		Computer Science for Biologists		1-54

9/11	"		Genbank and Bio-perl tools 		web-notes
9/13	Rosh Hashanah (class cancelled)

9/18	Assembly	Data structures for sequences		318-324   HW1 out
9/20 	"		Shortest common superstring		247-265

9/25	"		Phrap, Drosophila assembly		275-287
9/27	Projects Out

10/2	Homology search Exact string matching 			311-318
10/4	"		Pairwise global alignment 		147-177   HW1 in

10/9	"		Pairwise local alignment		177-184   
10/11	"		BLAST, FASTA, GCG			324-337   HW2 out

10/16	MIDTERM EXAM
10/18	Gene prediction	Statistical/homological approaches	193-211

10/23	"		Hidden Markov Models			387-397	
10/25	"		Genmark, Grail				397-407	  Proposal in

10/30*			Proteomics guest lecture (Rob Rizzo)
11/1*			Systems Biology guest lecture (David Green)

11/6	Array analysis	Affymetrics/Microarrays			339-343   HW2 in
11/8	"		Sequencing by Hybridization		265-275

11/13	"		Clustering and time series analysis	343-354   
11/15	"		Microarray analysis software		web-notes HW3 out

11/20	"		Tour of DNA Microarray Facility	(tent.)		  Progress in
11/22	Thanksgiving (class cancelled)

11/27	Proteins	Protein motifs, Swiss Prot, PDB		91-116
11/29	"		De novo and threading approaches	web-note  

12/4	Phylogenies	Distance metrics			354-368
12/6	"		parsimony methods			368-384

12/11	"		reversal sorting			125-142
12/13	"		student presentations / review 		1-417     Project in

12/20	Final Exam (2PM-4:30PM) 

(*) Possible substitute lecturer