CSE 648 - Computational Biology 
		Lecture Schedule - Fall 2000

date	subject		lecture topic				primary reading	
----	-------		-------------				---------------
9/5	Preliminaries	Biology for Computer Scientists		Watson
9/7	"		Computer Science for Biologists		Gusfield

9/12	"		Genbank and Bio-perl tools 		(students)
9/14	Fragment asmbly	Data structures for sequences		Gusfield

9/19	"		Shortest common superstring		Gusfield
9/21 	"		Phrap, Drosophila assembly		(students)

9/26	Homology search Exact string matching 			Gusfield
9/28	"		Pairwise alignment (*)			Gusfield

10/3	"		Multiple sequence alignment		Durbin
10/5	"		BLAST, FASTA, GCG			(students)

10/10	Gene prediction	Statistical and homological approaches	Durbin
10/12	"		Hidden Markov Models			Durbin

10/17	"		Genmark, Grail				(students)
10/19	Array analysis	Affymetrics/Microarrays			Gusfield

10/24	"		Tour of DNA Microarray Facility		
10/26	"		Sequencing by Hybridization		Gusfield

10/31	"		Clustering and time series analysis	Gusfield
11/2	"		Microarray analysis software		(students)

11/7	Folding		Lattice and energy models		Bishop/Rawlings
11/9	"		Threading approaches			Bishop/Rawlings

11/14	"		RNA/protein folding programs, CASP-3	(students)
11/16	Proteomics	Protein motifs				Bishop/Rawlings

11/21	"		Docking and drug discovery		Bishop/Rawlings
11/23	Thanksgiving (class cancelled)

11/28	"		Mass Spectrometry
11/30	"		Swiss Prot, PDB				(students)

12/5	Phylogenies	Distance metrics			Durbin
12/7	"		parsimony methods			Durbin

12/12	"		Genome rearrangements			Gusfield
12/14	"		Phylip and PAUP				(students)


(*) Possible substitute lecturer