CSE 549 - Computational Biology 
		Tentative Lecture Schedule - Fall 2013
		Tuesday-Thursday 4-5:20PM MELVILLE LBR W4330


date	subject		lecture topic				reading	  deadline
----	-------		-------------				-------   --------
8/27	Preliminaries	Biology for Computer Scientists		57-79
8/29	"		Computer Science for Biologists		1-54

9/3	Labor day after (no class)
9/5*	Rosh Hashana	Protein docking/interaction (Rob Rizzo)

9/10	"		Genbank and Bio-perl tools 		web-notes
9/12	Assembly	Data structures for sequences		318-324   

9/17 	"		Shortest common superstring		247-265
9/19	"		Phrap, Drosophila assembly		275-287

9/24	Projects Out
9/26	Homology search Exact string matching 			311-318

10/1	"		Pairwise global alignment 		147-177   
10/3	"		Pairwise local alignment		177-184   

10/8	"		BLAST, FASTA, GCG	324-337   
10/10	MIDTERM EXAM

10/15	Gene prediction	Statistical/homological approaches	193-211
10/17	"		Hidden Markov Models			387-397	  Proposal in

10/22*	"		Genmark, Grail				397-407	  
10/24*	Array analysis	Affymetrics/Microarrays			339-343   

10/29	"		Sequencing by Hybridization		265-275
10/31	"		Clustering and time series analysis	343-354   

11/5	"		Microarray analysis software		web-notes
11/7	"		Tour of DNA Microarray Facility (?)	Progress in

11/12	Proteins	Protein motifs, Swiss Prot, PDB		91-116
11/14	"		De novo and threading approaches	web-note  

11/19	Phylogenies	Distance metrics			354-368
11/21	"		parsimony methods			368-384

11/26*	RNA folding/Synthetic Biology? (Ruhksana Yeasmin)
11/28	Thanksgiving (class cancelled)

12/3	"		reversal sorting			125-142
12/5	"		reviews					1-417
12/6+	student presentations						     Project in

12/16+	Final Exam (2:15PM-5M) 

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