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