Tentative Schedule

	Date	Lecture Topics	Reading	Assignments
Week #1	Feb 7, Tue Feb 10, Fri	Course Introduction Introduction to biology, biological databases, and high-throughput data sources. Overview of bioinformatics problems. Sequence Alignment	Class Web Page Bioinformatics - An Introduction for Computer Scientists Reading on Homology
Week #2	Feb 14, Tue Feb 17, Fri	Pairwise sequence alignment algorithms: Dynamic programming Database searches: BLAST	ISMB Tutorial on Sequence Analysis NCBI Handbook on BLAST Interesting article on BLAST	Assignment #1 Due Feb 24
Week #3	Feb 21, Tue Feb 24, Fri	Statistical significance of alignments - Part I Statistical significance of alignments - Part II	Recommended Reading from the book Handook of Statistical Genetics: Statistical Significance in Biological Sequence Comparison Additional Readings: Statistics of BLAST Making sense of score statistics for sequence alignments Statistical significance in biological sequence analysis
Week #4	Feb 28, Tue Mar 3, Fri	Suffix trees Suffix arrays	Lecture Notes on Suffix Trees A short note on Suffix Trees by Dan Gusfield Alignment of Whole Genomes Using Suffix Trees A paper on Suffix Trees and their applications	Assignment #2 Due March 17
Week #5	Mar 7, Tue Mar 10, Fri	Multiple sequence alignment Review for Midterm Practice Questions	Lecture notes on multiple alignment A survey on recent techniques A comparative study on MSA
Week #6	Mar 14, Tue Mar 17, Fri	Midterm Exam I Solutions for the Midterm Exam Phylogenetic trees	Origins of Europeans
Week #7	Mar 21, Tue Mar 24, Fri	Phylogenetic trees continued Introduction to protein structures, structure prediction Protein structures, secondary structure prediction	Phylogeny of Chain Letters	Assignment #3 Due March 31
Week #8	Mar 28, Tue Mar 31, Fri	Pairwise protein structural alignment	A survey on structure comparison Another survey on structure comparison DALI paper STRUCTAL paper A paper about conducting flexible structural alignments
Week #9	Apr 4, Tue Apr 7, Fri	Geometric hashing, Multiple Structural Alignment Geometric hashing (continued)	Geometric Hashing: an overview Geometric Hashing for pairwise protein structure alignment Geometric Hashing for multiple protein structure alignment
Week #10	Apr 11, Tue Apr 14, Fri	Structural motif finding. Protein Structure Classification	Example motifs GASPS: a tool for 3d motif finding Using fragment transformation for discovering variable motifs
Week #11	Apr 18, Tue Apr 21, Fri	Microarray data analysis, clustering techniques. Clustering techniques: k-means, hierarchical clustering, and Self-organizing Maps	Microarray intro paper #1 Microarray intro paper #2 Microarray intro paper #3
Week #12	Apr 25, Tue Apr 28, Fri	Gene regulatory networks Midterm Exam II Solutions for the Midterm Exam
Week #13	May 2, Tue May 5, Fri	Biological pathways. Construction of large scale protein networks Yeast-two-hybrid movie Computing the interaction likelihood from microarray experiments Analysis of Protein Networks Using Monte Carlo sampling	A Bayesian Network approach for predicting protein interactions A probabilistic functional network of yeast genes	Assignment #4 Due May 24
Week #14	May 9, Tue May 12, Fri	Analysis of protein networks: Random Walks on Graphs Finding best paths of length k	Color coding paper