Tentative Schedule

	Date	Lecture Topics	Reading
Week #1	Sep 28, Wed	Course overview Introductory biology, key characteristics of biological data Lecture slides	Class Web Page Bioinformatics - An Introduction for Computer Scientists
Week #2	Oct 5, Wed	Next generation sequencing: Transcriptome assembly Lecture slides	RNA-Seq Intro IsoLasso paper
Week #3	Oct 12, Wed	Pathway Reconstruction Problem Lecture slides	SPINE paper
Week #4	Oct 19, Wed	Querying Biological Networks	Network Querying by Conditional Random Fieldspaper
Week #5	Oct 26, Wed	Text mining for PPI extraction	Text mining for PPI extraction
Week #6	Nov 2, Wed	Multiple protein structural alignment Lecture Slides	SMOLIGN paper
Week #7	Nov 9, Wed	Kurban Bayrami. NO CLASS
Week #8	Nov 16, Wed	Co-expression networks	Co-expression networks paper
Week #9	Nov 23, Wed	Microarray data classification	Microarray classification paper
Week #10	Nov 30, Wed	Project proposals are due on November 30 Genome-Wide Association Studies Decision trees AdaBoost	Genome-Wide Association paper
Week #11	Dec 7, Wed	Metabolic Pathway Analysis	Metabolic Pathway Analysis Paper
Week #12	Dec 14, Wed	Bioimage Informatics	Image Analysis Paper
Week #13	Dec 21, Wed	Student paper presentations
Week #14	Dec 28, Wed	Student paper presentations
Week #15	Jan 4, Wed	Project presentations Final exam of 20061 Final exam of 20081