Tentative Schedule

	Date	Lecture Topics	Reading	Assignments
Week #1	Feb 12, Tue Feb 14, Thur	Introduction to molecular biology and genetics, biological databases, and high-throughput data sources. Overview of bioinformatics problems. Lecture Slides Syllabus	Class Web Page Bioinformatics - An Introduction for Computer Scientists Introduction to Molecular Biology More reading on cells and genomes: Cells and Genomes How cells read the genome
Week #2	Feb 19, Tue Feb 21, Thur	Pairwise sequence alignment algorithms: Dynamic programming Lecture Slides Sequence alignment C code Sample input for alignment	Pairwise Sequence Alignment
Week #3	Feb 26, Tue Feb 28, Thur	Statistical significance of alignments Lecture Slides Suffix Trees, Suffix Arrays Lecture Slides	Statistical Significance of Alignments Statistical Significance of Alignments (Reading 2) Fast alignment with Burrows-Wheeler transform
Week #4	Mar 5, Tue Mar 7, Thur	Patterns, Profiles, and Multiple Alignments Hidden Markov Models Lecture Slides	Chapter 6 from the textbook A recent applications note about profile Hidden Markov Models	Assignment #1 DUE DATE: March 21, 23:55 via ODTU-Class
Week #5	Mar 12, Tue Mar 14, Thur	Hidden Markov Models continued
Week #6	Mar 19, Tue Mar 21, Thur	Multiple Sequence Alignment Algorithms Week 5 Lecture Slides Continued		Assignment #2 DUE DATE: April 4, 23:59 via ODTU-Class
Week #7	Mar 26, Tue Mar 28, Thur	Phylogenetic trees Lecture Slides
Week #8	Apr 2, Tue Apr 4, Thur	Phylogenetic trees continued. Midterm review on Tuesday Midterm Exam (at 18:00 on April 5 Friday) Sample midterm
Week #9	Apr 9, Tue Apr 11, Thur	Introduction to protein structures Lecture Slides		Assignment #3 DUE DATE: April 21, 23:59 via ODTU-Class
Week #10	Apr 16, Tue Apr 18, Thur	Protein Structure Prediction Structural Alignment of Proteins Lecture Slides (continued)
Week #11	Apr 23, Tue Apr 25, Thur	Microarray data analysis Clustering techniques Lecture Slides K-means Empty Cluster Example K-means Demo Self Organizing Maps Demo	RNA-Seq differential expression analysis RNA-Seq differential expression in Bioconductor Microarrays Intro Paper - 1 Microarrays Intro Paper - 2 Microarrays Intro Paper - 3	Assignment #4 DUE DATE: May 14, 23:59 via ODTU-Class
Week #12	Apr 30, Tue May 2, Thur	Introduction to Systems Biology Lecture Slides	Reading: Algorithmic Systems Biology A systems view of protein-protein interactions A systems view of metabolism A systems view of regulatory mechanisms
Week #13	May 7, Tue May 9, Thur	Analysis of biological networks Lecture Slides
Week #14	May 14, Tue May 16, Thur	Final review.