Tentative Schedule

Week	Lecture Topics	Reading	Assignments
Week #1	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	Pairwise sequence alignment algorithms: Dynamic programming Lecture Slides Sequence alignment C code Sample input for alignment	Pairwise Sequence Alignment
Week #3	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	Assignment #1
Week #4	Patterns, Profiles, and Multiple Alignments Hidden Markov Models Lecture Slides	Chapter 6 from the textbook A recent applications note about profile Hidden Markov Models
Week #5	Hidden Markov Models continued
Week #6	Multiple Sequence Alignment Algorithms Week 5 Lecture Slides Continued		Assignment #2
Week #7	Phylogenetic trees Lecture Slides
Week #8	Midterm Exam (in class on May 3 Monday) Sample midterm
Week #9	Introduction to protein structures Lecture Slides
Week #10	Protein Structure Prediction Structural Alignment of Proteins Lecture Slides (continued)
Week #11	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
Week #12	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	Analysis of biological networks Lecture Slides
Week #14	Final review.