Biostatistics & Medical Informatics 576
Computer Sciences 576
Introduction to Bioinformatics (Fall 2017)

General Course Information
Course overview
Announcements
Syllabus, Readings, Lecture Notes
Schedule
Homework Assignments
Grading criteria
DNA

Tentative Course Schedule

Week Date Section Lecture topicsHW assigned HW due
1 9/7 Introduction Class Overview
2 9/12 Molecular biology 101
9/14 Sequence assembly Sequence assemblyHW0
3 9/19 Sequence assemblyHW1HW0
9/21 Sequence assembly
4 9/26 Sequence alignment Pairwise sequence alignment
9/28 Pairwise sequence alignment
5 10/3 Intro to Probability for Discrete Variables
10/5 Heuristic methodsHW2HW1
6 10/10 Multiple sequence alignment
10/12 Multiple sequence alignment
7 10/17 Phylogenetic Trees Intro to Phylogenetics
10/19 Distance-based methods (Neighbor Joining algorithm)HW3HW2
8 10/24 Parsimony methods
10/26 Probabilistic methodsHW3
9 10/31 Mid-term Mid-term
11/2 Genome annotation Introduction to sequence annotation/Markov models
10 11/7 Hidden Markov models: forward/backward/viterbi algorithmHW4
11/9 Hidden Markov models: Parameter estimation
11 11/14 Applications of Markov models (ChromHMM)
11/16 Clustering of omic datasets Introduction to "omic" datasets and Flat Clustering
12 11/21 Gaussian mixture model-based clusteringHW5HW4
11/23 Thanksgiving. No class.
13 11/28 Hierarchical clustering, Cluster evaluation, and Clustering in practice
11/30 Modeling and analysis of networks Introduction to biological networks
14 12/5 Bayesian networksHW6HW5
12/7 Bayesian networks
15 12/12 Bayesian networksHW6
12/21 Final Exam Final Exam