TENTATIVE SCHEDULE FOR INTRO TO
BIOINFORMATICS (BMI/CS 576) Fall 2013 
Date 
Section 
Lecture topics 
3Sep 
Introduction 
Introduction to computational biology/class overview 
5Sep 

Molecular biology basics/Genomic sequence problems 
10Sep 
Sequence alignment 
Pairwise Sequence alignment 
12Sep 

Sequence alignment 
17Sep 

Sequence alignment in practice 
19Sep 

Multiple sequence alignment 
24Sep 

Sequence alignment in practice 
26Sep 
Evolutionary processes and phylogenetic trees 
Phylogenetic trees 
1Oct 

Phylogenetic trees 
3Oct 

Phylogenetic trees 
8Oct 

Phylogenetic trees in practice 
10Oct 

Midterm 
15Oct 
Annotating genomes 
Markov models 
17Oct 

Hidden Markov models 
22Oct 

HMMs 
24Oct 

HMMs in practice 
29Oct 
Clustering approaches to analyzing Omic datates 
Functional genomics 
31Oct 

Clustering 
5Nov 

Clustering 
7Nov 
Modeling and learning regulatory networks 
Network intro 
12Nov 

Modeling networks: Probabilistic graphical models 
14Nov 

Probabilistic graphical models: Dependency networks,
Markov networks 
19Nov 

Regression methods 
21Nov 

Network inference in practice 
26Nov 
Network analysis and applications 
Network properties 
28Nov 

thanksgiving 
3Dec 

Networks in diseases 
5Dec 

Networks to integrate data/study perturbations 
10Dec 

Networks to integrate data/study perturbations 
13Dec 

Class review 
15Dec 

Final exam 