Download MMG 232: Methods In Bioinformatics Spring 2016, 3 credits

MMG 232: Methods In Bioinformatics
Spring 2016, 3 credits
Wednesdays 12:00-3:00, Ira Allen Lecture Hall/MLK Room
Instructor: Julie Dragon, PhD
Director, Bioinformatics Shared Resource (BSR)
4 Hills Building (ground floor)
802-656-7777; [email protected]
Office hours by appointment
“The course provides a methodological survey of bioinformatics techniques. Particular
emphasis is given to popular bioinformatics applications. The final project of the course
will be to demonstrate an understanding of bioinformatics approaches within the context
of a biological scenario.”
MMG232
Date
Syllabus
Topic
20-Jan Applied Bioinformatics
27-Jan Biological Databases
Functional Domains & Sequence
3-Feb Similarity
Sequence Alignment & Mapping:
10-Feb Microbiome
17-Feb Phylogenetics
24-Feb Metagenomics
2-Mar Mid-Term Projects
9-Mar Spring Break
16-Mar Structural Variation
Gene Expression & Comparative
23-Mar Genomics
30-Mar Copy Number Variation
6-Apr Molecular Interactions
13-Apr Genomic variation
20-Apr Gene annotation
27-Apr Genome Wide Association Studies
4-May Presentations
Discussion
Survey bioinformatics applications &
databases
Database mining (continued)
BLAST searches and Protein visualization
Amplicon sequencing & OTU identification
Inferring evolutionary history
Metagenomics: the complete picture
What have you learned so far?
Structural changes & DNA integration:
inversion/translocation & viral insertion
The effects of differential gene expression
Identification of copy number variations and
their impact on disease
Protein binding sites and chromosomal
conformation
Is a variant real: frequentist vs bayesian
models
Variant annotation and functional
consequences
The association of genotype and phenotype
Wrapping the tools together!
This course provides a methodological survey of bioinformatics techniques. Particular
emphasis is given to popular bioinformatics applications. Classes will include about an
hour of theory/background, followed by an hour of hands on bioinformatics tool
application at your laptop. Lastly we will summarize what we did and review any
confusing points.
This is not a course for learning to program. Most activities will involve databases and
freeware with web-interfaces, or limited commercial software. I cannot guarantee that you
will learn to use your favorite bioinformatics tool or learn to analyze your own genomics
data, though I can work with folks who have their own data to include those in their
project.
Your grade will be based on 1) attendance and participation (20%), 2) the mid-term
project (40%), and 3) the final project (40%). The projects will require you to employee a
set of bioinformatics tools to address a question. Your comprehension of bioinformatics
methods will be assessed by the competency and depth at with which you apply
appropriate bioinformatics tools.