CAP 5510: Introduction to Bioinformatics
 

Lecture: MW 1:30PM - 2:45PM

Location: BA 209

Instructor: Dr. Haiyan Nancy Hu

Email: haihu@cs.ucf.edu

Office: HEC- 233

Phone Number: 407-882-0134

Office Hours: MW 10:00AM - 11:00AM

 
 

Description:

This course will introduce students to the rapidly developing bioinformatics field, and will train graduate students so that they are aware of current research problems in bioinformatics and they are prepared to develop more advanced methods and tools for bioinformatics applications.
Bioinformatics is an active and interdisciplinary research area. This course is open to all students with background such as computer science, biology, mathematics or statistics who are interested in bioinformatics research.

 

Prerequisite:

No formal prerequisite and open to all graduate students.

 
 

Book Reference:

Durbin, Eddy, Krogh, Mitchison "Biological Sequence Analysis"
Gusfield "Algorithms on Strings, Trees, and Sequences"
 

Grading:

Assignments (30%), Midterm (20%) and Final project (50%).

 

Preliminary Schedule:

Date Topic Notes and References*
W1: 08/22 Introduction/Administrivia Notes
08/24 DNA the genome Notes
W2: 08/29 Sequence alignment and dynamic programming Notes
08/31 Sequence alignment and BLAST Notes,
W3: 09/05 Labor day, no class  
09/07 Sequence alignment and Hidden Markov Model Notes
W4: 09/12 Sequence alignment and Hidden Markov Model Notes,
09/14 Sequence alignment and Hidden Markov Model Notes,
W5: 09/19 Conditonal Random Fields
09/21 Context Free Grammars Notes
W6: 09/26 Gene Regulation Notes,
09/28 motif finding Notes;
W7: 10/03 motif finding Notes,
10/05 motif finding Notes,
W8: 10/10 motif finding Notes,
10/12 motif finding Notes,
W9: 10/17 midterm
10/19 mRNA gene expression Notes,
W10: 10/24 functional element prediction Notes,
10/26 gene expression data analysis Notes
W11: 10/31 clustering Biclustering Notes;
11/02 Cancer classification using gene expression data Notes;
W12: 11/07 Gene ontology and function annotation

Notes;
11/9 Gene ontology and function annotation Notes,

W13: 11/14 Most current topics Notes;
11/16 Most current topics
W14: 11/21 Most current topics
11/23 Most current topics
W15: 11/28 Most current topics
11/30 Most current topics