CAP 5991: Introduction to Bioinformatics (3 cr)

Fall 2003

 

Instructor Information

Instructor: Giri Narasimhan, ECS 389, Phone x-3748, Office Hours: Thursday 11AM - 12:30 PM.

Course Web Page: http://www.cs.fiu.edu/~giri/teach/5991F03.html 

Justification & Course Overview

 

This is an introductory graduate course in Bioinformatics. The idea is to teach standard tools and techniques used to analyze and interpret Bioinformatics data.

 

Prerequisite Knowledge

 

Data Structures & Algorithms (COP 3530 or equivalent), Discrete Math (MAD 2104 or equivalent), Probability & Statistics (STA 3033 or equivalent).

 

Topics

 

·        Fundamentals of Biology, Statistics, and the Internet

·        Overview of Bioinformatics, Computational Biology and Biotechnology

·        (*) Databases and Software Packages, BioPerl and BioJava.

·        (*) Sequence Alignment: problems and algorithms; Multiple Sequence Alignment

·        (*) Phylogenetic Analysis

·        Sequencing and Mapping

·        (*) Predictive Methods: Nucleotide Sequences and Protein Sequences

·        (*) Pattern Discovery Techniques and applications

·        (*) Machine Learning Methods: Neural Networks, Hidden Markov Models, Self-Organizing Maps, Support Vector Machines, etc.

·        (*) Molecular Structural Analysis

·        (*) Analysis of Gene Expression Data

·        Image Processing & Mathematical Modeling.

The course will contain a lab component to learn Bioinformatics analysis tools. The tentative list of topics covered by the lab component are marked with a (*). Evaluation will include several homework assignments, exams and a semester project.

 

Evaluation

• Exams: 20%

• Homework: 20%

• Semester Project: 50%

• Class Participation: 10%

 

Texts and References

 

[Required]

·        Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Eds. A. D. Baxevanis and B. F. Ouellette, Wiley Interscience, 2^nd ed., 2001. ISBN: 0471383910

·        Bioinformatics – Sequence & Genome Analysis, David Mount, CSHL Press, 2002, Paperback, ISBN: 0879696087

 [Reference]

·        Computational Molecular Biology, P. Pevzner, MIT Press. 

·        Developing Bioinformatics Computer Skills, Gibas & Jambeck, O’Reilly Publishers.

·        Algorithm on Strings, Trees, and Sequences, Gusfield, Cambridge Univ. Press, 1997.

·        Biological Sequence Analysis, Durbin, Eddy, Krogh & Mitchison, Cambridge Press.

·        Bioinformatics: The Machine Learning Approach, P. Baldi and S. Brunak. MIT Press.