Joint Biology and Computer Science Track in Bioinformatics

Bioinformatics is an emerging discipline that integrates molecuar biology, genetics, biochemistry and computer science. It provides tools that allow scientists to make use of the vast amount of biological data generated in recent years and to answer questions unimaginable just a decade ago. Bioinformatics has revolutionized gene discovery and analysis, and offers excellent career opportunities for those who master it.

Link to companies and institutions in the Bay Area.

The departments of Biological Sciences and Computer Science at San Jose State University designed a new BSCS Track in Bioinformatics.

Recommended Prerequisite for CS Majors

Molecular Biology for Computer Scientists
Biology 23
Not offered in Fall 2009
The aim of this course is to help computer science students become familiar with the principles of molecular biology as they relate to bioinformatics. The emphasis will be on the molecular workings of a cell, including the fundamental processes by which coded genetic information is decoded during the production of useful macromolecular structures and machines.
Prerequisites: CS 46A; No college biology required.

Required Courses

Bio/CS 123A
Offered in Fall 2009
Tuesdays and Thursdays from 9:00 to 10:15 in MH450.
Instructor: Dr. Sami Khuri
This practical course, cross-listed with the biology department, provides an introduction to the main public domain tools, databases and methods in bioinformatics, including DNA and protein databases, such as Genbank and PDB, software tools such as BLAST, FASTA, Smith-Waterman; and methods including those for aligning sequences. More precisely, the course analyzes the algorithms behind the most successful tools, such as the local and global sequence alignment packages mentioned above; and the underlying methods used in fragment assembly packages. This course is intended both for biology and computer science students, to work together to solve complex biological questions requiring modification of standard code.
Prerequisites: Interest in Biology for CS majors.

Bio/CS 123B
Offered in Spring 2010.
Instructor: Dr. Sami Khuri
This practical course, cross-listed with biology, continues to cover the computational methods used for searching, classifying, analyzing, and modeling protein sequences. The course also continues to cover tools for analyzing DNA and RNA sequences. More advance topics, such as genetic algorithms and simulated annealing which can be used to address folding problems, are covered.
Prerequisites: Bio/CS 123A or instructor approval.

Overview of the program

Additional Courses of Interest

Advanced Programming with PERL
CS 122
Offered in Spring 2010
Instructor: Natasha Khuri This course introduces the Perl programming language with an emphasis on data manipulation, file processing and database access. The course will deal with real life applications in various fields such as system administration, networking and bioinformatics.
Prerequisites: CS146 or by permission of the instructor.

Statistics for Bioinformatics
Math 162
Not offered in Fall 2009
Instructor: Dr. Martina Bremer
Introduction to data analysis methods which are widely used in bioinformatics. Methods deal with prediction, classification, optimization, and clustering. The methods are placed into the context of principles and models of statistical science, with emphasis on Bayesian methods.
Prerequisite: Math 161A or instructor consent.

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