Specialized Track in Bioinformatics

Track Faculty: Profs. Martin Schultz, Avi Silberschatz, Mark Gerstein and Kei-Hoi Cheung

Track prerequisites: Admission to the MS program and one year of undergraduate courses in biology. Advanced biology is recommended.

Core Courses:
CPSC 537 Introduction to Databases. An introduction to database systems. Data modeling. The relational model and the SQL query language. Relational database design, integrity constraints, functional dependencies, and normal forms. Object-oriented databases. Implementation of databases: file structures, indexing, query processing, transactions, concurrency control, recovery systems, and security.

CPSC 545 Introduction to Data Mining. A study of algorithms and systems that allow computers to find patterns and regularities in databases, to perform prediction and forecasting, and to improve their performance generally through interaction with data.

CPSC 752 Genomics and Bioinformatics. Genomics describes the determination of the nucleotide sequence and many further analyses to discover functional and structural information on all the genes of an organism. Topics include the methods and results of functional and structural gene analysis on a genome-wide scale as well as a discussion of the implications of this research. Bioinformatics describes the computational analysis of genomes and macromolecular structures on a large scale. Topics include sequence alignment, biological database design, comparative genomics, geometric analysis of protein structure, and macromolecular simulation.

CB&B 750 Core Topics in Biomedical Informatics. Introduction to common unifying themes that serve as the foundation for different areas of biomedical informatics, including clinical, neuro-, and genome informatics. The course is designed for students with significant computer experience and course work who plan to build computational tools for use in bioscience research. Emphasis is on understanding basic principles underlying informatics approaches to biomedical data modeling, interoperation among biomedical databases and software tools, standardized biomedical vocabularies and ontologies, modeling of biological systems, and other topics of interest. The course involves lectures, class discussions, student presentations, and computer programming assignments.

CPSC 692 Indpendent Project. Individual research for students in the MS program. Requires a faculty supervisor (one of the track faculty) and the permission of the director of graduate studies.

Three additional electives to fulfill the MS course requirements selected by the student with the advice of the track advisor. Generally one of these courses will be in statistics.