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Graduate Education

 

Program description

Bioinformatics (we also include Systems Biology here) and Medical Informatics (also called Biomedical, Health, or Clinical Informatics) are related multidisciplinary fields that rely on data mining and pattern recognition techniques to discover biological or clinical patterns in large amounts of data, e.g. data mining. The majority of research and development (R&D) in the two fields can be categorized into one of three branches. The first branch is the algorithm development branch in which R&D specialists use mathematical and engineering techniques (sometimes also approaches from physical sciences) to develop new, more efficient, and/or more accurate methods to mine biological or clinical data. The second branch falls within the software engineering paradigm and primarily focuses on R&D in human-computer interface. Specifically, the branch deals with data visualization and the design of graphical user interface (GUI) that allows the user to easily visualize and interpret the results of the algorithms developed by the first branch. The third branch includes those who work on finding answers to specific biological or medical questions. This includes those working to uncover the underlying mechanisms involved in specific biological systems or specific diseases. This branch also includes much of the work being conducted in the area of Systems Biology. This program offers training for all three branches of the two fields. Students can specialize in their area of interest in the second year of the program, while the first year is individually tailored to primarily fill in the holes in the student’s background required for her/his desired specialization. During the first year, students usually take basic courses within two of the following four disciplines (depending on their background): Biology, Chemistry, Computer Science, and Mathematics/Statistics. All students are required to hold a thesis proposal presentation, but the oral thesis defense is only required for students in the classical MS track.

For specialization in the algorithm development branch, students can choose courses and projects in areas such as statistics, data mining, pattern recognition, artificial intelligence, search strategies, network architecture, digital image processing and advance imaging, modeling, decisions systems design, and analytical studies in various biological and clinical specializations. For specialization in the human-computer interface branch, students can choose courses and projects in areas such as principles of software design, human interface design, network architecture, usability studies, database design and management, computer graphics and animation, computer-aided design (CAD), and programming languages (especially object-oriented programming or OOP). Those who choose specialization in the third branch and wish to conduct targeted study of a specific biological/medical problem may require a mix of courses from the other two branches plus some training in the biology of the chosen problem of study.

This program is multidisciplinary in nature and combines expertise from the areas of Biology, Chemistry, Computer Science, and Mathematics in order to address the growing need for graduates with some level of knowledge of the four domains. In the industry, the need for these graduates spreads beyond the Biotech and Health Care sectors, and is felt in sectors such as Homeland Security and Information Technology.

Regional and industrial fit

Because San Diego is a major hub for the biotech industry (the largest in the country), the proposed program is especially well-suited to the region. The purpose of the program is to first serve the growing need of the local industry for graduates who are familiar with leading edge biological and clinical problems and have the skills to apply computing and mathematical techniques to solve them. Because of the high shortage in graduates in the field on a national scale, it is anticipated that some graduates of this program will find employment in other parts of the state or the country. Furthermore, it is also anticipated that a portion of the graduates will choose to continue their education or work in the academia. The program sets the goal of providing graduates for the above four needs.

Target student population

myGAP_LogoThe curriculum of the program is designed to accommodate students from four corners of sciences as well as engineering. The program will accept students with backgrounds in Biology, Chemistry, Computer Science, Mathematics, or Engineering. The first year of the program is designed to fill in the deficiencies in the students’ backgrounds, while in the second year they will take specialized courses to deepen their knowledge and skill in specific areas of Bioinformatics and Medical Informatics.

This program also has specific paths designed for working professionals who are interested in the program, as well as for those who are currently working in the Biotech or Health Care industries. When applying, please indicate whether you fall into either of these categories.

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