Bioinformatics and Medical Informatics

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OFFICE: South Life Science 373
TELEPHONE: 619-594-5371
E-MAIL: skelley@sdsu.edu

Faculty:

Director: Kelley, Scott T., Professor of Biology, Director (B.A., Cornell University; Ph.D., University of Colorado)

Tenured and Tenure-Track Faculty:

Bohonak, Andrew J., Associate Dean of Graduate Studies; Professor of Biology (B.S., Allegheny College; Ph.D., Cornell University)

Amir, Nader, Professor of Psychology (B.A., B.S., University of Illinois at Urbana-Champaign; M.S., Ph.D., The  Herman M. Finch University of Health Sciences/The Chicago Medical School)

Fields, Willa L., Professor of Nursing (B.S.N., Temple University; M.S.N., San Diego State University; D.N.Sc., University of San Diego)

Flores Renteria, Lluvia H., Assistant Professor of Biology (B.S., M.S., Ph.D., National Autonomous University of Mexico, Mexico)

Kelley, Scott T., Professor of Biology, Director (B.A., Cornell University; Ph.D., University of Colorado)

Kiene, Susan M., Professor of Public Health, Associate Director for Research (B.S., University of Nebraska; M.A., University of Connecticut; M.P.H., Harvard University School of Public Health; Ph.D., University of Connecticut)

Kumar, Sunil, Professor of Electrical and Computer Engineering, Thomas G. Pine Faculty Fellow (B.S., S.V. National Institute of Technology, India; Ph.D., Birla Institute of Tech & Science, India)

Levine, Richard A., Professor of Statistics (B.S., State University of New York at Binghamton; M.S., Ph.D., Cornell University)

Lipson, David A., Professor of Biology (B.A., University of California, Berkeley; Ph.D., University of Colorado at Boulder)

Madanat, Hala N., Albert W. Johnson Distinguished Professor and Director of School of Public Health (BSc, University of Jordan; M.S., Ph.D., Brigham Young University)

Matt, Georg E., Professor of Psychology (Dipl., Albert-Ludwigs-Universitat, Freiburg, Germany; Ph.D., Northwestern University)

Mi, Chunting Chris, Professor of Electrical and Computer Engineering (B.S., Northwestern Polytechnical University, China; Ph.D., University of Toronto, Canada)

Müller, Ralph-Axel, Professor of Psychology (M.A., Ph.D., University of Frankfurt, Main, Germany)

Murphy, Claire, Professor of Psychology (B.S., Loyola University; M.S., Ph.D., University of Massachusetts)

Ozturk, Yusuf, Interim Associate Dean for Undergraduate Studies, College of Engineering; Professor of Electrical and Computer Engineering (B.S., Middle East Technical University (METU); Ph.D., Ege University)

Rohwer, Forest L., Professor of Biology (B.A., Albertson College of Idaho; Ph.D., San Diego State University)

Sarkar, Mahasweta, Professor of Electrical and Computer Engineering (B.S., San Diego State University; Ph.D., University of California San Diego)

Segall, Anca M., Professor of Biology (B.S., University of Maryland; Ph.D., University of Utah)

Sinha, Usha, Professor of Physics, Director of Medical Physics (B.S., Osmania University, India; M.S., Indian Institute of Technology, India; Ph.D., Indian Institute of Science, Bangalore, India)

Talavera, Gregory A., Professor of Psychology (B.A., M.P.H., San Diego State University; M.D., University of Utah)

Valafar, Faramarz, Professor of Public Health (Vordiplom, Kaiserslautern University, Germany; M.S., Michigan Technological University; Ph.D., Purdue University)

Waters, Elizabeth R., Professor of Biology (B.A., Grinnell College; M.S., North Carolina State University; Ph.D., Washington University)

Xie, Tao, Professor of Computer Science (B.E., Anhui Institute of Technology, China; M.E., Hefei University of Technology, China; Ph.D., New Mexico Institute of Mining and Technology)

Zayas Ventura, Ricardo M., Professor of Biology (B.S., Fairfield University; Ph.D., Tufts University)

Zeller, Robert W., Professor of Biology (B.A., Boston University; Ph.D., California Institute of Technology)

Ashrafi, Ashkan, Associate Professor of Electrical and Computer Engineering (B.Sc., M.Sc., K.N., University of Technology, Tehran, Iran; M.S.E., Ph.D., University of Alabama, Huntsville)

Baek, Jong-Deuk, Associate Professor of Public Health (B.A., M.B.A., Kyung Hee University, South Korea; Ph.D., University of South Carolina)

Bailey, Barbara Ann, Associate Professor of Statistics (B.S., Springfield College in Illinois; M.S., University of Illinois at Urbana-Champaign; Ph.D., North Carolina State University)

Bergdahl, B. Mikael, Associate Professor of Chemistry and Biochemistry (B.S., M.S., Ph.D., Chalmers University of Technology, Sweden)

Kalyuzhnaya, Marina G., Associate Professor of Biology (B.S., M.S., Dnepropetrovask State University, Ukraine; Ph.D., Russian Academy of Sciences, Russia)

Lin, Chii-Dean, Associate Professor of Statistics (B.A., National Chiao Tung University, Taiwan; M.S., New Jersey Institute of Technology; Ph.D., Texas A&M University)

Liu, Xiaobai, Associate Professor of Computer Science (B.S., Fudan University, China; Ph.D., Huazhong University of Science and Technology, China)

Love, John J., Associate Professor of Chemistry and Biochemistry (B.S., State University of New York; Ph.D., University of California, San Diego)

Marinkovic, Ksenija, Associate Professor of Psychology (B.A., University of Zagreb, Croatia; M.S., Occidental College; Ph.D., University of Southern California)

Swairjo, Manal A., Associate Professor of Chemistry and Biochemistry (B.S., Kuwait University; Ph.D., Boston University)

Wang, Wei, Associate Professor of Computer Science (B.S., M.A., Xian Jiaotong University, China; Ph.D., University of Nebraska)

Forsberg, Erica, Assistant Professor of Chemistry and Biochemistry (B.S., Ph.D., McMaster University, Canada)

Luque Santolaria, Antoni, Assistant Professor of Mathematics (B.S., M.S., Ph.D., Universitat de Barcelona, Spain)

Roach, Dwayne R., Assistant Professor of Biology and Conrad Prebys Chair of Virology (B.S., Ph.D., St. Catherine University)

Schiaffino, Melody K., Assistant Professor of Public Health (B.A., University of Missouri-Columbia; M.P.H., University of South Florida; Ph.D., University of Florida)

Sukumaran, Jeet, Assistant Professor of Biology (B.S., University of Texas, Austin; M.S., University of Malaya, Malaysia; Ph.D., University of Kansas)

Verbyla, Matthew E., Assistant Professor of Civil, Construction, and Environmental Engineering (B.S., Lafayette College; M.S., Ph.D., University of South Florida)

Wiggins, Jillian L., Assistant Professor of Psychology (B.S., Wheaton College; M.S., Texas A&M University; Ph.D., University of Michigan. State  University)

Xu, Xiaofeng, Assistant Professor of Biology (B.A., Henan Normal University, China; M.S., Chinese Academy of Sciences, China; Ph.D., Auburn University)

Emeritus:

Novotny, Thomas E., M.D., 2009-2015, Professor of Public Health

Tarokh, Mahmoud, Ph.D., 1990-2019, Professor of Computer Science

Adjunct Faculty:

University of California, San Diego:

Catanzaro, Antonino, Professor of Pulmonary Health (M.D.)

Ohno-Machado, Lucila, Professor of Medicine (M.D., Ph.D.)

Rodwell, Timothy, Associate Professor of Pulmonary Health (M.D., Ph.D., M.P.H.)

Kim, Hyeon-Eui, Assistant Professor of Biomedical Informatics (Ph.D, M.P.H., R.N.)

La Jolla Institute for Allergy and Immunology:

Peters, Bjoern, Center for Infectious Disease (Ph.D.)

Rao, Anjano, Signaling and Gene Expression Research (Ph.D.)

VA Hospital:

Calvitti, Alan, System Biology (Ph.D.)

Graduate Information

General Information

Bioinformatics and Medical Informatics (BIOMI) are multidisciplinary fields at the intersection of computing and informatics, mathematics and statistics, biology, chemistry, and engineering.

The explosion in genomic information and in the elucidation of pathways of various types has created an unprecedented, but largely unmet, need for professionals with a working knowledge of the biological sciences and computing/statistical methods. The shortage, which is especially severe in the biotechnology and pharmaceutical industries, has been documented by various studies and discussed in the press. We can also observe a comparable demand in hospital and other clinical settings as the impact of new technologies spreads into clinical research and medical practice.

Research and development (R&D) in BIOMI 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 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. The third branch seeks to find answers to specific biological or medical questions including drug development or working to uncover the underlying mechanisms involved in specific biological systems or specific diseases. In the first year of the program, students in consultation with their graduate adviser will take basic courses within two of the following four disciplines: biology, chemistry, computer science, and mathematics/statistics.

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, CAD, and programming languages. For the third specialization students take a combination of courses in the areas listed above plus some specialized courses such as computer aided drug design.

The change toward quantitative analysis in life and clinical sciences has been so rapid that universities have been caught unprepared: few offer suitable courses, and virtually none offer a well integrated curriculum that meets the needs that are sure to grow and evolve as life sciences become increasingly conceptual and quantitative.

San Diego State University’s BIOMI graduate program offers two related but distinct tracks. The first is a professional science master concentration preparing students for immediate productivity in industrial or clinical settings. The second is a traditional master of science preparing students for academic setting or continuation in a Ph.D. program.

Admission to Graduate Study

In addition to the general requirements for admission to the university with classified graduate standing, as described in Admission and Registration , a student must satisfy the following requirements before being considered for recommendation to enter the masters program.

1. Meet the requirements deemed equivalent to a baccalaureate degree in biology, chemistry, computer science, mathematics, statistics, or a field in engineering.
2. Be considered as capable of graduate work in bioinformatics or medical informatics by at least two references who have submitted letters to the BIOMI program director.

Students applying for admission should electronically submit the university application available at http://www.calstate.edu/apply along with the application fee.

Students who do not meet all of the above requirements for admission with classified graduate standing may be admitted with conditionally classified graduate standing upon the recommendation of the research program. Students so admitted will be advised as to the nature of their deficiency and the time to be allowed to achieve full classified graduate standing. Conditions may include satisfactory passing of certain undergraduate courses. These courses will be in addition to the minimum of 33-38 units required for the program.

Graduate Admissions

All applicants must submit admissions materials separately to SDSU Graduate Admissions and to the Bioinformatics and Medical Informatics program.

The following materials should be submitted as a complete package directly to:

Graduate Admissions
Enrollment Services
San Diego State University
San Diego, CA 92182-7416

1. Official transcripts (in sealed envelopes) from all postsecondary institutions attended;
   • Students who attended SDSU need only submit transcripts for work completed since last attendance.
   • Students with international coursework must submit both the official transcript and proof of degree. If documents are in a language other than English, they must be accompanied by a certified English translation.
2. GRE scores (http://www.ets.org SDSU institution code 4682);
3. English language score, if medium of instruction was in a language other than English (http://www.ets.org SDSU institution code 4682).

Master of Science Degree in Bioinformatics and Medical Informatics

The following materials should be mailed or delivered to:

Bioinformatics and Medical Informatics
(BIOMI) Graduate Program
(Attention: Graduate Adviser)
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-7720

1. Two letters of recommendation (in sealed and signed envelopes) from persons in a position to judge academic ability.
2. Personal statement of motivating interest for the program; also briefly describe research interests and educational and professional goals.

Programs

• Bioinformatics and Medical Informatics, M.S.
• Bioinformatics and Medical Informatics, Professional Science Master Concentration, M.S.

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