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Program in Bioinformatics and Systems Biology


An International Leader in Bioinformatics and Systems Biology Research

The University of California at San Diego was one of the first major universities to initiate a bioinformatics graduate program and continues to be an international leader in the field. Located in Southern California, UC San Diego is a premier research institution that has fostered interdisciplinary research since its inception. The world is witnessing the birth of a new era in biology and medicine. The confluence of unprecedented measuring capabilities and computational power has dramatically changed the questions that may be addressed in the biological and biomedical sciences and promised to empower clinical practice in fundamental ways. UCSD's Bioinformatics and Systems Biology Graduate program (including the graduate Biomedical Informatics Track) is an inter-departmental academic program. It is supported broadly by five schools and divisions and by the faculty from participating departments, including the Jacobs School of Engineering, the Division of Biological Sciences, the Division of Physical Sciences the School of Medicine, and the Skaggs School of Pharmaceutical Sciences. The graduate program is supported by the respective schools, divisions, and departments, as well as by the National Institutes of Health (NIH) Training Grant and over 60, associated faculty.

Student-Faculty Member Ratio Is Nearly One-to-One

The cutting-edge research projects undertaken by UCSD's outstanding faculty members and exceptional graduate students focus on emerging frontiers in bioinformatics and computational biology. The program is one of the largest on campus, offering a student-faculty member ratio of nearly one-to-one.

Meeting the Challenges of a New Era in Biology

Addressing the challenges of biological datasets at the genomic, sub-cellular, molecular, and biology systems levels requires the development of sophisticated computational methods (bioinformatics) for computational biology. Moving biology into the realm of a quantitative, predictive, and theory-driven science requires an interdisciplinary research structure dedicated to developing intellectual and human capital in bioinformatics and systems biology. As such, there is an enormous need for trained professionals who are experts in both biology and computing.

The Ph.D. in Bioinformatics and Systems Biology

The interdisciplinary bioinformatics graduate program offers two tracks: "Bioinformatics and Systems Biology (BISB)" and "Biomedical Informatics (BMI)." Students are able to switch tracks during their course of studies. Each track is organized around a formal course requirement of four compulsory core courses and 16 units of elective courses to be completed within the first two years of study. Students must also each participate in a Seminar Series, student research talks, and research rotations. They complete one of two ethics courses, and two research units with their dissertation advisers. They also serve as a teaching assistant for two quarters. Incoming first-year students also each spend a week at the program's Boot Camp which introduces students to faculty members, courses, and research opportunity and conveys the work ethic and bar of the program's best students. It also provides student support to remedy deficiencies prior to beginning coursework.

Research Rotations

Each graduate undertakes three, 10-week research rotations in three different laboratories within the first calendar year. The purpose of the research rotations is to train students in specific research methodologies, and identify a laboratory in which students will pursue doctoral thesis research. All students, regardless of their backgrounds and elective tracks, are expected to identify a thesis research laboratory and join that laboratory by the beginning (fall quarter) of their second year.

Ph.D. Requirements

Students take second-year qualifying exams that consists of a 10-page research project proposal and an oral exam that tests the students' ability to think critically, analytically, and independently. Students also sit for a written and oral exam on their dissertation topics at the end of the third year to qualify for advancement to Ph.D. candidacy. Ph.D. candidates then submit their dissertations and defend them in oral examinations.

Wide-Ranging Research Opportunities in Bioinformatics

UCSD's large faculty offers a broad range of research opportunities in bioinformatics. Faculty member research interests include cell cycle, apoptosis, computational modeling of the genetic basis of diseases, proteomics, metabolomics, genomics, biological circuits, medical decision support systems, and many other areas. A sampling of the leading-edge doctoral theses completed by recent graduates of the UC San Diego bioinformatics program include: "Computational Tools for Analysis of Mass Spectrometry Imaging Data;" "Structural Systems Biology Perspective on the Metabolic Impact of Physicochemical Stress;" "Insights from Reconstructing Cellular Networks in Transcription, Stress and Cancer;" "Electromicrobiology: A Systems Perspective;" and "The Human Gut Microbiome: Characterization Challenges and HIV Disease Association."

UCSD: A Nationally Ranked Research University in a Beautiful Region

Established in 1960 in the San Diego community of La Jolla, the University of California San Diego soon became one of the country's top universities. The Southern California campus spreads from the scenic coastline, where the Scripps Institution of Oceanography is located, across a large, wooded portion of the Torrey Pines Mesa overlooking the Pacific Ocean. One of 10 campuses in the University of California System, UCSD boasts over 70 miles of beaches and one of the world's best climates. One can move from the beach to the mountains to the desert within a few hours and enjoy a year-round active lifestyle. A marvelous climate, a beautiful campus, and the lovely city of La Jolla are a perfect match for UC San Diego's superb academic environment for graduate education.

Degrees & Awards

Degrees Offered

Degree Concentration Sub-concentration
Doctor of Philosophy (PhD)

Degrees Awarded

Doctoral Degrees 8

Earning Your Degree

Part-time study available? No
Evening/weekend programs available? No
Distance learning programs available? No

Degree Requirements

Doctoral Degrees Entrance Exam GRE General Test
Comp Exam Required
Thesis Required
Two quarters as teaching assistant


Acceptance Rate



Application Fee - Domestic
Application Fee - International
applications accepted?

Application Deadlines

Type Domestic International Priority date
Fall deadline December 19th Not reported No

Entrance Requirements

Doctoral Degree Exam GRE General Test
International Students Exam Details
TOEFL: Required TOEFL Paper score: 550
TOEFL IBT score: 80
IELTS: Required IELTS Paper score: 7

Tuition & Fees

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Financial Support

Financial award applicants must submit FAFSA
Types of financial support available Scholarship and/or loans

Student Body

Total Graduate Students
Not Reported
International Breakout (representing other countries)
Out-of-state students


Male (72%)
Female (27%)


Focus of faculty research: Quantitative foundations of computational biology, structural bioinformatics and systems pharmacology, proteomics and metabolomics, epigenomics and gene expression control, genetic and molecular networks
Externally sponsored research expenditures last year: 0

Location & Contact

Address 9500 Gilman Drive
La Jolla, CA  92093
United States
Contact Vineet Bafna
Email: vbafna@ucsd.edu
Phone: 858-822-4978