Graduate Requirements — M.S. and Ph.D. in Bioinformatics
Program description
The program in bioinformatics is a multidisciplinary program sponsored by the Department of Biomolecular Engineering. The program offers B.S., M.S., and Ph.D. degrees in bioinformatics and a minor in bioinformatics.
Bioinformatics combines mathematics, science, and engineering to explore and understand biological data from high-throughput experiments, such as genome sequencing, gene expression chips, and proteomics experiments. The program builds upon the research and academic strengths of the faculty in the Center for Biomolecular Science and Engineering.
The Human Genome Project, the international collaboration to determine the sequence of human DNA and understand its function, had its origin in a conference that took place at UC Santa Cruz in 1985. One notable output from our research is that UCSC is the primary release site for the public version of the human genome and its annotation: <http://genome.ucsc.edu>. We are also a major player in protein-structure prediction, and have a strong research group in DNA microarray analysis.
Both M.S. and Ph. D. students must complete nine 5-credit courses (seven core courses and two electives; see below) and a 3-credit research and teaching course. In addition, M.S. students must complete 4 seminar credits, while Ph. D. students must complete 8 seminar credits. Also, M.S. students must complete two (1-credit or 2-credit) research project courses (such as BME 220L, BME 230L, BME 297F, or BME297), and Ph.D. students must complete three research lab rotations (BME 296) with different supervisors.
Core courses (5-credit)—7 are required:
- Biomolecular Engineering 100+L, Introduction to Bioinformatics + Laboratory
- Biomolecular Engineering 220, Protein Bioinformatics
- Biomolecular Engineering 230, Computational Genomics
- Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society
or Philosophy 245 Brave New World: Ethical Issues in Genetics
One graduate-level course, approved by the faculty, in each of the following three areas:
- Statistics (Engineering 206 recommended)
- Biology (Biology 200B recommended)
- Chemistry (Chemistry 200B recommended)
Electives (5-credit)—2 are required:
The electives should be graduate-level courses selected with approval of the faculty to ensure a coherent, balanced program. For M.S. students, 5 units of independent research (297) or thesis research (299) may count as electives toward the degree requirements upon approval of the faculty. For Ph.D. students, independent or thesis research cannot be counted as electives.
Students must choose their electives with faculty guidance and approval to balance their preparation and make up for deficiencies in background areas. In addition to fulfilling background needs, students may choose to emphasize one of the breadth areas: molecular biology, biochemistry, statistics, computational biology, genetics, computer science, computer engineering, applied mathematics, cell biology, and computer graphics/visualization. Alternatively, students may take a cross-sampling of the electives to achieve a broad knowledge base.
Other curriculum requirements:
- Biomolecular Engineering 200, Research and Teaching in Bioinformatics (3 credits)
- Seminars:
M.S. students: a minimum of two seminar courses, including at least one quarter of the 2-credit BME 280, Bioinformatics Seminar (formerly CMPE 280B).
Ph.D. students: a minimum of four seminar courses, including at least two quarters of the 2-credit BME 280, Bioinformatics Seminar (formerly CMPE 280B). - Research experience:
M.S. students: a minimum of two research project courses (BME 220L, BME 230L, BME 297F, or BME 297)
Ph.D. students: three quarters of laboratory rotations (BME 296), generally completed within the first 12 months; at least one rotation must be with a faculty supervisor who does wet-lab research, though the rotation project may be purely computational.
Graduate students receiving two or more U (unsatisfactory) grades or grades below B in courses relevant to the program are not making adequate progress and will be placed on academic probation for the next three quarters of registered enrollment.
Graduate students who fail (unsatisfactory or lower than B) a relevant course while on probation may be dismissed from the program. Students may appeal their dismissal. Graduate students who fail a relevant course after being removed from probation are immediately returned to academic probation.
Graduate students experiencing circumstances that may adversely affect their academic performance should consult with their advisor and the graduate director.
Thesis and dissertation requirements
In addition to completing the course requirements, students must fulfill the following thesis or dissertation requirements:
M.S. students must submit a written thesis proposal to a faculty member by the end of the fourth academic quarter. If the faculty member accepts the proposal, he or she will become the student's advisor and will be in charge of supervising the writing of the master’s thesis. When the thesis is completed, it will be submitted to and must be accepted by a faculty review committee consisting of the thesis advisor and at least two additional readers. The committee must include a School of Engineering faculty member, may include participants from the Division of Physical & Biological Sciences and from industry as appropriate, and must be approved by the bioinformatics program director. Students are required to present the thesis project in a public seminar.
Ph.D. students are encouraged to select a faculty research advisor by the beginning of the second year and must select one by the end of the second year. A written dissertation proposal is required before the end of the third year. A qualifying committee is then formed, consisting of the advisor and three additional members approved by the bioinformatics program director and the campus graduate dean. The student must submit his or her written dissertation proposal to all members of the committee and to the graduate assistant one month in advance of the examination. The dissertation proposal is publicly and formally presented in an oral qualifying examination given by the qualifying committee.
Ph.D. candidates will submit the completed dissertation to a reading committee at least one month prior to the dissertation defense. The reading committee, formed upon advancement to candidacy, consists of the dissertation supervisor and two readers appointed by the bioinformatics program director upon the recommendation of the dissertation supervisor. The candidate will present his or her research in a public seminar. The seminar will be followed by a defense of the dissertation to the reading committee and attending faculty, who will then decide whether the dissertation is acceptable or requires revision.
Up to two courses may be transferred from other graduate institutions, with the approval of the faculty advisor and the graduate director.