Program Description
PhD Program in Computational Biology & Bioinformatics (CBB, formerly BGT)
Prerequisites: Students admitted to the CBB program will generally have taken prerequisite courses in both computational and biological sciences to an advanced level. Students are expected to have taken mathematics through differential equations and linear algebra; two courses in statistics; two courses in computer science; at least one course in genetics and cell & molecular biology; and at least one semester of organic chemistry. Otherwise competitive students lacking one or more of these requirements will be expected to satisfy them prior to or during their first year in the program.
Student Advisory Committee: A Student Advisory Committee, composed of the Director of Graduate Studies and six additional faculty members of the CBB program, advises first and second year students with respect to their coursework, research rotations and advisor selection.
Required Courses: The CBB program is explicitly designed to be responsive to the breadth, newness and rapidly evolving nature of the CBB arena, and so does not have a heavy emphasis on required courses. However, students in the CBB Graduate Program must complete the following three core courses:
- CBB 220 Genomic Tools and Technologies
- CBB 230 Algorithms in Computational Biology
- CBB 240 Statistical Methods for Computational Biology
The CBB core curriculum emphasizes the integration of biology and computation. This integration is reflected in the syllabus of each core course, which includes lectures on biological applications of the informatics and computational principles being discussed. In addition to the core courses, all CBB graduate students will receive formal exposure to ethical and legal issues related to genomics, bioinformatics and genome technology through a series of workshops in conjunction with the Duke Graduate School as well as the IGSP Center for Genome Ethics, Law & Policy.
Elective courses: Additional CBB courses are offered as electives. Most students take a broad set of CBB courses as they define their own paths through the program. The Student Advisory Committee and the Dissertation Committee (beyond the second year) work with the student to design a series of elective courses to be taken beyond the core courses. Acceptable electives include not only genomics, statistics, genome technology or computer science courses, but can entail course offerings, particularly in the biological sciences, that advance the educational ends of the student's specific graduate program.
Rotation: During their first year in residence, students should complete three "research rotations", each consisting of a tutorial-level independent study or a laboratory experience with different faculty members in the CBB Program. Except in unusual circumstances, these rotations should be carried out with Program faculty from more than one participating department. Students are strongly encouraged to select one rotation experience with a primarily biological faculty member, and at least one with a primarily computational faculty member. Typically, the duration of each rotation is 12 weeks.
Graduate seminars: Throughout their participation in the CBB Graduate Program, students are expected to attend the weekly Computational Biology Seminar Series, which includes a combination of presentations from students, faculty and invited external speakers.
Advisor and Dissertation Committee: Typically, before the end of the fall semester of their second year the student selects a graduate advisor. The program strongly encourages the selection of a co-advisor who is complimentary to the primary advisor so that together, advisors represent both computational and experimental science.
Early in the spring semester the student forms a permanent Dissertation Committee, in consultation with their advisor(s). The Dissertation Committee advises the student about additional courses, oversees their PhD research, and guides the student in preparing for the Preliminary Examination. The committee consists of five faculty, including advisor(s). At least three committee members must be members of the CBB Graduate Program Faculty and one member (minor area representative) must be from a department outside of those of the advisor(s). The selection and approval of advisor(s) and committee follows the standard procedures of the Graduate School.
Preliminary examination: The PhD preliminary examination is administered in accordance with the guidelines set out by the Graduate School, generally at or before the end of the fifth semester. As part of this examination process, the candidate submits a written proposal in their expected area of thesis research to be presented and discussed at the examination. In addition to addressing the student's readiness to conduct independent research, the oral preliminary examination features questions and discussion designed to evaluate the competence and preparedness of the student in both the biological and computational components of the field. Successful completion of the exam qualifies the student as a PhD candidate.
Financial Support: The CBB Graduate Program provides support for students admitted directly into the Program for the first two years of doctoral study. Each student admitted into the must designate a faculty advisor no later than the beginning of the fourth semester in residence. Beginning July 1st of the second in residence, the faculty advisor will become responsible for the 's stipend and fees for the duration of the student's dissertation work.