The First Year
The time to degree (normative time) of the Computational Biology PhD is five years. The first year of the program emphasizes gaining competency in computational biology, the biological sciences, and the computational sciences (broadly construed). Since student backgrounds will vary widely, each student will work with faculty and student advisory committees to develop a program of study tailored to their background and interests. Specifically, all first-year students must:
- Perform three rotations with Core faculty (one rotation with a non-Core faculty is acceptable with advance approval)
- Complete course work requirements (see below)
- Complete a course in the Responsible Conduct of Research
- Attend the computational biology seminar series
- Complete experimental training (see below)
Entering students are required to complete three laboratory rotations during their first year in the program to seek out a Dissertation Advisor under whose supervision dissertation research will be conducted. Students should rotate with at least one computational Core faculty member and one experimental Core faculty member.
Course Work & Additional Requirements
Students must complete six courses in the first three (up to four) semesters:
- COMPBIO 293, Doctoral Student Seminar (required Fall/Spring Semester). This one-year interactive seminar builds skills, knowledge and community in computational biology for first year PhD and second year DE students. Topics covered include concepts in human genetics/genomics, laboratory methodologies and data sources for computational biology, workshops on use of various bioinformatics tools, critical review of current research studies and computational methods, preparation for success in the PhD program and career development. Faculty members of the graduate program in computational biology and scientists from other institutions will participate.
- STAT 201A/B Intro to Probability at an Advanced Level/Intro to Statistics at an Advanced Level. It is recommended to take A & B in the same semester; however, it is possible to take them in separate Fall semesters. Alternatively, students can demonstrate they have completed the equivalent by passing a proctored assessment exam on Campus the week before instruction begins. Information about the time/location/content of exam will be provided to each student before the semester begins. NOTE: Students who are offered admission and are not prepared to complete STAT 201A/B will be required to complete STAT 134 or PH 142 first.
- CS61A, The Structure and Interpretation of Computer Programs (Fall Semester) or demonstrate they have completed the equivalent in another course; a syllabus is required for approval.
- Three additional courses, drawn from existing campus offerings. These courses are intended to resolve deficiencies in training and ensure competency in the fundamental knowledge of each discipline. Students are expected to develop a course plan for remaining program requirements (such as biology coursework) and any additional electives, and to consult with the Head Graduate Advisor before the Spring semester of their first year for formal approval (signature required). The course plan will take into account the student’s undergraduate training areas and goals for PhD research areas.
- Attend the computational biology seminar series. A schedule is circulated to all students by email and is available on the Center website.
- Complete a Responsible Conduct of Research course, most likely through the Department of Molecular and Cell Biology .
- Complete an experimental training component in one of three ways: 1) complete a laboratory course at Berkeley (or equivalent) with a minimum grade of B, 2) complete a rotation in an experimental lab (w/ an experimental project), with a positive evaluation from the PI, 3) demonstrate proof of previous experience, such as: a biological sciences undergraduate major with at least two upper division laboratory-based courses, a semester or equivalent of supervised undergraduate experimental laboratory-based research at a university, or previous paid or volunteer/internship work in an industry-based experimental laboratory. Students will provide a brief summary of this experience to the Head Graduate Advisor for approval before taking the QE.
Satisfactory completion of first year requirements will be evaluated at the end of the spring semester of the first year. If requirements are satisfied, students will formally choose a Dissertation advisor from among the core faculty with whom they rotated and begin dissertation research.
Second Year & Beyond
At the beginning of the fall of the second year, students begin full-time dissertation research in earnest under the supervision of their Dissertation advisor. It is anticipated that it will take students three (up to four) semesters to complete the 6 course requirement. Students are required to continue to participate annually in the computational biology seminar series.
Students are expected to take and pass an oral Qualifying Examination (QE) by the end of the spring semester (June 15th) of their second year of graduate study. Students must present a written dissertation proposal to the QE committee no fewer than four weeks prior to the oral QE. The write-up should follow the format of an NIH-style grant proposal (i.e., it should include an abstract, background and significance, specific aims to be addressed (~3), and a research plan for addressing the aims) and must thoroughly discuss plans for research to be conducted in the dissertation lab.
Advancement to Candidacy
After successfully completing the QE, students will Advance to Candidacy. At this time, students select the members of their dissertation committee and submit this committee for approval to the Graduate Division. Students should endeavor to include a member whose research represents a complementary yet distinct area from that of the dissertation advisor (ie, biological vs computational, experimental vs theoretical) and that will be integrated in the student’s dissertation research.
Meetings with the Dissertation Committee
After Advancing to Candidacy, students are expected to meet with their Dissertation Committee at least once each year.
Dissertation projects will represent scholarly, independent and novel research that contributes new knowledge to Computational Biology by integrating knowledge and methodologies from both the biological and computational sciences. Students must submit their dissertation by the May Graduate Division filing deadline (see Graduate Division for date) of their fifth–and final–year.
Students will be required to present their research either orally or via a poster at the annual retreat beginning in their second year.