PhD Program

Prospective students who have completed a bachelor’s degree may apply for admission to the post-bachelor’s PhD program. The PhD requires a total of 64 credits, consisting of lecture/laboratory courses and research or seminar courses. While there is a set of required core courses, the precise course of study will be determined in consultation with the student’s academic advisor, and will reflect the student’s background and interests.  Students who have completed a bachelor’s degree as well as a master’s degree in a discipline related to the field—biological science, computer science, physical science, mathematics, engineering may apply up to 32 credits toward the PhD, including fulfillment of the core course requirements with a minimum of four lecture/laboratory courses, as recommended by the student’s academic advisor.

In order to be admitted to PhD candidacy, students must demonstrate mastery of the core subject matter (no lower than a “B” in core courses) and successfully complete the oral qualifying examination by the end of the second year.

Required Core Courses

ENG BE 562: Computational Biology: Genomes, Networks, Evolution (4 cr.)

ENG BE 605: Molecular Bioengineering (4 cr.)

ENG BF 690: Bioinformatics Challenge Project (2 cr./2 cr.)

ENG BF 768: Biological Database Analysis (4 cr.)

ENG BF 752: Legal & Ethical Issues of Science and Technology  (4 cr.)

GRS MA 681: Accelerated Introduction to Statistical Methods for Quantitative Research (4 cr.)

ENG BF 571: Dynamics and Evolution of Biological Networks (4 cr.)

ENG BF 820: Research Opportunities in Bioinformatics (1 cr.)

ENG BF 821: Bioinformatics Graduate Seminar (2 cr./2 cr.)


All students enrolled in the post-bachelor’s PhD program are required to take at least one non-research elective course. Elective courses are optional for students enrolled in the post-master’s PhD program.

Lab Rotation Requirement

Three lab rotations are required during a Ph.D. student’s first year, each lasting approximately 9 weeks. One rotation must be experimental, one computational, and the third can be either. At least two must be at Boston University, on either the Charles River campus or the Medical School campus.  Only rotations done in laboratories located on-campus fulfill the rotation residency requirement. Students in the NIH GPP have a modified rotation requirement.  They must complete three rotations, but two of these may be done at the NIH, preferably in the summer preceding and/or following their first year of graduate school.  The third rotation must be taken at Boston University. Students that are awarded an IGERT Fellowship will receive credit toward one of the required rotations for their wet lab training during the summer prior to their first semester.

Annual Report

All students are required to submit an annual report each fall. The report includes a list of courses completed, research projects and committee updates, journal publications, conference presentations or posters, teaching, Bioinformatics Community Service, financial support, report of oral  examination, as well as a brief program evaluation.

Teaching Requirement

There is a one semester teaching requirement for all PhD students in the Bioinformatics Program .

Qualifying Examination

The goal of the oral qualifying exam is for the student to demonstrate his or her general proficiency in bioinformatics, as well as command of the area(s) in which he or she intends to conduct research. Each student in the Bioinformatics Program will select a Qualifying Committee (QC) of 4 faculty members in the program during the first semester of their second year.  The Qualifying Committee must include faculty members with biological/experimental expertise, as well as members with computational expertise.

Ph.D. Dissertation

All Ph.D. students are expected to defend the significance, originality and methodologies employed in their thesis research. This defense consists of two parts. The first is the public seminar open to the University community and based on the work by the student. The second is an oral defense of the work, which usually follows the public seminar, and is done privately before the student’s Thesis Committee. The committee members ensure that the research is complete and understood by the candidate. At this time they can voice any concerns over the data or the preparation of the dissertation document. Depending on how well the thesis experiments are designed, performed, and defended, and how well the thesis is prepared, the committee will vote whether or not the thesis is complete and satisfactory.