Biomolecular Engineering and Bioinformatics Ph.D.


Program coursework is designed to provide the technical skills in programming and other technical skills required for independent and advanced scientific discovery. Incoming students undertake rigorous core coursework, conduct laboratory rotations, and are exposed to a rich environment of regular seminars and group meetings. Students interact closely with biomolecular engineering and bioinformatics (BME) faculty members while undertaking their dissertation research, and have firsthand access to state-of-the-art computation tools and laboratory facilities throughout their training, including cluster computing and high-throughput sequencing facilities.

Advancement to Candidacy

Course Requirements

Ph.D. students must complete a total of at least 55 credits as described below.

Core Courses

The following courses:
BME 201Scientific Writing


BME 205Bioinformatics Models and Algorithms


BME 201 is typically taken as a second-year Ph.D. student, in winter quarter.

Plus one of the following courses:
BME 229Protein and Cell Engineering


BME 230AIntroduction to Computational Genomics and Systems Biology


BME 278Stem Cell Biology


Graduate-Level Quantitative Science Course

Students must take one 5-credit graduate-level course focused on quantitative science. Suitable courses are to be selected in consultation with the Biomolecular Engineering Graduate Advising Committee, the student, and the student’s faculty mentor.

Ethics Course:

Choose one of the following courses:

Bioethics in the 21st Century: Science, Business, and Society


/BME 268A/FMST 268A/CRES 268A
Science and Justice: Experiments in Collaboration


BME 80G can be taken to meet the ethics requirement, but the credits will not be counted toward the overall credit requirement for the Ph.D. since it is a lower-division course. In other words, students who choose to take BME 80G for the ethics requirement, must take another 5-credit BME graduate-level course to fulfill their course credits.

Graduate-Level Biomolecular Engineering Electives

Students must take at least two 5-credit, graduate-level BME courses. Suitable courses are to be selected in consultation with the Biomolecular Engineering Graduate Advising Committee, the student, and the student’s faculty advisor. Alternative electives may be considered with the approval of a student's faculty advisor and the graduate director.


BME 280BSeminar on Bioinformatics and Bioengineering


A minimum of six seminar courses (12 credits), including at least two quarters of the 2-credit Biomolecular Engineering seminar. Because the intent of the seminar requirement is to ensure breadth of knowledge, laboratory group meetings (BME 281-series courses) do not count for the seminar requirement.

Before and after advancement, full-time Ph.D. students are required to enroll in at least one seminar course each quarter (e.g., BME 280 or BME 281), and must present the results of their ongoing research at least once each year.

Lab Rotations

Students must take at least two quarters of BME 296, during which students do three research laboratory rotations. Students must enroll in BME 296 during fall and winter quarters of their first year. Laboratory rotations for Ph.D. students are generally completed in the first two quarters (three 7-week rotations).

BME 296Research in Bioinformatics


Bootcamp Activity

Entering graduate cohorts are expected to participate in the hands-on “bootcamp” just before the start of the fall quarter. Bootcamp activities include program orientation, laboratory safety training, teaching assistant (TA) training, fellowship advice, cohort building activities, practical advice for navigating graduate school, and a hands-on research project.

Transfer Limitations

Up to two graduate courses may be transferred from other graduate institutions with the approval of the faculty advisor and the graduate director.

Further Study Outside the Department

No further courses are required. However, with faculty guidance students often choose to take upper-division undergraduate courses or graduate courses outside the department to make up for deficiencies in background areas of particular importance.

With consent of the graduate director, variations in the composition of the required courses may be approved.

Teaching Requirement

Ph.D. students will be required to serve as teaching assistants for at least one quarter during their graduate study. Certain exceptions may be permitted for those with extensive prior teaching experience, for those who are not allowed to be employed due to visa regulations, or for other reasons approved by the graduate director.

Ph.D. students whose native language is not English must demonstrate English fluency for Teaching Assistantship purposes before serving as a TA. Detailed information about TA eligibility is available at the Baskin Engineering Graduate Affairs website.

Qualifying Examination

Ph.D. students must select a faculty research advisor by the end of the first year. A qualifying examination committee is then formed in the second year, which consists of the advisor and three additional members, and which is approved by the graduate director and the campus graduate dean. At least two of the four must be members of the Department of Biomolecular Engineering. The student must submit a written dissertation proposal to all members of the committee and the graduate program advisor 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. students are strongly recommended to pass the qualifying examination and advance to candidacy by the end of their second year. They are required to do so by the end of their third year.



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 graduate director upon the recommendation of the dissertation supervisor. At least one of the three must be a member of the Department of Biomolecular Engineering.

Dissertation Defense

The candidate will present their 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.

Academic Progress

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.

Applying for Graduation

All candidates for a degree must submit an Application for PhD Degree to the Graduate Division by the date stated in the Academic and Administrative Calendar for the quarter they wish to receive the degree. The deadline for degree applications is typically in the second week of the quarter. For more information about applying for graduation, visit the Baskin Engineering Graduate Studies website.