Biomolecular Engineering and Bioinformatics M.S.


The unifying theme of our research training program is using quantitative approaches to addressing fundamental questions in biology and biomedical science. The master of science (M.S.) program is designed to prepare students for careers in contemporary biomedical research settings in the biotechnology industry.

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 and are exposed to a rich environment of regular seminars and group meetings. Students interact closely with biomolecular engineering and bioinformatics faculty members while undertaking capstone projects (M.S.), 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.


Course Requirements

M.S. students must complete a total of at least 41 credits as described below. 

Core courses (5-credit) six are required

The following course:
BME 205Bioinformatics Models and Algorithms


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/ANTH 267A
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 M.S. since it is a lower-division course.

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.


A minimum of three seminar courses, including at least one quarter of the 2-credit biomolecular engineering seminar (BME 280B):

BME 280BSeminar on Bioinformatics and Bioengineering


Because the intent of the seminar course requirement is to ensure breadth of knowledge, BME 281-series courses do not count as a seminar, since these are lab group meetings.

Research Experience

At least 5 credits of independent study from the following courses:

BME 297AIndependent Study or Research


BME 297BIndependent Study or Research


BME 297CIndependent Study or Research


Transfer Limitations

Up to two courses may be transferred from other graduate institutions with the approval of the faculty advisor and the graduate director. However, please note that students will still be required to complete 35 credits while in the graduate program at UC Santa Cruz, pursuant to UCSC's rules on minimum units for the master's degree.

Other Requirements

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.

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.

M.S. Capstone Requirement

This is a Plan II capstone. Students must complete an individual project or a group project with a final written report submitted as part of the final evaluation. That project must be proposed by the student or student-group and be approved by BME faculty. Group projects must include a mechanism for evaluating the contributions of each member of the group.

Adequate 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 Master's 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