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, which may include graduate and upper-division undergraduate courses, but no more than 15 credits may be upper-division undergraduate courses.

Core courses

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/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 M.S. 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.

Biomolecular Engineering Electives

Biomolecular engineering graduate courses suitable for fulfilling the 41-credit requirement include, but are not limited to, BME 215, Applied Gene Technology; BME 230B, Advanced Computational Genomics and Systems Biology; BME 232, Evolutionary Genomics; BME 272, Precision Medicine; BME 278, Stem Cell Biology. Up to 5 credits of Independent Study or Research (BME 297A) sponsored by an individual faculty member could be used to fulfill the 41-credit requirement. In addition to these graduate courses, up to 15 credits may be upper-division undergraduate courses. Suitable courses are to be selected in consultation with the Biomolecular Engineering Graduate Advising Committee, the student, and the student’s faculty mentor. Upon approval, these courses are selected to address specific interests, cover topics specific for the capstone project, or address specific deficiencies of each student.


A minimum of three seminar courses (6 credits total), 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.

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. 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 encouraged 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. Students will usually spend two to three quarters on the project and must include a BME faculty member for approval of the final written report. Group projects must describe in the written report a mechanism for evaluating the individual contributions of each member of the group.

Upon admission into the M.S. program, students should immediately seek out a faculty member to oversee their individual or group project. The faculty member must agree to oversee the project. Should the student have difficulty in finding a faculty member, they should seek assistance from the BME graduate advisor by the end of the winter quarter. A faculty advisor must be identified by the end of the first year of the M.S. program.

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.