Biomolecular Engineering and Bioinformatics Ph.D.

• Introduction
• Advancement to Candidacy
• Dissertation

Introduction

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

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Course Requirements Expand and Collapse

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

Core Courses Expand and Collapse

The following courses:

BME 205	Bioinformatics Models and Algorithms	5
BIOL 200F	Logic and Approaches to Scientific Discovery	5
BME 201	Scientific Writing	3

BIOL 200F is typically taken as a first-year Ph.D. student, in winter quarter.

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

Plus one of the following courses:

BME 230A	Introduction to Computational Genomics and Systems Biology	5
BME 229	Protein and Cell Engineering	5

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:

BME 80G /PHIL 80G	Bioethics in the 21st Century: Science, Business, and Society	5
SOCY 268A /BME 268A/FMST 268A/ANTH 267A	Science and Justice: Experiments in Collaboration	5

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.

Graduate-Level Biomolecular Engineering Electives

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

Seminars Expand and Collapse

BME 280B

Seminar on Bioinformatics and Bioengineering

2

A minimum of six seminar courses, 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 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 Expand and Collapse

Three research laboratory rotations (BME 296 - must enroll in fall and winter quarters of their first year) with different supervisors. Laboratory rotations for Ph.D. students are generally completed in the first two quarters (three 7-week rotations).

BME 296

Research in Bioinformatics

5

Bootcamp Activity Expand and Collapse

Entering graduate cohorts are strongly 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.

Transfer Limitations Expand and Collapse

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

Further Study Outside the Department Expand and Collapse

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.

Qualifying Examination Expand and Collapse

Ph.D. students must select a faculty research adviser by the end of the first year. A qualifying examination committee is then formed in the second year, which consists of the adviser 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 adviser 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 required to pass the qualifying examination and advance to candidacy by the end of their second year.

Dissertation

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Dissertation Expand and Collapse

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 Expand and Collapse

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 Expand and Collapse

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 adviser and the graduate director.

Applying for Graduation Expand and Collapse

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 School of Engineering Graduate Studies website.