Academics

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Flexible courses, research focused!

The Biomedical Engineering Graduate Program offers a flexible curriculum that focuses on dissertation research.

Degree Requirements

Biomedical Engineering graduate program curriculum

To graduate from the Biomedical Engineering PhD program the following requirements must be fulfilled:

  • Successful completion of core courses and 4 electives equivalent to 8 credits
  • Maintain 3.0 GPA throughout the program
  • Pass Qualifying Exam
  • Meet every 6 months with Dissertation Advisory Committee (DAC)
  • Perform dissertation research, write and defend dissertation
  • Successful completion of 135 credits, including 54 credits of PhD dissertation research.

For detailed program requirements, please refer to the BME Program Guidelines 

Required Courses

BME 605 Readings in Biomedical Engineering
Credits - 1 / Fall term
This course is designed to teach critical evaluation of information in the field of Biomedical Engineering.  Students will read articles and papers on timely topics related to the student’s area of interest.  Students are required to present summaries of the readings and to lead class discussions. 

BME 607 Seminar Series
Credits - 0 / every term

This seminar course will feature presentations and discussions on topics in biomedical engineering that exemplify the wide range of applications of biomedical engineering to science and medicine. The goals are to provide the students with an overview of the diverse opportunities for research and application, to foster development of critical analysis and thinking, and to stimulate creative problem solving and research planning.

BME 608 Grant Writing and Qualifier Preparation
Credits - 1 / Fall and Spring term

Students will be instructed in the preparation of a 6 page NRSA-style grant proposal per the BME Program Guidelines for submission to their qualifying exam committee. The topic of the proposal will be determined by each student. In addition to didactic instruction on grant writing skills, the student will serve as reviewers for their fellow students' proposals.   

CONJ 620 Introduction to Biostatistics for the Basic Sciences
Credits - 3 / Winter term

This course is designed for students enrolled in basic science graduate programs to provide an introduction to biostatistics concepts and analysis methods that are required to conduct research in these fields. The course is a combination of lectures (some of which may be online), statistical computing tutorial sessions and journal clubs. Some homework/projects will require the use of a statistical software package.

MGRD 650 The Practice and Ethics of Science
Credits -1 / Fall term

This course is designed to provide students in biomedical research with survival skills and an understanding of ethical conduct. Topics covered include: being a trainee, scientific integrity and misconduct, scientific publication, oral presentations, lab safety, use of laboratory animals, human subjects research, and research funding. Ethical dilemmas and issues are discussed in context of the practice of science. 

MATH 630 Probability & Statistical Inference for Scientists and Engineers
Credits - 3
This course is can be taking in place of CONJ 620 Introduction to Biostatistics for the Basic Sciences and introduces fundamental concepts underlying statistical data display, analysis, inference and statistical decision making. The topics include presentation and description of data, basic concepts of probability, Bayes' theorem, discrete and continuous probability distributions, estimation, sampling distributions, classical tests of hypotheses on means, variances and proportions, maximum likelihood estimation, Bayesian inference and estimation, linear models, examples of nonlinear models and introduction to simple experimental designs. One of the key notions underlying this course is the role of mathematical modeling in science and engineering with a particular focus on the need for an understanding of variability and uncertainty. Examples are chosen from a wide range of engineering, clinical, and social domains. 

BME Elective Courses

BME requires students to successfully complete at least four elective graduate courses, equivalent to 8 or more credits, offered by BME or other OHSU School of Medicine graduate programs prior to taking their Qualifying Exam. Below is a list of BME elective courses:

BME 640 Fluid Mechanics and Biotransport
Credits - 3 / Fall or Winter term

This course introduces basic concepts of fluid mechanics and convective mass transport.  It will start with a derivation of mass, momentum and energy conservation equations for fluid flows.  The importance of non-dimensional parameters such as Reynolds number and the Womersley parameter will be extensively discussed, and non-dimensional equations will be derived.  Other topics to be covered include Bernouilli’s equation, low and high Reynolds number flows, oscillatory flows, interactions of fluid flows with tissue and boundary layers.  The final part of the course will cover the derivation and use of mass transport equations in fluid flows.  Examples from different areas of biomechanics will be discussed throughout the course.

BME 645 - Biocompatibility: Host - Implant Interactions
Credits - 3 / Spring term

This course provides the student with a firm understanding of how the body reacts to implanted biomaterials at the cell, tissue, organ, and systemic levels. In addition, specific characteristics that hinder or improve the biocompatibility of materials will be addressed. The concepts of biocompatibility with regards to biomaterials in experimental and clinical situations are presented.  The influences of the molecular interactions between materials with different bulk and/or surface chemistry will be discussed.  Issues related to the consequences of degradation products, inflammation and infection are discussed at the cellular and molecular level.  Techniques to characterize biomaterials in vitro, as well as the in vivo / ex vivo analysis of implanted and explanted biomaterials are presented.

BME 673: Cancer Systems Biology
Credits - 3 / Spring term

Cancer systems biology is an integrative approach to understanding cancer as a complex biological system that is made up of more than the sum of its parts. Interactions between components are a primary focus, as is the behavior of subsystems made up of several components. This course is designed to provide an understanding of the rationale and approaches used in cancer systems biology. The class will transition through discussions of the biological basis for cancer, experimental methods, experimental model systems, large-scale data resources, analytical methods, and will provide practical experience with analyzing data from a systems perspective.

BME 674: Foundation of Measurement in Science
Credits - 3
 / Fall term
This course is intended for first and second year graduate students in the BME program or quantitative students in other programs who are interested in quantitative biosystems approaches to biomedical research and seek a deeper understanding of the technologies used in their research. The course will examine the physical principles underlying the instrument design and function and discuss analysis of their output and their practical use in actual research settings.

BME 675: Analysis of Quantitative Bioscience
Credits - 3 / Fall term

This introductory computational biology course is geared toward students comfortable with quantitative methods, but extensive programming experience is not necessary.  The course introduces and employs python notebooks for analyses of genomic and related 'big' biological data.  Key statistical concepts are introduced and used throughout the course in the discussion of algorithms for the analysis and simulation of biological data.  Topics covered typically included sequence alignments, analysis of RNA sequence data, pathway analysis, Markov modeling, and machine learning.

BME 680 (EE682 cross-listed) Signals and Linear Systems
Credits - 3 / Fall term

This course will teach students the core principals of digital signal processing.  We will survey a variety of topics in class lecture/discussion based on assigned readings while exploring specific topics/applications in depth through lab assignments and a final project.  Specifically, we will cover the core topic areas in digital signal processing including an overview of discrete-time signals and systems, the discrete-time Fourier transform, the z-Transform and transform analysis, the discrete Fourier Series, the discrete Fourier transform, circular convolution, network structures for FIR systems, design of IIR and FIR filters, multi-rate processing, and linear prediction.  If time permits, we will also provide an introductory lecture on the Kalman filter and the extended Kalman filter.

BME 683 Physiologic modeling and model predictive control
Credits -3 / Winter term

This course will teach students the core principals of modeling of physiologic processes and then teach how to use these models within a model-predictive control configuration.  Models of physiology can be used to improve our understanding of a system and for educational purposes and as a means to support clinical processes.  Model predictive control (MPC) is a method for controlling systems based on prior knowledge about the process being controlled and using a horizon of predicted responses of the process to determine optimal input control parameters.   This class will provide an introduction to modeling of physiologic processes. 

BME 690 Topics in Nanomedicine
Nanomedicine involves the development and application of materials and devices to study biological processes and to treat disease at the level of single molecules and atoms. Through the study and treatment of disease at the molecular cell level, this exciting new field of nanotechnology and medicine is offering unique capabilities in disease diagnosis and management.  This course offers a survey of timely concepts in the rapidly emerging nanomedicine. We will introduce basic principles underlying nanomedicine and review how nanomedicine is redefining clinical research in areas such as diagnostic imaging agents, nanomaterial-based drug delivery, and nanoscale proteomics. Specific attention will be directed to disease processes including: cancer, kidney, and neurodegenerative diseases.

OHSU Graduate Courses

In addition to the elective courses offered with in the Biomedical Engineering Graduate Program, student have access to most graduate courses at OHSU. Under the guidance of their mentor, students can take courses that support their research from graduate programs across OHSU.

Explore the course offerings of graduate programs at OHSU.

Course Collaboration at Portland State University

Students may also choose to take an elective graduate level course at our neighboring institution, Portland State University (PSU).

Find out more about these inter-institutional courses.

Registration

Register for classes by logging into the OHSU Student Information System (SIS). For detailed information about registration or assistance in registering, please visit the Office of the Registrar

Student Self Service Guide

Registration dates and deadlines for 2020-21

Fall term 2020
Term - 9/28/2020 - 12/18/2020
Registration begins - 8/17/2020 
Last day to add/drop - 10/5/2020

Winter term 2021
Term - 1/4/2021 - 3/19/2021
Registration begins - 11/23/2020
Last day to add/drop - 1/11/2021

Spring term 2021
Term - 3/29/2021 - 06/18/2021
Registration begins - 2/15/2021
Last day to add/drop - 4/5/2021

Academic Calendar 2020-21

Timeline and Milestones

Year one: Core courses

The main goal for the first year is to work with your mentor to identify those courses most relevance to your area of research, and to take as many core and additional courses as practical during the first 9 months in preparation for your Qualifying Exam proposal development and oral exam.

Students are required to complete the following course requirements:

BME 605 Reading in Biomedical Engineering
BME 607 Seminar Series (3 terms)
BME 608
Grant Writing and Qualifier Preparation

CONJ 620 Introduction to Biostatistics for the Basic Sciences
MATH 630* Probability & Statistical Inference for Scientists and Engineers
MGRD 650 The Practice and Ethics of Science

4 Elective courses = 8 credits total

In addition, students should continuously be enrolled in BME 601 pre-qualifying research credits or BME 603 Dissertation Research credits post Qualifying Exam.

*Recommended for Computational students in lieu of CONJ 620

Year two: Complete course requirements and Qualifying Exam

Students should enroll in any remaining course requirements and BME 608 Grant Writing/Qualifying Prep to fulfill all requirements for taking the Qualifying Exam, offered fall or spring terms. The majority of the student’s time and effort should be in research. A major goal for the second year is to begin to acquire the laboratory, computational or analytical skills and conceptual framework necessary for thesis work. The student should also be spending free moments reading the scientific literature.

Year three and beyond

Immediately following passing the qualifying exam, students in consultation with their mentor, should nominate a Dissertation Advisory Committee which must be approved by the Program Director.

The student must present a departmental research seminar during the third year. It is expected that most Ph.D. graduate students will defend their dissertation sometime in their fifth calendar year and the School of Medicine requires that the student be continuously enrolled until the thesis is bound. Students may not use a leave of absence to make corrections to the thesis.

Qualifying Exam

The goal of the Qualifying Exam is for students to develop the necessary skills to propose a research project. Students will formulate their own hypotheses, develop the background to justify the proposal and develop the experimental approach to test the proposed hypotheses. Students should also be thoroughly familiar with key historical and background publications that provide the foundation for their proposal, as well as any current literature that directly pertains to their specific aims.

The exam is both written and oral.  The written portion of the exam is in the form of an NIH-NRSA grant and is supported by an oral presentation, which is typically 2 hours long. The Qualifying Exam Committee, composed of four faculty members, will ask the students probing questions, testing students on breadth and depth of their knowledge of the purposed hypothesis.

BME students should take the Qualifying Exam during the second year of the Ph.D. program and are required to pass by their 12th term. The exam is offered both in spring and fall terms. Upon successful completion of the Qualifying Exam, students will become eligible for recommendation for advancement to candidacy.

Learn more about the Qualifying Exam

Dissertation Advisory Committee

A Dissertation Advisory Committee (DAC) is a committee of faculty, chosen by the student, to advise them through their dissertation research, provide additional mentorship and evaluate progress toward degree completion. We recommend forming the DAC between the seventh and twelfth terms to receive advice earlier in students’ graduate careers’ careers concerning research, courses, and preparing for the Qualifying Exam.

The DAC should be composed of multidisciplinary faculty and consists of at least four members: a Chair, the student’s mentor and 2-3 other faculty who could best serve the research aims of the student and approved by the Program Director and Associate Dean of Graduate Studies.

Students are responsible for scheduling and meeting with their DAC every six months. For each DAC meeting, students should prepare an organized presentation of their recent progress, including a summary of the goals outlined by the DAC during their previous meeting. After each DAC meeting, a short report that summarizes the issues raised during the meeting, called the DAC Meeting Summary, should be prepared by the student in consultation with the mentor, approved by the DAC and sent to the Program Coordinator.

Learn more about the Dissertation Advisory Committee.

Dissertation and Defense

Dissertation

Students present a written description of the research carried out during their course of study in the form of a dissertation. The dissertation demonstrates the student’s ability to plan and execute original research, and must represent a definite contribution to scientific knowledge. Although there is flexibility in the amount of work required for the dissertation, in general, the thesis should represent the equivalent of at least two first-author publications in significant, peer-reviewed journals, and should be submitted for publication prior to the defense.

Students have 6 months to electronically submit their dissertation to the Library after a successful Oral Exam. During this time, students must be registered for at least 1 credit to remain enrolled at OHSU.

Guidelines for preparation of dissertation and thesis

Dissertation Defense/Oral Exam

Once a student is close to completing their dissertation research, they can start to plan for their dissertation defense otherwise known as Oral Examination. Students will need to form an Oral Exam Committee (OEC) comprised of no fewer than 4 members of the Graduate Faculty who do not all have primary appointments in the same department or institute. The committee must also include at least 1 member who is not a member of the student’s Dissertation Advisory Committee. Students should check with the Program Director or Program Coordinator to make sure the majority of the members are Graduate Faculty.

The student and their OEC find a date and time that works for everyone and the oral examination is made public. The defense seminar lasts 1 hour including questions from the public followed by the oral examination. Students should send an abstract to the Program Coordinator for announcement of oral exam.

The dissertation needs to be sent to the OEC at least 2 weeks prior to oral exam.

Request for Oral Examination

9 Steps to Graduation

1. Complete Program Requirements

Find out if all program requirements have been completed by logging into the Student Information System. For questions about the degree audit or program requirements contact Dr. Monica Hinds, Program Director, or Erica Hankins Regalo, Program Coordinator.

2. Apply for Degree

The Office of the Registrar requires an Application for Degree be submitted one term prior to completing degree requirements. This can be submitted online by logging into the Student Information System.

Instructions on how to apply for degree

3. Request for Oral Examination

A signed Request for Oral Examination (OEC) form must be submitted to the Office of Graduate Studies at least 4 weeks before the scheduled oral defense date. The Oral Exam must be open to the public and advertised.

Note: Students on academic probation or with an (I) incomplete on their transcript may not take the Oral Exam.

4. Distribute a Copy of the Dissertation to Your OEC

This needs to happen at least 2 weeks prior to your Oral Exam.

5. Recording the Outcome of the Oral Examination

The OEC members individually evaluate the student's performance as satisfactory or unsatisfactory and record their votes on the certification form. A majority is necessary for a satisfactory outcome. 

Students can petition for re-examination if either the preparation or defense of the dissertation are not approved. 

6. After the Dissertation Defense

After the Oral Exam, students have 6 months to make all necessary corrections to their dissertation required by the Oral Exam Committee. Students must be registered for at least 1 credit during this time. Once all corrections have been approved by the OEC, the original of the signed Certificate of Approval has to be submitted to the Office of Graduate Studies.  

7. Dissertation Submission

The final dissertation must be electronically submitted to the OHSU Library for
publication at least 2 weeks prior the 6 month deadline. Please see the OHSU Library’s website for current instructions on how to electronically submit.

8. Survey of Earned Doctorates

Complete the required Survey of Earned Doctorates online.

9. Graduating

An Exit Contact & Information Form should be submitted to the Office of Graduate Studies. Degrees are awarded at the end of each term when all academic requirements are met. Debts and other unmet obligations prevent the release of diplomas and transcripts, including the graduation fee.

OHSU commencement is held at the beginning of June for all students who graduated in that academic year.

Guidelines for Degree Completion - Doctor of Philosophy