Doctoral Program

Megan Armstrong, Columbia University Biomedical Engineering PhD student

Megan Armstrong, BME PhD student

The Department of Biomedical Engineering offers a variety of graduate programs: the Master’s of Science degree (M.S.), the Doctor of Philosophy degree (Ph.D.), and the Doctor of Engineering Science degree (Eng.Sc.D). Applicants who have an M.S. or equivalent are welcome to apply directly to a doctoral degree program. Additionally, the department offers an M.S.-leading-to-Ph.D. track for applicants who have not yet completed their master’s degree, and a combined MD/Ph.D. program in conjunction with Columbia University School of Physicians and Surgeons.

All applicants are expected to have earned a bachelor’s degree in engineering or other science, and are required to take the Graduate Record Examination (GRE – general test only). Students who earned their bachelor’s degree in a country where English is not the dominant language will be required to take the TOFEL. 

Doctoral Candidate Requirements

Doctoral candidates are expected to complete 30 credits beyond the master's degree, pass an oral and written qualifying examination, and successfully defend their doctoral dissertations, which are based on individual research. In addition, all doctoral students must demonstrate teaching competence as part of their training.

The core course requirements (9 credits) for the doctoral program include the course in computational modeling of physiological systems (BMEN E6003), plus at least two graduate mathematics courses. If BMEN E6003 or a graduate level mathematics course has already been taken for the master’s degree, a technical elective can be used to complete the core course requirements. Students must register for BMEN E9700: Biomedical engineering seminar and for research credits during the first two semesters of doctoral study. Remaining courses should be selected in consultation with the student’s faculty adviser to prepare for the doctoral qualifying examination and to develop expertise in a clearly identified area of biomedical engineering. Up to 21 credits of research may be applied toward doctoral degree course requirements.

All graduate students admitted to the doctoral degree program must satisfy the equivalent of two semesters’ experience in teaching (one semester for M.D./Ph.D. students). This may include supervising and assisting undergraduate students in laboratory experiments, grading, and preparing lecture materials to support the teaching mission of the department. The Department of Biomedical Engineering is the only engineering department that offers Ph.D. training to M.D./Ph.D. students. These candidates are expected to complete their Ph.D. program within 3.5 years, with otherwise the same requirements as those outlined for the Doctoral Degree program. 

  • 30 credits beyond M.S. degreee
  • 2 advanced math courses required
  • Up to 21 credits can be research with consultation from adviser
  • Other courses can be selected in consultation with adviser

For information on specific courses see and .

Doctoral Qualifying Exam

 The BME doctoral qualifying exam is an important evaluation of a student’s mastery of broad, coursework-based knowledge and their ability to analyze, synthesize, present, and discuss contemporary concepts in a specific area of research.

  • These skills are fundamental for high-impact, creative doctoral research.
  • The qualifier is an opportunity for students to demonstrate the capacity for critical thinking and for the faculty to identify any areas that need strengthening.
  • The qualifier is distinct from any individual course or exam, emphasizing the use of fundamental concepts in research as appropriate for an early graduate student.  It is also distinct from the dissertation proposal and defense, as it does not require original research by the student.

The qualifier consists of the following three components:

  1. Written component (6-8 pages): summary, critical analysis, and syntheses of three papers from literature, and description of the state of the art in the chosen research problem/topic of interest.
  2. Oral presentation (between 30 and 45 minutes):  summary, critical analysis and synthesis of three papers within the context of a chosen research problem.
  3. General examination (approx. 60 minutes) in which the candidate answers questions posed by the examination committee.

I. Eligibility

To be eligible for the Qualifying Examination, a candidate must:

  • Be admitted to the doctoral (PhD) or M.S. leading to doctoral (MS/PhD or MD/PhD) degree program
  • Have completed 30 credits but no more than 45 credits with a cumulative GPA of ≥3.2 (the GPA calculation excludes all research credit)
  • Have received permission from his/her DBME thesis advisor to take the qualifying exam.  

II. Preparation

Please consult with your advisor on how to prepare for the written and oral component of the exam, including the preparation time and balancing against coursework and research. From past history, 2 months is a typical preparation time, but the time may vary, depending on your background. 

III. Format

Selection of papers (by November 30).  With your advisor, select three papers from the literature.  You are encouraged to select papers related to your intended thesis research.  The papers should not include your PI or any research faculty in the BME department as an author.  At least one of the papers must have an extensive mathematical basis.  You will have to explicitly state in the email which area of mathematics is being covered.  It should be within the topic areas of your graduate mathematics classes (excluding statistics).  Sample topics are: "partial differential equations", "vector calculus", and "linear algebra".  Topics not normally accepted are statistics, or purely equations fitting experimental data without an underlying mathematical or physical model.  During the examination, you should be prepared to describe the mathematical framework from first principles in the written paper, oral presentation, and/or general examination.  Send the 3 papers (PDFs) to James, and cc the advisor.  The advisor will have to respond to James to confirm their approval for this step to be complete.

Selection of examination committee (by November 30).  Work with your research advisor to form an examination committee of three BME faculty members: 1) your advisor; 2) the qualifier examiner appropriate for your track (listed at the end of this document); and 3) a BME research faculty at large.  If your advisor is also the qualifier examiner for your track, include a member of the graduate committee (also listed below) as the third member.  Please invite each potential committee member by email, and after you confirm, please email the committee membership to James.

Written component (by January 12).  Write a paper that describes the cohesive topic represented by the three selected papers.  Students should express the impact, scientific method, and technical details of the selected papers, and critique the strengths and limitations of the papers.  It is important to put the papers in the context of an overall research approach or question; the students should synthesize multiple, discrete studies as parts of a single, cohesive concept.  The title of the written component and oral presentation should reflect this cohesive research question or concept.  This document is to be 6 to 8 single-spaced pages, with 11 pt font and 1” margins, including original figures (students should avoid unnecessarily posting figures directly from the papers) but excluding references.  The document should follow this format:

  • Description of the cohesive research question or concept
  • Significance of research questions
  • Background (focusing on the 3 selected papers, and including other papers as needed)
  • Critiques of strengths/weaknesses of papers
  • Outline of future research to address research question (student should apply information from the background section and courses to describe research approaches that could further tackle the research question; detailed experimental designs are not expected)

Although others can provide input on the written component, the entire document must ultimately be written by the candidate alone.  A PDF of the written component, and PDFs of the three selected papers, must be emailed to all committee members by January 13.

Oral presentation (between January 20 and February 10).  Schedule a 2-hr period for this exam, in consultation with your committee members.  Coordinate with Zachary Corter on reserving a time and location for this exam.  Oral exams will be given priority for scheduling in the BME conference rooms during the designated period.  

In the first component, student will present the three papers.  The presentation itself should last no longer than 30 minutes (or about 45 minutes total with questions).  The format of the presentation should follow the outline set out above for the written component.  Committee members may ask questions at any time during your presentation.  Questions can focus on your understanding of the techniques used in the papers, critique of the authors’ conclusions, and presentation of these papers as different facets of a single research direction.

In the second component, the students will undergo an oral "general exam".  Committee is encouraged to begin the line of questions with topics related to the papers presented, but questions can be broad-ranging.  Questions will include at least one with a quantitative physiology basis, and one with a mathematical basis.  Additional questions can come from all topics of biomedical engineering, with an emphasis on the following list of topics, as guided by the students proposed area of research.  The level of expertise expected in each area is illustrated by the suggested list of courses (although the questions will not be taken directly from any one class).

Mathematics (APMA E4001, APAM E4200):  

  • vector algebra and calculus, partial/ordinary differential equations, linear algebra, Fourier series
  • mathematical models that relate to the topic presented by the student

Physiology/Biology (BMEN E4001/E4002/E6003, BIOL 2005/2006):

  • molecular-, cellular-, tissue- and system-level physiology
  • mathematical models and quantitative analysis of control mechanisms 

Biomechanics Track (BMEN E4300, BMEN E4305, BMEN E4340, and BMEN E4702) 

  •  solid mechanics; fluid mechanics; musculoskeletal biomechanics, cardiac mechanics,  cell mechanics

Biomedical Imaging Track (BMEN E4410, BMEN 4420, BMEN E4898, ELEN E4810, BMEN E4893, BMEN E4430):  

  • digital signal and image processing; image formation and contrast mechanisms, including tomographic reconstruction in X-Ray CT, SPECT, and PET; magnetic resonance imaging and spectroscopy; radiography; ultrasound; optical tomographic imaging; optical microscopy and spectroscopy; image analysis, quantification and evaluation

Cellular and Tissue Engineering Track (BMEN E4501/E4502, BMEN E4210; BMEN E6001):  

  • biomolecular processes (enzymatic reactions; molecular-, cell-, and organ-level transport; drug delivery, thermodynamics; electrochemistry; signal transduction)
  •  cell function (cell adhesion, migration, apoptosis, proliferation, and differentiation; cell-cell, cell-matrix, and cell-material interaction)
  • design at the molecular-, cellular-, and tissue-level (biocompatibility; biomaterials; scaffold design, bioreactor design; assay design)

IV. Exam grading

Immediately after the oral examination, the committee votes to pass, conditional pass, or fail.  The results will be reviewed by the DBME faculty in mid-February, with final decisions on the qualifier reported to the students shortly after.

In issuing the final recommendation, the committee will explicitly consider each of the following five grading components:


Out of 10
(10 = best)

1.  The student accurately presented the results of the papers.


2.  Was the student able to synthesize the papers into a cohesive concept?


3.  The student demonstrated technical ability to carry out doctoral level research in Biomedical Engineering.


4.  The student demonstrated knowledge of biology and physiology required to carry out doctoral level research in Biomedical Engineering.


5.  Written component


For any deficiencies, the committee should distinguish whether they are due to the scientific aptitude as opposed to language barrier.

In a conditional pass, the student may (for example) be requested to take a specific course and receive a minimum grade.

If the student fails, he or she may have one more chance to take the exam, upon approval by the graduate committee.

Please contact your advisor or Prof. Sam Sia with any questions or concerns.   

2017-2018: graduate committee:

Samuel Sia, Henry Hess, Elisa Konofagou, Helen H. Lu, Elizabeth Olson, Ken Shepard, Qi Wang, Joshua Jacobs, and Gordana Vunjak-Novakovic.

2017-2018: qualifier examiners:

            Josh Jacobs, Henry Hess, Sam Sia

Doctoral Committee and Thesis

Students who pass the qualifying examination choose a faculty member to serve as their research adviser. Each student is expected to submit a research proposal and present it to a thesis committee that consists of at least four faculty members.

The committee considers the scope of the proposed research, its suitability for doctoral research and the appropriateness of the research plan. The committee may approve the proposal without reservation or may recommend modifications.

In general, the student is expected to submit his/her research proposal after five semesters of doctoral studies. In accord with regulations of the School, each student is expected to submit a thesis and defend it before a committee of five faculty, at least one of whom hold primary appointments in another department.

Every doctoral candidate is expected to have had accepted at least one full-length paper for publication in a peer-reviewed journal prior to recommendation for award of the degree.

Proposal Defense

• Expected after four semesters of doctoral studies (2 years after qualifying exam)
• Committee of at least four faculty members

Thesis Defense

• Committee of at least five faculty members, at least one of whom hold primary appointments outside BME


Chair of the Graduate Affairs Committee
Professor Elisa Konafagou (

Student Affairs Manager
James Ihn (

Graduate Student Council 
Andrew Kang (

Individual Professors/Advisors

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