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As required by the university, to advance to Ph.D. Candidacy, the student must pass three Comprehensive Examinations: I) comprehensive written exam, II) comprehensive oral exam, and III) final thesis defense. For timelines of when the oral and written exams need to be scheduled, please refer to Important Deadlines; the final thesis defense is completed at the conclusion of the student’s graduate work.

I. Comprehensive Written Exam

The comprehensive written exam is an open-book exam to test your knowledge, comprehension, and analytical ability. Passing is required to remain in the program. It is suggested that students take the written comprehensive exam in their second year. Several weeks prior to the exam, relevant reading materials are provided to students by the faculty exam committee. The combination of these readings plus the core course requirements is sufficient to prepare students to succeed in the exam requirements for their chosen track (Biochemistry or Biophysics). Students typically have one week to complete the exam.

SECTION I: Molecular and Cellular Biology

SECTION II: Biophysics, Enzymology, Structural Biology

  • A questions – probe comprehension and ability to critically evaluate scientific work
  • B questions – analyze, interpret and/or devise scientific experiment(s) to address unresolved issues.

Topic 1: A-type question

Topic 3: A-type question

Topic 1: B-type question

Topic 3: B-type question

Topic 2: A-type question

Topic 4: A-type question

Topic 2: B-type question

Topic 4: B-type question

Each student answers 5 total questions to complete exam:

  • Biochemistry track students answer all four questions in Section I and one type A or type B question from section II.
  • Biophysics track students answer all four questions in Section II and one type A or type B question from section I.

II. Comprehensive Oral Exam


  1. Follow NIH F31 Guidelines. Your proposal should be in a format that could be submitted to NIH.
  2. Page limits should also meet F31 Guidelines.
    • Project Summary: includes an Abstract (no more than 30 lines of text, with aims listed) and statement of Relevance to Public Health (no more than two or three sentences)
    • Specific Aims (no more than 1 page)
    • Research Strategy (no more the 6 pages, including figures) Includes sections on a. Significance, b. Innovation, and c. Approach
    • References (no page limit) Includes the names of all authors, article title, journal title, volume number, page numbers, and year of publication.
    • Proper formatting Arial or Helvetica font, 11 points or larger, half-inch margins, single spaced”
  3. Proposals are due to your Advisory Committee during Spring semester (usually mid April). One copy should be emailed to each member and one paper copy given to the Holly Shepherd. Committee Members and Holly Shepherd must receive them by 5:00pm on the assigned due date. Electronic proposals should be in pdf format.

Oral Presentation:

  1. Your uninterrupted presentation should be 20-30 minutes in length.
  2. However, during the actual exam, you should expect to be interrupted by questions during your presentation, with a general discussion and question session after the presentation.
  3. The presentation should walk your committee through each section of the proposal (i.e. Background, Significance, Specific Aims, and Experimental Design, etc.). They will want to know what you are proposing and how you will achieve your goals.
  4. You should not have more than ~30 slides, although you can have additional data slides on hand if you anticipate detailed questions on any particular experiment. For the main presentation, you must decide which experiments are the most important to explain your work and consider carefully how to present these clearly and succinctly..
  5. You should allow two hours for the entire exam.

III. Final Thesis Defense

The final oral thesis defense will be held only after all members of the committee have had adequate opportunity to review a draft of the doctoral dissertation. The dissertation advisor is responsible for determining that the draft is in an appropriate form for committee evaluation. If substantial revisions are necessary, they should be completed before the final oral defense is scheduled. All committee members are expected to be present at the defense.

The final oral defense may be open to the public or limited in attendance to the candidate and the committee. Questions that relate the dissertation to the field are appropriate. A dissertation is accepted only after the approval of a majority of the examining committee members. At the conclusion of the final oral defense, all committee members should sign Part III of the Doctoral Exam Report Form.

At the time of the final oral defense, but no later than the oral, the committee may require alterations and corrections, but these should constitute relatively minor changes agreed to by a majority of the committee members. The dissertation advisor is responsible for verifying that the changes required by the committee have been made. When changes have been verified, the advisor should sign Part IV of the Doctoral Exam Report Form.


For more information, please refer to the Graduate School’s Thesis and Dissertation Guide.