Candidacy Exam

The purpose of the Candidacy Exam is for students to demonstrate preparation for PhD level research. Once a student passes their exam, they can begin full-time research toward the PhD. Candidacy Exams are given to second year PhD students and first year Combined Degree students in May. The Candidacy Examination consists of 2 parts: a written Proposal describing plans for the thesis project, and an oral Defense of that document. If there is not a well-developed thesis project of the candidacy exam year, the proposal can be focused on a possible thesis project, or previous lab rotation.

The proposal guidelines closely follow those for a Predoctoral Fellowship application to the NIH (NRSA F31). Thus, students should craft their proposal with the following section headings, using single spaced, 11 point Arial font, 0.5 inch margins, and the indicated page limits.

  • Cover page (1 page): proposal title, student’s name, and thesis lab.

  • Project Abstract (30 lines or less): Clear, concise description of the proposed work, understandable to any scientifically literate reader.

  • Specific Aims (limit of 1 page): There are three objectives for this page. First, focus the reader's attention on the problem being addressed; second, present the hypothesis to be tested; third, provide an outline of the experiments testing that hypothesis. Use one or two paragraphs to address the first two objectives. Then outline the experimental approach in (usually) two Specific Aims, where each aim reflects a major experiment or experimental category.

  • Research Strategy (limit 6 pages): There are two objectives in this section:

    • Communicate the Significance of the question using a brief, but scholarly review of the field to explain the importance of the problem central to the proposal. Move from the general to the more specific. Additionally, describe how scientific knowledge would be increased if the proposed aims were achieved.

    • Convey the Approaches proposed to address each aim, by restating its hypothesis, and briefly describing the rationale behind it. Then, for each aim, describe the Experimental Approach and Analysis, Expected Results and Interpretations, and Potential Pitfalls and Alternative Approaches.

There is no expectation that extensive preliminary data should exist, but if it does, present it within the Research Strategy section (remaining within the 6 page limit). For example, such data might be included as part of the rationale or justification for a particular approach. Any preliminary work that represents unpublished data of others from the thesis lab should be explicitly approved by those providing such data and be properly cited.

  • Human tissue or Animal use (limit of 0.5 page): For proposals involving the use of human tissues or vertebrate animals, please justify why this use is essential to achieving the goals of the proposal. For animal use also justify the numbers required to accomplish the proposed experiments.

  • Literature Citations (no page limit): Each citation should be numbered in the body of the proposal; in the bibliography, each citation must include names for all authors, article title, journal (or book name), volume and page numbers, and year of publication.

The emphasis of the proposal should not be on a review of the literature but on dealing creatively with the problem selected. The proposal should be "hypothesis-driven". That is, it should aim explicitly to address a working hypothesis regarding an unresolved issue in Genomics and Computational Biology.


For the Proposal Defense, there is an expectation of substantial depth of knowledge in the thesis area, broadly defined. Thus, it will not be sufficient to defend only the particulars of the proposed experiments. A key element of the oral examination will be to explain and defend the importance of the questions to be addressed, and to place these questions in the broader context of the field. Thus, in both the Significance section of the written Proposal and in the subsequent oral Defense, the student should be able to marshal knowledge from the relevant literature and from broader areas of Genomics and Computational Biology. Each student's performance will be evaluated on: 1) quality of the written proposal; 2) quality of the oral presentation; 3) defense of the proposal; and 4) general knowledge of computational biology, their Approach, and their Biological Specialty (covered in coursework).


The student is encouraged to consult with their Thesis Advisor during preparation for the Candidacy Examination. The student is also free to consult with any other faculty, students, or postdocs as they develop their ideas. Thesis advisors should not give copies of current or former grant applications to students nor should they edit the student's written proposal. It is the Thesis Advisor's responsibility to ensure that the overall objectives of the proposal are worthwhile. The student can discuss potential experimental approaches with their advisor or others. The Thesis Advisor is excluded from being on the committee for their own student and has no role in determining the composition of the committee.


The purpose of having a Uniform Examiner on the committee is to be able to compare all exams with respect to rigor and the decision making processes of the different exam committees. With this information, uniformity in decisions can be established. These examiners will be responsible for the evaluation forms that constitute the written record for the exam.

The remainder of the committee will be chosen by the GCB chair and will consist of three faculty members with a reasonable degree of expertise covering core knowledge and the student’s chosen Approach and Biological Specialty.


A Week before the Exam

As indicated in the timetable for preparation of the preliminary exam proposal, each student will provide each member of their committee with a copy of the proposal. In addition, the GCB office will provide a copy of the student's file to each examiner. Faculty should read and review both of these documents prior to the exam. Any problems with the submitted proposal should be held for discussion at the committee meeting.

Prior to the Exam

To facilitate independent review of the student's proposal, each committee member will write and submit comments to the GCB coordinator prior to the student's exam date. These comments will be shared with the examination committee to evaluate the proposal, and will be shared with the student after the exam.

On the Day of the Exam

The Uniform Examiner will serve as the chair of each examining committee. Examinations will be scheduled to allow 1.5-2 hours for each exam. When the committee has gathered and the members have been introduced to the student, the Uniform Examiner should ask the student to leave the room briefly. The topics to be discussed in the student's absence are:

  • The student's overall record. Any deficiencies that might need special attention in the oral questioning should be identified.
  • The quality of the written proposal. If the quality is so poor as to be unacceptable, the student can be given a "fail" at this point.
  • If the proposal is generally acceptable, any specific deficiencies revealed in the written proposal should be identified and pursued in the oral questioning.
  • The "ground rules" for the examination should be established. The student should prepare a 15 minute presentation. The committee members should plan to let the student give the presentation uninterrupted except for questions of clarification.

The student will then be invited to return to the room. The chair should explain the ground rules to the student and ask the student to begin the presentation. The student may prepare a 1-2 page handout for members of the committee if a complex diagram is needed for the oral presentation. With the exception of this handout, the student will be expected to use the whiteboard if needed. If questioning is slow in getting started, the committee chair should lead off by asking a question. The chair should then turn over the questioning to one of the other examiners. In a rotating fashion, the other examiners should question the student.

Exam questions should be designed to probe the student's depth of knowledge on the subject of the proposal, both theoretical and technical. In addition, exam questions should determine the student's general knowledge, especially as it relates to lecture and seminar courses taken and independent study and rotations completed. Special emphasis should be placed on questions designed to elicit the ability of a student to describe how an experiment was or will be done and to interpret it appropriately. When the Uniform Examiner feels that the student has been examined sufficiently, they will ask the student to leave the room while the committee discusses the performance.

Each student's performance should be evaluated in four areas: 1) quality of the written proposal, 2) quality of the oral presentation, 3) defense of the proposal, and 4) general knowledge of computational biology, their Approach, and their Biological Specialty. Each faculty examiner will be asked to fill out a form providing a numerical assessment of the performance in the four areas on a 1 to 9 scale according to the NIH scale (1 = superlative to 9 = unacceptable).



This is the outcome for most students. It can represent a range from absolutely stellar performance to a good, generally solid one. It is appropriate to give a pass when the performance is good, but not perfect, and perhaps was not all that the examiners think the student might be capable of doing. All four aspects listed above should come into play in the discussion, and a very strong performance in one area may serve to offset a weak performance in another area.

Conditional Pass

This is the outcome for students who do well, but perhaps exhibit a significant weakness in a specific, single area. For example, an excellent presentation, oral defense and impressive fund of general knowledge in the setting of a written proposal that is significantly below average could lead to the recommendation of a Conditional Pass. In the event of a "conditional pass" recommendation, the committee must suggest to the Graduate Group Chair what the student should be required to do to address the deficiency (such as rewrite the proposal, do an independent study, etc.). If the student is expected to consult with the committee members individually, this should be stated, and a time frame for completing the remediation should be established. This should typically take less than one month. It is important for the committee chair to put this in writing so that there is no ambiguity about what is being asked of the student. At the end of all the exams, the Graduate Group Chair will evaluate and compare all Conditional Passes to make sure they are fair decisions and to assure that the proposed remedial action is equitable from student to student. When the Chair communicates the outcome of the exams, they will discuss the conditions of a conditional pass with the student involved.


This is the outcome when the written proposal, the oral defense, and/or grades from coursework are unacceptable. The GCB chair, in consultation with the committee, the Uniform Examiner, and the thesis advisor(s) will decide if the student should be given a chance to retake the oral exam. Students who are given this option must do so within the time frame decided by their committee and GCB chair. If no remediation is granted, the student will be dismissed from GCB. In the case where dismissal is deemed necessary, the student may be eligible for a terminal Master’s degree if all other requirements have been met.