Qualifying Examination and Dissertation Proposal

The purpose of the qualifying exam is to assure that the student has sufficient knowledge and skills to begin a research project. The exam will be taken within nine months after the completion of required coursework. The exam consists of an oral presentation and defense of a research proposal (described below).  In advance of the qualifying examination, the student, in coordination with their advisor, will select a committee consisting of five members to serve as the qualifying examination review committee.  At least four of the members must be from the list of approved faculty for the bioinformatics Ph.D. program, with at least one representative from each of the three areas (Biomedical and Natural Sciences; Computational Sciences; Mathematics and Statistics).

Prior to writing the final Research Proposal, the student will develop an outline of the proposed experiments in coordination with their advisor and then present this outline to their committee.  It is at this point, prior to writing the Research Proposal that the committee should recommend any changes in the research plan, regarding, for example, too many or too few experiments, experiments that are too difficult, or experiments that may be more appropriate for addressing the research question. Once the committee is satisfied with the proposed experiments, the student will write a Research Proposal containing the following information, synthesized in a clearly written proposal, which may be organized as follows:

Literature Review and Significance
Section one will be an extensive literature review (similar to an expanded Background and Significance section of a National Institutes of Health grant proposal). This review should provide evidence that the student has a sufficient command of the background information relevant to the proposed research.

Specific Aims, Hypotheses and Experiments

This section will consist of a list of the proposed specific aims. Each Aim should include hypotheses to be tested and a brief description of the experiments that will be used to test these hypotheses. 

Experimental Design and General Methods
This section will consist of a detailed description of the experimental design as well as the methods that will be used to carry out the proposed experiments.

Expected Outcomes
This section will describe the expected results and how they will be interpreted.

Potential Problems
This section will describe any potential problems that could occur, how they might affect interpretation of their research results, and how the student will address any potential problems.

Upon completion of a draft of the research proposal, the student will distribute a copy to each committee member, who will have two weeks to read the proposal.  After this two week period, the review committee will provide feedback and develop a set of questions for the student based on the proposal and perceived weaknesses in terms of both breadth and depth competencies, which can be incorporated directly into the proposal where appropriate and/or provided separately with detailed responses.  The student will have two weeks to develop responses to questions/requested revision.  At that point in time, the student will distribute a copy of the completed proposal, along with a separate set of answers to the provided questions, to each committee member.  The committee will have two weeks to read the final research proposal.   At the conclusion of these two weeks, the student will give an oral presentation.

Students must consider the total required time of six weeks (two weeks for reading initial draft; two weeks for responding to questions; and two weeks for reading final version) when preparing the document and scheduling the oral portion of the exam. The qualifying exam itself will be chaired by the student’s advisor. The exam will begin with an oral presentation, open to the public, in which the student will present an overview (approximately 40 min) of the research plan. The presentation will be followed by an oral defense to assess the student’s readiness to conduct the proposed research, and their knowledge of background information relevant to the proposed research. Non-committee members in the audience will have an opportunity to ask questions first. The general audience will then be dismissed and the student will defend his/her proposal before the committee. Success or failure will be determined by majority vote of the committee. A student who fails the exam will have 2 months to retake the exam. Failure on the second attempt will result in dismissal from the program. The review committee will provide, as part of the student’s annual evaluation, any remedial steps that should be addressed as part of the examination results. 

Upon successful completion of the exam, a Proposal Defense Evaluation Form stating the outcome of the exam will be completed and signed by each committee member and will become a permanent part of the student’s record. A passing vote indicates that the student has completed the course requirements. At this point the student becomes a doctoral candidate and must register for and maintain candidacy (DOCT 600) until the successful completion of his/her dissertation.  This registration must be maintained year round (Fall, Spring and Summer). The statute of limitation for obtaining a Ph.D. degree is four years from the beginning of Doctoral Candidacy. University wide official maximums for fellowships and Graduate Assistantships are typically 6 years.

Annual presentation of research progress
Ph.D. students who have completed their classwork (i.e. are in candidacy status) are required to present their research accomplishments annually. This presentation should be 30-50 minutes in length, and time and location of the presentation should be formally announced to the department faculty, staff and students at least one week prior to the planned presentation. Selection of the time and date is to be done in consultation with the student’s committee.  Presentations at journal clubs are encouraged, but cannot be used as a substitute for the annual presentation requirement.


1. All eligible students are encouraged to submit (in coordination with their advisor) an application for a National Institutes of Health Predoctoral National Research Service Award (F31) or a National Science Foundation Predoctoral Award. Therefore, the Research Proposal may be submitted in the format of a relevant application with the exception that the background and significance section should be expanded to include a more extensive literature review than permitted by the NIH or NSF page limitations.