Academic PHD Bioinformatics Plan of Study

Please check the Manual of Rules and Regulations of the Graduate College for a complete description of the Ph.D. guidelines and requirements of the Graduate College. The requirements described here, specific to the Bioinformatics Ph.D. program, are in addition to the University-wide requirements for doctoral degrees.

The Ph.D. program in the Bioinformatics and Computational Biology subprogram inherits all course requirements of the Informatics Ph.D. program; that is, a total of 72 semester hours (37 semester hours of coursework) beyond the bachelor’s degree, consisting of 21 semester hours in core coursework (Bioinformatics and Computational Biology, Genetics, Biology, and Informatics), seminar hours in Ethics, and 6 hours in Grad Statistics coursework. The remaining 6 hours consist of electives selected in consultation with the student’s advisor.

The Ph.D. also requires satisfactory performance on the comprehensive exam, and the production and formal defense of a dissertation that describes original research results.


Every Ph.D. student must have a faculty advisor with an appointment in the Bioinformatics program. Upon admission, each student is assigned a temporary academic advisor who can assist in guiding the individual’s curriculum and plan of study. During their first year in the program, it is expected that the student will choose a faculty member whose research interests align with their own to serve as academic and research advisor, and chair of the student’s thesis committee. The advisor / advisee relationship requires the consent of both parties and can be terminated by either upon notice. It is required that a student will complete a Plan of Study form in consultation with his/her advisor every semester, and submit the completed form to the IGPI office for approval. The Plan of Study form is located at the bottom of this page.


Examination committees must be composed of a minimum of five faculty members, per graduate college guidelines. IGPI-BCB students’ committees must include their research Advisor and at least 2 program-affiliated faculty from any of the following disciplines: Engineering, Genetics, Biology, Biosciences, and IGPI. At minimum, two committee members must have never coauthored a peer-reviewed journal article with the student.

Ph.D. Guidelines & Milestones


  • Complete by fall of Year 2
  • Minimum committee of 5 professors, including the advisor
  • Format: Research or project in the form of a paper with a prepared presentation, turn in the written portion of the exam to your committee at least 2 weeks prior to oral exam – pass or fail

Students must choose one of the following qualifier formats:

  • A) An NIH-style proposal (typically proposed by the student and advisor; may also be assigned by the committee). Students are encouraged to submit the proposal as a pre-doctoral NIH Fellowship (F31). The purpose of this individual pre-doctoral research training fellowship is to provide support for promising doctoral candidates who will be performing dissertation research and training in scientific health-related fields relevant to the missions of the participating NIH Institutes and Centers (ICs) during the tenure of the award. These fellowships allow a student to develop a research idea and provide support for typically 2-3 years. The advisor and/or committee may decide to have on- or off-topic proposals. The committee (which includes the advisor), has the final say regarding on- or off-topic proposals by majority vote. The format gives students a year to polish and improve the proposal for submission to the NIH (
  • B) Open-ended research question: Students who select this qualifier option will be assigned, by their examining committee, an open-ended problem in the area of the student's intended thesis research. Ideally, the student will be presented with this problem no later than the end of the spring semester of the first year of study, along with a designated date/time for the examination (typically at the beginning of the fall semester), and the student will be expected to develop a solution during the summer. On the assigned examination date, the student will submit a written response to the assigned problem. The student will be expected to defend this response at an oral examination during the fall semester before the Examining Committee. The actual format of the response will depend on the specific problem assigned and specified by the Committee in the problem description, but is expected to involve the application of bioinformatics techniques towards the solution of a specific problem within the student's research area. Under certain circumstances, these guidelines, with respect to the problem due date and oral examination, might require modification to suit extenuating circumstances of the student or the Committee.

Successful completion of the Ph.D. Qualifying Exam is required before a student is to be considered a Ph.D. graduate student. Students will have two chances to pass the Ph.D. Qualifying Exam. If students receive an evaluation of “unsatisfactory” on their first Qualifying Exam attempt, a different topic will be selected for the open-ended problem. The Qualifying Exam is designed to ensure that the student starts early in gaining research experience; it also ensures that the student has the potential to conduct doctoral-level research. The student may retake the qualifier once. A second failure will result in termination from the program.

Comprehensive Exam

  • Expected in Fall Year 3, allowing flexibility to accommodate scheduling of specific courses
  • Format: On-topic thesis proposal
  • Committee: Minimum of five professors, two of whom are affiliated IGPI faculty.

Note: This examination satisfies the University’s comprehensive exam requirement.

After 2-3 years of working in conjunction with a research advisor on a problem in Bioinformatics, the size and scope of the research project becomes evident to the student, as well as the advisor. To clearly define a problem or hypothesis under examination and describe a clear, logical process to solve that problem or test the hypothesis, the student will develop a written document describing the problem/hypothesis and solution/experiments. This document represents the Ph.D. Comprehensive Exam. The Ph.D. Comprehensive Examination consists of a proposal, formatted in the style of an NIH grant proposal, outlining the student's Ph.D. research. It is expected that the Ph.D. Comprehensive Exam will be completed one year after the Ph.D. Qualifying Exam, but might be completed later, at the discretion of the student's examining committee. The quality of the proposal will be determined through its assessment by the Examining Committee, and a formal oral presentation is required. The final document will consist of a 12-page NIH-style grant application on the thesis, plus a comprehensive literature review (no page limit).

The proposal should include the following:

    • Student name
    • Committee members and their academic departments
    • Committee chair (research adviser)
    • Provide a detailed description of the research, including:
      • Specific Aims
      • Background and Significance
      • Preliminary Studies (optional, but recommended)
      • Research Plan (include expected results and their significance, and a discussion of potential pitfalls / workarounds)
    • Provide a specific schedule for the completion of the proposed studies, with explicit reference to the work proposed in the Research Plan.
    • A complete list of cited references.

Proposal Defense

The proposal defense is part of the Comprehensive Exam.

Final Oral Defense/ Final Examination (Thesis Defense)

  • Format: Written thesis and presentation
  • Committee: Minimum of five professors, with at least two affiliated with the IGPI.

Upon satisfactory completion of the Ph.D. thesis, the student will submit a final draft of the dissertation to the members of their Examining Committee. Following an assessment of the dissertation by the student's Examining Committee, the student will defend it orally in an open and public forum. The Examination Committee may then ask additional questions in a meeting between the candidate and the committee. Satisfactory performance in this final examination will result in a recommendation by the Committee to the Graduate College that the student be awarded a Ph.D. in Interdisciplinary Graduate Program in Bioinformatics and Computational Biology.

In addition to the formal examination process, students in the Ph.D. program are evaluated on a yearly basis to ensure that they are making satisfactory academic progress. By September 15th, each student and the student’s advisor are required to submit an evaluation assessment of the student’s progress, outlining past year accomplishments and plans for the current year, including Ph.D. milestones. The Advisory Board reviews these summaries and sends the student a letter summarizing their status in the program. Students who are failing to make satisfactory progress are expected to correct any deficiencies and move to the next milestone within one year. Failure to do so will result in dismissal from the program.