Doctoral Program

The core course work for the Ph.D. program is listed below. In addition to taking courses, Ph.D. students must perform at least two full research rotations in their first year. The students are then expected to identify their dissertation lab preferably by the end of their first year, but during their second year at the latest. The winter term of second year, Ph.D. students will complete preliminary examinations to achieve candidacy. The preliminary examination has both written oral components.  Once students become Ph.D. candidates, they are expected to devote most of their time to research and writing their dissertation. The students are expected to complete and defend their dissertation within 4 - 5 years of their studies here at the Bioinformatics Graduate Program.

For the Ph.D. program, there are two separate types of advising: academic advising and research advising. Upon entering the program, Ph.D. students will be assigned an academic advisor who will assist them to individually select their courses given their background and interests. Until the students have identified their thesis lab, the Principal Investigator (P.I.) of the lab that they rotate into will be their research advisor for that term. Once the student joins his or her thesis lab, the P.I. of that lab will become their academic and research advisor.

As a part of the Bioinformatics Ph.D. Program curriculum, students must reach a level of expertise in four core areas by either adequate background experience or by taking appropriate courses.
The four core areas are defined as:

• Introductory Bioinformatics
• Computing & Informatics
  
• Probability & Statistics
• Molecular Biology

In addition, students need to take:

• At least two major (3-4 credit) courses in advanced bioinformatics and/or computational biology, defined as applying the skills or computing and statistical analysis to a biological or medical problem. 
  
• Ph.D. students are also required to take at least one semester of Bioinformatics 602 (Journal Club) and must also take the Research Responsibility and Ethics course (PIBS 503).
  

A list of sample courses that can be taken to fulfill these requirements can be found on the courses page.  However, the program encourages students to find other courses that may meet the core area criteria.  All requests to place additional courses that may meet that particular core area's requirements should go directly to the Graduate Affairs Committee via the student services representative.

Students with a relevant Master degree can petition to take the preliminary exam after three terms. Such students will need to meet a minimum of 6 major (3-4 credit) courses. All other students need to take a minimum of 8 major (3-4 credit) courses. The remaining credits for Ph.D. students are filled by rotation and dissertation research credits (Bioinformatics 990 and 995 respectively) and electives.  To complete the Doctoral Degree, students must accumulate a minimum of 68 Required Fee Totals (RFTs) or make up the lack thereof by paying for the remaining RFTs.  Students who enter the Ph.D. Program with a Relevant Master’s Degree have a reduced RFT requirement of 50.

All Ph.D. students are required to perform at least two full research rotations.  Students will select rotation laboratories based on their skills and interests with the help of the academic advisors.  Ph.D. students are expected to find a lab to perform dissertation research by the end of their first year, but no later than the second year.

Becoming a GSI (Graduate Student Instructor) for a semester is a very valuable experience for Ph.D. students. All Ph.D. students are strongly encouraged to obtain one semester of teaching experience. Teaching opportunities are not limited to courses taught in the Bioinformatics Graduate Program.

The aims of the preliminary examination in Bioinformatics are two-fold. The first aim is to demonstrate that students have developed the ability to analyze a scientific problem and develop appropriate strategies to carry out a research plan.  The second aim is to demonstrate that students have enough Bioinformatics knowledge needed to carry out their thesis research. The preliminary examination in Bioinformatics consists of a written and oral component. For the written portion of the examination, each student will independently prepare a research proposal in a format modeled on standard NIH proposals, in a subject which may be somewhat relevant to, but is not their thesis project.  In the oral portion of the exam, the student will defend his or her research proposal. The examining committee has the further option of questioning the student on general subject matter that the committee feels is relevant to the candidate's proposed area of research.

Students who have successfully passed the preliminary examination will be reviewed by the Bioinformatics Graduate Affairs Committee who will make the decision on their advancement to Candidacy for the Ph.D. degree.

More information on the Preliminary Examination can be found here. 

A Ph.D. research project must be formally submitted to the Bioinformatics Graduate Affairs Committee (GAC) and must consist of original research and a brief review of pertinent literature on the subject and results of preliminary work. The student will present a one-page proposal summary and their nominations for members of their dissertation committee to the GAC. The make-up of the dissertation committee must meet Rackham's Guidelines and be approved by the Rackham Office of Academic Records and Dissertations. The committee should consist of at least 5 faculty members (the chair usually being the mentor, and at least two other Center for Computational Medicine and Biology affiliated faculty). (Please also note that one should submit a nomination for dissertation committee form to Rackham at least 6 months before defending.) After approval of the composition of the committee, the student meets with his/her dissertation committee for approval of the proposal before the dissertation committee is considered formally finalized. Research proposals and dissertation committee formations should usually take place within the third year of the student's studies. After the dissertation committee is formed, it is the committee's responsibility to keep the GAC informed of the student's status and progress with a progress report to be filled out annually.

The oral defense of the dissertation will consist of a public seminar, followed by possible questioning by the dissertation committee, and will need to follow Rackham guidelines.  The process of preparing the dissertation should begin while actively involved in the dissertation research. There are specific guidelines available from the Rackham Graduate School for the format and layout of the text of your dissertation.

One should consult the Dissertation Handbook regarding the dissertation committee composition, formatting requirements, and copyrighted material in the dissertation. The defending student should closely consult the Dissertation Handbook, the Student Handbook of Policies and Procedures, his/her mentor and his/her student services representative.