For Graduate Students in the Department of Microbiology & Immunology

Orientation and Introduction to the Graduate Program (Administered by the IBMG program)

Prior to the beginning of the fall term, the new student will receive an orientation to the graduate program which will include registration procedures, financial aid procedures, an orientation to the School of Medicine Library, and a series of brief descriptions of research programs that are seeking graduate students.

The student will be assigned a temporary graduate advisor, based on the student’s research interests.  The advisor will develop with the student a course schedule for the fall term and later for the spring semester.  Each new student will also be assigned a senior student to act as a mentor for the first year.

During the first semester the new student will begin a series of research rotations.  The student should develop their G718 rotations in consultation with the Departmental Graduate Advisor.  These rotations will consist of eight weeks of full time work in each of three faculty research laboratories.  At the completion of the three rotations the student will ordinarily select a major advisor.  This selection requires the mutual consent of the student and advisor and implies acceptance into the research program of the advisor.  Some students may require a fourth rotation before a selection is possible.


Upon choosing a laboratory and joining the Department, the major advisor will appoint an Advisory Committee. The Advisory Committee will include the major advisor, at least two associates from the major department, and a representative from the student's outside minor department or program.  At least one faculty member must have a primary appointment in the Department. The Chair of the Advisory Committee must be a primary or secondary faculty member.  If the Chair has not previously graduated a Ph.D. student in the Department, then at least one senior faculty member in the Department (Associate or Full Professor) must be included on the committee.   The Advisory Committee for combined degree candidates (M.D. or D.D.S. - Ph.D.) must include an appropriate representative from the Clinical Faculty. Secondary faculty in the department may serve as the minor representative for our Microbiology and Immunology students with the understanding that, regardless of their primary department affiliation, these faculty must be able to represent the student's minor.  It will be up to the Graduate Advisor/Department Chair to ensure that the constitution of the committee is appropriate for a given student.

It is the responsibility of the Advisory Committee to counsel the student both in coursework and in research, to determine academic deficiencies, and to suggest corrective measures for such deficiencies including appropriate coursework.  The Advisory Committee also will recommend for approval by the Graduate School the transfer of academic credits earned at another institution (see below and the Graduate Bulletin for limitations).  The Advisory Committee will determine satisfactory completion of the Qualifying Examination.  At each committee meeting, the Advisory Committee, mentor and trainee should review and approve the student’s educational plan for that year.  As part of this review, committee members should consider the student’s progress in courses required for the major and minor areas of study, completion of the teaching requirement in the department, trainees’ laboratory work and attendance at required seminars, journal clubs and scientific meetings.  Student participation in professional activities that are beyond the requirements of the graduate program must be approved by the advisory committee. 

Transfer of Academic Credits.  Upon recommendation of the department and with the approval of the dean, work taken for graduate credit at other institutions may be transferred in partial fulfillment of degree requirements.  No course may be transferred from another institution unless the grade is B or higher and unless the course was completed no more than seven years prior to passing the qualifying exam (typically within 5 years of entering the program).  Candidates for the Ph.D. degree may offer up to 30 hours of graduate credit from other institutions. 

Transfer of course credits requires comparison of course syllabi from both Universities to determine comparability of the course being transferred with an existing course in the program.  Transfer of credits is accomplished either by a transfer request form filled out by the Department Graduate Advisor and submitted to the Graduate School or, in the case of rotation research credits, a letter outlining the committee’s recommendation to the Graduate Advisor who will then seek approval from the Graduate Office. 


The Qualifying Examination will be administered within 25 months of matriculation.  Mentors and the student’s Advisory Committee may petition the faculty for a delay not to exceed 4 months.  In exceptional circumstances, a 2nd extension can be requested by the mentor and Advisory Committee.  Normally, the qualifying examination is taken after the student has completed all course work for the Ph.D.  However, occasionally, circumstances may arise that prevent a student from completing all coursework required by the program or recommended by the student's Advisory Committee within 25 months of matriculation; if the Advisory Committee considers the student sufficiently prepared, the student may progress to the Qualifying Examination prior to completion of required coursework.  In such circumstances, Advancement to Candidacy will be delayed until the student passes both the Qualifying Examination and all required coursework.  Students should confer with their Advisory Committee in planning the examination date, as the examination may be taken early, dependent on student progress.  Combined degree (M.D./Ph.D.) trainees must take the examination within 18 months of entry into the departmental program.

Components.  The Qualifying Examination consists of two parts.  The first part is a comprehensive written examination on the fields of Microbiology and Immunology, on a minor subject, and on related areas.  The second portion consists of an oral examination covering: a) questions in follow-up of answers on the written portion of the examination, and b) presentation and defense of a grant proposal submitted at least 3 weeks in advance to the members of the Advisory Committee.  The format for the Qualifying examination will follow the current NIH R01 guidelines.  The intent is to have the students give more attention to significance, innovation and approach (including outcomes and alternatives) and not provide specific methodological details (e.g., composition of buffers).  The written and oral examination will continue to be a forum for probing the student's background knowledge and experimental design as well as details pertinent to their proposal.

Scheduling the exam.  The Qualifying Examination has written as well as oral components, with passage of each of these sections required for students to move towards candidacy in the Ph.D. program.  At least 3 months before the examination, trainees should discuss with their mentor and their Advisory Committee the research topic and preliminary studies for their grant proposal, a timeline for preparing this grant, and a schedule for their written and oral examinations.  With the approval of their committee and mentor, the trainee can begin writing the grant proposal and planning for the examinations.  Setting a date and reserving rooms for the two steps of the Qualifying Examination is the responsibility of the trainee and their mentor.  The student is responsible for notifying the graduate secretary of the dates for both parts of the Qualifying Examination.

Grant Proposal.  The trainee researches and independently prepares a written proposal following the current NIH format (12-13 pages) with a page for specific aims, and sections on background, significance, innovation, and approach.  This proposal must originate from the trainee, although the mentor can provide some guidance in terms of the overall goals for the project, as well as minor comments or suggestions regarding the written document and experimental approach.  The ideas in the proposal and the writing should predominantly be the work of the trainee.  The trainee is not allowed to copy an existing grant from their mentor.  The grant should propose work that the trainee will conduct for 2-3 years to address a central hypothesis.  No budget or biographical information is needed.  The trainee can have other students or postdoctoral fellows read and make suggestions related to their proposal, but their mentor should provide minimal help.  Trainees can also review grant proposals prepared by senior students who have since advanced to candidacy, as a guide if needed.  The NIH website offers sample grants and information on standard grant formatting. 

Written Examination.  At least 3 weeks before the examination, the Advisory Committee should receive a copy of the grant proposal from the trainee.  The written examination should take place at least one week before the oral examination.  For the written examination the mentor should request from each committee member one or more questions for the trainee to complete in the written examination.  These questions can focus on any topic covered in graduate classes completed by the trainee at IUSM, topics related to the trainee’s proposal, or any subject that the committee member feels the trainee should be well informed about at this point.  Faculty may ask theoretical or learning based questions relevant to the student’s research focus and grant hypotheses and aims.  The trainee’s mentor should review the questions from faculty to ensure that these are appropriate and can be answered in the given time for the examination (8 hours total).  Mentors can contact members of the Advisory Committee to discuss the submitted questions and to avoid overlap in the examination.  The mentor distributes the examination questions to the trainee on the assigned date(s) for the written examination.  Trainees have one 8-hour day (or two 4-hour half-days) to complete the examination.  Mentors can also provide their students with one question at a time to answer.  The examination must be taken on campus in a manner consistent with Indiana University’s code of honor.  Typically a department conference room or office serves as the site for the written examination, and the mentor is encouraged to check on the trainee’s progress several times during the examination.  Trainees are not permitted to bring notes, text books, or any electronic devices, including cell phones, into the examination, except for a department-provided laptop (if used, see below).  Students are not permitted to consult others or access the internet or websites during the examination.  Only the trainee can answer the questions, and no help can be obtained from outside sources.  Typically, the mentor formats a blank page with one or more questions for the trainee to use in the examination.  The trainee can hand write or type the answers for the written examination.  Trainees should request a departmental laptop to use for the examination if they wish to type the examination answers.  If the trainee elects to take the examination over two half days, then the mentor gives the trainee half the questions each day to complete. 

Between Written and Oral Exam Components.  After the written examination, the trainee will return the questions and answers to their mentor.  The mentor sends a copy of each question and answer to each committee member so they can overall assess if the trainee is on track and if satisfactory answers were provided.  The mentor can consult each committee member before the oral examination to determine whether there is an overall sentiment that the trainee is ready to move on to the oral examination.  This is a pause point, typically about a week long, in the event that the Advisory Committee members are not satisfied with the trainee’s answers or have great concerns.  If there are only minor concerns, these can be addressed in two ways.  The trainee can talk to members of their Advisory Committee one on one to better explain their responses from the written examination, or a member of the Advisory Committee can suggest the trainee read more about a specific topic before the oral examination takes place.  Any member of the Advisory Committee can elect to ask the trainee more questions related to the written examination during the oral examination.  If all the members of the Advisory Committee along with the mentor agree that the trainee has performed satisfactorily to this point, the trainee can move on to the oral examination.  The mentor, research advisory committee, and trainee should discuss and review the format for the oral examination in advance.

Oral Examination.  On the day set for the oral examination, the trainee should come prepared with a copy of their grant proposal to the assigned room.  The mentor meets with the committee in the assigned room before the oral examination begins to talk about the trainee's overall progress and whether the trainee has put in the required effort on the grant proposal.  Trainees may give a very short overview of the proposal but this is not required.  Trainees and their mentors can decide in advance whether such a presentation will be helpful.  The committee must have sufficient time for the examination, thus students usually schedule a 3 hour block of time for this meeting.  During the oral examination, the mentor can ask questions but should not answer for the trainee.  If the mentor wants to rephrase a question to help clarify a point to the trainee, that is allowed.  At the end of the oral examination, the trainee is asked to leave the room, and the mentor and committee suggest a grade for the Qualifying Examination, which includes both the written and oral sections.  After the examination, the mentor should again meet with the trainee to discuss the results of the examination and suggest ways the trainee can improve as well as areas where the trainee performed well. 

Possible Outcomes.  The outcome of the examination may be one of the following:

a.  Unconditional pass with admittance to Doctoral Candidacy (upon completion of all coursework)

b.  Complete failure

c.  Or at the discretion of the committee, repetition of a part or all of the Qualifying Examination as detailed here.

Option C allows the following:

-  Further testing or preparation of responses by the trainee related to the written examination with a review of this revised examination by the Advisory Committee.

-  The preparation of a revised grant proposal or sections of the grant proposal with a formal review of this document by the Advisory Committee.

-  Scheduling a new oral examination with the trainee seeking faculty guidance to improve their performance and demonstrate proficiency.

The Advisory Committee can recommend one or more of these options to trainees.

Restrictions on Option C:

-  Trainees will be given only one opportunity to repeat a section of the examination.

-  Retaking of the either the oral or written examination must take place within 2 months of the first examination date.

Recording the Outcome.  Decisions and recommendations from the Advisory Committee must be recorded on the appropriate form, which can be obtained from the department graduate secretary or the department graduate advisor.  This form must include signatures from committee members and the mentor.  The Qualifying Examination can serve as a student committee meeting, with a grade assigned in the appropriate course based on the student's overall performance in the program at that point in time.

Depending on the Advisory Committee's evaluation of the performance on the Qualifying Examination the student will either be (i) admitted to Doctoral candidacy (upon completion of all coursework), (ii) recommended for a Masters degree upon submission of a thesis typically composed of appropriate parts of the papers submitted for the Qualifying Examination, or (iii) dismissed from the program.  Students who are admitted to candidacy may, thereafter, opt to submit a thesis and receive a Masters degree. 

Advancement to Candidacy Status.  Advancement to candidacy requires completion of the Qualifying Examination and all coursework.  Passing the Qualifying Examination must occur at least 8 months and no more than 5 years preceding the award of a Ph.D.


Doctoral degree students within the department must serve as a teaching assistant in MICR J210 Microbiology & Immunology for one semester during their graduate studies.  Students and their mentors will be notified that the student is needed for teaching at the start of a semester.  Under extenuating circumstances, a student’s mentor can make a written request asking to delay the student’s teaching requirement for one semester.  The letter should be directed to the Graduate Advisor and the director of the J210 course. 

Student participation in teaching activities beyond the assigned semester in J210 must be approved by their faculty thesis mentor.  The departmental Graduate Advisor and the director of the course in which students wish to teach must also give their approval before students can participate in additional teaching opportunities. 

Teaching activities are considered a part of our graduate training program, and students will not be provided with additional compensation beyond their annual stipend for time devoted to teaching. 

SPEAK test.  Students for whom English is not their native language must pass the IUPUI administered examination in oral English competency (the “SPEAK” test) prior to participating in teaching within the department.  If a student does show sufficient English proficiency in the SPEAK test, appropriate recommendations will be made to the student’s academic advisors.  Additional course work to improve English proficiency may be required before the student is allowed to teach.  Such coursework will not count toward the 90 credit requirement for the degree. 


Upon satisfactory completion of the Qualifying Examination, the Ph.D. candidate will form a Research Committee, the composition of which may be similar or identical to the Advisory Committee.  Once the major graduate advisor and the Research Committee have been selected, a form is generated and approved by the Departmental Graduate Advisor and Department Chairperson and forwarded to the Graduate Office.  The Research Committee will assist the student in thesis research and in thesis preparation and will determine satisfactory completion of the thesis and the thesis examination.  The Research Committee and a summary of the proposed research must be approved by the Graduate School at least 8 months prior to the thesis examination.

Ph.D. candidates in the Department of Microbiology and Immunology should not accept responsibilities apart from those of our training program until the thesis is formally approved.  If this commitment is not fulfilled, the student's Research Committee will not sign the thesis.  An exception to this requires a majority vote of the Research Committee.

Relevant Policies and Forms can be assessed by clicking on the appropriate word.

Campus Information:
Indiana University School of Medicine   and  IBMG
Indiana University-Purdue University at Indianapolis

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Department of Microbiology and Immunology | IU School of Medicine | 635 Barnhill Drive, MS 420 | Indianapolis, IN 46202 | (317) 274-0506