2nd Year

The second year of the program usually marks the beginning of thesis research. In addition, there are course requirements, teaching experience, and an important qualifying exam during the spring semester.  By the end of the second year, students must accumulate at least 24 semester hours of graded coursework.


Fall Semester

  • IMMUNOL 601 Immunology of Human Disease
  • IMMUNOL 731S Immunology Seminar - First and second year students enroll in this course. This course consists of two components: 1) a work-in-progress seminar for students and postdoctoral fellows on Mondays and 2) an invited speaker series on Tuesdays. Students are evaluated on attendance and a required presentation of at least one work-in-progress seminar per year. 
  • IMMUNOL 735 Current Topics in Immunology – Journal Club format, required each fall semester beginning in 2nd year.
  • Grant Writing Workshop – Facilitated by immunology faculty.
  • Electives or mini-courses may be chosen to complement the student's dissertation studies.
  • RCR forums 
  • Continuation is required each semester

Spring Semester

  • IMMUNOL 731S Immunology Seminar 
  • IMMUNOL 736 Current Topics in Immunology
  • Electives or mini-courses may be chosen to complement the student's dissertation studies
  • RCR forums
  • Continuation is required each semester

Summer Semester

  • Continuation is required each semester

Teaching Requirement

2nd Year

All students are required to participate in one semester of supervised teaching. The Program in Immunology believes doctoral students should be prepared to teach at the university level. Thus, the Program requires one semester of supervised teaching to undergraduate and graduate students in IMM 544 (Principles of Immunology) or to graduate students in IMM 701D (Pillars of Immunology). In IMM 544, trainees lead discussions and make didactic presentations within the framework of faculty-led classes. In IMM 701D, trainees take primary responsibility for all aspects of the course, with faculty oversight. The teaching requirement will normally be completed by the third year of doctoral training.

Student Advisory Committees

During the Fall semester of the second year, students and their Ph.D. supervisors shall propose an advisory and examinations committee. Approval must be obtained from the DGS by the end of October.  Students shall submit a Committee Approval Form to the DGS for initial approval. The DGSA must then submit to The Graduate School for final approval, at least 30 days prior to the Preliminary Examination.

This committee will consist of at least five graduate faculty members (including the student's dissertation mentor) who are considered best able to advise the student. At least three members of the committee should come from the primary departmental faculty; at least three members of the committee should hold a senior academic rank (tenured). One member of the committee, the “outside member,” must hold an appointment in the graduate faculty through a department other than the Department of Immunology. The chair of the Advisory Committee cannot be the dissertation mentor. The chair must hold a primary appointment in the Department of Immunology and may hold a junior or senior academic rank, but must have ample experience serving on advisory committees as judged by the DGS. Committee chairs may be nominated by the candidate but his/her appointment will be determined by the DGS. 

Advisory committees are formed prior to the preliminary examination and most committees retain the same membership throughout the student’s academic tenure. However, after a student passes the preliminary examination, the committee composition requirement changes to two primary faculty members other than the mentor.  This allows any student whose thesis advisor holds a secondary appointment in Immunology to replace one of the three primary faculty with another member of the graduate faculty who may be able to offer expertise that will be valuable for progress on thesis research. For a committee member change – for this or any other reason - a student must obtain approval from the DGS. For approval, the DGS requires an email from the student's advisor and the incoming committee member acknowledging the change. The student can then submit a revised Committee Approval Form (check the box Change in student's previously approved committee) to the DGSA. This form will be sent to the DGS and then to The Graduate School for final approval.

It is the responsibility of the Advisory Committee to evaluate whether the student is making satisfactory progress towards the degree. The chair of the committee submits a Annual Committee Meeting Report Form annually to the Graduate Program. If at any time progress is determined to be unsatisfactory, this conclusion and a written description of all issues involved will be forwarded to the DGS who may then convene the Executive Committee in order to determine the appropriate course of action. When conditions merit it, the Executive Committee can recommend termination from the Program.





Qualifying Preliminary Exam (PRELIM) 


Students can use the on-topic format for prelim, starting from the Fall 2022 semester. Using the off-topic format is now optional.

  • Format: The written research proposal for the preliminary exams should follow the NIH F30/31 formatting guidelines. Components to be submitted are:
    • Specific Aims (1 page)
    • Research Strategy (6 pages)
    • Citations (no page limit)
  • The written and oral prelim examination must be completed by March 31st of the 2nd year.
  • The Duke grant writing course (BIOTRAIN720) is a prerequisite for the preliminary examination.
  • Students must hold a pre-prelim meeting with their committee 2 months prior to submitting the written documents. 
  • Although faculty advisors are encouraged to discuss ongoing research activities including content of their own grants with their students, they should not assist the student in the preparation of the prelim documents. The student is expected to present and defend their ideas with little input or coaching from their advisor.
    • Exception: If the student fails their preliminary examination and a re-take is required, the committee should provide general comments on the document to help guide the student
  • Students are encouraged to obtain critiques from others on the written exam and the oral presentation, but the final document must represent the student’s original work.
  • Exemptions from any of these guidelines should be discussed with the committee and the DGS.



All students will schedule a "pre-prelim meeting" before the end of the Fall semester of their second year and will take a preliminary examination (prelim) before April 1 of the Spring semester to establish candidacy for the Ph.D. degree.  Exceptions to the April 1 deadline must be for good cause and must have the approval of the Advisory committee chair, the thesis mentor, and the DGS. Students who otherwise do not meet their approved deadline are no longer considered in good academic standing.

The preliminary examination consists of a written research proposal – called the alternate proposal - on a subject selected and researched by the student, followed by an oral defense of the proposal before the student’s advisory/examination committee.  The topic of the research proposal must be substantially distinct from the major research focus of the student's mentor.  Interactions with other students are permissible while preparing for the preliminary exam. General questions can be addressed to faculty as well, but faculty (committee members and others) are not allowed to read and comment on the proposal prior to the exam.

 (a) Pre-prelim meeting

The goal of the pre-prelim meeting is advisory in nature and to ensure that the student will have a topic for the alternate proposal that is both unrelated to the mentor’s research program and appropriate for scientific defense. The Advisory Committee may meet as many times as is reasonable and necessary to define a suitable topic for the alternate proposal and a schedule for its completion and presentation.

The student will bring to this meeting two single-page outlines; one describing the alternate proposal and the other describing the dissertation work. These documents should be provided to the committee members at least three days before the scheduled pre-prelim meeting. 

These documents should be single-spaced, 1-2 pages each, including:

A) Background and Significance

B) Hypothesis

C) Specific Aims

The pre-prelim meeting is held for one hour.  The student is expected to present her/his plans for the alternate proposal in sufficient detail for the Committee members to understand the background, rationale and proposed research strategy well enough to offer appropriate advice. In general, better clarity results in better advice from the Committee. There is no requirement to use slides, but they are generally helpful to clarify the presentation.

Upon approval by the committee, the student will prepare the written alternate proposal for the preliminary examination, as described below.

(b) Preliminary examination (Prelim)

The completed alternate proposal must be in the hands of the examining/advisory committee seven days before the scheduled examination.

The written alternate proposal shall be well-formulated and presented in sufficient detail to be evaluated thoroughly for scientific merit. The alternate proposal must be conceived and written by the student. Students may, however, receive help in preparation for the preliminary examination. Interaction with other students is permissible and encouraged but only general questions should be presented to members of the faculty. No member of the faculty can read or comment on the proposal prior to the examination.

The proposal should include sufficient information to permit an effective review without reviewers having to refer to the literature. Identify all abbreviations used. Be specific and informative, and avoid redundancy. Brevity and clarity in the presentation are considered indicative of an applicant's approach to a research objective and ability to conduct a superior project. Only discuss background and significance relevant to this proposal; you should, however, be prepared to discuss other related information during the oral examination. The Experimental Design and Methods should comprise the bulk of the proposal. Pay particular attention to the experimental design, as it will be emphasized at the oral exam. It is particularly important that the student discuss potential problems that might arise in the conduct of the proposed research and specify how these problems might be overcome.

The format of the alternate proposal is as follows:

  • Double-spaced, one-inch margins, Arial 11-point
  • 20-25 pages, main text and figures.
  • No page limit for references.

 The document must include the following sections:

A) Specific Aims: State the specific question the research proposal is designed to address, as well as the hypothesis to be tested. Present the individual aims in outline format with a brief description of the experimental approach to be used for each.  Conclude with a brief statement about what will have been learned if the study is successful (2 pages).

B) Background and Significance: Sketch briefly (6-8 double-spaced pages) the background, the rationale, and the significance behind the proposal. This is an important consideration in the review of your proposal. State concisely the importance of the proposed research by relating the specific aims to broad, long-term objectives.

C) Experimental Design and Methods: For each specific aim, provide brief but cogent descriptions of: i. The experimental design and procedures necessary to accomplish each specific aim; ii. A proposed sequence for the proposed investigation or research; iii. Statistical or other quantitative procedures or criteria by which the data will be analyzed; iv. Potential experimental or analytical difficulties that might hamper the proposed work or strength of conclusions; v. Alternative experimental or analytical approaches that could achieve the scientific aims.

D) References: Adequate references justifying the proposed scientific aims and relevant background are placed at the end of the proposal. Each citation must include the names of all authors, name of the book or journal, volume number, page numbers, and year of publication. Providing titles of articles is required.

The defense of the alternative proposal is scheduled for a minimum of two hours. Students must present and defend the proposal submitted to the committee. The committee chair, not the mentor, is responsible for directing the examination. At the beginning of the examination meeting, the student will be excused from the room and the committee chair will review the student's academic record, receive an evaluation from the student's mentor, and discuss any initial critiques of the proposal. The student will then present and defend his/her alternate proposal. Questioning may begin at any time. Questions will focus on the proposal but students should be prepared to discuss related information that has been a part of the curriculum of the Graduate Program. Small deviations between the oral presentation and the submitted written document must be justified; substantial deviations will result in a Fail decision.

At the end of the oral defense, the candidate is excused from the meeting room, and the committee first deliberates and then votes by written, secret ballot, indicating “Pass” or “Fail”. On a committee of five or more, two “Fail” votes, or a vote of “Fail” by the mentor, constitutes a failure. In this case, the student may apply, with the consent of his/her advisory committee, the DGS and the Associate Dean of The Graduate School, for permission to take a second examination. This re-examination can be taken no sooner than three months after the first attempt. The committee must be unchanged for the second examination, and the committee vote must be unanimous for the student to pass the examination.

Following the committee decision, the DGS will act to advance or dismiss the student based on the committee’s written evaluation.