Course of Study

The first year is spent taking courses (two to three each semester) and performing three laboratory rotations. Students are encouraged to supplement the core courses in molecular and cellular immunology with additional courses selected from the wide range available in cell and developmental biology, molecular biology, microbiology, biochemistry, genetics, and molecular medicine. In conjunction with other BBS Tracks, the Immunology Track maintains an active and well attended weekly seminar series for which students participate. Informal interactions with other graduate students, postdoctoral fellows and faculty also form an important part of graduate education. By the end of the first year, the student chooses a Ph.D. thesis supervisor and begins thesis research. In most cases, this choice also determines from which department the student will receive the Ph.D. degree. For example, many students entering the Immunology Track will perform thesis research with a faculty member in the Department of Immunobiology and hence receive their Ph.D. degree from this department. However, students are free to work with any faculty member in any department.

Below is a description of the typical first year program for a student in the Immunobiology Track of BBS. Asterisks(*) mark courses that are required by the Immunobiology Graduate Program.

Course Work:

• The DGS, your faculty mentor, student liaison and student services officer are on hand to help you with your course decisions. Students are required to take at least four or five science courses for a grade in the first year. The typical load is 2-3 courses per semester.

First Semester:

• IBIO 530: Biology of the Immune System *REQUIRED
  Required unless consultation with DGS and course director determines that passing the previous year final exam shows sufficient knowledge in subject. This does not reduce the six course requirement.
• IBIO 600: Introduction to Research, Faculty Research Presentations *REQUIRED, Pass/Fail At least one elective graduate course
• IBIO 611, Laboratory Research training (not for a grade—Pass/Fail) *REQUIRED,
• IBIO 612: Laboratory Research Training (not for a grade—Pass/Fail)*REQUIRED
  
  NB: First year graduate students may not take the Immunobiology Seminar Course during their first semester. IBIO530 is a pre-requisite for the seminar courses. Rare exceptions may be given based on students past coursework in immunology.

Second semester:

• IBIO 531b: Advanced Immunology *REQUIRED
• IBIO 601b: Fundamentals of Research (responsible conduct in of research) *REQUIRED (Pass/Fail)
• IBIO 613b: Laboratory Research Training *REQUIRED (not for a grade—Pass/Fail);
• At least one elective graduate course.

Laboratory Rotations (611a, 612a, 613b) and Rotation Evaluation Forms

• Three rotations are required for all first year immunology graduate students. A rotation done during the summer prior to matriculation does not count as one of the three rotations required during the first year.

There are several ways for you to find out about the research going on at Yale

• meet the faculty in 600a, take notes, and then contact them individually for further discussion
• read about the faculty interests on the websites and in their published papers
• contact the faculty directly

Meet the faculty – IBIO 600a: The Immunobiology Department coordinates “Research Talks presented by two-three faculty per week for several weeks. After each session, if interested, contact the faculty through their admin assistants for a separate short meeting to discuss their research and possible rotation opportunity projects.

Read about the faculty interests: The BBS provides a rotation manual compiling opportunities in many labs within the 7 tracks. You can also visit the BBS website and peruse the Immunology track faculty research interests. Additionally, there are other faculty at Yale not necessarily in the Immunology Track, who have interests in Immunology, with who you may want to rotate. If they do not present their research in our series of short talks, please feel free to contact them to see if they are accepting rotation students.

Contact the faculty: If you are interested in rotating in a non-Immunology track faculty lab, then you will need to contact that faculty member. This is routine and you should not hesitate to do so.

All BBS faculty who have open rotation opportunities are open to all incoming BBS students.

How do I select a lab to rotate in?

After attending the faculty research presentations and meeting individually with faculty, you should feel confident to send a note to your faculty of choice. Dr. Rothlin and other faculty are available to discuss your choices and provide guidance on how to proceed. Consulting with more senior students in the program can be very helpful as well. Let Caroline and Carla know whose lab you are going to rotate in.

Choosing a Thesis Laboratory

Near the end of the third rotation, students will determine which lab they would like to do thesis research in and presumably have made arrangements with their mentor of choice. Once that is determined, let Caroline and Carla know.

Choosing a Graduate Program

This is a very important choice because it determines what requirements (courses, exams, etc.) you will have to fulfill for the remainder of your graduate career. The decision should be made by June 15, after consulting with the DGSs. See the discussion on the Transition between BBS Tracks and Departmental Graduate Programs.

Within BBS, there are approximately 350 participating faculty in numerous basic science and clinical Departments located on Yale’s North, South and West campuses. Graduate training begins within interest-based Tracks, each of which provides robust academic and advisory structures designed to prepare students for cutting-edge research. Recently, the BBS launched two new Tracks that epitomize our strong collaborative environment for graduate student training:

1. Biochemistry, Quantitative Biology, Biophysics, and Structural Biology
2. Computational Biology and Bioinformatics http://bbs.yale.edu/computational/
3. Immunology
4. Microbiology
5. Molecular Cell Biology, Genetics, and Development
6. Molecular Medicine, Pharmacology, and Physiology
7. Neuroscience
8. Plant Molecular Biology

In the second year, students take one or two courses each semester and focus considerable time on developing their thesis research project. In addition, they prepare for and take the qualifying exam, which consists of a written proposal concerning their thesis project and an oral examination. Students typically serve as a teaching assistant in one course during the second year, and one course during the third year. This fulfills the teaching requirement, although additional teaching opportunities are available for interested students.

In advance of the Pre-prospectus meeting, meet with your advisor to discuss your ideas. Prepare a short (one page maximum) description of your proposed project with Specific Aims and distribute it, in advance, to your committee members. Be in contact with your committee, during the process, keep them informed and certainly keep an open dialogue with your advisor.

The pre-prospectus should begin with a 20–30-minute presentation describing your current research and goals, and your committee members will provide guidance and suggestions on the proposed research. You and your advisor should come prepared with 4-5 suggested “Reading Topics” that you will need to master for your prospectus exam. You and your committee will discuss the possible topics and you then formulate a preliminary reading list for each of these Reading Topics for examination.

You should plan on meeting individually with your committee members to expand the reading lists so that the reading provides you with a thorough and broad understanding of the subject area. Reading lists are only a means of providing you with a starting point to investigate the literature and are not meant to be all-inclusive. You are expected to explore the literature broadly. You may wish to schedule one or more additional meetings with individual committee members to discuss questions and issues that arise during the reading.

Prospectus Meeting: The Prospectus is normally held within 2 months of the Pre-prospectus meeting and for BBS students, you must complete your Prospectus by May 31st of the second year. However, we strongly encourage students to start the process in the fall semester of the second year as the intellectual growth gained by the process is typically extremely valuable for students and helps them become more engaged in their thesis project.

For MD/PhD students, you should complete your Prospectus by the end of your first full year in the program. The written prospectus should be sent to all committee members at least a week in advance of the Prospectus Exam date. Students may seek advice in crystallizing their ideas, addressing general technical questions, and in preparing for the exam. The writing of the proposal, however, must be entirely by the student. Students may show drafts of their proposal to anyone they wish (including faculty and the student's PI).

Feedback should be given verbally concerning broad scientific aspects of the proposal (such as “this won’t work,” “unclear,” or “flesh this out”). The student remains fully responsible for the actual writing, including grammar, spelling, sentence structure, etc. Be sure that you put quotation marks around any text you take from anyone else’s work, whether from an online source or a formal publication. Failure to do so may result in charges of plagiarism, a very serious offense. Please speak with the DGS or another faculty member if you are unclear on the meaning of plagiarism. The oral Immunobiology Prospectus Exam tests a student's understanding of two general areas: the proposed thesis research and the specific subjects covered in the readings (typically 4-5 areas of biology/immunology).

Yale has a wonderful graduate school writing center with resources to help you with your project.

The remainder of the time is devoted to questions relating to the reading and to some extent to the thesis project. Questions test your ability to synthesize your knowledge of the relevant areas of biology/immunology (particularly as relates to the reading), to address questions through the design new experiments, to formulate testable hypotheses, and to interpret possible outcomes of experiments. In the course of this, it will become clear whether or not you have mastered relevant basic information derived from course work and the reading.

Your faculty will each have prepared two questions in advance of the exam, which are discussed by the exam committee during a short pre-meeting that takes place in your absence and before you begin presenting. This has two important functions. First, it forces faculty to give thought to their questions in advance and second, it allows the committee to screen out and/or modify questions that are deemed inappropriate (e.g., too difficult, too easy or off target).

The Written Prospectus: is to be in the format of an NIH R21 grant proposal and should not exceed 10-12 pages in length, including figures. (Single spaced, font 11 point Arial, 1 inch margins on all sides; references can go on additional pages). The written Prospectus should have the following sections and please visit this url for several helpful writing tips for each section:

https://www.niaid.nih.gov/researchfunding/grant/strategy/pages/3researchstrategy.aspx

• Title
• Abstract (1 paragraph- no more than 30 lines in length) Specific aims (1 page limit)
• Premise and Significance of work (typically 1 page) Innovation (typically 1 paragraph)
• Background and Preliminary data/experimental plan of each Aim (typically 6-8 pages) References
• Figures (figures should be embedded in the text and accompanied by clear legends) The four possible outcomes are:
  
  

Pass: the student’s presentation and paper is approved, has passed the prospectus exam unconditionally and, now, can receive graduate school certification on his/her transcript.

Fail: the student is not approved and can be asked to leave the Immunobiology Graduate Program

Conditional Pass: the student is conditionally approved for prospectus certification provided that specified additional work is completed satisfactorily. Such additional work could be, a research paper on one of the topics that the student was felt to be weak in, revisions of the written prospectus, or other requirements to be determined by the committee.

Re-examine: the student’s performance was judged to be substantially unsatisfactory, but the committee feels that extenuating circumstances exist that dictate that the student should be re- examined, perhaps using a different format (e.g., a written exam).

During the third year, the student now focuses almost entirely on thesis research, writing manuscripts for publication, and the Ph.D. thesis. The student also completes any remaining requirements, and by the end of the third year will have completed all departmental and university requirements required for being Advanced to Candidacy. The student works closely with his/her thesis supervisor and also benefits from advice and feedback from a Thesis Committee, consisting of the faculty supervisor and several other pertinent and knowledgeable faculty who are chosen by the student and her/his advisor. Students can take advantage of a myriad of resources to help in making progress toward completion of the degree.