Department of Immunobiology - Ph.D. Graduate Program Program and Policies Manual 2021-22 Yale University
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Department of
Immunobiology
Ph.D. Graduate Program
Program and Policies
Manual 2021-22
Yale University
School of Arts and Sciences
School of Medicine
Director of Graduate Studies:
Dr. Carla Rothlin
Director of Graduate Admissions:
Dr. Carrie Lucas
Student Services Officer/Registrar:
Caroline N. Lieber
Table of Contents
Immunobiology Program Overview 3
Requirements for the Ph.D. Degree 5
M.D./Ph.D. Students Who Join Immunobiology 7
Year by Year Outline 8
YEAR ONE 8
Choosing a Thesis Laboratory 9
Choosing a Graduate Program 10
BBS Tracks and Programs - Eight interest-based "Tracks" 10
YEAR TWO 12
Teaching 12
Pre-prospectus and Prospectus (Qualifying Exam) 13
Year Three and Beyond: Advance to Candidacy 17
Committee Meetings 18
Career development and the Individual Development Plan (IDP) 20
The Written Dissertation and Oral Defense 20
Checkpoints in the Graduate Program 24
Research in Progress (RIP) Guidelines 25
Department Interactions 27
Fellowships 28
Administrative and Academic Procedures 34
Important Graduate Resources 35
Safety Information 38
Guidelines for the Responsible Conduct of Research I. Introduction Error! Bookmark not defined.
2021-22 Immunology Track Faculty and Office Staff 42
2021-22 Immunobiology Graduate Students 43
Immunobiology Program Overview
Welcome to the Graduate Program in the Department of Immunobiology at Yale
University School of Medicine. Our goal is to provide you with the best possible education
in the field of Immunology, through a combination of course work and laboratory
research. The Department of Immunobiology and associated departments contain 50
faculty members whose laboratories are performing research in an extremely wide range
of topics in Immunology and related disciplines. The guiding philosophy of the Department
is that research and learning are fundamentally collaborative and are dramatically
enhanced by access to individuals with diverse expertise and interests. Therefore, we have
worked hard to create a supportive and cooperative environment that stresses
excellence in research. Students routinely make use of the technical and intellectual
expertise of multiple different laboratories, and we urge you to take advantage of the
superb resources (faculty, post-docs, graduate students and state-of-the-art technology)
that are all around you. As the Directors of Graduate Admission and Graduate Study, we,
together with the program’s Coordinator, are responsible for overseeing your progress and
ensuring that your program of study meets the highest educational standards. All of the
other faculty and staff in the Department of Immunobiology are here to help you make
the most of your graduate years. We wish you great success in your research and studies.
Carla Rothin, PhD, Carrie Lucas, PhD, Caroline Lieber,
Director of Graduate Studies Director of Graduate Admissions Student Services Coordinator
The Yale Immunobiology Graduate Program is an independent component of Yale Graduate
School. It is designed to provide the education, intellectual support and supervision necessary for
students to obtain the Ph.D. degree in Immunology. The guidelines and rules described on the
pages that follow are intended to provide high standards, firm guidance and flexibility, and to
ensure that students are directed towards research problems that are significant and technically
practical.
Students enter the program through the Biological and Biomedical Sciences (BBS) Program of
Yale Graduate School. Students are admitted to one of the eight “Tracks” of BBS, and during the
first year, BBS and the Tracks oversee student education. During this year, students take courses,
3
do three research rotations, and become familiar with the wide variety of research
opportunities available in the biological sciences at Yale. By the end of the first year, students
select a laboratory in which to do their thesis research.
The choice of a thesis laboratory will, in most cases, determine which degree-granting Graduate
Program a student enters. Hence, it is possible for a student in any Track of BBS in the first year to
become a member of any of the departmentally based Graduate Programs in the second (and
subsequent) years. For the Immunobiology Graduate Program, the typical route of entry is via the
Immunology Track of BBS. However, students from other tracks occasionally choose a thesis
supervisor in Immunobiology and enter the Immunobiology Graduate Program.
In the second year, students continue with course work, begin thesis research in earnest, and
take the Prospectus exam. In addition, during the second and third years, students serve as
teaching assistants in two or more courses. With the Prospectus exam successfully completed,
students are admitted to candidacy for the Ph.D. at the end of their third year, and in the fourth and
subsequent years, focus the great majority of their efforts on the research that will form the basis of
the Ph.D. dissertation. Our goal is for students to complete and defend their Ph.D. dissertation
within five or six years of matriculation. Semesters beyond the sixth year are possible but require
special approval. A Thesis Committee of three to five faculty carefully monitors progress toward
the Ph.D. degree; and mentored committee meetings occur annually.
4
Requirements for the Ph.D. Degree
BBS/PhD Students
Academic and Research Requirements
• Three research rotations (IBIO 611, 612, 613)
Summer rotations prior to matriculation do not count toward the three-rotation
requirement. Note that you must register for rotations, and independently select the labs in
which you would like to rotate by contacting the PI directly. Please let Carla and Caroline
know which labs you rotate in, and at the end of the spring semester, you will officially
choose your lab.
Rotation Shopping Period - Aug 30 – Sep 10
Rotation 1 Fall Sep 13 – Oct 29
Rotation 2 Fall Nov 1 – Jan 14
Rotation 3 Spring Jan 18 - Mar 4
Rotation 4 Spring Optional
• Six graduate level science courses, taken for a grade and passed in the first three years.
Pass/Fail courses (such as IBIO 600, 601, 611, 612, 613) and audited courses do not count
toward this requirement.
Required:
A grade average of at least High Pass and a minimum of two Honors required by the
end of the 4th semester. A grade of High Pass is minimally required in IBIO core program
courses*:
*IBIO 530: Biology of the Immune System (Fall)
The development of the immune system. Cellular and molecular mechanisms of immune
recognition. Effector responses against pathogens. Immunologic memory and vaccines. Human
diseases including allergy, autoimmunity, cancer, immunodeficiency, HIV/AIDS. E. Meffre
Required unless consultation with DGS and course director determine that passing the previous year final exam
shows sufficient knowledge in subject. Does not reduce the six-course requirement
*IBIO 531: Advanced Immunology (Spring)
The historical development and central paradigms of key areas in immunology. The course
attempts to develop a clear understanding of how these paradigms were established
experimentally. Landmark studies are discussed to determine how the conclusions were obtained
and why they were important at the time they were done. Lecture and discussion format;
readings of primary research papers and review articles. Prerequisite: IBIO 530 or equivalent.
Enrollment limited to fifteen. N. Palm
*Two advanced seminar courses (choose from IBIO 532, 536, 537, 538, 539)
Seminar courses are typically available three out of four semesters. First seminar must be taken for a grade. If
the student has completed six graded courses, then the seventh class (seminar) can be audited.
IBIO 600: Introduction to Research: Faculty Research Presentations (Fall)
Introduction to the research interests of the faculty. Required of all first-year Immunology/BBS
students. Pass/Fail. C.V. Rothlin
IBIO 601: Responsible Conduct in Research, all first-year students (Spring)
A weekly seminar presented by faculty trainers on topics relating to proper conduct of research.
Required of first year Immunobiology students, first-year CB&B students, and training grant-funded
postdocs. Pass/Fail.
5
IBIO 611, 612, 613: Laboratory Research Training (Fall and Spring)
Intensive experience in the design and execution of experiments in immunology or other areas of
biology. Students design a focused research project in consultation with a faculty mentor and
execute the designed experiments in the mentor’s laboratory. Students are expected to read
relevant background papers from the literature, design and perform experiments, interpret the
resulting data, and propose follow-up experiments. Students are also expected to attend the
mentor’s weekly lab meeting(s) as well as weekly Immunobiology departmental seminars and
Research in Progress seminar. After each rotation, the student must submit their evaluation of their
lab rotation, and the PI will also provide an evaluation of the student’s performance. Pass/Fail. 1
course credit; minimum of 20 hours/week. Required of all first-year Immunology/BBS students. C.V.
Rothlin
IBIO 503: Responsible Conduct in Research, Refresher Course. Required for all 4th years
(Spring)
The NIH requires that students receive training in the responsible conduct of research every four
years. This course meets that requirement for fourth-year students. The course has two
components: (1) one large-group session is held for all fourth-year students through the BBS; the
main topics are scientific misconduct and authorship; (2) two Immunobiology faculty facilitate
discussions based on RCR topics, gathered in advance from the students; anonymous or
hypothetical stories are selected by the faculty and discussed in a workshop environment in which
students are then asked to analyze each case and suggest courses of actions.
• Teaching: two, one semester–long science courses. (Year Two)
• Only one course needs to be taught to advance to candidacy; the second
teaching requirement can be fulfilled later, but is required for the Ph.D.
• The Yale Teaching & Learning offers a one-day seminar entitled “Teaching at Yale”
Attending this seminar is recommended prior to teaching
• Eligible students (green card or US) are strongly encouraged in year two to apply for an NSF
fellowship and in year three for an NIH. (Year Two/Three). Please contact the DGS if you are
unable to
• Pre-prospectus and successful completion of prospectus exam, both oral and written
components. (Year Two)
• First committee meeting (year three or first meeting post the prospectus/qualifying exam-
- usually one year later). Three forms with committee signatures required: i) committee
meeting form, ii) Advancement to Candidacy Form, iii) IDP certificate. (Year Two)
rd
• Advance to Candidacy by the end of semester six (all requirements met and 3 year
committee report submitted). (Year Three)
• Annual or semi-annual committee meetings following Advance to Candidacy meeting. (From
Year Three)
• Permission from the thesis committee to begin writing the PhD thesis, documented by the PI
in a written report submitted to the DGS, student, and all committee members.
• Written dissertation, approved by Thesis Committee and an outside reader.
• There is a very strong expectation that your thesis research will result in at least one first author
primary research paper, published (or at the very least submitted) prior to the oral defense of
your dissertation. Exceptions must be approved by your thesis committee and the DGS.
• Oral Dissertation defense
In addition, students must fulfill all requirements set forth in the Yale University Graduate School
Programs and Policies Manual: https://gsas.yale.edu/academic-requirements/policies
6
M.D./Ph.D. Students Who Join Immunobiology
An MD/PhD. student affiliates with the Immunobiology Graduate program through the MD/Ph.D.
program. You will have chosen your research Ph.D. course of study after matriculating through the
YSM and completing one or more research rotations during the course of your first two years of
medical school. In many cases, the first rotation is done during the summer between years one and
two of medical school. MD/PhD students are required to do a minimum of two rotations, which can
be done during a single summer.
Once a thesis laboratory is selected, the student completes an application for a Ph.D. department
filing it with both the MD/PhD and Immunobiology Registrar. MD/PhD students with interests in the
Immunobiology Graduate Program should discuss their situation with the Director of Graduate
Studies as early as possible and notify Caroline Lieber so that your graduate school paperwork can
be processed.
The MD/PhD student arrives further advanced than a first year BBS graduate student (course
work and teaching). It is possible to defend your pre-prospectus (preliminary description of your
prospectus research) after the first semester and prospectus (preliminary description of your thesis
project) after the second semester.
Courses / Requirements
• Six graduate level (science) courses, taken for a grade.
A grade average of at least High Pass and a minimum of two Honors required by the
end of the 4th semester. A grade of High Pass is minimally required in IBIO core
program courses
IBIO 530: Biology of the Immune System (Fall)
Required unless consultation with DGS and course director determines that passing the previous year final
exam shows sufficient knowledge in subject. Does not reduce the six-course requirement.
IBIO 531: Advanced Immunology (Spring)
Two advanced seminar courses (choose from IBIO 536, 537, 538, 539)
Seminar courses are typically available every Fall and every other Spring. First seminar must be taken for a
grade. If the student has completed six courses, then the seventh class (seminar) can be audited.
IBIO 601: Responsible Conduct in Research, unless taken in medical school (Pass/Fail) (Spring)
IBIO 503: Responsible Conduct in Research, Refresher Course. Required for all 4th
year students, unless taken in medical school. (Spring)
• Teaching: one semester–long science courses.
– The Yale Teaching & Learning offers a one-day seminar entitled “Teaching at
Yale” Attending this seminar is recommended prior to teaching
• Pre-prospectus and successful completion of prospectus exam, both oral
and written components. (By the start of Year Two of the PhD)
• First committee meeting, post your prospectus with a signed committee form
verifying student is in good standing, together with advisor summary report of
meeting, including IDP certificate. (Year Two)
• Advance to Candidacy, all requirements met and committee report submitted (Year
Two)
• Written dissertation, approved by Thesis Committee and an outside reader.
There is a very strong expectation that your thesis research will result in at least one
first author primary research paper, published (or at the very least submitted) prior
to the oral defense of your dissertation. Exceptions must be approved by your
thesis committee and the DGS.
• Oral Dissertation defense
In addition, students must fulfill all requirements in the Yale University Graduate School Programs
and Policies Manual: https://gsas.yale.edu/academic-requirements/policies
7
Year by Year Outline
YEAR ONE
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 unless consultation with DGS and course director- determines that passing the previous year final exam shows
sufficient knowledge in subject. Does not reduce the six-course requirement.
IBIO 600: Introduction to Research, Faculty Research Presentations
*REQUIRED, Pass/Fail
IBIO 611: Laboratory Research training
*REQUIRED (Pass/Fail)
IBIO612: Laboratory Research Training
*REQUIRED (Pass/Fail)
At least one elective graduate course
NB: First year graduate students may not take the Immunobiology Seminar Course during their
first semester. IBIO530a is a pre-requisite for the seminar courses. Rare exceptions may be
given based on student’s past coursework in immunology.
Second semester
IBIO 531: Advanced Immunology
*REQUIRED
IBIO 601: Fundamentals of Research (responsible conduct in of research)
*REQUIRED (Pass/Fail)
IBIO 613: Laboratory Research Training
*REQUIRED (Pass/Fail)
At least one elective graduate course.
Master of Science Degree: Students who complete at least one year of resident graduate study
at Yale with the quality of work judged satisfactory by the Department of Immunobiology
faculty and who have satisfied 10 courses with an average grade point average of High Pass
(graded) and Pass (ungraded) may petition for the award of the M.S. degree. Students must
petition through the Registrar’s Office of the Graduate School in early October for the
December award and by the middle of March for the May award.
Laboratory Rotations (611, 612, 613) 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. General rotation timeframes are below:
Rotation shopping period September
Rotation 1 September/October
8
Rotation 2 November/December
Rotation 3 January/February
Rotation 4 March/April (optional - students can begin selecting thesis lab)
After you complete each rotation, you and the rotation PI will need to complete an evaluation form:
Student form: https://yalesurvey.ca1.qualtrics.com/jfe/form/SV_2ujioAoi5nWqdzE
PI form: https://yalesurvey.ca1.qualtrics.com/jfe/form/SV_2ujioAoi5nWqdzE
How do you learn about Immunology Research at Yale?
There are several ways for you to find out about the research going on at Yale
a) meet the faculty in 600, take notes, and then contact them individually for further discussion
b) read about the faculty interests on the websites and in their published papers
c) contact the faculty directly
d) talk with your fellow graduate students. They are a phenomenal resource.
Meet the faculty – IBIO 600: Introduction to Research. 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 whom you may wish 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. See Appendix A is this manual for Faculty contacts, as well as their
administrators.
All BBS faculty who provide 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. Once you’ve chosen a
lab, let Caroline and Dr. Rothlin 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. A fourth rotation is allowed, with approval from
the DGS.
Choosing a lab!
Advice from IBIO Students: Choosing a Rotation/Thesis Lab
9Choosing 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 DGS. See the discussion on the Transition between BBS Tracks
and Departmental Graduate Programs.
BBS Tracks and Programs - Eight interest-based "Tracks"
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
http://medicine.yale.edu/bbs/biochemistry/
2. Computational Biology and Bioinformatics http://bbs.yale.edu/computational/
3. Immunology http://medicine.yale.edu/bbs/immunology/
4. Microbiology http://medicine.yale.edu/bbs/microbiology/
5. Molecular Cell Biology, Genetics, and Development
http://medicine.yale.edu/bbs/molecularcell/
6. Molecular Medicine, Pharmacology, and Physiology http://medicine.yale.edu/bbs/molmed/
7. Neuroscience http://medicine.yale.edu/bbs/neuroscience/
8. Plant Molecular Biology http://medicine.yale.edu/bbs/plantmolbio/
Special Programs:
Within the BBS there are 5 special programs that offer specialized training to students. The first
three require applicants to express interest in the program during the BBS application process.
Yale’s Cancer Biology Training Program
http://bbs.yale.edu/training/nihprograms/YaleCancerBio.aspx
With close proximity and teamwork by scientists, clinician-scientists, and clinicians, Yale
provides a rich environment for fundamental and translational cancer research. Yale is
home to the Yale Cancer Center, designated as a US National Cancer Institute
Comprehensive Cancer Center.
Yale’s Integrated Graduate Program in Physical and Engineering Biology
http://medicine.yale.edu/bbs/training/initiatives/peb.aspx
The Integrated Graduate Program in Physical and Engineering Biology combines traditional
training in the biological sciences with skills and techniques employed in physics and
engineering.
The Yale Medical Research Scholars Program
http://bbs.yale.edu/training/nihprograms/mrsp.aspx
The Medical Research Scholars Program bridges barriers between traditional predoctoral
and medical training by providing both medically oriented coursework and a mentored
clinical experience to select BBS students.
China Scholarship Council-Yale World Scholars Program
http://medicine.yale.edu/bbs/training/initiatives/csc.aspx
The CSC-Yale World Scholars in Biomedical Sciences recruits top applicants from five of
China's best universities for training in the BBS Program.
The Yale PhD/MBA Joint Degree Program Recognizing the long-standing applicability of the
PhD beyond the academy and the increasing relevance of sophisticated management
analysis in the highly varied positions held by many PhD recipients, the Graduate School of Arts
10and Sciences (GSAS) has joined with the School of Management (SOM) to offer one of the
first joint degrees of its kind, the MBA/Ph.D. Combined MBA-PhD are required to do a minimum
of two rotations, which can be done during a single summer.
The Transition Between BBS Tracks and Departmental Graduate Programs
Graduate students in the first year are members of one of the Tracks of BBS and are not affiliated
with a departmental graduate program. Students become affiliated with a departmental
graduate program at the beginning of the second year, based largely upon their choice of a
thesis supervisor. During the first year, therefore, students follow the guidelines established by the
Track they are in. In the second year and beyond, students are governed by the requirements
of the Departmental Graduate Program they enter at the beginning of the second year. The
guidelines of the Track are meant to prepare students in the first year for entry into a Department
in year two.
Some examples of how this might go
Student A enters the Immunology Track of BBS, and after three rotations during the first year,
decides to do thesis research in the laboratory of one of the faculty affiliated with the
Department of Immunobiology. Student A therefore enters the Immunobiology Graduate
program at the beginning of the second year. This is the most typical route of entering the
Immunobiology Graduate Program.
Student B enters the MCGD Track and ultimately chooses to do thesis research with a
professor in Immunobiology. Student B typically enters the Immunobiology Graduate
Program; alternatively, this student might choose to enter the Genetics, Cell Biology, or
MCDB Graduate Program.
Student C enters the Immunology Track of BBS and chooses to do thesis research with a
professor in the Department of Cell Biology. Student C typically enters the Cell Biology
Graduate Program; alternatively, this student might choose to enter the Immunobiology
Graduate Program.
It is clear from these examples that it is not always possible to predict at the beginning of the first year
which Departmental Graduate Program a student will eventually end up in. And since each
Graduate Program has its own requirements, it can be unclear what courses to take in the first
year (e.g., Student B above might not have taken IBIO 530 during his/her first year, thinking that
it would not be required – and then finds that it is required by virtue of the lab she/he chose to do
thesis research in).
Some guidelines for choosing courses:
Students in the Immunology Track will almost certainly take the courses outlined on the preceding
page during the first year because of the high likelihood of doing thesis research in Immunobiology.
If you find yourself interested in doing thesis research with a professor who is not in the Section
or Department you originally thought you’d be in (e.g., Student B and C above), don’t panic.
BBS and the various graduate programs have sufficient flexibility to help you through this without
having to do a lot of extra course work. If necessary, you and representatives of the involved
Tracks/ Departments will meet to determine what Graduate Program is most appropriate for you
to enter, and which additional courses it makes sense for you to be required to take. For example,
it is possible that Student C above might choose to enter the Immunobiology Graduate Program,
based on courses already taken and thesis research to be performed.
*During the first year, take the courses that meet the requirements of the program you think you
will be in, and choose electives based on your interests or gaps in your previous course work.
11YEAR TWO
In the second year, graduate students become affiliated with one of the departmentally-based
Graduate Programs. Students enter the Immunobiology Graduate Program by virtue of
choosing to do thesis research in the laboratory of a faculty member in the Department of
Immunobiology. Below is a description of the requirements and activities of the second year.
Course Work
The typical course load is 1-2 courses in the first semester and 1-2 courses in the second
First Semester: Second Semester:
Immunobiology seminar course Immunobiology seminar course or one
One elective graduate course might be taken elective graduate course might be taken
REMEMBER: You must take 6 science graduate courses for a grade
IBIO530 is a pre-requisite for the seminar courses. Rare exceptions may be given based on a
student’s past coursework in immunology.
Teaching
Students typically teach one, one-semester course in the second year.
How do you find out about teaching? Dr. John Alvaro (BBS director) and Caroline will send you
a link to a designated student application allowing you to directly apply for teaching positions.
* * * * Make sure you inform Caroline of any positions accepted to ensure it is duly noted on
your transcript. This is very important!
Yale Teaching Program
The Poorvu Center for Teaching and Learning one day seminar entitled “Teaching at Yale” is
offered each year. Attending this seminar is recommended prior to teaching.
https://poorvucenter.yale.edu/GraduateStudents
Teaching Protocol and Rules
1. Teaching in two semester long science courses is required
2. First year students do not teach
3. Teaching opportunities are first given to students who need the credit
4. Teaching for additional income is available when openings exist after those selected for
credit is provided with teaching slots
5. Maximum teaching load per semester is one course
***Teaching past the two-course requirement, which earns the student extra income, must be
approved by the advisor by providing an approval signature on the teaching application.
12Thesis Research
Most time not spent on course work is devoted to thesis research, with the goal being to
develop a clear conception and preliminary data for the Prospectus.
Advice from Students - Selecting a Project: The process of selecting a project varies a lot between
labs and between students. The key to this step is to be in good communication with your advisor.
Some ways to generate a project include:
• You can take over a project that someone else in the lab was working on before you.
• You can generate a completely new project based on a gap in the literature. The best way
to do this is do a lot of reading and thinking after you’ve joined a thesis lab, find
something that interests you, and see what knowledge gaps are present.
• You can dig through existing data in the lab and come up with a new project based on an
offshoot of an old one (e.g., take a CRISPR or scRNA-seq hit that was never pursued and
test how it affects xyz)
Pre-prospectus and Prospectus (Qualifying Exam)
Chronological steps for the pre-prospectus and prospectus are described below.
Select a project topic and speak with your thesis advisor. Your Advisor will be a huge
support during the prospectus process
Choose Prospectus Committee (Summer before or 1st semester of second year). Meet with
each one individually. Choose 4-5 faculty members, including your thesis advisor.
Select a Prospectus Chair from your committee (cannot be your PhD advisor, and
preferably a primary Immunobiology faculty member)
Schedule and hold Pre-prospectus meeting with your committee - preferably in the first
semester or early spring of second year. Assign a ‘reading topic’ for each committee
member. In this meeting, you will receive comments and suggestions from your
committee.
Schedule your Prospectus/Qualifying Exam about 8 weeks after your pre-prospectus.
Study for Prospectus/Qualifying Exam and prepare your reading list and send to your
committee for approval.
Begin your reading period and write your prospectus (8-12 pages).
Provide your committee with your written paper at least one week in advance of your
qualifying exam date.
Prepare your presentation for the qualifying exam. You will give a talk on your prospectus,
and field questions from your committee.
Complete the prospectus process before the end of the second year – May 31.
Your prospectus chair (not your Ph.D. advisor) fills out the form, sends to the DGS (Carla
Rothlin) cc’d to Caroline describing the outcome of your exam; this is also cc’d to the
rest of the committee.
Student sends Caroline a copy of the prospectus paper.
Advice from students: * Somewhere in this timeline, you’ll need to coordinate with your
committee members to set up an exam date. The sooner you can nail down a date with
your committee, the better. Be sure to set up a backup date in case something changes
and you need another time. It can be hard to meet with all of these faculty at the same
time for 1-2 hours. Depending on how busy the PI is, you might need to do this as early as
2-3 months in advance.Thesis Advisor & Committee:
These are the faculty you have chosen to work with towards your Ph.D. and who will read and
evaluate your pre-prospectus, prospectus and will, in many instances, end up being members of
your thesis committee. Provide Caroline with a list of your committee members; she needs this
information for your transcripts. Based upon your research, you and your advisor will choose 3 to
4 additional faculty members to serve on your committee (Your thesis advisor is a member of
the committee).
A total of four faculty on your committee is usually adequate and is easier to schedule than five.
You should formally meet with each potential member to discuss their involvement and your
research.
Advice from Students - Selecting Your Prospectus Committee: Your prospectus committee
will be composed of your advisor (or co-advisors) and two or three faculty members. The
committee will have a chair, usually chosen during the pre-prospectus meeting, which will
direct your prospectus meeting and enforce prospectus rules. You can have faculty who are
not from the Immunobiology Department in your committee. Do not be afraid to seek out
committee members outside of the department. If you are worried how the request will be
received, you can always have your PI reach out on your behalf. However, keep in mind
that the Chair of your Committee (who cannot be your advisor) has to be a IBIO faculty
member.
Each person you select for your committee should be an “expert” in a relevant topic for
your qualifying process. For example, if your project is on CD8 T cells during viral infection,
you likely want people with the following “topics” of expertise: T cells, adaptive immunity,
antigen presentation, viral pathogenesis, etc.
Your prospectus committee usually becomes your thesis committee (unless your project
shifts and you need new expertise). Thus, prospectus committee members will be key
mentors throughout your PhD process. Choose people who will be supportive, but also
choose people who will challenge you as a trainee. Ask other students in the department
for feedback about having these PIs on your committee and what they are like during the
exam period. You want them to be beneficial to your qualifying process, not a roadblock.
Pre-prospectus Exam:
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. Prior to the pre-prospectus meeting, you and your advisor should come up with a list of
4-5 reading topics. During the meeting, you and the committee members will discuss which
reading topic will be assigned to each committee member. After your meeting, follow up with
each committee member to craft a reading list and begin your reading period.
Preparing for the Prospectus:
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 teaching and learning center. Take a look at this website: https://poorvucenter.yale.edu -- they offer many workshops, and several are geared for the writing of the prospectus. The exam begins with a presentation by you on your thesis research project. The presentation is strictly limited to 30 minutes, including questions. You should provide a focused description of the proposed thesis research that emphasizes experimental design, data interpretation, and anticipated problems and potential solutions, and which touches on background very briefly (the committee should already be familiar with the background from the pre-prospectus process). The chair of your prospectus committee (who must not be your PI) shall enforce the time limit. During this 30-minute period, your PI remains silent, asks no questions and provides no answers or information related to questions asked by other committee members. 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 of 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 F31 grant proposal and should not exceed 10-12 pages in length, including figures. The written Prospectus should follow the NIH guidelines found here at this site, along with several helpful writing tips for each section: https://www.niaid.nih.gov/grants-contracts/write-research-plan
Advice from Students: Timeline Be aware of your time. The writing can overlap with the reading period if you choose. Your written prospectus is due one week prior to your prospectus exam and coming up with the final version will consume at least a week and a half. Make sure you don’t delay before beginning to write. If three weeks before the submission deadline you are still behind on reading, start writing anyways. You will have to make a LOT of drafts anyways. Format The format for writing the IBIO Prospectus largely follows the NIH F31 NRSA. Make sure you follow the IBIO rules on format but, when instructions are not specified, follow the NIH F31 NRSA format. The NIH uploads multiple examples of the F31 from the current cycles’ awardees. When examining these, you will notice that the format can vary. This is because unless otherwise specified, there is a degree of flexibility on how you structure certain sections of the F31. Skim through multiple examples to get ideas. Regardless of the format you follow, you’ll want to include: specific aims, background, significance, innovation, aims, expected outcomes, pitfalls/alternative approaches and conclusion. Figures can be added to your prospectus but must be included in the 8-12 page limit. Figures can be based on preliminary data or on diagrams illustrating experimental designs or key concepts. Writing Tips Your aims will likely morph as you read and write – this is okay! Keep thinking independently, change your aims as necessary, and keep discussing with your PI. It may feel like beating a dead horse but keep tying your expected outcomes and everything back to your hypothesis. Ask yourself constantly: How do the experimental approach and findings help answer the question you are asking? Answer this question throughout your writing and highlight this by underlining or bolding a key phrase or a few sentences in the aims/expected outcomes. Finally, you do not need any preliminary data. Having it will help shape your hypotheses, but this is not an expectation. You may use preliminary data from other members of your lab (with prior consent) if it helps. Workshops/Courses Yale BBS offers multiple grant writing courses. Additionally, the Poorvu Center for Teaching and Learning holds a few workshops on the F31 NRSA. Attending these are optional and feedback on how helpful they are is mixed. However, if you’re looking for a starting point, their workshops are recommended. Citation Managers It is essential for you to master EndNote or any other citation manager. Do not, by any means, rely on manually adding citations, it is not feasible and will take too much of your time. Requesting Feedback Your PI/thesis committee can only give you feedback on your ideas/concepts rather than specific writing. This must be written entirely by you and consist fully of your ideas. While your advisor will be unable to provide direct edits to your prospectus, they can provide general advice and intellectual feedback. You should send your advisor and/or lab members a copy of your draft(s) ahead of time so that you can thoroughly incorporate their feedback into your writing before handing in the written prospectus. Ask other lab members (especially PhD students or postdocs) to read over it and give feedback about your aims and approach. You want your project to be feasible and make sense to others. The more feedback, the better! 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).
The form for the Prospectus Chair to complete upon passing the qualifying exam is found here.
Advice from Students
• Do not hesitate to ask questions or ask for guidance. Be assertive and reach out to your
mentors ahead of time so they can guide you through any questions you may have.
Independence and drive are encouraged, but as a trainee you still have much to learn. While the
conceptualization and writing of your proposal is your responsibility, the help of your advisor
and fellow lab members may be essential for the crystallization of specific aims, experimental
designs, potential pitfalls and alternative strategies. It is important for your growth and your
performance as a trainee to reach out to your mentors if you feel stuck at any point during this
process (this advice also extends to the rest of your PhD).
• Do not avoid meetings with your advisor. Advisors are generally busy and may not be able to
closely track/monitor your progress. Be sure to communicate with your advisor and other lab
members frequently. If you feel stuck, do not avoid meeting with your advisor. Your advisor may
not know that you feel stuck/need help.
• Do not take criticism personally. You are a trainee and you are not expected to know everything.
Criticism or questions usually means that your mentors are invested in your project.
• Manage your own timeline. The timeline for your qualifying process is largely dependent on you.
o While the guidelines suggest you schedule your pre-prospectus meeting right after your
RIP, this is not required. Scheduling your pre-prospectus meeting is up to you and may be
done at any time of your choosing throughout your Second Year.
o The guidelines also state that you have eight weeks to qualify after you hold your pre-
prospectus meeting. In our experience, this is a “soft” deadline or suggestion. The reality
is your prospectus date will be dictated by multiple outside factors. Some examples
include the availability of your committee members, whether you require essential
preliminary data to support one of your aims, and your overall preparedness for the
qualifying exam.
o As time goes on, it will become clear to you, your advisors and your committee members
whether the 8-week mark is feasible. Be aware that the hard deadline for qualifying, as
dictated by GSAS, is May 31st of your second year so plan your timeline responsibly.
• Stay calm! Your committee will have prepared you for success!!!Year Three and Beyond: Advance to Candidacy
Advancement to Candidacy (all requirements met + satisfactory 3rd year
committee meeting)
An important requirement for advancing to candidacy and receiving the MPhil, Master of
Philosophy, is achieved following the first thesis committee meeting, post your
prospectus/qualifying exam. This meeting is your first yearly committee gathering. Plan on
providing your committee with a written summary (at least one week in advance) of your goals
and achievements from the previous year. The committee will critique your progress and let you
know if you are making sufficient advancement. If all is well then, the meeting concludes with
the committee signing off on three forms required for the student to continue in the graduate
program.
1. Committee Form Report (with IDP)
2. Certificate of Advancement to Candidacy
3. IDP Individual development certification. Because students must be advanced to
candidacy before the end of the third year, the thesis committee meeting should take
place relatively early in year 3 (no later than February), so that if problems are identified
by the committee, there is sufficient time for the student to attempt to address them prior
to the end of the third year.
Evaluation of student progress within the program: A faculty meeting is held each spring in
which each student's progress is reviewed. Research progress, course grades, performance in
the laboratory, attendance and participation in seminars are all considered.
Committee Meetings
The dissertation progress of each student is determined at least once per year at a thesis
committee meeting. Committee meetings should be held more frequently if the student or
committee believes it is appropriate, but each meeting should last no longer than one hour.
The Thesis Committee is usually made up of the faculty that served as the Prospectus
Committee and should consist of the student’s mentor plus three or four other faculty, chosen
for their expertise in areas relating to the student’s research. At least two members of the Thesis
Committee should have a primary or joint appointment in Immunobiology, although
exceptions can be made by the DGS under special circumstances.
The committee serves several critical functions
1. Provide the student with suggestions concerning the research and help redirect the
research into productive avenues.
2. Evaluate the student’s progress and ensure that the project is interesting, novel, well
focused and do-able.
3. Provide the student and the mentor with an opportunity to express privately any
concerns about the research environment or the progress of the research (see below).
Each committee meeting should conclude with a short meeting of the mentor with the
committee (in the absence of the student), and the student with the committee (in the
absence of the mentor).
The format of the Thesis Committee Meeting is as follows:
1. Prior to the meeting, the student will write up a one-page summary of their past progress
and future Aims/goals. It helps to just have a one paragraph describing the overarching
problem or hypothesis being studied, and then bulleting your accomplishments andfuture objectives. Please note the submission or receipt of any awards, fellowships or
other notable achievements. A timeline for publication(s) and/or graduation should be
at the very end of the progress report. This summary can also serve as the student’s
dissertation progress report (DPR) submitted to the graduate school.
2. Please get the committee report form from Caroline and bring to the meeting if you
don't have it already.
3. At the beginning of the meeting, the faculty may want to have a private meeting for few
minutes to discuss matters of importance, but this is not mandatory.
4. The student will then present their progress on their thesis to the committee in a
presentation planned to last no more than 30 minutes (less than 20 slides typically). After
a couple of intro and background slides, the next few slides should go over the main
findings and/or results generated to date (best if presented in the format of figures for a
paper) and then leave the remaining slides and discussion time for challenges,
technical issues, alternative approaches and future experiments being planned. The
committee discusses changes in emphasis or direction in the research as well as
providing technical expertise. It is intended that all matters relating to the student’s thesis
project can be freely discussed within a time frame of ~45-50 minutes.
The committee meeting ends with an executive session of two parts:
1. The Thesis Advisor meets with the committee (in the absence of the student) and the
committee fills out the student report form. The student then re-enters the room and will
be presented with the completed report form to summarize the main points of the
discussion and review their progress and scientific maturation.
2. The Graduate Student then meets with the committee (in the absence of the advisor).
At this time the student has the opportunity to talk openly and in confidence about any
issues they may be having in the lab, with their advisor, career directions or any other
topic they wish to talk about. Depending on the situation, the committee should report
any particular issues to the DGS and/or the advisor (as deemed appropriate). The
student and the Advisor should typically meet immediately afterwards to recap on the
highlights of the meeting and anything within the Report that requires attention.
The student should scan the report and send a copy to the DGS (carla.rothlin@yale.edu), the
Registrar (caroline.lieber@yale.edu) and the rest of the committee members.
Furthermore, a student’s progress in the program will be determined by evaluation of:
1. The quality of presentations (could be a RIP presentation).
2. The ability to discuss his/her research area and answer questions about the research and
its context.
3. Research progress.
Please be sure to inform Caroline each time you have a Thesis Committee Meeting. This ensures
that the meeting took place, and she will know to expect a committee report from your PI. Plan
in advance to book your meetings. One of the most challenging is coordinating everyone’s
time together in one place. It is not unusual to schedule a committee meeting many months
in advance. Here is a link to the committee form.
If the student’s progress is unsatisfactory, the committee may issue a warning to the student in
which the deficiencies are clearly identified, and a time period is set within which it is expected
that the student will correct the deficiencies. A copy of the warning is filed with the Director of
Graduate Studies. At the end of the warning period, the committee and student will meet to
assess progress. If upon re-evaluation, progress is found to be unsatisfactory, the committee will
draft a recommendation to be reviewed by the faculty as a whole. The DGS will inform the
student and committee members of the decision in writing. Two warnings by the committee
/faculty may lead to termination of the association of the student with the department.Career development and the Individual Development Plan (IDP) The Immunobiology Graduate Program, BBS, and Yale Graduate School are committed to helping students develop the skills, expertise, knowledge, and experience needed to pursue a productive and satisfying career after graduating with the PhD degree. This includes providing students with exposure to a wide range of possible career choices, both in and outside of scientific research. While many of our graduates take postdoctoral positions after graduating, many do not and instead pursue diverse career paths in teaching, business, law, writing, editing, government, and public policy. Our philosophy is that these should not be regarded as “alternative” careers, but rather as valid, valuable, and desirable careers to pursue with a PhD degree. Many career development resources are available at Yale, including workshops, symposia, career/job fairs, dinners with graduate alumni, panel discussions, etc and these are hosted and organized by various groups at Yale, including Immunobiology graduate students. We strongly encourage you to participate in these activities and get involved in organizing them if you are interested. The McDougal Center at Yale Graduate School offers career development opportunities, information, and support. We also strongly encourage you to start thinking about the development of your career early during your PhD training. To this end, all graduate students in Immunobiology (and more generally, in the BBS), are now required to complete and Individual Development Plan (IDP). Immunobiology students must do so prior to the end of their second year. Several good online IDP resources are available, but Immunobiology (and BBS more generally) has chosen as its standard myIDP (http://myIDP.sciencecareers.org) an interactive career-planning website organized by Science Careers with funding from AAAS and the Burroughs Wellcome Fund. myIDP is part of a tool to identify career possibilities that you might be interested in (and might not have thought of). But it should also help you identify areas in which you might want to develop skills, gain experience, identify opportunities, and start making contacts. It can help in identifying discrete goals that can move you closer to your chosen career. It is designed to be interactive: after filling it out the first time, you are encouraged to visit your personal IDP at the website and update it. You are also strongly encouraged to discuss career paths with your PhD supervisor and Thesis Committee. This discussion could be guided or informed by the results of your IDP, but it need not be. You are not required to disclose or discuss the results of your IDP. The only requirement is that you provide a certificate of completion to the Student Services Officer (Caroline). The myIDP website allows you to “print out” (as a PDF file you want) such a certificate once the IDP has been completed, and you can elect to have the certificate exclude any information you want. In short, we hope that the IDP will help initiate an ongoing dialogue that will help you identify and prepare for life after graduate school.
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