Department of Virology, Immunology & Microbiology Graduate Student Guide


Program overview:
The goal of the Microbiology Program is to provide rigorous training in the fields of virology, host-pathogen interactions, and immunology. To meet this goal, we provide specialized courses, hold journal clubs and seminars, provide practice qualifying exams and presentations, and scheduled dissertation advisory committee meetings, as well as mentored research projects. All of us in the Department of Virology, Immunology & Microbiology are committed to helping students to meet their goals, and students should feel free to ask for help from their mentors, dissertation advisory committee members, and other faculty, staff, researchers and students at any point in their training.

Program summary:
Students spend time prior to joining the Microbiology Program either in the PhD Program in Biomedical Sciences or the combined MD-PhD Program. In those programs, students take foundational courses and research rotations that prepare them for the Microbiology Program

Year 1 of the Microbiology Program:

June – December: Students take required and elective courses, attend seminars, perform dissertation research, prepare for practice qualifying exam.

January: Students take a practice qualifying exam.

January – May: Students give a journal club presentation, take required and elective courses, attend seminars, perform dissertation research, and prepare for the qualifying exam.

June: Students take their qualifying exam.

July – August: Students work with their advisors and the Director of Graduate Studies to select their dissertation advisory committees and continue their dissertation research.

Year 2 in the Microbiology Program and beyond:

Students complete any outstanding courses, continue their dissertation research, having regular meetings with their dissertation advisory committee, and give research in progress presentations to the department. When a student’s mentor and committee think that the student’s dissertation research meets the standard required for a PhD, the student defends their dissertation.

Learning outcomes:
By the time students complete their Ph.D. training they should be able to:

  • Demonstrate academic mastery in virology, immunology, and/ or host-pathogen interactions.
  • Demonstrate competencies in oral and written communication.
  • Generate an original body of research in virology, immunology, and/ or host-pathogen interactions.
  • Attain the skills and qualifications needed for employment in an academic, government, or private sector position related to biomedical sciences.



Dr. Rachel Fearns ( is the Chair of the Department of Virology, Immunology & Microbiology

Dr. Ratnakar Deole ( is the Director of Graduate Studies (DGS) for the Microbiology Program

Dr. Robert Davey ( is the Assistant DGS for the Microbiology Program.

Ms. Kathleen Marinelli ( administers the Microbiology Program.

Dr. Deole should be consulted for advice on and approval of courses, rotations, training options, dissertation advisors, research advisory committees, and dissertation defense preparation. He will review each student’s performance and progress on a regular basis and reassess curricular and research options. Dr. Davey will also provide advice and support for these issues.



For graded course work, a minimum grade of B- is considered a passing grade by the Division of Graduate Medical Sciences. Division rules state that students who fail 8 or more credits will be terminated from the program. The Department of Virology, Immunology & Microbiology requires that if a student gets a C+ or lower in any required course, s/he will be required to repeat the course(s); the original grade will be carried on the transcript. Credits in other failed courses must be made up with credits from the same or other courses.

Ph.D. student curriculum:
For Ph.D. students in the Microbiology program, a total of 24 graded credits is currently required.

Required courses (typically taken in the 1st year of the PiBS program, prior to joining the Microbiology Program):
GMS FC 701 FiBS I: Protein Structure, Catalysis and Interactions, 3 cr
GMS FC 702 FiBS II: Structure and Function of the Genome, 3 cr
GMS FC 703 FiBS III: Architecture and Dynamics of the Cell, 3 cr
GMS FC 704 FiBS IV: Mechanisms of Cell Communication, 3 cr
GMS FC 764 Professional Skills, 2 cr
GMS FC 708 Professional Development Skills, 2 cr

In addition, students in the Microbiology program are required to take the following:

GMS FC 721 Statistical Reasoning for the Basic Biomedical Sciences, 4 cr (another statistics course can be substituted with Dr. Deole’s permission)

At least 4 credits from one or more of the following courses:

GMS MI 701 Concepts in Virology, 2 cr
GMS MI 823 Special Topics in Microbiology (Microbial Pathogenesis), 2 cr

GMS MI 713 Comprehensive Immunology, 4 cr


GMS MI 811 (Fall), 812 (Spring) Microbiology Seminar, 2 cr (this is ungraded and is to be taken each year in the program)
GMS MI 911, 912 Microbiology Research, var cr

Responsible Conduct in Research (

M.D.-Ph.D. student curriculum:
M.D.-Ph.D. students are required to obtain 16 graded credits from relevant courses taken during their time in the Microbiology Program. They do not typically take the FiBS or Professional Skills/ Professional Development Skills courses. However, aside from these exceptions, the M.D.-Ph.D. students have the same course requirements as described above for the Ph.D. students.

Elective Courses for both Ph.D. and M.D.-Ph.D. students:
Students should take additional elective courses that will best complement their research studies. Students typically complete coursework by the end of their first year in the Microbiology program, except in cases where courses are only offered in alternate years. Course offerings change each year and so students are advised to consult the student link to identify courses that might be suitable, and to discuss course options with their advisor and with Drs. Deole or Davey.

Examples of elective courses taken by students in the Microbiology Program:

GMS GE 701 Principles of Genetics and Genomics, 4 cr

GMS BI 777 Techniques in Biomedical research, 2 cr

GMS BY 776 Macromolecular Assemblies I, 2 cr
GMS BY 777 Macromolecular Assemblies II, 2 cr

GMS MM 710 Stem Cells and Regenerative Medicine, 2 cr

GMS MM 725 Biology of the Lung and Pulmonary Disease, 2 cr

GMS FC 705 Foundations in Biomedical Sciences: Translational Genetics and Genomics, 2 cr
GMS FC 706 Foundations in Biomedical Sciences: Molecular Metabolism, 2 cr



The Department of Virology, Immunology & Microbiology hosts two seminar series: a trainee seminar series and an expert faculty seminar series. Seminars and journal clubs are important components of training throughout a scientific career and the trainee seminar series provides an opportunity for valuable practice of presentation skills. All students in the Microbiology Program are expected to attend and participate in departmental seminars throughout their graduate career and students are encouraged to attend seminars in a variety of disciplines.

Trainee seminar series:
The trainee seminar series is held on Mondays, from 12:00-1:00 ( It involves journal club presentations from students who are in their first year in the Microbiology Program, and research in progress presentations from more advanced graduate students, postdoctoral trainees, and research scientists. Journal club presentations are ~45-60 minutes in length and students will be provided guidance on how to prepare for their presentation. Research in progress seminars are ~ 20-25 minutes in length. These seminars should be well organized and will normally include the following components: 1) a brief but inclusive background summary of the general topic of the student’s dissertation project; 2) a statement of the student’s research goals (i.e. what question(s) the student is trying to answer); 3) a summary of the student’s results to date and conclusions drawn by the student from their results; and 4) future experiments that the student intends to carry out. Each student is expected to present once each year that they are in the program.

Expert faculty seminar series:
The expert faculty seminar series includes invited speakers from other institutions and is held on Wednesdays, from 12:00-1:00. These speakers typically are internationally recognized leaders in their field of expertise. See for more details. Following each of these guest speaker seminars, students have the opportunity to meet with the speaker over lunch. Each student who has completed their second-year coursework is expected to attend at least four lunches over the course of the academic year. We welcome input from students regarding seminar speakers and so please let your mentor know if you have any suggestions.

The Department of Virology, Immunology & Microbiology and the Immunology Training Program each provide graduate students to choose an external faculty member to invite to present a seminar. A student host invites the speaker and organizes the events on their visiting day.

In addition, all students are strongly encouraged to attend additional seminars offered within the Boston University Medical School community.



The qualifying exam is a key component of the PhD qualification. It takes place in June one year after the student has entered the Microbiology Program. This exam allows the faculty to evaluate if the student has the potential to meet the standards necessary for successful completion of their PhD training. To help prepare students for the qualifying exam, the Department of Virology, Immunology & Microbiology provides a mandatory practice qualification exam, which is typically held in the months of January/ February after the student has entered the Microbiology Program.

Practice qualifying exam:
The practice qualifying exam is a formative assessment (i.e. it is not graded). The purpose is to help the student to identify their strengths and areas for improvement, and to provide advice on how those weaknesses can be remedied (e.g. through course work or directed study) so that the student can fully prepare themselves for the formal qualifying exam. It is also intended to give students experience of an oral exam so that they are better prepared for the qualifying exam. Students are encouraged to seek advice and guidance from their mentor in preparing for this exam.

The practice qualifying exam has two parts: (1) an in-depth editorial on a paper related to their dissertation research and (2) an oral presentation in a closed session before members of an ad hoc qualifying exam committee. The written editorial should be 3-4 pages single spaced, Arial 11-point text (not including references). It can include a model figure or figures but should not include any of the results figures of the paper being discussed.

It should include the following elements:

  • An introduction to the field
  • Identification of the gap in knowledge that the paper addresses (why is the paper important)
  • A summary of the key findings of the paper
  • An explanation of what techniques/ methods were used and why
  • An explanation of the key strengths of the paper
  • An explanation of any weaknesses or caveats of the paper
  • Identification of what gaps in knowledge remain

For the oral component, the student prepares a slide show of the paper. In addition to assessing the student’s understanding of the paper, the practice qualifying exam committee will ask general concept questions to help them assess the student’s knowledge of their area of concentration, as well as their foundational knowledge in appropriate areas of the biomedical sciences, including cell biology, genetics, biochemistry, etc. The student’s mentor may be present for the oral component as an observer.

Students will receive written feedback from the exam committee after the exam according to the following rubric:

  • Foundational knowledge: an understanding of material from foundation courses and other required courses.
  • Scholarship: knowledge and understanding of the literature in the field of study with breadth and depth.
  • Ability to interpret data critically: an understanding of techniques used in the paper and underlying principles, an understanding of whether the experiments really address the question being asked, ability to determine if the experimental design is appropriate (e.g., positive and negative controls), ability to determine if the data are being interpreted correctly, and to determine if other interpretations are possible.
  • Creativity: ability to conceive of a novel hypothesis if the results had been different, ability to conceive of an experimental plan to test a hypothesis.
  • Presentation skills: ability to write clearly and fluently, to present data appropriately (graphs, or images etc.), cite references appropriately, verbally articulate thoughts clearly.

Qualifying exam:
The formal qualifying exam is a pass/fail exam. The examining committee evaluates if the student has the potential to fulfill the requirements for a Ph.D.

The qualifying exam committees are selected to match the student’s research interests to the extent possible and includes a committee chair who is a member of Virology, Immunology, & Microbiology faculty. The exam has three parts: (1) a short report, (2) a 30-minute presentation in an open session of the students and faculty of the training program(s), and (3) a closed session of questioning by the qualifying exam committee. Students are entitled to have up to two weeks fully dedicated to qualifying exam preparation during the month of May should they choose to do so.

The exam is based on what the student plans to do for their dissertation research (although it is not a binding document, and ultimately the dissertation research will be determined by the PhD student’s advisor in consultation with the student). The written component is a document written in the style of the Specific Aims and Research Strategy sections of an F31 grant application (for examples see ). The document should be ~6-7 pages (excluding references) with figures embedded within it. Although it is expected that students are technically competent, the goal of this document is for the student to demonstrate their ability and aptitude for Ph.D. research, and the amount of preliminary data that they themselves have generated is not assessed. The student is encouraged to seek guidance from their advisor regarding the scope of the aims and should ask for feedback from their advisor on the Specific Aims page. However, they should not receive help from the advisor or others in crafting and writing the proposal. The oral component consists of a 30-minute research seminar open to all students and faculty, followed by a closed oral exam before the qualifying exam committee. Students can seek help from more advanced students for practicing their research seminars (see list of students and responsibilities at the end of this guide).

The student’s written report must be submitted to the qualifying exam committee, Dr. Deole and Kathy Marinelli on June 1st. The research seminar and closed-door exam will typically be held in mid-June, but the exact dates might vary, depending on faculty availability. During the research seminar, the student is expected to explain clearly the background and rationale for the research questions. They must also explain the experimental approach and provide an interpretation of their data and how the data fit in with the existing scientific literature. Finally, they must be able to answer questions from the audience.

Following the research seminar, the qualifying exam committee meets and reviews the student’s performance in the laboratory with their advisor. Then the committee invites the student to join them and proceeds with the oral exam. The committee will ask questions to test the student’s understanding of the research project and of general concepts in virology, immunology and/or microbial pathogenesis. The committee will then excuse the student and determine whether the student has passed both the written and oral components of the exam. If the committee votes to fail the student, the committee chair will forward the decision to Dr. Deole who will consult with the student’s advisor and Drs. Davey and Fearns to decide if the student is allowed to retake the written and/or oral exam or should be recommended for dismissal from the program. When a student passes their exam, they are advanced to dissertation status.



After completing the qualifying exam, the student should assemble a Dissertation Advisory Committee (DAC) who will help guide them in their research project. A student should choose members of their committee in consultation with their advisor and Dr. Deole. The membership of the committee must be approved by Dr. Deole. All committee members must hold graduate appointments in the Division of Graduate Medical Sciences. Committee members from outside of the institution should hold graduate level faculty appointments at their home institutions and are able to receive special service appointments in the Division of Graduate Medical Sciences for the duration of their service on a student’s committee:

Dissertation advisory committee composition:
If the advisor is a member of the Virology, Immunology & Microbiology faculty:

  • Advisor
  • 2 other members of the Virology, Immunology & Microbiology faculty
  • 2 additional members with faculty appointments in the Division of Graduate Medical Sciences (at least 1 of whom should be from outside of the Virology, Immunology & Microbiology Department)

If the advisor is not a member of the Virology, Immunology & Microbiology graduate faculty:

  • Advisor
  • 3 members of the Virology, Immunology & Microbiology faculty
  • 1 other member with a faculty appointment in the Division of Graduate Medical Sciences (preferably from outside the Department of Virology, Immunology & Microbiology)

The DGS will appoint 1 of the 5 committee members, not the student’s advisor, to chair the committee. The chair will be a member of the Virology, Immunology & Microbiology faculty.

Dissertation advisory committee meetings:
The DAC should meet with the student no later than January following the qualifying exam date. Ideally, the first committee meeting should be held in the months of September to early December. The committee should then reconvene approximately every six months (unless otherwise determined by the Dissertation Advisory Committee or Dr. Deole) to discuss research progress with the student.

It is the student’s responsibility to schedule their committee meetings. Drs. Deole, Davey and Kathy Marinelli should be notified by E-mail at, and, respectively of the date, time, and place of each meeting as soon as the meeting is set but no later than 2 weeks prior to the meeting. Kathy can help with room bookings if necessary. If it is impossible for all committee members to agree on a meeting date, it is better to schedule a meeting in the absence of one committee member (not the advisor or committee chair) than to postpone committee meetings for months.

One week prior to a student’s first meeting with their DAC, the student must submit to committee members and Drs. Deole and Davey an outline of their proposed dissertation project. The first committee report should provide the committee members with the information necessary to understand the hypothesis to be tested and the rationale for the hypothesis. It should include a specific aims section, a background and rationale section, a preliminary results section, and a section describing the experimental approach that will be used to carry out the studies. This report should be no more than 5-6 pages in length. Typically, this report is adapted from the qualifying exam document in consultation with the student’s advisor.

At least three days prior to each subsequent committee meeting, each student should provide members of the committee and Drs. Deole and Davey with a brief outline of their research progress. The outline should include each of the specific aims and the progress that has been made to date in addressing those aims. It should also include the future studies that are planned to address the aims. The student should be sure to indicate how they have addressed issues or concerns raised at the previous meeting. This outline should be kept brief (no more than 1-2 pages). Experimental findings should be included separately as figures and/or tables. If there is a significant change in research directions, the student should supplement the report with a brief background and rationale section to explain the change in research direction.

At the conclusion of each committee meeting, the committee chair and the student will review comments raised in the meeting. It will be the responsibility of the student to prepare a short report summarizing the meeting. The student should forward the summary to the committee chair for additional review, comments, time frame for the next committee meeting, and approval. The committee chair will email the final and approved summary to Kathy Marinelli ( who will distribute copies to the student, committee members, and Dr. Deole.



As part of the Ph.D. requirements, a written dissertation describing the student’s research accomplishments must be submitted and defended. The dissertation is based on original laboratory research. Students are expected to finish their Ph.D. having made a significant contribution to their field of research.  The expectation is for at least 1-2 first (or co-first) author publications summarizing the work.  Exceptions can be considered in consultation with the student’s DAC.

Ph.D. degrees are awarded three times a year, January, May and September. There are specific deadlines to be met for each of these degree award dates, which if missed could delay the final oral examination and the degree award. Many of these are set by the registrar’s office and are not flexible. Advice on dissertation preparation and a deadline calendar can be found at the following URL:  “General Research, Thesis and Dissertation Information”  “PhD completion of degree checklist”. Students are encouraged to reach out to Dr. Deole 10 months before they plan to defend their dissertations to determine what is required.

Before the student begins to write a formal dissertation document, both the major advisor and the DAC must agree that the student has completed a significant body of original research. Once the dissertation has been written, the student is required to present a formal seminar followed by an oral defense of the dissertation in a closed exam with the DAC. A written dissertation that has been approved by the 1st reader must be delivered to the 2nd reader one month before the scheduled date of the oral defense. A revised dissertation that addresses the 2nd reader’s comments must be delivered to all committee members at least two weeks before the scheduled date of the oral defense. Failure to meet these deadlines will result in the delay of the oral defense. Exceptions may be granted but only with the full consent of the DAC and Dr. Deole and/or Davey. Each student is required to provide the Department with a final copy of their dissertation before the Department will sign off on the necessary paperwork in order for the student to complete their degree requirements.



Student performance will be evaluated by the qualifying exam committee at the end of year 2, and then by the dissertation advisory committee and Drs. Deole and Davey thereafter.

For students pre-qualifying exam, the expectations are:

  • Maintaining a B average (3.0) in courses
  • Receiving no grades below B-
  • Attending and participating in departmental journal clubs, seminars, and speaker lunches
  • Completing Responsible Conduct of Research
  • Completing laboratory rotations and successful identification of a dissertation laboratory

For students post-qualifying exam, the expectations are:

  • Scheduling and having timely dissertation advisory committee meetings
  • Performing satisfactory dissertation research (determined by the student’s advisor and Dissertation Advisory Committee)
  • Attending and participating in departmental journal clubs, seminars and speaker lunches

Students must adhere to the rules of conduct as they are outlined by the Division of Graduate Medical Sciences in its documents “Academic Standards and Disciplinary Procedures” and “Code of Student Responsibilities.” Students must also adhere to the rules and policies of Boston University regarding sexual harassment. Copies of documents describing these rules and policies can be obtained through the Division of Graduate Medical Sciences (

Dr. Deole will provide feedback to students, at their request, throughout their time in the graduate program and will reach out to students who are not meeting expectations.

If a student fails to meet expectations, appropriate action will be taken which could include one of the following recommendations:

  1. additional coursework and/or directed study to remediate deficiencies
  2. revocation of financial aid
  3. dismissal from the program



More detailed information will be distributed throughout the year as deadlines approach on the following graduate student awards.

Corwin Award: Awarded by the Department of Virology, Immunology & Microbiology to a pre-doctoral graduate student in the program, in recognition of exemplary scholarly and/or scientific achievement, values of collegiality and scientific integrity. The award is named for Dr. Laurence Corwin who was a Microbiology faculty member for many years before his untimely death in 1983, and consists of a $1000 cash prize, a certificate, and a luncheon. Eligible students are nominated and voted on by faculty.

Travel Awards: The Department of Virology, Immunology & Microbiology provides up to three travel awards per year, a possible 1-3 to VIM graduate students and up to 2 to post-docs to attend scientific meetings. There is one annual competition, and it is open to all graduate students in the Microbiology Program and those post-docs in the laboratories of primary Virology, Immunology & Microbiology faculty. The deadline is usually at the end of January and e-mails are sent approximately 1 month and 1 week prior to the deadline along with the application form. The first prize is in the amount of $750 and the second and third prizes are in the amounts of $500 each. The top prize can go to either a graduate student or a post-doc and the meetings must occur within 6 months prior to or after the travel award deadline. In addition, the Division of Graduate Medical Sciences provides travel awards to graduate students. More information on the GMS travel awards can be found at:

GMS Outstanding Student Achievement Awards: GMS offers student awards for outstanding research achievement and community service. Students are encouraged to self-nominate themselves for these awards. Please see the following link:,the%20awardee%20from%20GMS%20funds.



For any travel abroad, students are required to register with BU Global Programs. They will be able to help in the event of an emergency.



The Department of Virology, Immunology & Microbiology strives to provide a professional, nurturing, supportive and respectful environment for our faculty, staff, students and trainees. By doing so our community creates an atmosphere of mutual trust and collegiality and a positive learning and professional environment for every member of the Department.

Every member of the Department of Virology, Immunology & Microbiology is expected to:

  • Contribute to a welcoming and respectful academic atmosphere;
  • Promote the educational goals of the Chobanian & Avedisian School of Medicine through example by treating all others in a professional, respectful manner grounded in civility and honesty;
  • Maintain an inclusive learning environment that encourages open inquiry and expression among community members while recognizing and respecting diversity of background, values, and views.
  • Respond in the moment (where possible) to comments or actions by members of the department that are clearly discriminatory or disrespectful of others
  • Report observations of clearly discriminatory comments or actions immediately to the department Chair (and/or the University Ombuds or EthicsPoint if preferred

Title IX & BU Policies: Title IX of the Education Amendments of 1972 is a federal civil rights law that prohibits sex-based discrimination in federally funded education programs and activities. Sex-based discrimination includes sexual harassment and sexual violence, such as rape, sexual assault, sexual battery, and sexual coercion. The law covers sex-based discrimination against students, faculty, and staff.

Reporting infractions of Title IX or other negative behaviors:

Graduate Students

Under Title IX,

Gwyneth Offner, Director, M.A. Medical Sciences Program (GMS) / (617) 358-9541

Karen Symes, Ph.D., Assistant Dean of Student Affairs (MED) / (617) 358-4578


Under Ethics Point (see link and specifically look at the FAQ section)

All BU Faculty, Staff, Students, etc.

Office of the Ombuds see link



Students in the program receive full tuition coverage, fees, health insurance options and a stipend which is set by Graduate Medical Sciences. The Department of Virology, Immunology & Microbiology also provides $1,000 to second year, pre-qualifying exam students to help defray the cost of computers, books, or conferences. Students should contact Kathy Marinelli ( for additional information. The department also recognizes that graduate students may not have the means to wait for reimbursement of credit card charges for conference related expenses. Rebecca Washburn ( in the Virology, Immunology & Microbiology office will be available to pay for these expenses in advance using a departmental purchasing card. If students are interested in utilizing this option, they should contact Becky.



Graduate Student Representatives: Virology, Immunology & Microbiology graduate students are represented at departmental faculty meetings and other institutional meetings as the need arises. The term is 2 years and as one student rotates off, a new representative is elected. The current representatives are Elizabeth Chavez and Elias Nafziger.

Student responsibilities for the 2023-2024 academic year are listed below:

Student Representative to the Faculty
1. Elizabeth Chavez (1-year appointment)
2. Elias Nafziger (2-year appointment)

Representatives to the GMSSO
1. Elise Armstrong

Student representative for the VIM Retreat
1. Ellen Suder (2023)
2. Michael Vannini (2024)

Student Representative for Seminar Speaker Diversity Subcommittee
1. Christina McConney

VIM Community Outreach Chair
1. Jonathan Kilroy
2. Kara Vasilew

Order pizza for journal club
1. Ivy Hughes

Set up and breakdown X222 for seminars
1. Callie Donahue
2. Joelle Johnson
3. Joseph McWhirter

Organize Happy Hour
1. Scott Adams
2. Jonathan Kilroy

Purchase student gift for graduating students
1. Devin Kenney
2. Christina McConney

Organize qualifying exam oral presentation practice sessions
1. Sita Ramaswamy

Smooth transition for 2nd years joining VIM (getting paid, expectations, etc.)
1. Stephen Ross

Organize welcome party for incoming 2nd years
1. Jonathan Kilroy
2. Scott Adams