Graduate Student Guide

Boston University School of Medicine


This short guide is intended to summarize the requirements for graduate study in the Department of Microbiology and to provide some helpful information. Official documents regarding academic policies and procedures, registration information, etc. are available in the Division of Graduate Medical Sciences or online (


The Department of Microbiology is in the process of appointing a new Director of Graduate Studies (DGS). The DGS should be consulted for advice on and approval of courses, rotations, training options, dissertation advisors, research advisory committees, and just about all other academic matters in the Department. In addition, s/he will review each student’s performance and progress on a regular basis and reassess curricular and research options. The DGS will be available to students throughout their training in the Department should problems arise in meeting the particular requirements that a student has selected.


Students enter the Department and affiliated programs via the umbrella Ph.D. graduate program, Program in Biomedical Sciences (PiBS), which offers training by integrating the foundations of interdisciplinary biomedical research with focused investigation. Admissions criteria and online applications can be found on the Division of Graduate Medical Sciences website. Students may also enter through the M.D. / Ph.D. Program.

Specific information about the Department of Microbiology and its graduate programs can be obtained by contacting the Microbiology Office.

In addition to successfully completing prescribed course work, Ph.D. and M.D.-Ph.D. candidates must also complete rotations, participate in seminars, pass a qualifying examination, and successfully defend a dissertation based on original laboratory research.


The curricula for students in the Department of Microbiology were reviewed recently and the curricula below were designed to recognize each student’s interests, background and training.

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 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.

Host Pathogen Interactions Curriculum

M.A. and Ph.D. students.
M.D.-Ph.D. students should consult with the DGS for course exemptions.

Required Courses
GMS MI 701 Concepts in Virology, 2 cr
GMS MI 812 Microbiology Seminar, 2 cr
GMS MI 911,912 Microbiology Research, var cr
GMS FC 701 Foundations in Biomedical Sciences I: Protein Structure, Catalysis and Interactions, 2 cr
GMS FC 702 FiBS II: Structure and Function of the Genome, 2 cr
GMS FC 703 FiBS III: Architecture and Dynamics of the Cell, 2 cr
GMS FC 704 FiBS IV: Mechanisms of Cell Communication, 2 cr
GMS FC 764 Professional Skills, 2 cr
GMS FC 708 Professional Development Skills, 2 cr
GMS FC 720 Statistical Reasoning for the Basic Biomedical Sciences, 3 cr (another statistics course can be substituted with permission of the DGS)

Responsible Conduct in Research

Advanced Microbiology Courses
Choose 8 credits of the following
GMS MI 713 Comprehensive Immunology, 4 cr
GMS MI 823 Special Topics in Microbiology (2016 Microbial Pathogenesis), 2 cr

Elective Courses
Choose 4-8 credits of the following**
GMS BI 776 Gene Targeting in Transgenic Mice, 2 cr
GMS BI 777 Techniques in Molecular Biology, Proteins, 2 cr
GMS BI 787 Molecular Mechanisms of Growth and Differentiation, 2 cr
GMS BI 790 Receptor & Signal Transduction, 2 cr
GMS BY 762 Foundations of Biophysics and Structural Biology I, 2 cr
GMS BY 763 Foundations of Biophysics and Structural Biology II, 2 cr
GMS BY 776 Macromolecular Assemblies I, 2 cr
GMS BY 777 Macromolecular Assemblies II, 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
GMS FC 707 Foundations in Biomedical Sciences: Physiology of Specialized Cells, 2 cr
GMS FC 761 Critical Thinking in Biomedical Research, 2 cr
GMS IM 600 Bioimaging Foundations, 4 cr
GMS IM 620 Bioimaging Theory and Imaging Processing, 4 cr
GMS GE 701 Principles of Genetics and Genomics, 4 cr
GMS MS 700 Elementary Biostatistics for the Biomedical Sciences, 2 cr
GMS MM 703 Cancer Biology, 2 cr
GMS PA 500 Introduction to Pathology of Disease, 4 cr
GMS PH 730 Human Physiology, 4 cr

**Advanced Microbiology Courses can be substituted with the permission of the Director of Graduate Studies

Immunology Training Program/Microbiology Curriculum

In addition to the required courses listed above, ITP/Microbiology students are required to take the following:

  • Comprehensive Immunology (GMS MI713, 4 cr)
  • 10 credits of either the Advanced Microbiology or Elective courses listed above

Training Program in Inflammatory Diseases/Microbiology Curriculum

In addition to the required courses listed above, Inflammatory Diseases/Microbiology students are required to take the following:

  • Inflammatory Diseases and Therapeutics (GMS MM, 2 cr)


Advisory/review committees:

SARC (Student Advisory and Review Committee). This committee is responsible for annual review of student progress and making format recommendations to the faculty, which may include recommendations for remediation, probation and/or non-continuance.

The SARC includes:

  1. Program directors (HPI, ITP, etc.) or his/her designee
  2. Director of Graduate Studies (DGS) for Microbiology
  3. Three (3) additional members of the graduate faculty with appointments (primary or secondary) in microbiology.

Student evaluations:

There will be a formal evaluation by the Student Advisory/Review Committee (SARC) of all students at the end of each year.

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 journal clubs, seminars, and speaker lunches (Microbial Pathogenesis, Inflammation, and Immunology Seminar Series and Microbiology as well as Immunology Trainee Seminar and Journal Club Series)
  • Completing Responsible Conduct in 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 Mentor and Dissertation Advisory Committee)
  • Attending and participating in journal clubs, seminars and speaker lunches (Microbiology; ITP; as appropriate)

Implicit in a student’s evaluation and the definition of good standing is a student’s conduct which includes but is not limited to the following:

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.

Students who meet the expectations above will be deemed to be in good standing. A student must be in good standing to progress to Qualifying Exams.

The SARC is expected to provide feedback to students throughout their time in the graduate program.

If a student fails to meet these 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


In order to provide students with some teaching experience, all students are required to serve as a teaching assistant at least once in either the Microbiology component of the Medical School MS220 Disease & Therapy course or in one module of the Foundations in Biomedical Sciences (FiBS) Courses.


Seminars and journal clubs are important components of training at all stages of a scientific career and all students are encouraged to attend seminars in a variety of disciplines. In addition, all students in the Microbiology Department are expected to attend and participate in Departmental seminars throughout their graduate career. 

The Department of Microbiology, National Emerging Infectious Diseases Laboratories (NEIDL), Inflammatory Disorders Training Program, and the Immunology Training Program host a combined weekly seminar series. This joint seminar series includes invited speakers from other institutions and is held WEDNESDAYS, from 12:00-1:00 in the X715 Conference Room or in the NEIDL first floor conference room. See the seminar schedule for more details.

In addition, the Department of Microbiology and Immunology Training Program hold a Trainee Seminar Series and Journal Club which includes seminars and journal clubs by graduate students and postdoctoral fellows on MONDAYS, from 12:00-1:00 in the X715 Conference Room. Alternating with trainee seminars are journal clubs wherein trainees and faculty discuss research papers chosen from the current scientific literature. Students are expected to participate in journal clubs.

Check the Microbiology website at for information on both of these seminar series.

Both the Department of Microbiology and the Immunology Training Program will feature one invited speaker from another institute who is chosen by students in the department/program. These speakers typically are internationally recognized leaders in their field of expertise. Following both the Microbiology and the Immunology guest speaker seminars, students may meet with the guest speakers over lunch to discuss research.

Each student is required to present at least one seminar per year and this requirement holds whether or not a student is actually registered for the Microbiology seminar course. In an effort to provide feedback to students on their seminars, students and faculty are invited to critique student seminars after each presentation.

All graduate student seminars (except for dissertation defense seminars) will be limited to 20 minutes each with an additional 5 minutes for questions. There are 2 graduate students scheduled for each seminar slot.

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 his/her results; and 4) future experiments that the student intends to carry out.

All graduate students are required to complete the lecture series on the Responsible Conduct of Research presented by Boston University School of Medicine.

At the completion of a student’s graduate training and as an essential part of his/her Departmental and Divisional degree requirements, a dissertation seminar is required of all students. It will be the responsibility of the student and advisor to schedule this seminar at a time that will ensure maximum attendance by members of the Department and the Medical School community.

In addition, all students are strongly encouraged to attend additional seminars offered within the Boston University Medical School community. Our medical center is also fortunate to be in close proximity to other academic centers.


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 Microbiology to a Microbiology pre-doctoral graduate student, engaged in a research project, 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 by faculty.

Russek Award: Awarded to Ph.D. and/or M.D.Ph.D. students (usually 2 awards per basic science department, one first prize and one second prize) who have successfully completed their qualifying exam and are engaged in a research project. Students are nominated for this award which recognizes graduate student accomplishments and commitment to the pursuit of research in basic sciences. Awards are presented at the Henry I. Russek Student Achievement Day which is usually held in April and consists of poster sessions and oral presentations. The award is administered through the Division of Graduate Medical Sciences and is named for Dr. Henry I. Russek, a physician/scientist who made significant contributions to research and post-graduate education over a career of four decades.

Travel Awards: The Department of Microbiology provides up to three travel awards per year, a possible 1-3 to Microbiology graduate students and up to 2 to post-docs to attend scientific meetings. There is one annual competition and it is open to all Microbiology graduate students and those post-docs in the laboratories of primary Microbiology. 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 in the amount of $250 per semester. More information on the GMS travel awards can be found at:


Qualifying exams allow the training faculty to evaluate whether the student has accrued a level of scientific knowledge commensurate with his/her level in the program, as well as to determine a student’s organizational and analytical abilities based on the research s/he has carried out during the laboratory rotations. There are two components of the qualifying examination, both administered by appropriate members of the training faculty. Both exams allow the faculty to evaluate the student’s knowledge base, but the exams differ in depth of expertise required of the student.

The Qualifying Exam Committee composition changes regularly and follows the guidelines of the Division of Graduate Medical Sciences. The composition of the ad hoc Qualifying Exam Committee includes:

  1. A committee chair, who is a member of the Microbiology graduate faculty
  2. A minimum of four members of the program faculty in the student’s area of concentration
  3. Other members as needed

The student’s rotation advisors are excluded from sitting on their student’s Qualifying Exam Committee but may be asked to assess a student’s performance during the deliberations of the Qualifying Exam Committee.

1. First Preliminary Exam component

Format: This is an oral 30 minute presentation in a closed session before the members of an ad hoc Qualifying Examination Committee. Ph.D. students take the first Preliminary Exam, usually at the end of the Fall semester of the 2nd year. M.D./Ph.D. students typically take the exam at the end of the Fall Semester of their 1st year in the Program. The presentation can be based on one of the rotations carried out.

Purpose: The First Preliminary Exam is used to determine the strengths and weaknesses of the individual student at a point in the training process when deficiencies can be remedied through course work or directed study.

Content: During the presentation, the student must convey an understanding of the rationale for the project undertaken during the laboratory rotation, a critical understanding of the data generated, and a plan for future experiments. The Qualifying Exam Committee will ask general concept questions to help them assess the student’s knowledge of the student’s area of concentration, as well as appropriate areas of the biomedical sciences, including cell biology, genetics, biochemistry, etc.

Evaluation: The Qualifying Exam Committee will determine whether the student shows deficiencies, and forward its decision to the SARC. In this event, the Committee will forward recommendations for remedial action or acknowledgement of extenuating circumstances. If the SARC determines that the student is deficient, remedial action including additional coursework, presentations in journal clubs, or a re-exam will be assigned. The student will receive feedback on his/her performance.

2. Second Preliminary Exam component

Format: The Second Preliminary Exam has three parts: (1) a short paper, (2) a 30-45 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 ad hoc Qualifying Exam Committee. Students take the Second Preliminary Exam usually at the end of the 2nd year. M.D./Ph.D. students usually take the exam in the summer at the end of their 1st year in the program or the beginning of the Fall Semester of their 2nd year in the program.

Purpose: During this second component of the Preliminary Exam, the examining committee evaluates the student’s progress to determine if the student is qualified for Ph.D. level research. If the student passes the Second Preliminary Exam, the student should be advanced to Dissertation Status. No student may be advanced to Dissertation Status without passing this Qualifying Exam.

Content: The exam is based on the research project undertaken by the student during any of the 3 laboratory rotations (please note the rotation used for the first preliminary exam cannot be used for the second preliminary exam) and consists of written and oral components. The written component is a 5-7 page report (exclusive of references and data) that addresses the background, rationale for the research, the research findings, and data interpretation. The student may seek guidance from his/her rotation advisor about the proposal but not for help with the actual writing of the proposal. The oral component consists of a 30-45 minute research seminar open to all students and faculty followed by a closed oral exam before the Qualifying Exam Committee.

Evaluation: The student’s written report must be submitted to the Qualifying Exam Committee two weeks before the oral exam. The Committee will evaluate the report and determine whether the student has passed the written component of the exam. If the Committee votes to fail the student, its decision will be forwarded to the SARC. The SARC will decide if the student is allowed to retake the written exam or should be recommended for dismissal from the program. If the Qualifying Exam Committee votes to pass the student, they will notify the student of any potential weaknesses that should be addressed during the research seminar component of the exam.

Generally, there will be a 2 week interval between the oral and the written exams during which time the student will receive constructive feedback on his/her written proposal.

During the research seminar the student is expected to explain clearly the background and rationale for the research questions. S/he must also explain the experimental approach and provide an interpretation of his/her data and how the data fit in with the existing scientific literature. Finally, s/he must be able to answer questions from the audience.

Following the research seminar, the Qualifying Exam Committee will meet with the Rotation Advisor in a closed session and ask the Advisor to assess the performance of the student in the laboratory. The Committee will then excuse the Advisor and meet with the student in a closed session. At this time, the Committee will examine the student’s performance in the rotation and clarify issues raised by the written document and during the research seminar. The Committee will also ask questions to test the student’s understanding of the research project and of general concepts in immunology and/or microbial pathogenesis. The Committee will then excuse the student and determine whether the student has passed this component of the exam and should be advanced to Dissertation Status or be dismissed from the Program.

Notification: The student will be notified by the Qualifying Exam Committee.


Advancement to candidacy indicates that the student possesses the organizational and conceptual skills necessary for Ph.D. level research, and is judged capable and prepared to perform dissertation work.


Ph.D. and M.D.-Ph.D. students should assemble a Research Advisory Committee either prior to or shortly after completion of the qualifying exam procedure.

Student Dissertation Advisory Committees.

A student’s dissertation advisory committee should reflect a balance of expertise needed to guide a student in his/her research project. A student should choose members of his/her committee in consultation with his/her advisor and the DGS. The membership of the committee must be approved by the DGS. 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.

HPI (Host-Pathogen Interactions) track students: Five (or more) members, including the advisor:

If the advisor is a member of the Microbiology graduate faculty:

  • Advisor
  • 2 other members of the Microbiology graduate 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 Microbiology Department)

If the advisor is not a member of the Microbiology graduate faculty:

  • Advisor
  • 3 members of the Microbiology graduate faculty
  • 1 other member with a faculty appointment in the Division of Graduate Medical Sciences (preferably from outside the Department of 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 Microbiology graduate faculty.

ITP (Immunology Training Program) track students: Five (or more) members, including the advisor:

  • 3 members must be ITP faculty
  • 2 members must be Microbiology graduate faculty

TPID (Training Program in Inflammatory Disorders) track students: Five (or more) members, including the advisor:

  • 3 members must be TPID faculty
  • 2 members must be Microbiology graduate faculty

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


The Research Advisory Committee must meet with the student no later than the end of the semester following the qualifying exam date. The committee must then reconvene every six months (unless otherwise determined by the Advisory Committee or DGS) to discuss research progress with the student.

It is the student’s responsibility to schedule his/her committee meetings. The DGS and Kathy Marinelli should be notified by E-mail at (TBA) 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. The DGS and Kathy should also be notified of any changes in meetings. (NB: many students use the R504 Conference Room for their committee meetings. This room must be reserved through Kathy Marinelli at ( to avoid scheduling conflicts with other activities taking place in that room.

One week prior to a student’s first meeting with his/her Research Advisory Committee, the student must submit to Committee Members and the DGS, an outline of the 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 background and rationale section, a specific aims 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 5-10 pages in length. In addition, a limited number of well-selected figures or tables providing salient data should also be included. It is not necessary to include a copy of all the overheads or slides used in the Research-in-Progress seminar. Examples of acceptable proposal outlines are available from the DGS.

In general, it is best for students to have their subsequent committee meetings following their Departmental seminars, but since this is not always possible, it is acceptable to schedule each on a separate day. Also, it is inevitable that at some point there will be scheduling conflicts with committee members that will make it 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. At least three days prior to each subsequent committee meeting, each student should provide members of the committee and the DGS with a brief outline of the student’s 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 the student plans to carry out to address the aims. In essence, the outline should be a running compilation of the student’s dissertation research. 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.

In the event that 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 the meeting. It will be the responsibility of the student to prepare a short report summarizing the meeting. The student will 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 the DGS.


As part of the Ph.D. requirements, a written dissertation describing the student’s research accomplishments must be submitted and defended. Before the student begins to write a formal dissertation document, both the major advisor and the Research Advisory Committee 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 departmental or ITP seminar followed by an oral defense of the dissertation. Students should consult with the DGS at the beginning of the semester in which they plan to defend to schedule their seminar. 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 dissertation advisory committee and the DGS. Each student is required to provide the Department with a final copy of his/her dissertation before the Department will sign off on the necessary paperwork in order for the student to complete his/her degree requirements.


Ph.D. degrees are awarded three times a year, January, May and September. M.A. degrees are awarded three times a year, January, May, and September. It is important that students consult the Graduation Calendar available on the Division of Graduate Medical Sciences website for the timelines for submitting various documents, scheduling of final oral examinations, etc. There are some very specific deadlines, which if missed could delay the final oral examination.


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) 638-8221

Karen Symes, Ph.D., Assistant Dean of Student Affairs (MED) / M, T, Th (617) 638-4077or W, F (617) 638-4196,


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

All BU Faculty, Staff, Students, etc.

Office of the Ombuds  see link

Department of Microbiology: The Departmental Offices are located on the fifth floor of the Center for Advanced Biomedical Research Building, W508/W509. Some faculty offices and laboratories are also located on W5. Additional faculty offices, laboratories, general equipment rooms, and a small conference/lunch room are located on R5 as well as space in the NEIDL.

Departmental Retreat: The department holds an annual retreat each Fall. The retreat features short big picture talks by Microbiology faculty and a guest speaker from outside the department. The retreat also provides an opportunity for graduate students and post-doctoral trainees to present their research as iPoster PowerPoint presentations on laptop computers.

Websites: The address for the Department’s website is Seminar and journal club announcements are posted here. In addition, information on curricula, courses, faculty research interests, and departmental events can be found at this site. The Immunology Training Program has its own website at

E-mail: This is our primary means of communication. Make sure to check your email often.

Mail: All graduate student mail will be sent to their advisor’s laboratory.

Microbiology Conference Room (R504): There is a small conference room located in R504, which is used for lab meetings, student committee meetings, etc. There is a refrigerator and microwave available in this room as well, and again we ask all who use this room to keep it clean. To reserve this room for Committee Meetings, please contact Kathy Marinelli,

Lockers: Lockers are available on R5 and are assigned based on availability. Please contact Kathy Marinelli, to sign up for one.


Graduate Student Representatives: Microbiology graduate students are represented at Microbiology 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 representatives for 2017-2018 are Alexander Barron and Stephanie D’Souza. Stephanie will be rotating off for the 2018-2019 Academic year and a new representative will be elected at the annual fall graduate student meeting.

Primary teaching affiliate
of BU School of Medicine