Training Program in Pathogenesis & Host—Pathogen Interactions (HPI)

The Microbial Interactions training track includes a literature-based curriculum, prominent guest speakers, and spirited journal clubs, as well as extensive hands-on laboratory training. Small class size and extensive interaction between the various faculty in the basic and clinical sciences allow our students to become familiar with a number of research themes, and our collegial atmosphere and integrative approach to training provide a highly supportive environment for students.

Students may choose any of the faculty within the Department of Microbiology for their research training. Particular areas of expertise within the research community include:

  • Viral molecular biology
  • Viral-host cell interactions
  • Host defense and immune responses to viral and bacterial pathogens
  • Development of diagnostic tools
  • Development of therapeutics
  • Vaccine development

Please see the individual faculty research descriptions for a more complete picture of ongoing research programs.

Learning Outcomes

  • Demonstrate an in-depth and integrated knowledge of molecular virology and/or interactions of pathogens with the host.
  • Demonstrate the ability to perform laboratory research.
  • Demonstrate the ability to critically read and analyze the scientific literature, propose and test a hypothesis, and communicate findings clearly, incorporating them into the existing body of knowledge.


Students enter the HPI Training Program through the Department of Microbiology. Students must apply for admission through the Program in Biomedical Sciences (PiBS), Graduate Medical Sciences of BU Chobanian & Avedisian School of Medicine. Departmental preference should be noted on the application. Application information and forms are available through Graduate Medical Sciences. Any further inquiries can be addressed to the program.

Financial Aid

All trainees receive full stipend, tuition, and health insurance from institutional sources and from faculty research grants. Funding is also available for travel to scientific meetings. The average time for completion of all degree requirements is 5 1/2 years.

Students are also eligible to compete for support from outside sources, such as the National Institutes of Health, the National Science Foundation, and the Howard Hughes Medical Institute. While in graduate school, students are also eligible to apply for internal research and travel awards.


The curriculum for students in HPI offers flexibility in training and is designed with the interests of the student and their prior background and training in mind. Formal coursework emphasizes breadth and depth in various areas of microbiology, immunology, molecular biology, cell biology, and biochemistry. Formal coursework is normally completed within the first two years with the majority usually completed in the first year. Students should consult with the director of graduate students for program-specific coursework.

Seminars and Journal Clubs

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 HPI track are expected to attend and participate in departmental seminars throughout their graduate career.

The Department of Microbiology, National Emerging Infectious Diseases Laboratories (NEIDL), and Immunology Training Program host a combined weekly seminar series. This joint seminar series includes invited speakers from other institutions and is held Wednesdays, 12–1 pm, in the NEIDL first-floor conference room. Following these guest speaker seminars, students may meet with the speakers over lunch to discuss research. Each student is expected to attend at least four lunches over the course the academic year.

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, 12–1 pm, in the NEIDL first-floor conference room. Each student in the HPI track is required to present at least one seminar per year. Alternating with trainee seminars are journal clubs, in which trainees discuss research papers chosen from the current scientific literature.


Teaching is an important training experience for students who plan on an academic career, and the Department of Microbiology encourages students to avail themselves of opportunities to gain teaching experience within GMS.

Qualifying Exam

There are two components of the qualifying examination, both administered by appropriate members of the training faculty. The first preliminary exam has two parts: (1) an editorial on a paper related to their dissertation research and (2) an oral 30-minute presentation in a closed session before members of an ad hoc Qualifying Exam Committee. The paper and presentation are based on one of the rotations carried out, excluding the rotation in the lab of the chosen advisor. PhD students typically take the first preliminary exam at the beginning of the spring semester of their 2nd year. The second preliminary exam has three parts: (1) a short report, (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 usually take the second preliminary exam at the end of the 2nd year.

Laboratory Research

Research is the central part of the graduate student’s training and as such most of the time spent in graduate school is devoted to original laboratory research. This is carried out in the laboratory of a faculty member chosen by the student who serves as the student’s mentor and scientific advisor. A Research Advisory Committee composed of faculty scientists provides additional expertise and guidance to the student. The committee meets regularly with the student to help direct the course of research. Students are expected to publish the results of their original research in refereed scientific journals.

Dissertation—PhD Program

As part of the PhD requirements, a written dissertation describing the student’s research accomplishments must be submitted and defended.