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Graduate: Microbiology and Immunology

  • Program Overview

    Microbiology and immunology Department

    Graduate study in Molecular Genetics and Microbiology offers a diversified course of study leading to the Ph.D. degree. The major areas of study are the basic mechanisms of viral, bacterial, and fungal pathogenesis, immunology, and cancer biology.

    Studies are directed toward an understanding of cell biology, molecular genetics, immunology, and microbial pathogenesis and are designed to prepare a student to become an effective research scientist.

    Microbiology and Immunology Department

    David Thanassi, Life Sciences Building 280C (631) 632-4549

    Graduate Program Director
    Nicholas (Nick) Carpino, Life Sciences Building 160 (631) 632-4610

    Graduate Program Coordinator
    Jennifer Jokinen, Life Sciences Building 130 (631) 632-8812

    Degree Awarded
    Ph.D. in Microbiology and Immunology

    Web Site


  • Admissions

    Admission Requirements of Microbiology and Immunology 

    Pre-doctoral trainees in Microbiology and Immunology are admitted to the Graduate School of Stony Brook University by application to the Program.

    In addition to the minimum Graduate School requirements, the following elements are considered when making admissions decisions:

    A. Undergraduate performance in science courses.

    B. Three letters of recommendation.

    C. Research Experience

    All students who are accepted into the Microbiology and Immunology Program are accepted with full support. The level of support for 2019 is $29,000 per calendar year plus full tuition scholarship. Health insurance is provided for all students as a fringe benefit.

  • Degree Requirements

    Requirements for the Ph.D. Degree in Microbiology and Immunology

    The predoctoral training program offers its students the opportunity to study questions in virology, bacteriology, mycology, immunology, biochemistry, cancer biology, and cell and developmental biology utilizing the experimental approaches of the molecular biologist and geneticist.

    Instruction and course planning involve faculty members from the Department of Microbiology and Immunology and selected members from the Departments of Biochemistry and Cell Biology, Medicine, Pathology, Physiology and Biophysics, and Pharmacology, and from Cold Spring Harbor Laboratory. The general philosophy of the Program is that a successful research career in the diverse and heterogeneous area of molecular biology requires a broadly-based background, familiarity with at least all of the above areas, and a frame of mind that is receptive to new approaches.

    The Department of Microbiology and Immunology has an active seminar program of outside speakers who present topics relevant to Microbiology and Immunology, and there is a yearly retreat in which ongoing research in the Department and recent progress in the field are presented and discussed. This retreat is held early in the fall in order to introduce new students to the faculty, to other students, and to the areas of ongoing research within the Department. The Department also presents a colloquium periodically on human diseases, with outstanding scientists from throughout the world presenting their current work on the selected topic. Students in the program are encouraged to attend all of these programs as part of their training.

    In addition to the minimum requirements of the Graduate School, the following are required:

    A. Course Requirements

    It is the policy of the Department of Microbiology and Immunology that a student must obtain a grade of B or higher in each course. The decision to have students who receive a final grade below 3.0 re-take a course will be made by the Program’s Executive Committee on a case-by- case basis.

    First Year

    MCB 520 Graduate Biochemistry I

    HBM 503 Molecular Genetics  

    HBM 509 Experimental Microbiology and Immunology (laboratory rotations)*

    HBM 696 Professional Development


    HBM 522 Biology of Cancer

    MCB 656 Cell Biology

    HBM 510 Experimental Microbiology and Immunology (laboratory rotations)*

    HBM 692 Experimental Methods in Microbiology and Immunology

    HBM 696 Professional Development

    *Students rotate through three different laboratories over the course of their first year. At the end of that year, students must identify and enter the laboratory in which they will conduct their graduate and dissertation research.

    HBM 800 Full-time Summer Research

    Second Year


    HBM 640 Molecular Mechanisms of Microbial Pathogenesis

    HBP 533 Immunology

    HBM 599 Graduate Research

    HBM 691 Readings in Microbiology and Immunology Literature

    HBM 696 Professional Development


    HBM 599 Graduate Research

    HBM 693 Research Proposal Preparation in Microbiology and Immunology

    HBM 696 Professional Development

    HBM 800 Full-time Summer Research

    Third Year Until Completion
    Students register for HBM 599 Graduate Research every fall and spring semester until they advance to candidacy at which time they register for HBM 699 Dissertation Research every fall and spring semester. Students registers for HBM 800 Full-time Summer Research every summer until graduation.

    B. Qualifying Exam
    After the successful completion of all required courses, the student must write and defend a research proposal in an area distinct from his/her graduate research for the qualifying exam.

    C. Dissertation Proposal Exam
    Within 10 months of passing the qualifying exam, each student submits a written proposal of his or her dissertation research (similar to an NIH grant proposal) and orally defends the proposal before his or her dissertation committee shortly thereafter.

    D. Advancement to Candidacy
    After successfully completing all required and elective courses, the qualifying exam, and the dissertation proposal exam, the student will be recommended to the Graduate School for advancement to candidacy.

    E. Attendance and Participation in Student Seminar
    Students are expected to participate actively in the departmental seminar series. Students who perform their graduate and dissertation research off-campus are expected to participate in a similar seminar series at their off-campus location.

    F. Ph.D. Dissertation
    The research for the Ph.D. dissertation is conducted under the supervision of the dissertation committee, which is appointed by the Program and approved by the Dean of the Graduate School. A formal public oral defense of the dissertation is scheduled, at which the student presents his or her research and is questioned by members of the dissertation committee and other members of the audience. A closed oral examination before the dissertation committee follows the seminar.

    G. Teaching Practicum
    It is expected that each graduate student completing a doctoral degree will have functioned as a teaching assistant during at least one semester of his or her graduate studies.

    H. Publication Requirement
    All students must be the first author of at least one publication of original research in order to graduate.  Students may schedule the dissertation defense, with the approval of the dissertation advisor and advisory committee, once the first-author manuscript has been submitted for publication.

  • Facilities

    Facilities of Microbiology and Immunology Department

    The Department of Microbiology and Immunologhy occupies the second floor of the Life Sciences Building as well as space on the lower level, first and third floors of the Life Sciences Building. Program faculty members’ laboratories are also located on the first, second and third floors of the Centers for Molecular Medicine (CMM) and within other departments at Stony Brook University and Cold Spring Harbor Laboratory. Approximately 47,000 square feet of research space are available within the Department of Microbiology and Immunology. Each research laboratory is fully equipped, and, in addition, the Department provides access to a variety of communal central facilities and services. These include a flow cytometry facility, glassware washing and sterilization facility, analytical equipment lab, deconvolution microscopy facility, environmental rooms, and darkrooms. Major items of equipment are organized into these central facilities, which are readily available to trainees. The Centers for Molecular Medicine, a state-of-the-art research and teaching facility, serves as a physical and intellectual bridge between investigators in the adjacent Life Sciences Building and the nearby University Health Sciences Center. The Health Sciences Library and Barry S. Coller Learning Center, located in the Health Sciences Center, contains collections of biological and medical books and journals presently totaling 262,000 volumes, including more than 3,200 journal titles. In addition, the Health Sciences Library provides access to more than 2,300 full-text electronic journals. Other campus libraries include the Frank Melville, Jr. Memorial Library

  • Faculty

    Faculty of the Department of Microbiology and Immunology

    Toll Distinguished Professors

    Benach, Jorge, Ph.D., 1971, Rutgers University: Pathogenesis of spirochetal infections and their host responses.

    Distinguished Professors

    Wimmer, Eckard, Ph.D., 1962, University of Gottingen, Germany: The molecular biology of poliovirus replication and the molecular basis of picornaviral pathogenesis.


    Bliska, James B., Ph.D., 1987, University of California, Berkeley: Molecular and cellular basis of bacterial-host interactions.

    Carter, Carol A., Ph.D., 1972, Yale University: HIV and retroviral assembly and replication.

    Del Poeta, Maurizio, M.D., 1992, University of Ancona, Italy: Role of sphingolipids in mediating signaling pathways and fungal pathogenesis.

    Fries, Bettina1, M.D., 1991, Albert Ludwig Universitaet Freiburg, Germany: Staphylococcal enterotoxin B; Cryptococcal neoformans pathogenesis

    Futcher, Bruce, D.Phil., 1981, University of Oxford, England: Control of cell division in eukaryotic cells.

    Hayman, Michael J., Ph.D., 1973, National Institute for Medical Research, England: Mechanism of transformation by retroviral oncogenes; erythroid differentiation.

    Hearing, Patrick, Ph.D., 1980, Northwestern University: Viral molecular genetics; eukaryotic transcriptional regulation; gene therapy.

    Konopka, James B., Ph.D., 1985, University of California, Los Angeles: G-protein coupled receptor signal transduction; fungal pathogenesis (Candida albicans).

    Mackow, Erich R., Ph.D., 1984, Temple University: Rotavirus and hantavirus pathogenesis.

    Marshall, Nancy Reich, Ph.D., 1983, University at Stony Brook: Signaling switches in gene expression by hormones or viral infection.

    Thanassi, David, Ph.D., 1995, University of California, Berkeley: Secretion of virulence factors by bacterial pathogens; pilus biogenesis by uropathogenic E. coli.

    Associate Professors

    Bhaduri-McIntosh, Sumita, M.D., Ph.D., 1991, Byramjee Jeejeebhoy Medical College; Epstein-Barr virus-host interactions.

    Carpino, Nicholas, Ph.D., 1997, University at Stony Brook; Positive and negative regulation of T cell receptor signaling.

    Karzai, Wali4, Ph.D., 1995, Johns Hopkins University: Structure and function of RNA-binding proteins and biochemical studies of the SmpBSsrA quality control system.

    Krug, Laurie, Ph.D., 2001, Emory University: Virus-host interactions during chronic gammaherpesvirus infection.

    Leatherwood, Janet, Ph.D., 1993, The Johns Hopkins University: Cell cycle control of DNA replication.

    van der Velden, Adrianus, Ph.D., 2000, Oregon Health and Science University: Salmonella pathogenesis.

    Assistant Professors

    Kim, Hwan, PhD, 2011, University of Chicago; Pathogenesis of diseases caused by Rickettsia species

    Kumar, Pawan, DVM, PhD, 2009, University of Southampton, UK; Immunology and intestinal microbiota

    Seeliger, Jessica5, Ph.D., Stanford University; Membrane biosynthesis, structure and behavior in bacterial pathogenesis

    Sheridan, Brian, Ph.D., 2008, University of Pittsburgh; Mucosal immunity to microbial pathogen

    Salamango, Daniel, PhD, 2015, University of Missouri; HIV replication, regulation of cellular antiviral responses.


    Adjunct Faculty

    Stillman, Bruce W., Professor.6 Ph.D., 1979, Australian National University: Mechanism of eukaryotic DNA replication.

    Research Faculty

    Boon, Elizabeth, Associate Professor.7 Ph.D., 2002, California Institute of Technology: Biofilms.

    Hannun, Yusuf, Professor.8 M.D. American University in Beirut, Lebanon, 1983: lipid mediators of cancer cell signaling.

    Kew, Richard, Associate Professor.9 Ph.D., 1986, Stony Brook University: Leukocyte chemotaxis; inflammation; pulmonary immunopathology.

    Krainer, Adrian, Professor.6 Ph.D., 1986, Harvard University: Posttranscriptional control of gene expression; alternative splicing; splicing in genetic diseases and cancer; antisense therapeutics.

    London, Erwin, Professor.10 Ph.D., 1979, Cornell University: Membrane protein folding and lipid interaction.

    Moll, Ute, Professor.9 M.D., 1985, University of Ulm: Tumor suppressor genes; role of p53 in human cancer.

    Neiman, Aaron, Professor.10 Ph.D., 1994, University of California, San Francisco: Vesicle trafficking and intracellular signaling in yeast.

    Obeid, Lina, Professor.8, M.D., 1983, American University in Beirut, Lebanon: signaling lipids in cell stress and disease.

    Tonge, Peter J., Professor.7 Ph.D., 1986, University of Birmingham: Enzyme mechanisms and rational drug design.

    Vakoc, Christopher, Assistant Professor.6 M.D., Ph.D., 2007, University of Pennsylvania: chromatin regulators and oncogenic signal transduction cascades.

    Wigler, Michael, Professor.6 Ph.D., 1978, Columbia University: Signal transduction and growth control in eukaryotes.


    Number of teaching, graduate, and research assistants, fall 2019: 26


    • Joint appointment, Department of Medicine
    • Joint appointment, Department of Pathology
    • Joint appointment, Department of Pediatrics
    • Joint appointment, Department of Biochemistry and Cell Biology
    • Joint appointment, Department of Pharmacological Sciences
    • Cold Spring Harbor Laboratory
    • Department of Chemistry


  • Contact

    Microbiology and Immunology Department

    David Thanassi, Life Sciences Building 280C (631) 632-4549

    Graduate Program Director
    Nicholas (Nick) Carpino, Life Sciences Building 160 (631) 632-4610

    Graduate Program Coordinator
    Jennifer Jokinen, Life Sciences Building 130 (631) 632-8812

    Degree Awarded
    Ph.D. in Microbiology and Immunology

    Web Site