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The Department of Cell Biology is a multidisciplinary basic science department in the College of Medicine with a diverse research portfolio that emphasizes the mechanisms of gene expression in health and disease, particularly with respect to lipid metabolism, the cardiovascular system, microbiology, immunology, organ system development. Other areas of research include the anatomy of human evolution and medical education. Faculty are responsible for delivering pre-clinical (Foundation) years training in the COM, most notably Gross Anatomy, Histology, and Neuroanatomy labs, via lectures, and facilitating small group discussions.

Originally established as a traditional Department of Anatomy as part of the Long Island College of Medicine, the department was transferred to the new Downstate Medical Center in central Brooklyn in the mid-50s under the aegis of the State University of New York. The first chairman, James B. Hamilton, assembled a group of young anatomists, biochemists, electron microscopists and neuroanatomists to staff its curriculum in classical gross, microscopic, developmental and neural anatomy. The diverse background and training of the faculty favored the formation of a thriving and well-funded research and graduate training program with an overall emphasis on ageing and human genetics. The next chairman, Donald A. Fishman, recruited from the University of Chicago in the mid-70s, developed an EM facility and transformed the department into a Department of Anatomy and Cell Biology in keeping with the changes in teaching and research. In the late 1980s Dr. M.A.Q. Siddiqui, an expert in biochemistry and the cellular and molecular biology of the cardiovascular system, was appointed department Chair. He recruited new faculty members with expertise in different aspects of organ development, particularly cardiovascular disease, and lipid and glucose metabolism. He oversaw the merger of Anatomy and Cell Biology with the Department of Microbiology and Immunology and the addition of some faculty from the Department of Biochemistry in 2010. These changes expanded the size and scope of the department to include researchers focused on molecular biology of protein synthesis and viral gene expression, the immune response and autoimmune disease, schistosomiasis, and cancer. Research expertise was later added in ear, eye, and skin. Dr. Christopher Roman, originally part of Microbiology and Immunology, became interim Chair in 2013 after Dr. Siddiqui retired.

The Department presently occupies approximately 16,000 square feet of research and teaching space. Departmental resources include shared instruments and equipment such as confocal and conventional fluorescence microscopy, flow cytometry and cell sorting, fluorescent gel imaging, and qPCR, in addition to many common instruments, equipment and facilities, such as scintillation counters, ultracentrifuges, spectrophotometers, biosafety hoods, autoclaves and a glassware washer, dark rooms, and cold and warm rooms. The Department also sponsors the Stephen I. Morse Seminar Series that includes the Lipid Club, and a robust student achievement award program.