Bassem Allam

AllamMarinetics Endowed Professor

Ph.D. 1998, European Institute of Marine Sciences,
University of Western Brittany, Brest, France

Marine invertebrate physiology and health, Shellfish Genomics, Aquaculture

Dr. Allam’s web page



Research Interests

My research focuses on interactions between benthic invertebrates and waterborne microbes in general and in the framework of host-pathogen interactions in particular. This includes the mechanisms of resistance to pathogens (i.e. immunity) and the effect of environmental factors on host-pathogen interactions. My current projects encompass host/microbe interactions at molecular, cellular and organismal scales, and my approach to addressing these issues involves field studies and laboratory experiments. Because of the specific service responsibilities of our laboratory (reference lab for shellfish diseases in New York State), my research also includes a strong applied component aimed at enhancing knowledge and development of mitigation strategies for diseases affecting local shellfish species. Taken together, our research activities use a diverse range of experimental and technical approaches ranging from ecological physiology and traditional pathobiology and immunology to modern “omics” (genomics, transcriptomics and proteomics) tools and methods. Current funding of our activities derives from the National Science Foundation (mucosal immunity and mechanisms of food particle recognition in suspension-feeding bivalves), the National Oceanic and Atmospheric Administration (mechanisms and costs of resilience to ocean acidification in bivalve mollusks, ecological physiology of economically-important bivalve species and adaptation to changing environments), the United States Department of Agriculture (genetic markers -e.g. SNPs- associated with disease resistance and development of marker-assisted selection for disease resistance in bivalves) and the New York State Department of Environmental Conservation (biosecurity, shellfish restoration, marine diseases and human health). For more information about these projects and other activities, please visit:

Note to Prospective Students

There are often openings for different types of positions ranging from post-doctoral positions to high school internships. We expect to hire 2 graduate students in fall 2019 to work on shellfish physiology and genomics. Please contact Bassem Allam for more information.

Recent Seminars

NECAN Industry Webinar: Climate Change Impacts on the Health of Commercially Important Species (YouTube)

Selected Publications (2016-2018, * and ** designate graduate and undergraduate students, respectively. Full list available at:

Bassim S, Allam B. (2018). SNP hot-spots in the clam parasite QPX. BMC Genomics 19: 486.

Pales Espinosa E, Allam B. (2018). Reverse genetics demonstrate the role of mucosal C-type lectins in food particle selection in the oyster Crassostrea virginica. Journal of Experimental Biology.

*Lau Y-T, **Santos B, **Barbosa M, Pales Espinosa E, Allam B. (2018). Regulation of apoptosis-related genes during interactions between oyster hemocytes and the alveolate parasite Perkinsus marinus.  Fish and Shellfish Immunology 83: 180-189.

*Hartman R, Pales Espinosa E, Allam B. (2018). Identification of clam plasma proteins that bind its pathogen Quahog Parasite Unknown. Fish and Shellfish Immunology 77: 214-221.

*Hornstein J, Pales Espinosa E, Cerrato R, Lwiza K, Allam B. (2018). The influence of temperature stress on the physiology of the Atlantic surfclam, Spisula solidissima. Comparative Biochemistry and Physiology Part A 222: 66-73.

*Lau Y-T, **Gambino L, **Santos B, Pales Espinosa E, Allam B. (2018). Regulation of oyster (Crassostrea virginica) hemocyte motility by the intracellular parasite Perkinsus marinus: A possible mechanism for host infection. Fish and Shellfish Immunology 78: 18-25.

*Lau Y-T, **Gambino L, **Santos B, Pales Espinosa E, Allam B. (2018). Transepithelial migration of mucosal hemocytes in Crassostrea virginica and potential role in Perkinsus marinus pathogenesis. Journal of Invertebrate Pathology 153:122-129.

*Lau Y-T, *Sussman L, Pales Espinosa E, Katalai S, Allam B. (2017). Characterization of hemocytes from different body fluids of the eastern oyster Crassostrea virginica. Fish and Shellfish Immunology 71: 372-379.

*Rubin E, Tanguy A, Pales Espinosa E, Allam B. (2017). Differential gene expression in five isolates of the clam pathogen, quahog parasite unknown (QPX). Journal of Eukaryotic Microbiology 64: 647-654.

*Liu Q, Collier JL, Allam B. (2017). Seasonality of QPX disease in the Raritan Bay (NY) wild hard clam (Mercenaria mercenaria) population. Aquaculture Research 48: 1269-1278.

*Rubin E, *Werneburg GT, Pales Espinosa E, Thanassi DG, Allam B. (2016). Identification and characterization of peptidases secreted by quahog parasite unknown (QPX), the protistan parasite of hard clams. Diseases of Aquatic Organisms 122: 21-33.

*Wang K, Pales Espinosa E, Allam B. (2016). Effect of “heat shock” treatments on QPX disease and stress response in the hard clam, Mercenaria mercenaria. Journal of Invertebrate Pathology 138: 39-49.

Allam B, Pales Espinosa E. (2016). Bivalve immunity and response to infections: Are we looking at the right place? Fish and Shellfish Immunology, 53: 4-12.

*Wang K, Del Castillo C, Corre E, Pales Espinosa E, Allam B. (2016). Clam focal and systemic immune responses to QPX by RNA-Seq technology. BMC Genomics, 17:146.

Pales Espinosa E, Cerrato R, Wikfors G, Allam B. (2016). Modeling food choice in the two suspension-feeding bivalves, Crassostrea virginica and Mytilus edulis. Marine Biology, 163(2): 1-13.

*Wang K, Pales Espinosa E, Tanguy A, Allam B. (2016). Alterations of the immune transcriptome in resistant and susceptible hard clams (Mercenaria mercenaria) in response to Quahog Parasite Unknown (QPX) and temperature. Fish and Shellfish Immunology 49: 163-176.

Pales Espinosa E, Koller A, Allam B. (2016). Proteomic characterization of mucosal secretions in the eastern oyster, Crassostrea virginica. Journal of Proteomics 132: 63-76.

*Dahl S, Allam B. (2016). Clam transplant as a mitigation strategy for QPX disease in Mercenaria mercenaria. Aquaculture Research  47: 3445-1454.

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Joyce Lau (BS, 2006)

“Being in Stony Brook University gave me the opportunity to experience what it means to be a marine biologist and I am thankful I have been a part of MSRC. The Marine Sciences Research Center is full of faculty who are supportive and always willing to help. I will always remember as I was applying to graduate school, all the faculty who were willing to talk to me and give me advice even though I was never one of their students and they were not my assigned advisors. Having had a mentor like Bassem Allam has really helped me become who I am today. He was supportive, helpful, and taught me how to become a better scientist. With him as my mentor, I was able to do a URECA summer project, present a poster at the URECA poster presentation event, as well as learn numerous lab skills. As I continue my studies in marine science, I can only hope that one day I will become a professor who like Mary Scranton, is always willing to take time out to advise students, who like Bassem Allam, inspires students to pursue marine science and instills confidence in students to think for themselves, and like all the faculty at marine science, who always keep an open door and a willingness to help every student.”

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