Skip to toolbar

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.

Related News Articles

Summer Updates from SoMAS Faculty

Above: a close-up photo of a bay scallop (Photo by Chris Paparo). Congratulations to the recent research grants awarded to SoMAS faculty! Dr. Bassem Allam and co-PI Dr. Emmanuelle Pales Espinosa have received an Award from NSF in support of the project "RAPID: A...

Student Research Celebrated at URECA

From URECA’s 2020 Virtual Undergraduate Research Symposium on Stony Brook University News, May 6, 2020. URECA’s Celebration of Undergraduate Research & Creativity is an annual event organized by the URECA Program that showcases undergraduate research and is open...

Celebrating the Top Stories of the Decade

As 2019 draws to a close, so does another decade of Making Scientific Research Count.  The School of Marine and Atmospheric Sciences accomplished much in the years between 2010 and 2019, recording $82 million in research expenditures, and over 1,300 degree...

NY Sea Grant Contributes to Marine Aquaculture Research Projects

Photo above: SBU’s Bassem Allam is the lead PI on a study of hard clams (photo by Bassem Allam); Inset photo: A worker at Norm Bloom & Son Oysters offloads shellfish harvested from the company’s beds in Norwalk, CT (photo by Judy Benson, Connecticut Sea Grant)....

Bassem Allam Invested as Inaugural Marinetics Endowed Professor

Photo above: Bassem Allam was formally invested as the Marinetics Endowed Professor of Marine Science in Stony Brook University’s School of Marine and Atmospheric Sciences (SoMAS) on April 26. From left to right: Bassem Allam, SoMAS Dean’s Council Chair Bob Maze,...

Two SoMAS Teams Awarded Ocean Research Grants to Study Waters off NY

Photo above: New York Bight Whale Monitoring Program. Property of NYSDEC and the aerial survey contractor, Tetra Tech From Two SBU Teams Awarded Ocean Research Grants to Study Waters off NY on Stony Brook News, February 6, 2019. Nearly $570,000 in ocean research...

Retrospective Banquet 2017

Interim Dean Larry Swanson thanks everyone who joined us at our Retrospective Event: This wonderful event brought us all together to reminisce, reflect, and look hopefully to the future." Many thanks to our colleagues who helped put the evening together. They include:...

SoMAS Convocation 2017

Congratulations to our graduates!  The annual SoMAS Convocation occurred on Friday, May 19, 2017 at the Student Activities Center auditorium. Students gathered with their friends and family and SoMAS faculty and staff to celebrate the completion of their journey at...

SoMAS Undergraduates Participate in URECA Festival

The UNDERGRADUATE RESEARCH & CREATIVE ACTIVITIES (URECA) program, founded in 1987, awards research funding and travel grants to undergraduates, and is a central point of contact for students and faculty engaged in research and creative endeavors. URECA helps bring...

Print Friendly, PDF & Email

Subscribe By Email

This form is protected by reCAPTCHA and the Google Privacy Policy and Terms of Service apply.