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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 the framework of host-pathogen or predator-prey (filter-feeding) interactions. This includes the mechanisms of resistance to pathogens and the effect of environmental factors (e.g. ocean acidification) on host-pathogen interactions. My current projects encompass animal-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 activities use a diverse range of experimental and technical approaches ranging from ecological physiology, pathology and immunology to modern “omics” (genomics, transcriptomics and proteomics) tools and methods to answer a broad range of basic and applied questions (the publication list below provides a rapid overview of the diversity of our research activities). Current funding in my lab derives from the NSF (mucosal immunity and mechanisms of food particle recognition in suspension-feeding bivalves), NOAA (mechanisms and costs of resilience to ocean acidification in bivalve mollusks, ecological physiology of economically-important bivalve species and adaptation to changing environments, selective breeding), the USDA (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. Please contact Bassem Allam for information about current availabilities.

Recent Seminars

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

Selected Publications (2018-2020, *, ** and *** designate graduate, undergraduate and high school students, respectively. Full list available at:

Farhat S, Tanguy A, Pales Espinosa E, Guo X, Boutet I, Smolowitz R, Murphy D, Rivara G, Allam B. (2020). Identification of variants associated with hard clam, Mercenaria mercenaria, resistance to Quahog Parasite Unknown disease. Genomics 112: 4887-4896.

*Cerullo A, Lai T-Y, Allam B, Baer A, Barnes J, Barrientos Z, Deheyn D, Fudge D, Gould J, Harrington M, Holford M, Hung C-S, Jain G, Mayer G, Medina-Munoz M, Monge J, Napolitano T, Pales Espinosa E, Schmidt S, Thompson E, Braunschweig A. Comparative animal mucomics: Inspiration for functional materials from ubiquitous and understudied biopolymers. ACS Biomaterials Science & Engineering. In Press. DOI: 10.1021/acsbiomaterials.0c00713

***Allam S, Allam B, Pales Espinosa E. (2020). Regulation of mucosal lectins in the oyster Crassostrea virginica in response to food availability and environmental factors. Journal of Molluscan Studies. In Press.

*Zuykov M, Allam B, Gosselin M, Archambault P, Spiers G, Schindler M. (2020). First report of signs of infection by Coccomyxa-like algae in wild blue mussels, Mytilus spp., in the Gulf of Maine (USA, Maine). Journal of Fish Diseases 43: 775-778.

***Allam S, Allam B, Pales Espinosa E. (2020). Regulation of mucosal lectins in the oyster Crassostrea virginica in response to food availability and environmental factors. Journal of Molluscan Studies. In Press.

***Jones J, Allam B, Pales Espinosa E. (2020). Particle selection in suspension-feeding bivalves: Does one model fit all? Biological Bulletin 238: 41-53.

*Schwaner C, *Barbosa M, ***Connors P, Park TJ, *de Silva D, *Griffith A, Gobler CJ, Pales Espinosa E, Allam B. (2020). Experimental acidification increases susceptibility of Mercenaria mercenaria to infection by Vibrio species. Marine Environmental Research 154: 104872

*Barbosa M, *Schwaner C, *Schwemmer T, Pales Espinoa E, Allam B. (2019). Effect of food resource availability on the resilience of eastern oyster larvae to ocean acidification. World Aquaculture 5(30)

Rosani U, Shapiro M, Venier P, Allam B. (2019). A needle in a haystack: Tracing bivalve-associated viruses in high-throughput transcriptomic Data. Viruses 11, 205; doi:10.3390/v11030205

Fernández-Robledo JA, Yadavalli R, Allam B, Pales-Espinosa E, Gerdol M, Greco S, Stevick RJ, Gómez-Chiarri M, Zhang Y, Heil CA, Tracy AN, Bishop-Bailey D, Metzger MJ. (2019). From the raw bar to the bench: Bivalves as models for human health. Developmental and Comparative Immunology 92: 260-282.

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.

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...

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