Bassem Allam

bassem1School of Marine and Atmospheric Sciences

Stony Brook University
NY 11794-5000,  USA
Phone: +1 (631) 632 8745
Fax: +1 (631) 632 8915


Dr Allam also holds a Courtesy Faculty appointment at Cornell University’s College of Veterinary Medicine

Main research interests:

  • Pathology and immunology of marine invertebrates
  • Early interactions at water-tissue interfaces between suspension feeding bivalves and waterborne microbes (tissue colonization by microbes, particle sorting in suspension-feeders)
  • Marine genomics

Current research projects can be accessed here.

Recent publications: (since 2012 , complete listing is available here)

Bassim S, Allam B. SNP hot-spots in the clam parasite QPX. BMC Genomics. Submitted.

Bassim S, Pales Espinosa E, Allam B. Network analysis of dual RNA-Seq reveals a repertoire of virulence and survival mechanisms in the clam parasite QPX. BMC Genomics. Submitted.

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. pdf

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. In Press.

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. In Press.

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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. pdf

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

Rosa M, Ward JE, Ouvrard M, Pales Espinosa E, Shumway SE, Allam B. (2015). Examining the physiological plasticity of particle capture by the blue mussel, Mytilus edulis (L.): Confounding factors and potential artifacts with studies utilizing natural seston. Journal of Experimental Marine Biology and Ecology 473: 207-217. pdf

Allam B, Raftos D. (2015). Immune responses to infectious diseases in bivalves. Journal of Invertebrate Pathology 131: 121-136. (review paper that is part of a special issue of JIP on mollusk diseases). pdf

Mars M, McElroy A, Pales Espinosa E, Allam B. (2015). Antimicrobial activity in the cuticle of the American lobster, Homarus americanus. Fish and Shellfish Immunology 44: 542-546. pdf.

Allam B, Pales Espinosa E. (2015). Mucosal immunity in mollusks. Book chapter In: Mucosal Health in Aquaculture. Benjamin Beck and Eric Peatman (Eds). Academic Press. pp. 325-370. ISBN: 978-0-12-417186-2.

Rubin E, Pales Espinosa E, Koller A, Allam B (2015). Characterization of the secretome of the clam parasite QPX. International Journal for Parasitology 45: 187-196. pdf

Allam B, Tanguy A, Jeffroy F, Le Bris C, Pales Espinosa E, Paillard C. (2014). Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to brown ring disease. Fish and Shellfish Immunology 41(1): 2-11. pdf

Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, et al. (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biology, 12(6), e1001889. pdf

Pales Espinosa E., Corre E, Allam B. (2014). Pallial mucus of Crassostrea virginica regulates the expression of putative virulence genes of its pathogen Perkinsus marinus. International Journal for Parasitology 44: 305-317. pdf

Rubin E, Tanguy A, Perrigault M, Pales Espinosa E, Allam B. (2014). Characterization of the transcriptome and temperature-induced differential gene expression of in quahog parasite unknown QPX, the thraustochytrid parasite of hard clams. BMC Genomics 15: 245. pdf

Pales Espinosa E, Boutet I, Le Panze S, Allam B, Tanguy A. (2013). Endobacteria in Loripes lacteus: Characterization, localization and some aspect of host-symbiont regulation. Journal of Experimental Marine Biology and Ecology 448: 327-336. pdf

Levinton J, Doall M, Allam B. (2013). The two-year eastern oyster mortality syndrome in impacted waters. Journal of Shellfish Research 32(2): 417-427. pdf

Rosa M, Ward JE, Shumway SE, Wikfors GH, Pales Espinosa E, Allam B. (2013). Effects of Particle Surface Properties on Feeding Selectivity in the Eastern oyster Crassostrea virginica and the Blue mussel Mytilus edulis. Journal of Experimental Marine Biology and Ecology 446: 320-327. pdf

Pales Espinosa E., Winnicki S, Allam B. (2013). Early host-pathogen interactions in marine bivalves: Pallial mucus of Crassostrea virginica modulates the growth and virulence of its pathogen Perkinsus marinus. Diseases of Aquatic Organisms 104: 237-247. pdf

Pales Espinosa E., Allam B. (2013). Food quality and season affect the expression of the mucosal lectin MeML and food sorting abilities in the blue mussel Mytilus edulis. Marine Biology 160(6): 1441-1450. pdf

Allam B, Carden WE, Ward JE, Ralph G, Winnicki S, Pales Espinosa E. (2013). Early host-pathogen interactions in marine bivalves: Evidence that the alveolate parasite Perkinsus marinus infects through the oyster mantle during rejection of pseudofeces. Journal of Invertebrate Pathology 113: 26-34. pdf

Perrigault M., Dahl S.F., Pales-Espinosa E., Allam B. (2012). Effects of salinity on hard clam (Mercenaria mercenaria) defense parameters and QPX disease dynamics. Journal of Invertebrate Pathology 110(1): 73-82. pdf

Perrigault M, Allam B. (2012). Differential immune response in the hard clam (Mercenaria mercenaria) against bacteria and the protistan QPX (Quahog Parasite Unknown). Fish and Shellfish Immunology 32(6): 1124-1134. pdf

Homerding M, McElroy A, Taylor G, Dove A, Allam B. (2012). Investigation of epizootic shell disease in American lobsters (Homarus americanus) from Long Island Sound: II. Immune parameters in lobsters and relationships to the disease. Journal of Shellfish Research 31(2):495-504. pdf

Bell SL, Allam B., McElroy A, Dove A, Taylor GT. (2012). Investigation of epizootic shell disease in American lobsters (Homarus americanus) from Long Island Sound: I. Characterization of associated microbial communities. Journal of Shellfish Research 31(2):473-484. pdf

Sokolowski M, Allam B, Dunton K, Clark M, Kurtz E, Fast M. (2012). Spatio-temporal differences in immunophysiology of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus (Mitchill), and the relationship to parasitic copepod, Dichelesthium oblongum, (Abilgaard) infection. Journal of Fish Diseases 35(9): 649-660. pdf