Recent publications: (since 2016 , complete listing is available here)

Schwaner C, Farhat S, Boutet I, Tanguy A, Barbosa M, Grouzdev D, Pales Espinosa E, Allam B. (2023). Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica). Marine Biotechnology. In Press.

Czaja R, Beal B, Pepperman K, Pales Espinosa E, Munroe D, Cerrato R, Busch E, Allam B. (2023). Interactive roles of temperature and food availability in predicting habitat suitability for marine invertebrates. Estuarine, Coastal and Shelf Science. In Press.

Brianik C, Bouallegui Y, Allam B. (2023). Triploid animals, a potential model for ETosis research: Influence of polyploidy on the formation and efficacy of extracellular traps in the eastern oyster. Fish and Shellfish Immunology. In Press.

Czaja R, Pales Espinosa E, Cerrato R, Lwiza K, Allam B. (2023). Using meta-analysis to explore the roles of global upwelling exposure and experimental design in bivalve responses to low pH. Science of The Total Environment. In Press.

Brianik CJ, Allam B. (2023). The need for more information on the resistance to biological and environmental stressors in triploid oysters. Aquaculture. In Press.

Czaja Jr R, Holmberg R, Pales Espinosa E, Hennen D, Cerrato R, Lwiza K, O’Dwyer J, Beal B, Root K, Zuklie H, Allam, B. (2023). Behavioral and physiological effects of ocean acidification and warming on larvae of a continental shelf bivalve. Marine Pollution Bulletin, 192, 115048.

Brianik CJ, Bopp J, Piechocki C, Liang N, O’Reilly S, Cerrato RM, Allam B. (2023). Infection prevalence, intensity, and gill coverage by the parasitic flatworm, Bdelloura candida, in the American horseshoe crab (Limulus polyphemus). Hydrobiologia 850: 3655-3669.

Pales Espinosa E, Bouallegui Y, Grouzdev D, Brianik C, Czaja R, Geraci-Yee S, Kristmundsson A, Muehl M, Schwaner C, Tettelbach ST, Tobi H, Allam B. (2023). An apicomplexan parasite drives the collapse of the bay scallop population in New York. Scientific Reports, 13(1), 6655. pdf

Tettelbach ST, Czaja R, Tobi H, Hughes S, Peterson BJ, Heck S, MacGregor J, DeLany F, Scannell B, Pales Espinosa E, Allam B. (2023). Collapse of the New York Bay Scallop Fishery Despite Sustained Larval and Juvenile Recruitment. Marine Ecology Progress Series 714, 45-56. pdf

Schwaner C, Barbosa M, Schwemmer T, Pales Espinosa E,  Allam B. (2023). Increased food resources help eastern oyster mitigate the negative impacts of coastal acidification. Invited Research Paper. Animals 13(7): 1161. https://www.mdpi.com/2076-2615/13/7/1161

Schwaner C, Pales Espinosa E,  Allam B. (2023). RNAi silencing of the biomineralization gene Perlucin impairs oyster ability to cope with ocean acidification. International Journal of Molecular Sciences, 24(4), 3661; https://doi.org/10.3390/ijms24043661

Czaja R, Hennen R, Cerrato R, Lwiza K, Pales Espinosa E, O’Dwyer J, Allam B. (2023). Using LASSO regularization to project recruitment under CMIP6 climate scenarios in a coastal fishery with spatial oceanographic gradients. Canadian Journal of Fisheries and Aquatic Sciences. https://doi.org/10.1139/cjfas-2022-0091

Guo X, Puritz J , Wang Z, Proestou D, Allen S, Small J, Verbyla K, Zhao H, Haggard J, Chriss N, Zeng D, Lundgren K, Allam B, et al. (2023). Development and evaluation of high-density SNP arrays for the eastern oyster Crassostrea virginica. Marine Biotechnology. In Press. https://rdcu.be/c24XS

Tomasetti S, Hallinan B, Tettelbach S, Doherty O, Allam B, Gobler C. (2023). Warming and hypoxia reduce performance and survival of northern bay scallops Argopecten irradians irradians amid a fishery collapse. Global Change Biology. Epub ahead of print. doi.org: 10.1111/gcb.16575

Schwaner C, Farhat S, Barbosa M, Boutet I, Tanguy A, Pales Espinosa E, Allam B. (2023). Molecular features associated with resilience to ocean acidification in the northern quahog, Mercenaria mercenaria. Marine Biotechnology. In Press. doi: 10.1007/s10126-022-10183-3. Epub ahead of print. PMID: 36417051.

Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. (2022). Proteomic and transcriptomic responses enable clams to correct the pH of calcifying fluids and sustain biomineralization in acidified environments. International Journal of Molecular Sciences 23, 16066. pdf

Geraci-Yee S, Collier JL, Allam B. (2022). Mucochytrium quahogii (=QPX) Is a Commensal, Opportunistic Pathogen of the Hard Clam (Mercenaria mercenaria): Evidence and Implications for QPX Disease Management. Journal of Fungi 8: 1128. pdf

Geraci-Yee S, Allam B, Collier JL. (2022). A nested, quantitative PCR assay for detection of the hard clam pathogen, Mucochytrium quahogii (=QPX), in environmental samples. Frontiers in Marine Science: 2215. doi: 10.3389/fmars.2022.988918. pdf

Barbosa M, Schwaner C, Pales Espinosa E, Allam B. (2022). A transcriptomic analysis of phenotypic plasticity in Crassostrea virginica larvae under experimental acidification. Genes 22(13): 1529. pdf

Boutet I., Monteiro HJA, Takeuchi T, Baudry L, Bonnivard E, Billoud B, Farhat S, Gonzales-Haraya R, Salaun B, Andersen A, Toullec J-Y, Lallier F, Flot J-F, Guiglielmoni N, Guo X, Cui L, Allam B, Pales-Espinosa E, Hemmer-Hansen J, Marbouty M, Koszul R, & Tanguy A. (2022). Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic ressource for aquaculture. Evolutionary Applications. In Press.

El-Sayed H, Elshobary M, Barakat K, Khairy H, El-Sheikh M, Czaja R, Allam B, Senousy H. (2022). Ocean acidification induced changes in Ulva fasciata biochemistry may improve Dicentrarchus labrax aquaculture via enhanced antimicrobial activity. Aquaculture 560: 738474. https://doi.org/10.1016/j.aquaculture.2022.738474

Pales Espinosa E, Eckstein M, Allam B. (2022). Density of compatible ligands on the surface of food particles modulates sorting efficiency in the blue mussel Mytilus edulis. Frontiers in Marine Sciences 9: 882356. https://doi.org/10.3389/fmars.2022.882356 pdf

Geraci-Yee S, Allam B, Collier J. (2022). Keeping up with advances in qPCR pathogen detection: an example for QPX disease in hard clams. Diseases of Aquatic Organisms 148: 127-144. pdf

Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. (2022). Transcriptomic, proteomic, and functional assays underline the dual role of extrapallial hemocytes in immunity and biomineralization in the hard clam Mercenaria mercenaria. Frontiers in Immunology 13: 838530. doi: 10.3389/fimmu.2022.838530 pdf

Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot J-F, Allam B. (2022). Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. BMC Genomics 23:192. doi: 10.1186/s12864-021-08262-1 pdf

Kim S-H, Nam K-W, Allam B, Choi K-S, Park K-H, Park K-I. (2021). Quantification of the Inflammatory Responses to Pro-and Anti-Inflammatory Agents in Manila clam, Ruditapes philippinarum. Fish & Shellfish Immunology 115: 22-26. pdf

Geraci-Yee S, Brianik CJ, Rubin E, Collier JL, Allam B. (2021). Erection of a New Genus and Species for the Pathogen of Hard Clams ‘Quahog Parasite Unknown’(QPX): Mucochytrium quahogii gen. nov., sp. nov. Protist 172(1): 125793. Open access: https://doi.org/10.1016/j.protis.2021.125793

Pales Espinosa E, Allam B. (2021). High spatial resolution mapping of the mucosal proteome of the gills of Crassostrea virginica: implication in particle processing. Journal of Experimental Biology 224, jeb233361. doi:10.1242/jeb.233361  pdf

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. (2020). Comparative animal mucomics: Inspiration for functional materials from ubiquitous and understudied biopolymers. ACS Biomaterials Science & Engineering 6(10): 5377-5398. pdf

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(6): 4887-4896. pdf

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 87(1): eyaa037. pdf

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. pdf

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

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 pdf

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) pdf

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 pdf

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. pdf

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. pdf

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

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 222: 66-73. pdf

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. pdf

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. 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