About

Bassem Allam is the Marinetics Endowed Professor in the Office of the Dean at Stony Brook University, affiliated with the School of Marine and Atmospheric Sciences. His research focuses on interactions between benthic invertebrates and waterborne microbes, particularly within the framework of host-pathogen and predator-prey (filter-feeding) interactions. His work includes studying mechanisms of resistance to pathogens and examining the effects of environmental factors such as ocean acidification on host-pathogen interactions. His current projects involve animal-microbe interactions at molecular, cellular, and organismal levels, utilizing both field studies and laboratory experiments. As part of his research activities, he serves as a reference laboratory for shellfish diseases in New York State, which adds an applied component aimed at developing mitigation strategies for diseases affecting local shellfish species. His research employs a diverse array of approaches, including ecological physiology, pathology, immunology, and modern 'omics' tools such as genomics, transcriptomics, and proteomics. His work is funded by agencies such as the NSF, NOAA, USDA, and the New York State Department of Environmental Conservation, supporting projects on mucosal immunity, resilience to ocean acidification, genetic markers for disease resistance, biosecurity, shellfish restoration, and marine diseases. He holds a PhD from the University of Brittany, obtained in 1998.

Research topics

• Biology
• Ecology
• Oceanography
• Environmental science
• Geology
• Computer Science
• Evolutionary biology
• Fishery
• Computational biology
• Chemistry
• Genetics
• Physics
• Zoology
• Environmental chemistry
• Nanotechnology
• Materials science
• Microbiology

Selected publications

• Effect of host background and environmental conditions on disease susceptibility and mortality in the northern bay scallop, Argopecten irradians irradians

  Scientific Reports · 2026-05-05

  articleOpen access1st authorCorresponding

  Since 2019, outbreaks of an apicomplexan parasite caused catastrophic mortalities of adult northern bay scallops (Argopecten irradians irradians) in New York, USA. Anecdotal observations suggested different levels of mortality between different scallop stocks and mortality outbreaks appeared to occur in years displaying positive temperature anomalies. In this study, field and laboratory experiments were designed to evaluate the effect of environmental conditions and host (scallop) background on disease susceptibility and mortality. Wild and aquacultured scallops originally sourced from the same area were deployed in lantern nets (suspended in the water column) or oyster culture bags (on bottom) at two different enzootic sites showing contrasting environmental conditions. Subsets of wild and aquacultured stocks were also used in laboratory experiments exposing scallops to different temperatures and dissolved oxygen levels, mimicking different environmental scenarios. Results showed higher mortality in aquacultured scallops compared to wild scallops, especially in the more stressful conditions. Laboratory experiments showed that the trajectories of disease development and mortality were significantly affected by initial disease levels and environmental factors. For instance, high temperature and low dissolved oxygen were shown to favor disease development when initial disease levels were low (wild scallops) but also appear to lead to an overall reduction in disease via culling of the most heavily infected scallops when initial disease levels and mortality during the experiment were high (aquacultured scallops). Altogether, these findings underline the impact of environmental conditions, in particular temperature, on host-parasite interactions and suggest the potential existence of more resilient scallop stocks.

  PublisherDOI

• Transcriptomic characterization of mucosal hemocytes in the eastern oyster (Crassostrea virginica) underlines their potential role as immune sentinels

  Frontiers in Immunology · 2026-03-30

  articleOpen accessSenior author

  Substantial progress has been made in understanding hemocytes within the hemolymph (herein referred to as circulatory hemocytes), which are essential for immune defense and various physiological functions in bivalve mollusks. Yet, our knowledge of peripheral immunity, particularly the role of hemocytes associated with mucosal surfaces covering pallial (gills, mantle) organs (herein referred to as mucosal hemocytes), remains limited. While mucosal and circulatory hemocytes share similar morphologies, they exhibit distinct functional profiles and cell surface epitopes. The molecular mechanisms underlying these functional differences remain poorly understood. To address this knowledge gap, we characterized gene expression profiles (using RNA sequencing) in granulocytes and agranulocytes isolated via flow cytometry from hemolymph and mucus covering pallial tissues of the eastern oyster, Crassostrea virginica . Mucosal hemocytes showed overexpression of genes related to cell motility, cytokine activity, signaling, and cell adhesion, supporting the hypothesis that they may have sentinel functions. Despite a consistent dichotomy in gene expression between granulocytes and agranulocytes across both body fluids, it was more pronounced in circulatory hemocytes. Circulatory granulocytes showed functions linked to phagocytosis and pathogen killing, whereas circulatory agranulocytes overexpressed genes associated with mitosis and early inflammation compared to their mucosal counterparts. To our knowledge, this is the first study combining flow cytometry sorting and transcriptomic methods to characterize hemocytes from different body fluids in a marine invertebrate. Results underline the potential role of mucosal hemocytes as immune sentinels, although more studies, possibly using single-cell transcriptomic methods and functional assays associated with pathogen challenge experiments, are needed to probe their specific functions.

  PublisherOA PDFDOI

• Genome annotation and phylogenomic dataset for Margolisiella madlensis 23004-MA1

  Figshare · 2026-05-22

  datasetOpen accessSenior author

  This dataset contains derived genome annotation, functional annotation, repeat annotation, BUSCO completeness summaries, and phylogenomic analysis files generated for the draft nuclear genome assembly of<i> Margolisiella madlensis</i> 23004-MA1, an apicomplexan parasite infecting the bay scallop <i>Argopecten irradians</i>. The dataset accompanies the genome descriptor reporting the first draft nuclear genome assembly for the apicomplexan class Marosporida. The M. madlensis assembly comprises 41 Mb distributed across 6,697 scaffolds, with a GC content of 33.7%. Structural annotation identified 11,867 protein-coding genes, 14,385 protein-coding transcripts, 100 tRNA genes, and 6 rRNA genes. Files included in this dataset provide derived outputs used for genome characterization and reuse, including structural annotation files, predicted protein and coding sequences, InterProScan and eggNOG-mapper functional annotation results, RepeatMasker outputs, and phylogenomic files used to place <i>M. madlensis </i>within the broader apicomplexan/alveolate phylogenomic framework. The raw sequencing data and genome assembly <i>of M. madlensis </i>have been deposited at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA1404218

  PublisherDOI

• Genome annotation and phylogenomic dataset for Margolisiella madlensis 23004-MA1

  Figshare · 2026-05-22

  datasetOpen accessSenior author

  This dataset contains derived genome annotation, functional annotation, repeat annotation, BUSCO completeness summaries, and phylogenomic analysis files generated for the draft nuclear genome assembly of<i> Margolisiella madlensis</i> 23004-MA1, an apicomplexan parasite infecting the bay scallop <i>Argopecten irradians</i>. The dataset accompanies the genome descriptor reporting the first draft nuclear genome assembly for the apicomplexan class Marosporida. The M. madlensis assembly comprises 41 Mb distributed across 6,697 scaffolds, with a GC content of 33.7%. Structural annotation identified 11,867 protein-coding genes, 14,385 protein-coding transcripts, 100 tRNA genes, and 6 rRNA genes. Files included in this dataset provide derived outputs used for genome characterization and reuse, including structural annotation files, predicted protein and coding sequences, InterProScan and eggNOG-mapper functional annotation results, RepeatMasker outputs, and phylogenomic files used to place <i>M. madlensis </i>within the broader apicomplexan/alveolate phylogenomic framework. The raw sequencing data and genome assembly <i>of M. madlensis </i>have been deposited at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA1404218

  PublisherDOI

• Referee report. For: The genome sequence of the Pacific oyster, Magallana gigas (Thunberg, 1793) [version 2; peer review: 2 approved, 1 approved with reservations]

  Faculty of 1000 Research Ltd · 2025-01-01

  peer-reviewOpen access1st authorCorresponding
  PublisherDOI

• Genome-wide association mapping for heat shock tolerance in Mercenaria mercenaria through SNP microarray analysis

  BMC Genomics · 2025-05-30 · 2 citations

  articleOpen accessSenior author

  Abstract Background The northern quahog Mercenaria mercenaria is a major aquaculture species on the US East Coast, and heat resistance is the most sought trait for aquaculture. This study aimed to establish a genome-wide association for heat tolerance using a 66K SNP array for M. mercenaria . Quahogs from three farms were combined for a heat challenge at 1 °C per day from 24 °C to 35 °C and stay for two days (Phase I), decreasing to 27 °C in 24 h, to 24 °C in another 24 h, and maintaining at 24 °C (Phase II) until no one dead within 48 h at 24 °C (Phase III). Dead and live quahogs were sampled for genotyping using the SNP array. Results During the heat challenge, different mortalities among the quahogs from the three farms were identified at 38, 46, and 55% at Phase I, and 36, 30, and 29% at Phase II. For the survivors (Phase III), no changes were found in body weight before and after the heat shock challenges ( p &lt; 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with quahog survival under heat stress across the different farms. The heritability of the heat tolerance was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait on chromosome 7 ( p = 1.98 × 10 − 5 ). More significant SNPs ( p &lt; 10 − 3.5 ) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11 , and some genes found within 50 K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 ( TLRs 4 and TLRs 6 ), uracil-DNA glycosylase , and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 ( ADAMT s). Conclusion The fastStructure analysis revealed the proportions of different ancestral components within the quahogs from different farming stocks, highlighting that the genetic factors may contribute to their varying survival rates under heat stress. The associated genes have potential roles in immune response, cellular stress, and tissue repair. The findings highlighted the power of high-throughput approaches for the identification of superior quahog genotypes for further breeding.

  PublisherOA PDFDOI

• Survival of the fittest: genomic investigations of the bay scallop reveal a shift in population structure through a summer mortality event

  BMC Genomics · 2025-02-15

  articleOpen accessSenior author

  BACKGROUND: Understanding the genetic basis of resilience in marine organisms is critical for conservation and management, particularly in the face of escalating environmental stress and disease outbreaks. The bay scallop Argopecten irradians is a commercially and recreationally important shellfish species found in estuarine and coastal environments of the United States from New England to the Gulf of Mexico. In New York, adult bay scallop populations have been decimated every summer since 2019 leading to the collapse of their fishery. These mortality events were associated with annual outbreaks of an undescribed apicomplexan parasite recently named Bay Scallop Marosporida (BSM) that disrupts scallop kidneys. RESULTS: This study investigates host-pathogen interactions and assesses changes in population structure during BSM-associated mortality events. The research compared wild and aquacultured scallops used for stock enhancement in New York, revealing significant change in population structures throughout the mortality outbreak. The results underscore the selective pressures exerted by BSM infection and environmental stressors, as evidenced by shifts in genetic divergence and allele frequencies particularly in genes associated with kidney function, stress and infection response. Through a detailed genomic and population genetic approach, this research represents a unique case study highlighting the impact of disease on marine biodiversity and advances our understanding of the impact of summer mortality events on the scallop population in NY. CONCLUSIONS: This study highlights changes in the genomic structure of bay scallops during a BSM-associated mortality event. Identified mutations (such as the one in the nephrocystin-3-like gene) represent prime candidates for specific targeted investigations to link genotypes to phenotypes. By integrating genomic and epidemiological data, the research provides a basis for understanding the impact of disease on scallop biodiversity. These findings may help guide conservation strategies for sustainable fisheries in the face of environmental change and disease outbreaks.

  PublisherOA PDFDOI

• Chromosome-level genome assembly of the bay scallop Argopecten irradians

  Scientific Data · 2024-09-28 · 5 citations

  articleOpen accessSenior author

  The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.

  PublisherOA PDFDOI

• In silico identification of neuropeptide genes encoded by the genome of Crassostrea virginica with a special emphasis on feeding-related genes

  Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology · 2024-12-16 · 2 citations

  articleSenior author
  PublisherDOI

• In Silico Identification of Neuropeptides Encoded by the Genome of Crassostrea Virginica with a Special Emphasis on Feeding-Related Genes

  SSRN Electronic Journal · 2024-01-01

  preprintOpen accessSenior author
  PublisherDOI

Recent grants

• EID: Collaborative Research - Linking Marine Pathogens to Molluscan Shellfish; The Ecological Role of Marine Aggregates

  NSF · $241k · 2004–2008

• Collaborative Research: Host-Pathogen Interactions at Pallial Interfaces in Marine Bivalves: Cellular and Molecular Pathways for Host Colonization and Invasion

  NSF · $468k · 2011–2015

Frequent coauthors

• Emmanuelle Pales Espinosa

  Stony Brook University

  95 shared

• Christine Paillard

  41 shared

• Arnaud Tanguy

  Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier

  36 shared

• Gary H. Wikfors

  Rogers (United States)

  36 shared

• Isabelle Boutet

  Adaptation et Diversité en Milieu Marin

  25 shared

• Mickael Perrigault

  Université de Bordeaux

  23 shared

• Tessa Getchis

  20 shared

• Julie M. Rose

  Rogers (United States)

  20 shared

Education

• Ph.D.

  Stony Brook University