Research

My research integrates comparative genomics, transcriptomics, microbiome analyses and bioinformatics to investigate how aquatic organisms respond to environmental and husbandry-related perturbations. A central objective of my work is to understand the molecular processes underlying organism performance, resilience and adaptation through the combined analysis of host biology, microbial communities and environmental context.

My current research focuses primarily on marine organisms of aquaculture relevance, particularly bivalves, where I develop and apply reproducible computational approaches for genome annotation, RNA-seq, microbiome profiling and metabarcoding. These studies aim to identify molecular and microbial signatures associated with physiological responses, larval performance and environmental conditions.

An increasing focus of my research is the application of these approaches to the genomics of adaptation in aquatic systems, integrating host genomics, transcriptomics, microbiome data and environmental genomics to better understand how organisms and biological communities respond to environmental change.

Comparative genomics and transcriptomics

  • Comparative genomics and genome annotation in non-model aquatic organisms.
  • Transcriptomic analyses of host responses to environmental and husbandry-related perturbations.
  • Functional interpretation of molecular pathways associated with physiology, stress responses and adaptation.

Host–microbiome interactions

  • Characterization of microbial communities associated with aquatic organisms and aquaculture systems.
  • Integration of host transcriptomic profiles with microbiome dynamics.
  • Identification of microbial and molecular signatures associated with robustness, health and production performance.

Environmental genomics and biodiversity

  • Metabarcoding approaches for profiling biological communities in aquatic environments.
  • Comparative analyses linking environmental communities with host-associated processes.
  • Progressive expansion toward environmental DNA (eDNA) and biodiversity-oriented applications in ecosystem monitoring and adaptation studies.

Reproducible bioinformatics and omics analysis

  • RNA-seq analysis, differential expression and functional annotation.
  • Comparative genomics and genome annotation workflows.
  • Microbiome and metabarcoding data analysis.
  • Integration of multi-omics datasets for biological interpretation.
  • Development of reproducible, containerised and HPC-ready computational workflows following FAIR principles.