Projects
Selected research compendia, computational workflows, and emerging resources
These projects bring together field studies, non-model resources and reproducible analysis around environmental stress and biological organisation.
Reproducible eco-omics and field ecotoxicology
EchoGO
Problem: Functional interpretation can depend on the annotation resource used, especially for non-model organisms.
Contribution: An R framework for annotation-context-aware interpretation after differential-expression analysis, anchored to the target experimental enrichment.
Programme link: Supports transparent and transferable interpretation across non-model eco-omics.
R · RNA-seq · GO enrichment · non-model organisms · reproducibility
Holtemme Gammarus Ecotoxicogenomics
Problem: Relating environmental micropollutant mixtures to molecular responses in wild Gammarus pulex across a river gradient.
Contribution: A reproducible analysis integrating environmental chemistry, transcriptome-wide structure, differential expression, functional interpretation and gene-network analysis.
Programme link: Connects a real-world stress gradient with molecular and network-level responses.
field ecotoxicology · RNA-seq · environmental chemistry · WGCNA · research compendium
Non-model organism workflows and resources
Cottus Genomics
Problem: Building genome and transcriptome resources for European sculpins.
Contribution: A reproducible workflow combining genome annotation, RNA evidence, de novo transcriptomics, HPC execution, validation gates and release-oriented provenance.
Programme link: Develops reusable molecular resources for non-model aquatic organisms.
genomics · BRAKER · Trinity · HPC · non-model organisms
Skåne Environmental Metagenomics
Problem: Characterising microbial genomes and environmental viruses across spatially structured metagenomes.
Contribution: A Snakemake/HPC workflow across seven sites, including MAG recovery, vOTU catalogues, taxonomy, quantification and evidence-aware virus–host linkage.
Programme link: Extends my work into microbial and viral community organisation, environmental metagenomics and host–virus ecological structure.
metagenomics · viromics · MAGs · Snakemake · HPC
Zebrafish Exposure Transcriptomics
Problem: Comparing molecular responses across two chemical-exposure experiments in zebrafish larvae.
Contribution: A reproducible RNA-seq workflow integrating differential expression, target enrichment, annotation-context interpretation, KEGG analysis and mechanism-focused synthesis.
Programme link: Adds a comparative experimental exposure context to my work with environmental stress responses.
zebrafish · RNA-seq · DESeq2 · functional genomics
Emerging programme
TROPECO-OMICS / Hi-SGH
Question: How does biological coordination change as environmental stress increases, and when might compensation give way to loss of resilience?
Status: Proposal under evaluation.
Programme link: Hi-SGH provides a testable framework for studying cross-layer coordination, compensation and resilience along real-world stress gradients.
multi-omics · holobiont · field gradients · resilience · systems ecology
Project philosophy
Across these projects, I preserve data provenance, connect analytical outputs to primary evidence and document the decisions that shape biological interpretation.