Daniel J. Macqueen

The paper generates high-quality genome assemblies for two manta and devil ray species and identifies structural variations linked to pelagic adaptation.

The paper analyzes a duplicate-resolved paddlefish genome to study rediploidisation and Hox cluster evolution, finding links between genome rearrangements, 3D architecture, and rediploidisation timing.

This study presents a transcriptomic analysis of Atlantic salmon embryogenesis, identifying key transcriptional events and regulatory mechanisms during early development.

The paper identifies regulatory variation driving lineage divergence in European sea bass by analyzing epigenomic and genomic data from Atlantic and Mediterranean populations.

This paper presents a high-quality genome assembly and tissue expression atlas for the European lobster, along with divergence time estimates and gene duplication analyses related to immunity and longevity.

This study identifies a metabolic-ageing profile in Atlantic salmon similar to humans and shows that spermidine supplementation reduces inflammation and improves metabolic flexibility in aged fish.

This study identifies STBD1 as a conserved glycophagy receptor in bilaterians, showing its structural evolution supports metabolic adaptation across species.

This study identifies a biphasic regulatory program for shell formation in bivalve molluscs and shows how dynamic chromatin remodeling allows evolutionary innovation within conserved gene regulatory networks.

The paper studies gene regulatory evolution in salmonids after autotetraploidization, finding that it is influenced by developmental and tissue-specific factors, with constraints at advanced embryogenesis.

This study uses single-nucleus RNA sequencing to identify two distinct endothelial response patterns to ISAV infection in Atlantic salmon.

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

This study shows that rapamycin-induced autophagy enhances lipid breakdown and reduces lipotoxicity in Atlantic salmon cells.

The paper imputes SNVs and SVs from low-coverage WGS data in Atlantic salmon, showing improved accuracy with SV genotype likelihoods.

The paper examines sex chromosomes in 14 elasmobranch species, identifying conserved X chromosomes and a shared candidate gene for sex determination.

The paper integrates multi-omics data to study the epigenomic and transcriptomic responses to viral and bacterial stimulation in turbot, identifying gene regulation patterns and chromatin state changes.

This study creates a comprehensive epigenomic atlas of turbot embryogenesis, revealing chromatin dynamics and regulatory elements important for development and aquaculture.

This study investigates the origins and functional significance of genomic diversity in bivalves, focusing on oysters, and identifies haplotype divergent sequences as key drivers of genetic innovation and adaptation.

The paper presents a chromosome-level reference genome for the European flat oyster, enabling high-resolution genomics for conservation and aquaculture.

This study evaluates genomic selection for improving growth traits in European flat oysters using low-density SNP panels and finds that similar prediction accuracies can be achieved with fewer markers.

This study reconstructs genome-wide rediploidization after autopolyploidization in salmonids over 100 million years, showing two waves of rediploidization and lineage-specific ohnologue divergence.

This study identifies 15,483 high-confidence structural variants in 492 Atlantic salmon genomes, revealing their role in population structure, functional impact, and domestication traits.

The paper introduces FAASG, an initiative to study salmonid genomes to understand phenotypic variation and improve aquaculture and conservation.

The paper proposes LORe as a model explaining delayed rediploidization and its impact on salmonid evolution, showing lineage-specific ohnologue divergence and functional adaptation.