Simen R. Sandve

This paper presents a chromosome-level genome assembly of cloudberry, revealing its octoploid origin through multiple polyploidization events involving four subgenomes.

OmniCorr is an R package that clusters and visualizes multi-omics data to identify putative host-microbiota interactions across different biological systems.

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.

The paper analyzes eQTL data in Atlantic salmon to show long-term dosage balance maintenance after a 100 million-year-old genome duplication.

The paper introduces nf-RASQUAL, a Nextflow pipeline for molQTL mapping in small datasets, applied to Atlantic salmon to identify expression and chromatin accessibility QTLs.

The paper shows that the saccus vasculosus transcriptome response to seawater exposure in Atlantic salmon depends on photoperiodic history and identifies ependymin as a major secretory output.

This study examines the evolution of gig immune genes in teleosts, focusing on Atlantic salmon, revealing distinct evolutionary trajectories and regulatory mechanisms.

The paper identifies a major locus on chromosome 14 associated with gill gene expression and somatic growth in Atlantic salmon during smoltification.

This paper develops a deep learning framework to predict the regulatory impact of non-coding variants in farmed animals using chromatin data, improving genomic prediction for livestock and aquaculture.

This study examines the impact of different light regimes on growth, survival, and genetic parameters of Atlantic salmon, finding no significant long-term effect on size but increased mortality under continuous light.

This study assesses the effects of gamma radiation on Norway spruce stem cells, finding dose-dependent DNA damage and transcriptomic changes, but retained stemness despite cellular abnormalities.

The paper investigates strain-specific gene regulation of lipid and carotenoid production in Mucor circinelloides under calcium starvation using genomic and transcriptomic analyses.

The paper develops gene expression-based predictive models for survival and growth in seawater using gill transcriptomes of Atlantic salmon, finding photoperiod-sensitive genes are more important than previously thought sodium pump genes.

This study examines how dietary chitin affects chitinase activity, gene expression, and gut microbial composition in Atlantic salmon.

This study evaluates microbiota-directed fibers (MDFs) in Atlantic salmon diets, finding negligible effects on gut microbiome and host physiology, but identifying potential endogenous lactic acid bacteria for future MDF strategies.

The paper presents a chromosome-level genome assembly for the snowy owl and identifies evolutionary new centromeres seeded by a transposable element, showing lineage-specific centromere evolution.

This study investigates the genome regulatory changes in Atlantic salmon liver during smoltification, finding that metabolic remodeling occurs in freshwater and transcription factor dynamics drive gene expression changes, while DNA methylation is not correlated with expression shifts.

This study investigates how transposon activity and whole genome duplication interact to shape cis-regulatory element evolution in Atlantic salmon, finding a strong link between TE insertions during WGD and TE-CRE evolution.

The paper links genomic prediction of muscle fat content in Atlantic salmon to changes in lipid metabolism by analyzing gene expression and eQTLs.

The paper investigates the expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon using comparative genomics, transcriptomics, and chromatin accessibility data.

This paper develops a method for efficiently transfecting Atlantic salmon primary hepatocytes for functional assays and gene editing.

SALARECON links the Atlantic salmon genome to metabolic fluxes and growth, showing that marine feed efficiency can be achieved by supplementing plant- and insect-based feeds with specific amino acids.

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 examines the relationship between gut microbiota and metabolism in Atlantic salmon, finding significant associations between specific microbial OTUs and metabolic phenotypes.

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.

This study uses single-nuclei RNAseq to analyze Atlantic salmon gill during smoltification, identifying 20 cell clusters and showing immune reprogramming associated with seawater transfer.

This study compares lipid metabolism in domesticated and wild Atlantic salmon fed different diets, finding domesticated salmon show distinct metabolic responses to vegetable oil.

The paper analyzes the grayling genome to study regulatory divergence of Ss4R duplicates after whole genome duplication, finding purifying selection and adaptive divergence in brain-related and immune functions.

The paper uses RNA-seq to analyze phospholipid and lipoprotein metabolism development in Atlantic salmon fry intestines, finding increased synthesis capacity in pyloric caeca and specific gene expression patterns.

The paper compares cold response gene regulation across five Pooideae species to understand evolutionary adaptations to temperate climates.