This study uses structural bioinformatics and AlphaFold to reconstruct a salmonid alphavirus virion, revealing a distinctive helical feature in the E2 envelope protein and its implications for virulence.

iScience · Feb 18, 2026Peer-reviewedMicrobiology

Characterization of interindividual DNA methylation variability in rainbow trout (Oncorhynchus mykiss)

Gaëlle Lefort, Aurélien Brionne, Benoît Piégu, Frédéric Terrier, Antoine Pigeon, Linda Beauclair, Jérôme Roy, Marandel Lucie, Stéphane Panserat, Delphine Lallias, Vincent Coustham

This study characterizes interindividual DNA methylation variability in rainbow trout using whole-genome bisulfite sequencing, identifying variable methylation regions enriched at gene regulatory elements and showing intraindividual correlation in some loci.

Genomics · Feb 3, 2026Peer-reviewedGenomics

Empowering bioinformatics communities with Nextflow and nf-core

Björn E. Langer, Andreia Neves do Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip Ewels, Sonia E Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, , The Nf-Core Community

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

Genome biology · Jul 29, 2025Peer-reviewedBioinformatics

Isogenic lines of rainbow trout (Oncorhynchus mykiss) as a tool to assess how growth and feeding behaviour are correlated to feed efficiency in fish

Simon Pouil, Thierry Kernéis, Edwige Quillet, Laurent Labbé, Delphine Lallias, Florence Phocas, Mathilde Dupont‐Nivet

The paper assesses correlations between feed efficiency (FE) and feeding behavior in rainbow trout using isogenic lines and indirect measurements.

Aquaculture · Jul 21, 2023Peer-reviewedGenetics

Analysis of DNA methylation in rainbow trout spermatozoa: the strengths and limitations of RRBS

Marina El Kamouh, Aurélien Brionne, Sayyari Amin, Delphine Lallias, Catherine Labbé, Audrey Laurent

The paper evaluates RRBS as a method for analyzing DNA methylation in rainbow trout spermatozoa, finding it effective for genome-wide scanning but with limitations in coverage and data processing choices.

bioRxiv · Jun 20, 2023 · PreprintMolecular Biology

Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits

Henri Lagarde, Delphine Lallias, Pierre Patrice, Martin Prchal, Yoannah François, Jonathan D’Ambrosio, Emilien Segret, Ana Acin Perez, Frédéric Cachelou, Pierrick Haffray, Audrey Dehaullon, Mathilde Dupont‐Nivet, Florence Phocas

This study identifies the genetic architecture of acute hyperthermia resistance in rainbow trout and shows it is polygenic with no major genetic correlations to production traits.

Genetics Selection Evolution · Jun 12, 2023Peer-reviewedGenomics

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Maria Bernard, Audrey Dehaullon, Guangtu Gao, Katy Paul, Henri Lagarde, Mathieu Charles, Martin Prchal, Jeanne Danon, Lydia Jaffrelo, Charles Poncet, Pierre Patrice, Pierrick Haffray, Edwige Quillet, Mathilde Dupont‐Nivet, Yniv Palti, , Florence Phocas

The paper develops a high-density 665 K SNP array for rainbow trout and demonstrates its utility in detecting linkage disequilibrium at shorter genomic distances.

Frontiers in Genetics · Jul 18, 2022Peer-reviewedGenomics