Article
Sveen L, Fast MD, Tengs T, Kline RA, Marti JA, Kurian D, Timmerhaus G, Vaadal M, Houston RD, Bron JE, Monaghan SJ, Mohammed HH, Daniels RR, Salisbury S & Robledo D (2025) Local inflammation at the salmon louse (Lepeophtheirus salmonis) attachment site contributes to copepodid rejection in coho salmon (Oncorhynchus kisutch). Cell and Tissue Research, 401, pp. 181-211. https://doi.org/10.1007/s00441-025-03976-0
Article
Taylor RS, Ruiz Daniels R & Macqueen DJ (2025) Cell type resolved expression of duplicate genes retained from whole genome duplication in Atlantic salmon. Van De Peer Y (Editor) Genome Biology and Evolution, Art. No.: evaf076. https://doi.org/10.1093/gbe/evaf076
Article
Transcriptomic characterization of transitioning cell types in the skin of Atlantic salmon
Ruiz Daniels R, Salisbury SJ, Sveen L, Villamayor PR, Taylor RS, Vaadal M, Tengs T, Krasnov A, Monaghan SJ, Penaloza C, Fast MD, Bron JE, Houston R, Robinson N & Robledo D (2025) Transcriptomic characterization of transitioning cell types in the skin of Atlantic salmon. BMC Biology, 23 (1). https://doi.org/10.1186/s12915-025-02196-w
Article
Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon
Salisbury SJ, Daniels RR, Monaghan SJ, Bron JE, Villamayor PR, Gervais O, Fast MD, Sveen L, Houston RD, Robinson N & Robledo D (2024) Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon. BMC Biology, 22, Art. No.: 160. https://doi.org/10.1186/s12915-024-01952-8
Article
Andresen AM, Taylor RS, Grimholt U, Daniels RR, Sun J, Dobie R, Henderson NC, Martin SA, Macqueen DJ & Fosse JH (2024) Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics. Fish & Shellfish Immunology, 146, Art. No.: 109357. https://doi.org/10.1016/j.fsi.2024.109357
Article
Sun J, Ruiz Daniels R, Balic A, Andresen AM, Bjørgen H, Dobie R, Henderson NC, Koppang EO, Martin SA, Fosse JH, Taylor RS & Macqueen DJ (2024) Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection. Fish & Shellfish Immunology, 145, Art. No.: 109358. https://doi.org/10.1016/j.fsi.2024.109358
Article
Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin
Sveen LR, Robinson N, Krasnov A, Daniels RR, Vaadal M, Karlsen C, Ytteborg E, Robledo D, Salisbury S, Dagnachew B, Lazado CC & Tengs T (2023) Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin. G3: Genes, Genomes, Genetics, 13 (11), Art. No.: jkad215. https://doi.org/10.1093/g3journal/jkad215
Article
Single cell genomics as a transformative approach for aquaculture research and innovation
Daniels RR, Taylor RS, Robledo D & Macqueen DJ (2023) Single cell genomics as a transformative approach for aquaculture research and innovation. Reviews in Aquaculture, 15 (4), pp. 1618-1637. https://doi.org/10.1111/raq.12806
Article
Ruiz Daniels R, Taylor RS, Dobie R, Salisbury S, Furniss JJ, Clark E, Macqueen DJ & Robledo D (2023) A versatile nuclei extraction protocol for single nucleus sequencing in non-model species–Optimization in various Atlantic salmon tissues. Winter S (Editor) PLOS ONE, 18 (9), Art. No.: e0285020. https://doi.org/10.1371/journal.pone.0285020
Article
Matz H, Taylor RS, Redmond AK, Hill TM, Ruiz Daniels R, Beltran M, Henderson NC, Macqueen DJ & Dooley H (2023) Organized B cell sites in cartilaginous fishes reveal the evolutionary foundation of germinal centers. Cell Reports, 42 (7), Art. No.: 112664. https://doi.org/10.1016/j.celrep.2023.112664
Article
Applying genetic technologies to combat infectious diseases in aquaculture
Robinson NA, Robledo D, Sveen L, Ruiz Daniels R, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl-Wilson A, Samsing F & Difford G (2023) Applying genetic technologies to combat infectious diseases in aquaculture. Reviews in Aquaculture, 15 (2), pp. 491-535. https://doi.org/10.1111/raq.12733
Other
Ruiz Daniels R A versatile nuclei extraction protocol for single cell multiome ATAC and gene expression in non model species v1. Refers to: 10.17504/protocols.io.bp2l69wnrlqe/v1. PLoS ONE. https://doi.org/10.17504/protocols.io.bp2l69wnrlqe/v1
Article
Common microgeographical selection patterns revealed in four European conifers
Scotti I, Lalagüe H, Oddou‐Muratorio S, Scotti‐Saintagne C, Ruiz Daniels R, Grivet D, Lefevre F, Cubry P, Fady B, González‐Martínez SC, Roig A, Lesur‐Kupin I, Bagnoli F, Guerin V & Plomion C (2023) Common microgeographical selection patterns revealed in four European conifers. Molecular Ecology, 32 (2), pp. 393-411. https://doi.org/10.1111/mec.16750
Book Chapter
Taylor RS, Daniels RR, Morata DP, Gundappa MK & Macqueen DJ (2022) Evolution of ray-finned fish genomes: Status and directions with a primer on microRNA characterization. In: Cellular and Molecular Approaches in Fish Biology. Amsterdam: Elsevier, pp. 309-346. https://doi.org/10.1016/b978-0-12-822273-7.00010-0
Article
Taylor RS, Ruiz Daniels R, Dobie R, Naseer S, Clark TC, Henderson NC, Boudinot P, Martin SAM & Macqueen DJ (2022) Single cell transcriptomics of Atlantic salmon (Salmo salar L.) liver reveals cellular heterogeneity and immunological responses to challenge by Aeromonas salmonicida. Frontiers in Immunology, 13. https://doi.org/10.3389/fimmu.2022.984799
Article
Macqueen DJ, Eve O, Gundappa MK, Daniels RR, Gallagher MD, Alexandersen S & Karlsen M (2021) Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages. Viruses, 13 (12), Art. No.: 2549. https://doi.org/10.3390/v13122549
Article
Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine (Pinus halepensis)
Ruiz Daniels R, Taylor RS, González-Martínez SC, Vendramin GG, Fady B, Oddou-Muratorio S, Piotti A, Simioni G, Grivet D & Beaumont MA (2019) Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine (Pinus halepensis). Genes, 10 (9), Art. No.: 673. https://doi.org/10.3390/genes10090673
Article
Ruiz Daniels R, Taylor RS, Serra‐Varela MJ, Vendramin GG, González‐Martínez SC & Grivet D (2018) Inferring selection in instances of long‐range colonization: The Aleppo pine (Pinus halepensis) in the Mediterranean Basin. Molecular Ecology, 27 (16), pp. 3331-3345. https://doi.org/10.1111/mec.14786
Article
Serra‐Varela MJ, Alía R, Daniels RR, Zimmermann NE, Gonzalo‐Jiménez J & Grivet D (2017) Assessing vulnerability of two Mediterranean conifers to support genetic conservation management in the face of climate change. Brotons L (Editor) Diversity and Distributions, 23 (5), pp. 507-516. https://doi.org/10.1111/ddi.12544
Article
RUIZ DANIELS R, BELTRAN S, POULIN R & LAGRUE C (2013) Do parasites adopt different strategies in different intermediate hosts? Host size, not host species, influencesCoitocaecum parvum(Trematoda) life history strategy, size and egg production. Parasitology, 140 (2), pp. 275-283. https://doi.org/10.1017/s0031182012001564