Advancing fish breeding in aquaculture through genome functional annotation

Authors: Johnston, Ian A., Kent, Matthew P., Boudinot, Pierre, Looseley, Mark, Bargelloni, Luca, Faggion, Sara, Merino, Gabriela A., Ilsley, Garth R., Bobe, Julien, Tsigenopoulos, Costas S., Robertson, Joseph, Harrison, Peter W., Martinez, Paulino, Robledo, Diego, Macqueen, Daniel J., Lien, Sigbjørn

Source: In Aquaculture 30 March 2024 583

Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics

Authors: Andresen, Adriana M.S., Taylor, Richard S., Grimholt, Unni, Daniels, Rose Ruiz, Sun, Jianxuan, Dobie, Ross, Henderson, Neil C., Martin, Samuel A.M., Macqueen, Daniel J., Fosse, Johanna H.

Source: In Fish and Shellfish Immunology March 2024 146

Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection

Authors: Sun, Jianxuan, Ruiz Daniels, Rose, Balic, Adam, Andresen, Adriana M.S., Bjørgen, Håvard, Dobie, Ross, Henderson, Neil C., Koppang, Erling Olaf, Martin, Samuel A.M., Fosse, Johanna Hol, Taylor, Richard S., Macqueen, Daniel J.

Source: In Fish and Shellfish Immunology February 2024 145

Single cell genomics as a transformative approach for aquaculture research and innovation

Authors: Daniels, Rose Ruiz, Taylor, Richard S., Robledo, Diego, Macqueen, Daniel J.

Source: Reviews in aquaculture. 15(4):1618-1637

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100193054072.0x000001&indx=1&recIds=ETOCvdc_100193054072.0x000001

Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes

Authors: Clark, Thomas C., Naseer, Shahmir, Gundappa, Manu Kumar, Laurent, Audrey, Perquis, Aline, Collet, Bertrand, Macqueen, Daniel J., Martin, Samuel A.M., Boudinot, Pierre

Source: In Genomics July 2023 115(4)

Transcriptomic characterisation of acute myeloid leukemia cell lines bearing the same t(9;11) driver mutation reveals different molecular signatures.

Authors: Georges, Elise, Ho, William, Iturritza, Miren Urrutia, Eory, Lel, Malysz, Kamila, Sobhiafshar, Ulduz, Archibald, Alan L., Macqueen, Daniel J., Shih, Barbara, Garrick, David, Vernimmen, Douglas

Source: BMC Genomics; 3/29/2025, Vol. 26 Issue 1, p1-13, 13p

High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.

Authors: Gundappa, Manu Kumar, Robledo, Diego, Hamilton, Alastair, Houston, Ross D., Prendergast, James G. D., Macqueen, Daniel J.

Source: Genetics Selection Evolution; 3/28/2025, Vol. 57 Issue 1, p1-18, 18p

Chromosome‐level reference genome for European flat oyster (Ostrea edulis L.)

Authors: Gundappa, Manu Kumar, Peñaloza, Carolina, Regan, Tim, Boutet, Isabelle, Tanguy, Arnaud, Houston, Ross D., Bean, Tim P., Macqueen, Daniel J.

Source: Evolutionary applications. 15(11):1713-1729

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100165484583.0x000001&indx=1&recIds=ETOCvdc_100165484583.0x000001

Two parallel chromosome‐level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis

Authors: Bean, Tim P., Tanguy, Arnaud, Peñaloza, Carolina, Gundappa, Manu Kumar, Boutet, Isabelle, Houston, Ross D., Macqueen, Daniel J., Boudry, Pierre

Source: Evolutionary applications. 15(11):1709-1712

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100165484572.0x000001&indx=1&recIds=ETOCvdc_100165484572.0x000001

A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae

Authors: Sambade, Inés Martínez, Casanova, Adrian, Blanco, Andrés, Gundappa, Manu K., Bean, Tim P., Macqueen, Daniel J., Houston, Ross D., Villalba, Antonio, Vera, Manuel, Kamermans, Pauline, Martínez, Paulino

Source: Evolutionary applications. 15(9):1408-1422

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161221961.0x000001&indx=1&recIds=ETOCvdc_100161221961.0x000001

Genome-wide target enriched viral sequencing reveals extensive ‘hidden’ salmonid alphavirus diversity in farmed and wild fish populations

Authors: Gallagher, Michael D., Matejusova, Iveta, Ruane, Neil M., Macqueen, Daniel J.

Source: In Aquaculture 30 May 2020 522

Organized B cell selection sites in cartilaginous fishes reveal the evolutionary foundation of germinal center-based selection

Authors: Matz, Hanover, Taylor, Richard S., Redmond, Anthony K., Hill, Thomas, Daniels, Rose Ruiz, Beltran, Mariana, Henderson, Neil C., Macqueen, Daniel J., Dooley, Helen

Source: Developmental and comparative immunology. 148

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195823394.0x000001&indx=1&recIds=ETOCvdc_100195823394.0x000001

Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes

Authors: Clark, Thomas, Naseer, Shahmir, Gundappa, Manu Kumar, Laurent, Audrey, Perquis, Aline, Collet, Bertrand, Macqueen, Daniel J., Martin, Samuel A.M., Boudinot, Pierre

Source: Developmental and comparative immunology. 148

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195823453.0x000001&indx=1&recIds=ETOCvdc_100195823453.0x000001

Phylogenetic origins of the complement system in the ancestor of animals

Authors: Redmond, Anthony K., Mohanty, Dibya Swarupa, McLysaght, Aoife, Macqueen, Daniel J., Dooley, Helen

Source: Developmental and comparative immunology. 148

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195822609.0x000001&indx=1&recIds=ETOCvdc_100195822609.0x000001

Organized B cell sites in cartilaginous fishes reveal the evolutionary foundation of germinal centers

Authors: Matz, Hanover, Taylor, Richard S., Redmond, Anthony K., Hill, Thomas M., Ruiz Daniels, Rose, Beltran, Mariana, Henderson, Neil C., Macqueen, Daniel J., Dooley, Helen

Source: Cell reports. 42(7)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100194799262.0x000001&indx=1&recIds=ETOCvdc_100194799262.0x000001

Proteomic comparison of selective breeding and growth hormone transgenesis in fish: Unique pathways to enhanced growth

Authors: Causey, Dwight R., Kim, Jin-Hyoung, Stead, David A., Martin, Samuel A.M., Devlin, Robert H., Macqueen, Daniel J.

Source: In Journal of Proteomics 10 February 2019 192:114-124

Evolutionary history of the T cell receptor complex as revealed by small-spotted catshark (Scyliorhinus canicula)

Authors: Pettinello, Rita, Redmond, Anthony K., Secombes, Christopher J., Macqueen, Daniel J., Dooley, Helen

Source: In Developmental and Comparative Immunology September 2017 74:125-135

Divergent regulation of insulin-like growth factor binding protein genes in cultured Atlantic salmon myotubes under different models of catabolism and anabolism

Authors: Garcia de la serrana, Daniel, Fuentes, Eduardo N., Martin, Samuel A.M., Johnston, Ian A., Macqueen, Daniel J.

Source: In General and Comparative Endocrinology 1 June 2017 247:53-65

Haptoglobin Is a Divergent MASP Family Member That Neofunctionalized To Recycle Hemoglobin via CD163 in Mammals

Authors: Redmond, Anthony K., Ohta, Yuko, Criscitiello, Michael F., Macqueen, Daniel J., Flajnik, Martin F., Dooley, Helen

Source: Journal of immunology. 201(8):2483-2491

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN617611841&indx=1&recIds=ETOCRN617611841

Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution

Authors: Gundappa, Manu Kumar, To, Thu-Hien, Grønvold, Lars, Martin, Samuel A M, Lien, Sigbjørn, Geist, Juergen, Hazlerigg, David, Sandve, Simen R, Macqueen, Daniel J

Source: Molecular biology and evolution. 39(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100139844090.0x000001&indx=1&recIds=ETOCvdc_100139844090.0x000001