Defining genome activity

2024

Genome-wide variation study and inter-tissue communication analysis unveil regulatory mechanisms of egg-laying performance in chickens

Wang, D., Tan, L., Zhi, Y., Bu, L., Wang, Y., Wang, Z., Guo, Y., Tian, W., Xu, C., Li, D., Li, Z., Jiang, R., Han, R., Li, G., Wang, Y., Xia, D., Tian, Y., Dunn, I., Hu, X., Li, H., & 3 othersZhao, Y., Kang, X. & Liu, X., Dec 2024, In: Nature Communications. 15, 1, p. 1-18 18 p., 7069.

Research output: Contribution to journal › Article › peer-review

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The DoGA consortium expression atlas of promoters and genes in 100 canine tissues

DoGA Consortium & Schoenebeck, J. J., Dec 2024, In: Nature Communications. 15, 1, p. 1-12 12 p., 9082.

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The DRB3 gene of the bovine major histocompatibility complex: discovery, diversity and distribution of alleles in commercial breeds of cattle and applications for development of vaccines

Andrade, T. E. G., Peña, M. S., Fiorotti, J., de Souza Bin, R., Caetano, A. R., Connelley, T. & de Miranda Santos, I. K. F., Dec 2024, In: Journal of Dairy Science. 107, 12, p. 11324-11341 18 p.

Research output: Contribution to journal › Review article › peer-review

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Establishing African genomics and bioinformatics programs through annual regional workshops

Sharaf, A., Nesengani, L. T., Hayah, I., Kuja, J. O., Mdyogolo, S., Omotoriogun, T. C., Odogwu, B. A., Beedessee, G., Smith, R. M., Barakat, A., Moila, A. M., El Hamouchi, A., Benkahla, A., Boukteb, A., Elmouhtadi, A., Mafwila, A. L., Abushady, A. M., Elsherif, A. K., Ahmed, B., Wairuri, C., & 91 othersNdiribe, C. C., Ebuzome, C., Kinnear, C. J., Ndlovu, D-F., Iraqi, D., El Fahime, E., Assefa, E., Ouardi, F., Belharfi, F. Z., Tmimi, F. Z., Markey, F. B., Radouani, F., Zeukeng, F., Mvumbi, G. L., Ganesan, H., Hanachi, M., Nigussie, H., Charoute, H., Benamri, I., Mkedder, I., Haddadi, I., Meftah-Kadmiri, I., Mubiru, J. F., Domelevo Entfellner, J-B. K., Rokani, J. B., Ogwang, J., Daiga, J. B., Omumbo, J., Ideozu, J. E., Errafii, K., Labuschagne, K., Komi, K. K., Tonfack, L. B., Hadjeras, L., Ramantswana, M., Chaisi, M., Botes, M. W., Kilian, M., Kvas, M., Melloul, M., Chaouch, M., Khyatti, M., Abdo, M., Phasha-Muchemenye, M., Hijri, M., Mediouni, M. R., Hassan, M. A., Piro, M., Mwale, M., Maaloum, M., Mavhunga, M., Olivier, N. A., Aminou, O., Arbani, O., Souiai, O., Djocgoue, P. F., Mentag, R., Zipfel, R. D., Tata, R. B., Megnekou, R., Muzemil, S., Paez, S., Salifu, S. P., Kagame, S. P., Selka, S., Edwards, S., Gaouar, S. B. S., Reda, S. R. A., Fellahi, S., Khayi, S., Ayed, S., Madisha, T., Sahil, T., Udensi, O. U., Ras, V., Ezebuiro, V., Duru, V. C., David, X., Geberemichael, Y., Tchiechoua, Y. H., Mungloo-Dilmohamud, Z., Chen, Z., Happi, C., Kariuki, T., Ziyomo, C., Djikeng, A., Badaoui, B., Mapholi, N., Muigai, A., Osuji, J. O. & Ebenezer, T. E., Aug 2024, In: Nature Genetics. 56, 8, p. 1556-1565

Research output: Contribution to journal › Review article › peer-review

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Multiscale 3D genome organization underlies duck fatty liver with no adipose inflammation or serious injury

Ning, M., Song, L., Niu, X., Wang, Y., Liu, W., Hu, J., Cai, H., Song, W., Liu, L., Li, H., Gong, D., Smith, J. & Huang, Y., Jun 2024, In: International Journal of Biological Macromolecules. 271, Pt 1, p. 1-14 14 p., 132452.

Research output: Contribution to journal › Article › peer-review

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MeCP2 binds to methylated DNA independently of phase separation and heterochromatin organisation

Pantier, R., Brown, M., Han, S., Paton, K., Meek, S., Montavon, T., Shukeir, N., Mchugh, T., Kelly, D., Hochepied, T., Libert, C., Jenuwein, T., Burdon, T. & Bird, A. P., 8 May 2024, In: Nature Communications. 15, 1, p. 1-14 14 p., 3880.

Research output: Contribution to journal › Article › peer-review

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Effects of foetal size, sex and developmental stage on adaptive transcriptional responses of skeletal muscle to intrauterine growth restriction in pigs

Cortés Araya, Y., Cheung, S., Ho, W., Stenhouse, C., Ashworth, C., Esteves, C. & Donadeu, X., 11 Apr 2024, In: Scientific Reports. 14, p. 1-13 13 p., 8500.

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Advancing fish breeding in aquaculture through genome functional annotation

Johnston, I. A., Kent, M. P., Boudinot, P., Looseley, M., Bargelloni, L., Faggion, S., Merino, G., Ilsley, G. R., Bobe, J., Tsigenopoulos, C. S., Robertson, J., Harrison, P., Martínez, P., Robledo, D., Macqueen, D. & Lien, S., 30 Mar 2024, In: Aquaculture. 583, p. 1-13 13 p., 740589.

Research output: Contribution to journal › Review article › peer-review

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

Andresen, A. M. S., Taylor, R. S., Grimholt, U., Daniels, R. R., Sun, J., Dobie, R., Henderson, N. C., Martin, S. A. M., Macqueen, D. J. & Fosse, J. H., Mar 2024, In: Fish and Shellfish Immunology. 146, p. 1-18 18 p., 109357.

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

Sun, J., Ruiz Daniels, R., Balic, A., Magalhaes Santos Andresen, A., Bjørgen, H., Dobie, R., Henderson, N. C., Koppang, E. O., Martin, S. A. M., Hol Fosse, J., Taylor, R. & Macqueen, D., Feb 2024, In: Fish and Shellfish Immunology. 145, p. 1-17 17 p., 109358.

Research output: Contribution to journal › Article › peer-review

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A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii)

Wu, Z., Miedzinska, K., Krause, J., Perez, J., Wingfield, J. C., Meddle, S. & Smith, J., 18 Jan 2024, In: Scientific Data. 11, 1, p. 1-10 10 p., 86.

Research output: Contribution to journal › Article › peer-review

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Building in vitro tools for livestock genomics: chromosomal variation within the PK15 cell line

Johnsson, M., Hickey, J. M. & Jungnickel, M. K., 11 Jan 2024, (E-pub ahead of print) In: BMC Genomics. 25, 1, p. 1-11 11 p., 49.

Research output: Contribution to journal › Article › peer-review

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A compendium of genetic regulatory effects across pig tissues

PigGTEx Consortium, Jan 2024, In: Nature Genetics. 56, 1, p. 112-123

Research output: Contribution to journal › Article › peer-review

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Delineation of chicken immune markers in the era of omics and multicolour flow cytometry

Härtle, S., Sutton, K., Vervelde, L. & Dalgaard, T. S., 2024, In: Frontiers in Veterinary Science. 11, p. 1-19 19 p.

Research output: Contribution to journal › Article › peer-review

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Innovative construction of the first reliable catalog of bovine circular RNAs

Robic, A., Hadlich, F., Monteiro Moreira, G. C., Clark, E., Plastow, G., Charlier, C. & Kuhn, C., 2024, In: Rna biology. 21, 1, p. 52-74 22 p.

Research output: Contribution to journal › Article › peer-review

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Transitioning from Triton X-100 to Tergitol 15-S-9: impacts on diagnostic assays using viral PCR sample solution

Zorzoli, A., MacLean, A., Nicholson, S., Daniels, A., Hughes, S., Bennet-Slater, S., Tait-Burkard, C., Sakka, N. E., Gunson, R. & Templeton, K., 2024, In: Biotechniques. 76, 7, p. 295-298 4 p.

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2023

Selection on the promoter regions plays an important role in complex traits during duck domestication

Yin, Z-T., Li, X-Q., Sun, Y-X., Smith, J., Hincke, M., Yang, N. & Hou, Z-C., 21 Dec 2023, (E-pub ahead of print) In: BMC Biology. p. 1-19 19 p., 303.

Research output: Contribution to journal › Article › peer-review

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A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes

Zhu, F., Yin, Z-T., Zhao, Q-S., Sun, Y-X., Jie, Y-C., Smith, J., Yang, Y-Z., Burt, D. W., Hincke, M., Zhang, Z-D., Yuan, M-D., Kaufman, J., Sun, C-J., Li, J-Y., Shao, L-W., Yang, N. & Hou, Z-C., Dec 2023, In: Communications Biology. 6, 1, p. 1-15 15 p., 1233.

Research output: Contribution to journal › Article › peer-review

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Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis: Honeybee cell heterogeneity during development

Patir, A., Raper, A., Fleming, R., Henderson, B., Murphy, L., Henderson, N. C., Clark, E., Freeman, T. & Barnett, M., 30 Sept 2023, In: G3: Genes | Genomes | Genetics. 13, 10, p. 1-13 13 p., jkad178.

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A versatile nuclei extraction protocol for single nucleus sequencing in non-model species – optimization in various Atlantic salmon tissues

Ruiz Daniels, R., Taylor, R., Dobie, R., Salisbury, S., Furniss, J., Clark, E., Macqueen, D. & Robledo, D., Sept 2023, In: PLoS ONE. 18, 9, p. 1-9 9 p.

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Association between blood miR-26a levels following artificial insemination and pregnancy outcome in dairy cattle

Tzelos, T., Lee, S., Pegg, A. & Donadeu, X., Aug 2023, In: PLoS ONE. 18, 8, p. 1-11 11 p., e0289342.

Research output: Contribution to journal › Article › peer-review

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Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing

Salavati, M., Clark, R., Becker, D., Kühn, C., Plastow, G. S., Dupont, S., Moreira, G. C. M., Charlier, C. & Clark, E., Aug 2023, In: G3: Genes | Genomes | Genetics. 13, 8, p. 1-38 38 p., jkad108.

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High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure

Vasoya, D., Tzelos, T., Benedictus, L., Karagianni, A., Pirie, S., Marr, C., Oddsdottir, C., Fintl, C. & Connelley, T., 10 Jul 2023, In: Genes. 14, 7, p. 1-30 30 p., 1422.

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Association of plasma miRNAs with early life performance and aging in dairy cattle

MacLeay, M., Banos, G. & Donadeu, X., Jul 2023, In: PLoS ONE. 18, 7, p. 1-18 18 p., e0288343.

Research output: Contribution to journal › Article › peer-review

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

Clark, T. C., Naseer, S., Gundappa, M. K., Laurent, A., Perquis, A., Collet, B., Macqueen, D. J., Martin, S. A. M. & Boudinot, P., Jul 2023, In: Genomics. 115, 4, p. 1-13 13 p., 110663.

Research output: Contribution to journal › Article › peer-review

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Livestock phenomics and genetic evaluation approaches in Africa: current state and future perspectives

Houaga, I., Mrode, R., Opoola, O., Mizeck G.G, C., Mwai, O. A., Rege, J. E. O., Olori, V. E., Nash, O., Banga, C., Okeno, T. O. & Djikeng, A., 8 Jun 2023, (E-pub ahead of print) In: Frontiers in Genetics. 14, p. 1-13 13 p.

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Open Institute of the African BioGenome Project: Bridging the gap in African biodiversity genomics and bioinformatics

Sharaf, A., Ndiribe, C. C., Omotoriogun, T. C., Abueg, L., Badaou, B., Markey, F. J. B., Beedessee, G., Diouf, D., Duru, V. C., Ebuzome, C., Eziuzo, S. C., Jaufeerally Fakim, Y., Formenti, G., Ghanm, N., Guerfali, F. Z., Houaga, I., Ideozu, J. E., Katee, S. M., Khayi, S., Kuja, J. O., & 15 othersKwon-Ndung, E. H., Marks, R. A., Moila, A. M., Mungloo-Dilmohamud, Z., Muzemi, S., Negussie, H., Osuji, J. O., Ras, V., Tchiechoua, Y. H., Zoclanclounon, Y. A. B., Tolley, K. A., Ziyomo, C., Mapholi, N., Muigai, A. & Djikeng, A., 30 May 2023, (E-pub ahead of print) OSF Preprints, p. 1-18, 18 p.

Research output: Working paper › Preprint

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CAGE sequencing reveals CFTR-dependent dysregulation of type I IFN signaling in activated cystic fibrosis macrophages

Gillan, J. L., Chokshi, M., Hardisty, G. R., Clohisey Hendry, S., Prasca-Chamorro, D., Robinson, N. J., Lasota, B., Clark, R., Murphy, L., Whyte, M. K. B., Baillie, J. K., Davidson, D. J., Bao, G. & Gray, R. D., 26 May 2023, In: Science Advances. 9, 21, p. 1-17 17 p., eadg5128.

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Profiling the immune epigenome across global cattle breeds

Powell, J., Talenti, A., Fisch, A., Hemmink, H., Paxton, E., Toye, P., Santos, I., Ferreira, B. R., Connelley, T., Morrison, L. & Prendergast, J., 22 May 2023, In: Genome Biology. 24, p. 1-31 31 p., 127.

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Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans

Gao, C., Amador, C., Walker, R., Campbell, A., Madden, R., Adams, M. J., Bai, X., Liu, Y., Li, M., Hayward, C., Porteous, D. J., Shen, X., Evans, K. L., Haley, C. S., McIntosh, A. M., Navarro, P. & Zeng, Y., 15 May 2023, In: Genome Biology. 24, p. 1-28 28 p., 117.

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nf-core/isoseq: Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing

Guizard, S., Miedzinska, K., Smith, J., Smith, J., Kuo, R., Davey, M. & Watson, M., 4 May 2023, In: Bioinformatics. 39, 5, p. 1-2 2 p., 24323.

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The transcriptome of chicken migratory primordial germ cells reveals intrinsic sex differences and hallmark germ cell genes

Doddamani, D., Woodcock, M., Taylor, L., Nandi, S., McTeir, L., Davey, M., Smith, J. & McGrew, M., 13 Apr 2023, In: Cells. 12, 8, p. 1-15 15 p., 1151.

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RNA-Seq profiling between commercial and indigenous Iranian chickens highlights differences in innate immune gene expression

Sadr, A. S., Nassiri, M. R., Ghaderi-Zefrehei, M., Heidari, M., Smith, J. & Dolatabady, M. M., Apr 2023, In: Genes. 14, 4, p. 1-15 14 p., 793.

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Defining the pig microglial transcriptome reveals its core signature, regional heterogeneity, and similarity with human and rodent microglia: Pig microglial transcriptome signature

Shih, B., Brown, S., Barrington, J., Lefevre, L., Mabbott, N., Priller, J., Thompson, G., Lawrence, A. & McColl, B. W., Feb 2023, In: Glia. 71, 2, p. 334-349

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Defining genome activity

Research output

Search results