Publications - Centre for Genomic Research

Selected publications from 2024/2025

Paine, L.W., Higham, J.P., Barker, K.H., Pavlou, S., Welsh, F., Smith, E.S.J. and Bulmer, D.C., 2025. IL-17 sensitises sensory neurons and colonic afferents to noxious stimuli in a PI3K dependent manner. bioRxiv, pp.2025-04.
Mulindwa, J., Lujumba, I., Musiime, C., Namulondo, J., Kimuda, M.P., Nyangiri, O., Cuu, G., Mwubaha, C., Tukwasibwe, S., Ssemaganda, A. and Ssewanyana, I., 2025. High Schistosoma mansoni infection intensity is associated with distinct gut microbiota and low levels of systemic cytokines in children along the Albert-Nile, Northern Uganda. BMC microbiology, 25(1), p.506.
Fresneda Alarcon M, Abdullah GA, Beggs JA, Kynoch I, Sellin A, Cross A, Haldenby S, Antczak P, Gutiérrez EC, Wright HL. Complexity of the neutrophil transcriptome in early and severe rheumatoid arthritis. A role for microRNAs? J Leukoc Biol. 2025 Jun 18:qiaf090. doi: 10.1093/jleuko/qiaf090
Cunningham-Oakes E, Perez-Sepulveda BM, Li Y, Hinton JCD, Nelson CA, McIntyre KM, Wardeh M, Haldenby S, Gregory R, Iturriza-Gómara M, Hertz-Fowler C, O'Brien SJ, Cunliffe NA, Darby AC; INTEGRATE consortium. Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples. Genome Med. 2025 May 20;17(1):55. doi: 10.1186/s13073-025-01478-w. PMID: 40390150.
Adams, S.E., Cawley, A.K., Arnold, D., Hoptroff, M.J., Slomka, V., Matheson, J.R., Marriott, R.E., Gemmell, M.R. and Marsh, P.D., 2025. A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function. Scientific Reports, 15(1), p.8136.
Ebrahim, H., Haldenby, S., Moore, M.P., Dashti, A.A., Floyd, R.V. and Fothergill, J.L., 2025. Genotypic and phenotypic analyses of two distinct sets of Pseudomonas aeruginosa urinary tract isolates. Journal of Medical Microbiology, 74(2), p.001971.
Renaudineau, Y., Charras, A., Natoli, V., Congy-Jolivet, N., Haldenby, S., Liu, X., Fang, Y., Smith, E.M., Beresford, M.W., Hedrich, C.M. and Roberts, C., 2025. Across ancestries, HLA-B* 08: 01∼ DRB1* 03: 01 (DR3) and HLA-DQA* 01: 02 (DR2) increase the risk to develop juvenile-onset systemic lupus erythematosus through low complement C4 levels. Journal of Translational Autoimmunity, p.100268.
Lehr K, Oosterlinck B, Then CK, Gemmell MR, Gedgaudas R, Bornschein J, Kupcinskas J, Smet A, Hold G, Link A; ENIGMA: European Network for the Investigation of Gastrointestinal Mucosal Alterations. Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition. mSystems. 2025 Jan 28:e0135824.
Walters, M., Skovgaard, K., Heegaard, P.M., Fang, Y., Kharaz, Y.A., Bundgaard, L., Skovgaard, L.T., Jensen, H.E., Andersen, P.H., Peffers, M.J. and Jacobsen, S., 2025. Identification and characterisation of temporal abundance of microRNAs in synovial fluid from an experimental equine model of osteoarthritis. Equine veterinary journal.
Hares, M.F., Griffiths, B.E., Barningham, L., Vamos, E.E., Gregory, R., Duncan, J.S., Oikonomou, G., Stewart, C.J. and Coombes, J.L., 2025. Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis. Animal microbiome, 7(1), p.3.
Knight, C.G., Nicolitch, O., Griffiths, R.I., Goodall, T., Jones, B., Weser, C., Langridge, H., Davison, J., Dellavalle, A., Eisenhauer, N. and Gongalsky, K.B., 2024. Soil microbiomes show consistent and predictable responses to extreme events. Nature, pp.1-7.
Sokouri, E.A., Ahouty, B., Abé, I.A., Yao, F.G., Konan, T.K., Nyangiri, O.A., MacLeod, A., Matovu, E., Noyes, H. and Koffi, M., 2024. Evaluation of the epidemiological situation of intestinal schistosomiasis using the POC-CCA parasite antigen test and the Kato-Katz egg count test in school-age children in endemic villages in western Côte d’Ivoire. Parasite, 31, p.66.
Morgan, G., Pinchbeck, G., Haldenby, S., Schmidt, V. and Williams, N., 2024. Raw meat diets are a major risk factor for carriage of third-generation cephalosporin-resistant and multidrug-resistant E. coli by dogs in the UK. Frontiers in Microbiology, 15, p.1460143.
Bragg, J.G., Potter, S., Bi, K., Catullo, R., Donnellan, S.C., Eldridge, M.D., Joseph, L., Keogh, J.S., Oliver, P., Rowe, K.C. and Moritz, C., 2017. Resources for phylogenomic analyses of Australian terrestrial vertebrates. Molecular ecology resources, 17(5), pp.869-876.
Wiener, E., Cottino, L., Botha, G., Nyangiri, O., Noyes, H., McLeod, A., Jakubosky, D., Adebamowo, C., Awadalla, P., Landouré, G. and Matshaba, M., 2024. An assessment of the genomic structural variation landscape in Sub-Saharan African populations. Research square, pp.rs-3.
Nambala, P., Noyes, H., Namulondo, J., Nyangiri, O., Alibu, V.P., Nerima, B., MacLeod, A., Matovu, E., Musaya, J., Mulindwa, J. and TrypanoGEN+ Research Group as Members of the H3Africa Consortium, 2024. Transcriptome profiles of Trypanosoma brucei rhodesiense in Malawi reveal focus specific gene expression profiles associated with pathology. PLOS Neglected Tropical Diseases, 18(5), p.e0011516.
Sokouri, E.A., Ahouty Ahouty, B., N’Djetchi, M., Abé, I.A., Yao, B.G.F.D., Konan, T.K., MacLeod, A., Noyes, H., Nyangiri, O., Matovu, E. and Koffi, M., 2024. Impact of environmental factors on Biomphalaria pfeifferi vector capacity leading to human infection by Schistosoma mansoni in two regions of western Côte d'Ivoire. Parasites & vectors, 17(1), p.179.
Astuti, Y., Raymant, M., Quaranta, V., Clarke, K., Abudula, M., Smith, O., Bellomo, G., Chandran-Gorner, V., Nourse, C., Halloran, C. and Ghaneh, P., 2024. Efferocytosis reprograms the tumor microenvironment to promote pancreatic cancer liver metastasis. Nature cancer, pp.1-17.

Publications from previous years can be found by following the links below:

The CGR has the following Research Resource Identifier (RRID): SCR_027394

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