Publications - Centre for Genomic Research

Selected Publications from 2023/2024

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.
Iannucci, S., Harvey, W.T., Hughes, J., Robertson, D.L., Poyade, M. and Hutchinson, E., 2023. The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. Journal of Visual Communication in Medicine, 46(3), pp.122-132.
Pascall, D.J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N. and Fjodorova, L., 2023. Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection.
Pascall, D.J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N. and Fjodorova, L., 2023. The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis. Plos one, 18(4), p.e0284187.
Cook, K.F., Beckett, A.H., Glaysher, S., Goudarzi, S., Fearn, C., Loveson, K.F., Elliott, S., Wyllie, S., Lloyd, A., Bicknell, K. and Lumley, S., 2023. Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK. Frontiers in cellular and infection microbiology, 12, p.1968.
Burnside, G., Cheyne, C.P., Leeming, G., Humann, M., Darby, A., Green, M.A., Crozier, A., Maskell, S., O’Halloran, K., Musi, E. and Carmi, E., 2023. COVID-19 risk mitigation in reopening mass cultural events: population-based observational study for the UK Events Research Programme in Liverpool City Region. Journal of the Royal Society of Medicine, p.01410768231182389.
Foxley-Marrable, M., D’Cruz, L., Meredith, P., Glaysher, S., Beckett, A.H., Goudarzi, S., Fearn, C., Cook, K.F., Loveson, K.F., Dent, H. and Paul, H., 2023. Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust. Plos one, 18(3), p.e0283447.
Cox, M., Peacock, T.P., Harvey, W.T., Hughes, J., Wright, D.W., Willett, B.J., Thomson, E., Gupta, R.K., Peacock, S.J., Robertson, D.L. and Carabelli, A.M., 2023. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature Reviews Microbiology, 21(2), pp.112-124.
Colton, H., Parker, M.D., Stirrup, O., Blackstone, J., Loose, M., McClure, C.P., Roy, S., Williams, C., McLeod, J., Smith, D. and Taha, Y., 2023. Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. Journal of Hospital Infection, 131, pp.34-42.
Cotton, S., McHugh, M.P., Dewar, R., Haas, J.G., Templeton, K., Robson, S.C., Connor, T.R., Loman, N.J., Golubchik, T., Nunez, R.T.M. and Bonsall, D., 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection, 135, pp.28-36.
Bailey, C., Sanderson, T., Townsley, H., Goldman, J., Black, J.R., Young, G., Goldstone, R., Fowler, A.S., Ward, S., Jackson, D.J. and Cubitt, L., 2023. Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London. The Lancet.
Dunn, J.C., Thomas, R.C., Hipperson, H., Sheehan, D.J., Orsman, C., Mallord, J. and Goodman, S.J., 2023. Evidence for strain-specific virulence of Trichomonas gallinae in African columbiformes. Parasitology, 150(2), pp.206-211.
Ransome, E., Hobbs, F., Jones, S., Coleman, C.M., Harris, N.D., Woodward, G., Bell, T., Trew, J., Kolarević, S., Kračun-Kolarević, M. and Savolainen, V., 2023. Evaluating the transmission risk of SARS-CoV-2 from sewage pollution. Science of The Total Environment, 858, p.159161.
Barnes, K., Levy, J., Andersen, K., Gauld, J., Rigby, J., Kanjerwa, O., Uzzell, C., Chilupsya, C., Anscombe, C., Tomkins-Tinch, C. and Mbeti, O., 2023. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems. Research Square.
Laine, V.N., Sävilammi, T., Wahlberg, N., Meramo, K., Ossa, G., Johnson, J.S., Blomberg, A.S., Yeszhanov, A.B., Yung, V., Paterson, S. and Lilley, T.M., 2023. Whole-genome analysis reveals contrasting relationships among nuclear and mitochondrial genomes between three sympatric bat species. Genome biology and evolution, 15(1), p.evac175.
Wanelik, K.M., Begon, M., Bradley, J.E., Friberg, I.M., Jackson, J.A., Taylor, C.H. and Paterson, S., 2023. Effects of an IgE receptor polymorphism acting on immunity, susceptibility to infection, and reproduction in a wild rodent. Elife, 12, p.e77666.
Brunner, F., Payne, A., Cairns, E., Airey, G., Gregory, R., Pickwell, N., Holmes, N., Wilson, M., Carlile, M., Hill, V. and Child, H., 2023. Wastewater genomic surveillance tracks the spread of the SARS-CoV-2 Omicron variant across England. medRxiv, pp.2023-02.
Taylor, C.H., Friberg, I.M., Jackson, J.A., Arriero, E., Begon, M., Wanelik, K.M., Paterson, S. and Bradley, J.E., 2023. Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent. Molecular ecology, 32(5), pp.1197-1210.
Fenn, J., Taylor, C., Goertz, S., Wanelik, K.M., Paterson, S., Begon, M., Jackson, J. and Bradley, J., 2023. Discrete patterns of microbiome variability across timescales in a wild rodent population. BMC microbiology, 23(1), p.87.
Maestri, A., Pursey, E., Chong, C., Pons, B.J., Gandon, S., Custodio, R., Chisnall, M., Grasso, A., Paterson, S., Baker, K.S. and van Houte, S., 2023. Bacterial defences interact synergistically by disrupting phage cooperation. bioRxiv, pp.2023-03.
Child, H.T., O’Neill, P.A., Moore, K., Rowe, W., Denise, H., Bass, D., Wade, M.J., Loose, M., Paterson, S., van Aerle, R. and Jeffries, A.R., 2023. Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing. PLoS One, 18(4), p.e0284211.
Bassano, I., Ramachandran, V.K., Khalifa, M.S., Lilley, C.J., Brown, M.R., van Aerle, R., Denise, H., Rowe, W., George, A., Cairns, E. and Wierzbicki, C., 2023. Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples. Microbial Genomics, 9(4).
Keshaviah, A., Diamond, M.B., Wade, M.J., Scarpino, S.V., Ahmed, W., Amman, F., Aruna, O., Badilla-Aguilar, A., Bar-Or, I., Bergthaler, A. and Bines, J.E., 2023. Wastewater monitoring can anchor global disease surveillance systems. The Lancet Global Health, 11(6), pp.e976-e981.
Wanelik, K.M., Begon, M., Bradley, J.E., Friberg, I.M., Taylor, C.H., Jackson, J.A. and Paterson, S., 2023. Early life immune expression profiles predict later life health and fitness in a wild rodent. Molecular ecology.
Kharaz, Y.A., Fang, Y., Welting, T., Peffers, M. and Comerford, E.J., 2020. Small RNA signatures of the anterior cruciate ligament from patients with knee joint osteoarthritis. MedRxiv, pp.2020-05.
Nyangiri, O.A., Mulindwa, J., Namulondo, J., Kitibwa, A., Nassuuna, J., Elliott, A., Kimuda, M.P., Boobo, A., Nerima, B., Adriko, M. and Dunton, N.J., 2023. Variants of IL6, IL10, FCN2, RNASE3, IL12B and IL17B loci are associated with Schistosoma mansoni worm burden in the Albert Nile region of Uganda. PLOS Neglected Tropical Diseases, 17(11), p.e0011796.
Nambala, P., Mulindwa, J., Noyes, H., Alibu, V.P., Nerima, B., Namulondo, J., Nyangiri, O., Matovu, E., MacLeod, A., Musaya, J. and TrypanoGEN+ Research Group as Members of the H3Africa Consortium, 2023. Differences in gene expression profiles in early and late stage rhodesiense HAT individuals in Malawi. PLOS Neglected Tropical Diseases, 17(12), p.e0011803.
Namulondo, J., Nyangiri, O.A., Kimuda, M.P., Nambala, P., Nassuuna, J., Egesa, M., Nerima, B., Biryomumaisho, S., Mugasa, C.M., Nabukenya, I. and Kato, D., 2023. Transcriptome analysis of peripheral blood of Schistosoma mansoni infected children from the Albert Nile region in Uganda reveals genes implicated in fibrosis pathology. bioRxiv, pp.2023-06.
Zamboulis, D.E., Marr, N., Lenzi, L., Birch, H.L., Screen, H.R., Clegg, P.D. and Thorpe, C.T., 2023. The interfascicular matrix of energy storing tendons houses heterogenous cell populations disproportionately affected by ageing. bioRxiv, pp.2023-01.
Panca, M., Blackstone, J., Stirrup, O., Cutino-Moguel, M.T., Thomson, E., Peters, C., Snell, L.B., Nebbia, G., Holmes, A., Chawla, A. and Machin, N., 2023. Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals. Journal of Hospital Infection.
Fisher, A.M., Airey, G., Liu, Y., Gemmell, M., Thomas, J., Bentley, E.G., Whitehead, M.A., Paxton, W.A., Pollakis, G., Paterson, S. and Viney, M., 2023. The ecology of viruses in urban rodents with a focus on SARS-CoV-2. Emerging microbes & infections, (just-accepted), p.2217940.
Olsson-Brown, A., Yip, V., Ogiji, E.D., Jolly, C., Ressel, L., Sharma, A., Bergfeld, W., Liu, X., Khirwadkar, N., Bellon, T. and Dickinson, A., 2023. TNF-α‒Mediated keratinocyte expression and release of matrix metalloproteinase 9: Putative mechanism of pathogenesis in stevens‒johnson syndrome/toxic epidermal necrolysis. Journal of Investigative Dermatology, 143(6), pp.1023-1030.
Quinn, L.M., Haldenby, S., Antzcak, P., Fowler, A., Bullock, K., Kenny, J., Gilbert, T., Andrews, T., Diaz-Nieto, R., Fenwick, S. and Jones, R., 2023. Genomic profiling of idiopathic peri-hilar cholangiocarcinoma reveals new targets and mutational pathways. Scientific Reports, 13(1), p.6681.
Sollazzo, G., Gouvi, G., Nikolouli, K., Aumann, R.A., Djambazian, H., Whitehead, M.A., Berube, P., Chen, S.H., Tsiamis, G., Darby, A.C. and Ragoussis, J., 2023. Genomic and cytogenetic analysis of the Ceratitis capitata temperature-sensitive lethal region. G3: Genes, Genomes, Genetics, p.jkad074.
Charras, A., Haldenby, S., Smith, E.M., Egbivwie, N., Olohan, L., Kenny, J.G., Schwarz, K., Roberts, C., Al-Abadi, E., Armon, K. and Bailey, K., 2023. Panel sequencing links rare, likely damaging gene variants with distinct clinical phenotypes and outcomes in juvenile-onset SLE. Rheumatology, 62(SI2), pp.SI210-SI225.
Pérez-Hernández, T., Hernández, J.N., Machín, C., McNeilly, T.N., Nisbet, A.J., Matthews, J.B., Burgess, S.T. and González, J.F., 2023. Exploring the transcriptomic changes underlying recombinant vaccine efficacy against Teladorsagia circumcincta in 3-month-old lambs. Veterinary Parasitology, p.109960.
Dimitriu, T., Souissi, W., Morwool, P., Darby, A., Crickmore, N. and Raymond, B., 2023. Selecting for infectivity across metapopulations can increase virulence in the social microbe Bacillus thuringiensis. Evolutionary Applications, 16(3), pp.705-720.
Mewamba, E.M., Noyes, H., Tiofack, A.A.Z., Kamga, R.M.N., Kamdem, C.N., Mengoue, L.E.T., Ofon, E., Ngassam, R.I.K., Nyangiri, O., Bucheton, B. and Njiokou, F., 2023. Association between polymorphisms of IL4, IL13, IL10, STAT6 and IFNG genes, cytokines and immunoglobulin E levels with high burden of Schistosoma mansoni in children from schistosomiasis endemic areas of Cameroon. Infection, Genetics and Evolution, 111, p.105416.
Beesley, N.J., Cwiklinski, K., Allen, K., Hoyle, R.C., Spithill, T.W., La Course, E.J., Williams, D.J., Paterson, S. and Hodgkinson, J.E., 2023. A major locus confers triclabendazole resistance in Fasciola hepatica and shows dominant inheritance. PLoS Pathogens, 19(1), p.e1011081.

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

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