2021

Faber, M., Yoon, S., Shaw, S., de Paiva Alves, E., Wang, B., Zhitao, Q., Okamura, B., Hartikainen, H., Secombes, C.J., Holland, J.W. (2021) Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease. Scientific Reports. Link.

2020

Smith, N.M., Maloney, N.G., Shaw, S., Horgan, G.W., Fyfe, C., Martin, J.C., Suter, A., Scott, K.P., Johnstone, A.M. (2020) Daily Fermented Whey Consumption Alters the Fecal Short-Chain Fatty Acid Profile in Healthy Adults. Frontiers in Nutrition. Link.

Wenzel, M., Johnston, C., Müller, B., Pettitt, J. & Connolly, B. (2020) Resolution of polycistronic RNA bySL2 trans-splicing is a widely-conserved nematode trait. RNA. Link.

Afouda, B., Nakamura, Y., Shaw, S., Charney, R. M., Paraiso, K. D., Blitz, I. L., Cho, K. W. Y. & Hoppler, S. (2020) Foxh1/Nodal defines context-specific direct maternal Wnt/β-catenin target gene regulation in early development. iScience. Link.

Krol, E., Noguera, P., Shaw, S., Costelloe, E., Gajardo, K., Valdenegro, V., Bickerdike, R., Douglas, A. & Martin, S. (2020) Integration of transcriptome, gross morphology and histopathology in the gill of sea farmed Atlantic salmon (Salmo salar): Lessons from multi-site sampling. Frontiers in Genetics. Link.

Hijazi, K., Morrison, R.W., Mukhopadhya, I., Martin, B., Gemmell, M., Shaw, S. & Santoro, F. (2020) Oral bacterial diversity is inversely correlated with mucosal inflammation. Oral Diseases. Link.

Gusachenko, O.N., Woodford, L., Balbirnie-Cumming, K., Campbell, E.M., Christie, C.R., Bowman, A.S., & Evans, D.J. (2020) Green Bees: Reverse Genetic Analysis of Deformed Wing Virus Transmission, Replication, and Tropism. Viruses. 12(5), 532. Link.

McFarland, M.R., Keller, C.D., Childers, B.M., Adeniyi, S.A., Corrigall, H., Raguin, A., Carmen Romano, M.  & Stansfield, I. (2020) The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Nucleic Acids Research. 48 (6), 3071–3088. Link.

Beaurepaire, A., Piot, N., Doublet, V., Antunez, K., Campbell, E., Chantawannakul, P., Chejanovsky, N., Gajda, A., Heerman, M., Panziera, D., Smagghe, G., Yañez, O., de Miranda, J.R. & Dalmon, A. (2020) Diversity and Global Distribution of Viruses of the Western Honey Bee, Apis mellifera. Insects. 11(4), 239. Link.

Alessi, A.M., Gray, V., Farquharson, F.M., Flores‐López, A., Shaw, S., Stead, D., Wegmann, U., Shearman, C., Gasson, M., Collie‐Duguid, E.S.R, Flint, H.J. & Louis P. (2020) β‐glucan is a major growth substrate for human gut bacteria related to Coprococcus eutactus. Environmental Microbiology. Link.

2019

Siemienowicz, K., Filis, P., Shaw, S., Douglas, A., Thomas, J., Mulroy, S., Howie, F., Fowler, P., Duncan, W.C. & Rae, M. (2019) Fetal androgen exposure is a determinant of adult male metabolic health. Scientific Reports. 9: 20195 (2019). Link.  

Figeac, N., Mohamed, A.D., Sun, C., Schönfelder, M., Marallanas, D., Garcia-Munoz, A., Missiaglia, E., Collie-Duguid, E., De Mello, V., Pobbati, A.V., Pruller, J., Jaka, O., Harridge, S.D.R., Hong, W., Shipley, J., Vargesson, N., Zammit, P.S. & Wackerhage, H. (2019) VGLL3 operates via TEAD1, TEAD3 and TEAD4 to influence myogenesis in skeletal muscle. Journal of Cell Science. 132(13). Link

Wasi, M., Khandelwal, N.K., Moorhouse, A.J., Nair, R., Vishwakarma, P., Bravo Ruiz, G., Ross, Z.K., Lorenz, A., Rudramurthy, S.M., Chakrabarti, A., Lynn, A.M., Mondal, A.K., Gow, N.A.R. & Prasad, R. (2019) ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes. Frontiers in Microbiology. 10:1445. Link

Lahari, Z., Ribeiro, A., Talukdar, P., Martin, B., Heidari, Z., Gheysen, G., Price, A.H. & Shrestha, R. (2019) QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.). Euphytica. 215:117. Link

Hsu, T., Gemmell, M.R., Franzosa, E.A., Berry, S., Mukhopadhya, I., Hansen, R., Michaud, M., Nielsen, H., Miller, W.G., Nielsen, H., Bajaj-Elliott, M., Huttenhower, C., Garrett, W.S. & Hold, G.L. (2019) Comparative genomics and genome biology of Campylobacter showae. Emerging Microbes and Infections. 8(1):827-840. Link

Derous, D., Sahu, J., Douglas, A., Lusseau, D. & Wenzel, M. (2019) Adaptations of energy metabolism in cetaceans have consequences for their response to foraging disruption. bioRxiv. https://doi.org/10.1101/709154.

Lopes, B.S., Strachan, N.J.C., Ramjee, M., Thomson, A., MacRae, M., Shaw, S. & Forbes, K. (2019) Nationwide stepwise emergence and evolution of multidrug-resistant Campylobacter jejuni sequence type 5136, United Kingdom. Emerging Infectious Disease. 25(7). Link 

Wenzel, M.A., Johnston, C., Müller, B., Pettitt, J., & Connolly, B. (2019) Deep evolutionary origin of nematode SL2 trans-splicing revealed by genome-wide analysis of the Trichinella spiralis transcriptome. bioRxiv. https://doi.org/10.1101/642082.

Pascoe, B., et al. (2019) Domestication of Campylobacter jejuni NCTC 11168. Microbial Genomics. 10.1099/mgen.0.000279. Link

2018

Brunner, K., John, C.M., Phillips, N.J., Alber, D.G., Gemmell, M.R., Hansen, R., Nielsen H.L., Hold, G.L., Bajaj-Elliott, M., & Jarvis, G.A. (2018) Novel Campylobacter concisus lipooligosaccharide is a determinant of inflammatory potential and virulence. Journal of Lipid Research. 59: 1893-1905. Link.

Norton, G.J., Travis, A.J., Douglas, A., Fairley, S., De Paiva Alves, E., Ruang-areerate, P., Naredo, M.E.B., McNally, K.L., Hossain, M., Islam, R.M. & Price, A.H. (2018) Genome wide association mapping of grain and straw biomass traits in the rice Bengal and Assam Aus Panel (BAAP) grown under alternate wetting and drying and permanently flooded irrigation. Frontiers in Plant Science. 9:1223. Link.

Dalby, M.J., Aviello, G., Ross, S., Walker, A.W., Barrett, P. & Morgan, P.J. (2018) Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N. Scientific Reports. 8: 15648. Link

Perez Calderon, L.J., Gontikaki, E., Potts, L.D., Shaw, S., Gallego, A., Anderson, J.A. & Witte, U. (2018) Effects of pressure and temperature on deep sea hydrocarbon-degrading microbial communities in subartic sedmiments. Microbiology Open. 16(e768). Link

Mukhopadhya, I., Gomez, J., Duncan, S., Louis, P., Shaw, S., Collie-Duguid, E., Crost, E., Juge, N. & Flint, H. (2018) Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in cocultures of acetogenic and amylolytic human gut bacteria. Environmental Microbiology. Link

Wenzel, M.A., Douglas, A. & Piertney, S.B. (2018) Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons). PLoS ONE 13(8): e0202212. Link

Hiraga, S., Monerawela, C., Katou, Y., Shaw, S., Clark, K., Shirahige, K. & Donaldson, A. (2018) Budding yeast Rif1 bind to replication origins and protects DNA at blocked replication forks. EMBO reports. e46222. Link.

Edwards, C., Baird, J., Zinser, E., Woods, D., Shaw, S., Campbell, E.M. & Bowman, A. (2018) RNA-interference in the cat flea, Ctenocephalides felis: approaches for sustained gene knockdown and evidence of involvement of Dicer-2 and Argonaute2. International Journal for Parasitology. S0020-7519(18)30207-8. Link.

Gemmell, M.R., Berry, S., Mukhopadhya, I., Hansen, R., Nielsen, H.L., Bajaj-Elliott, M., Nielsen, H., & Hold, G.L. (2018) Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential. Emerging Microbes & Infections. 7:116. Link.

Garg, M., Hendy, P., Ding, J.N., Shaw, S., Hold, G., & Hart, A. (2018) The effect of vitamin D on intestinal inflammation and faecal microbiota in patients with ulcerative colitis. Journal of Crohn's and Colitis. jjy052. Link.

Hansen, R., Gibson, S., de Paiva Alves, E., Goddard, M., MacLaren, A., Karcher, A.M., Berry, S., Collie-Duguid, E., El-Omar, E., Munro, M., & Hold G.L. (2018) Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin. Scientific Reports. 8:6470. Link.

Afouda, B.A., Lynch, A.T., de Paiva Alves, E., & Hoppler, S. (2018) Genome-wide transcriptomics analysis of genes regulated by GATA4, 5 and 6 during cardiomyogenesis in Xenopus laevis. Data in Brief. Link.

2017 

Afouda, B.A., Lynch, A.T., de Paiva Alves, E., & Hoppler, S. (2017) Genome-wide transcriptomics analysis identifies sox7 and sox18 as specifically regulated by gata4 in cardiomyogenesis. Developmental Biology. Link.

Swortwood, M.J., Bartock, S.H., Scheidweiler, K.B., Shaw, S., Filis, P., Douglas, A., O'Shaughnessy, P.J., Soffientini, U., Lucendo-Villarin, B., Iredale, J.P., Hay, D.C., Fowler, P.A., Huestis, M.A. (2017) Quantification of ethyl glucuronide, ethyl sulfate, nicotine, and its metabolites in human fetal liver and placenta. Forensic Toxicology. Link

Sun, C., De Mello, V., Mohamed, A., Ortuste Quiroga, H.P., Garcia-Munoz, A., Al Bloshi, A., Tremblay, A.M., von Kriegsheim, A., Collie-Duguid, E., Vargesson, N., Matallanas, D., Wackerhage, H., & Zammit, P.S. (2017) Common and distinctive functions of the Hippo effectors Taz and Yap in skeletal muscle stem cell function. Stem Cells. epub ahead of print. Link

Pradhan, A., Herrero-de-Dios, C., Belmonte, R., Budge, S., Garcia, A.L., Kolmogorova, A., Lee, K.K., Martin, B.D., Ribeiro, A., Bebes, A., Yuecel, R., Gow, N.A.R., Munro, C., MacCallum, D.M., Quinn, J., & Brown, A.J.P. (2017) Elevated catalase expression in a fungal pathogen is a double-edged sword of iron. PLoS Pathogens. 13(5):e1006405. Link.

Morrice, N., McIlroy, G.D., Tammireddy, S., Reekie, J., Shearer, K.D., Doherty, M.K., Delibegovic, M., Whitfield, P.D., & Mody, N. (2017) Elevated Fibroblast growth factor 21 (FGF21) in obese, insulin resistant states is normalised by the synthetic retinoid Fenretinide in mice. Scientific Reports. 7: 43782. Link.

Dehler, C. E., Secombes, C. J., & Martin, S. A. (2016). Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.). AquacultureLink.

Carroll, A., Cheng, R., Collie-Duguid, E., Meharg, C., Scholz, M. E., Fiering, S. N., Fields, J. L., Palmer, A. A., Lionikas, A. (2017) Fine mapping of genes determining extrafusal fiber properties in murine soleus muscle. Physiological Genomics Jan 13:physiolgenomics.00092.2016. Link.

2016

Ballou, Elizabeth R., et al. "Lactate signalling regulates fungal β-glucan masking and immune evasion." Nature Microbiology 2 (2016): 16238. Link.

Watt, E., Gemmell, M. R., Berry, S., Glaire, M., Farquharson, F., Louis, P., ... & Hold, G. L. (2016). Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies. Microbiome, 4(1), 61. Link.

Ikeh, M. A., Kastora, S. L., Day, A. M., Herrero-de-Dios, C. M., Tarrant, E., Waldron, K. J., ... & MacCallum, D. M. (2016). Pho4 mediates phosphate acquisition in Candida albicans and is vital for stress resistance and metal homeostasis. Molecular Biology of the Cell27(17), 2784-2801. Link.

Hijazi, K., Mukhopadhya, I., Abbott, F., Milne, K., Al-Jabri, Z. J., Oggioni, M. R., & Gould, I. M. (2016). Susceptibility to chlorhexidine amongst multidrug-resistant clinical isolates of Staphylococcus epidermidis from bloodstream infections. International journal of antimicrobial agentsLink.

Shaw, S., Le Cocq, K., Paszkiewicz, K., Moore, K., Winsbury, R., de Torres Zabala, M., Studholme, D., Salmon, D., Thornton, C.R. and Grant, M.R., (2016). Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil. Molecular plant pathology. Link.

Leach, M. D., Farrer, R. A., Tan, K., Miao, Z., Walker, L. A., Cuomo, C. A., ... & Cowen, L. E. (2016). Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nature communications7. Link.

Nakamura, Y., de Paiva Alves, E., Veenstra, G.J.C. & Hoppler, S. (2016) Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules. Development; 143(11):1914-25. Link.

Lehtovirta-Morley, L. E., Ross, J., Hink, L., Weber, E. B., Gubry-Rangin, C., Thion, C., ... & Nicol, G. W. (2016). Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS microbiology ecology92(5), fiw057. Link.

Derous, D., Mitchell, S.E., Green, C.L., Chen, L., Han, J.J., Wang, Y., et al. (2016) The effects of graded levels of calorie restriction: VI. Impact of short-term graded calorie restriction on transcriptomic responses of the hypothalamic hunger and circadian signaling pathways. Aging. Link


2015

Ribeiro, A., A. Golicz, C.A. Hackett, I. Milne, G. Stephen, D. Marshall, A.J. Flavell, and M. Bayer. 2015. An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome. BMC Bioinformatics 16(1):1–16. Link

Li, R., Redmond, A. K., Wang, T., Bird, S., Dooley, H., & Secombes, C. J. (2015). Characterisation of the TNF superfamily members CD40L and BAFF in the small-spotted catshark (Scyliorhinus canicula). Fish & shellfish immunology47(1), 381-389. Link.

Strachan, N. J., Rotariu, O., Lopes, B., MacRae, M., Fairley, S., Laing, C., ... & Ashton, P. (2015). Whole genome sequencing demonstrates that geographic variation of Escherichia coli O157 genotypes dominates host association. Scientific reports, 5. Link.

Lusseau, D., Mitchell, S.E., Barros, C., Derous, D., Green, C., Chen, L., et al. (2015) The effects of graded levels of calorie restriction: IV. Non-linear change in behavioural phenotype of mice in response to short-term calorie restriction. Sci Rep. 5:13198. Link

Shearer, K., Morrice, N., Henderson, C., Reekie, J., McIlroy, G., McCaffery, P., Delibegovic, M., Mody, N. (2015) Fenretinide prevents obesity in female mice via the interaction between retinoid and estrogen signalling. Obesity; 23:1655-62. Link

Mitchell, S.E., Tang, Z., Kerbois, C., Delville, C., Konstantopedos, P., Bruel. A, et al. (2015) The effects of graded levels of calorie restriction: I. impact of short term calorie and protein restriction on body composition in the C57BL/6 mouse. Oncotarget; 6:15902–15930. Link

Mitchell, S.E., Delville, C., Konstantopedos, P., Hurst, J., Derous, D., Green, C., et al. (2015) The effects of graded levels of calorie restriction: II. impact of short term calorie and protein restriction on circulating hormone levels, glucose homeostasis and oxidative stress in male C57BL/6 mice. Oncotarget. 6:23213–23237. Link

Mitchell, S.E., Delville, C., Konstantopedos, P., Derous, D., Green, C.L., Chen, L., et al. (2015) The effects of graded levels of calorie restriction: III. impact of short term calorie and protein restriction on mean daily body temperature and torpor use in the C57BL/6 mouse. Oncotarget. 6:18314–18337. Link

Zou, J., Redmond, A.K., Qi, Z., Dooley, H., Secombes, C.J. (2015) The CXC chemokine receptors of fish: insights into CXCR evolution in the vertebrates. Gen Comp Endocrinol; 215:117-31. Link

Weber, E.B., Lehtovirta, L.E., Prosser, J.I., Gubry-Rangin, C. (2015). Ammonia oxidation is not required for growth of Group 1.1c soil thaumarchaea. FEMS Microbiology Ecology; 91:3 Link


2014

Flink, L. G., Allen, R., Barnett, R., Malmström, H., Peters, J., Eriksson, J., ... & Larson, G. (2014). Establishing the validity of domestication genes using DNA from ancient chickens. Proceedings of the National Academy of Sciences111(17), 6184-6189. Link.