Publications
2023
Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis
Hares, M. F., Griffiths, B. E., Johnson, F., Nelson, C., Haldenby, S., Stewart, C. J., . . . Coombes, J. L. (2023). Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis. Animal Microbiome, 5(1). doi:10.1186/s42523-023-00265-5
Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: A metagenomic analysis
Enhancing Infectious Intestinal Disease diagnosis through metagenomic and metatranscriptomic sequencing of over 1000 human diarrhoeal samples
2022
Author Correction: SARS-CoV-2 evolution during treatment of chronic infection.
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., . . . Gupta, R. K. (2022). Author Correction: SARS-CoV-2 evolution during treatment of chronic infection.. Nature, 608(7922), E23. doi:10.1038/s41586-022-05104-2
Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., . . . Gupta, R. K. (2022). Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.. Nature, 608(7922), E24. doi:10.1038/s41586-022-05103-3
Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.
Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2022). Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.. Nature, 606(7915), E18. doi:10.1038/s41586-022-04887-8
Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Donovan-Banfield, I., . . . Hiscox, J. A. (2022). Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. GIGASCIENCE, 11. doi:10.1093/gigascience/giac045
SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.
Ashford, F., Best, A., Dunn, S. J., Ahmed, Z., Siddiqui, H., Melville, J., . . . McNally, A. (2022). SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.. Journal of clinical microbiology, 60(4), e0240821. doi:10.1128/jcm.02408-21
2021
Genomic reconstruction of the SARS-CoV-2 epidemic in England
Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), 506-511. doi:10.1038/s41586-021-04069-y
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells
de, S. T. I., Liu, G., Lindsey, B. B., Dong, D., Moore, S. C., Hsu, N. S., . . . Dong, T. (2021). The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. ISCIENCE, 24(11). doi:10.1016/j.isci.2021.103353
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., . . . Gupta, R. K. (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. NATURE, 593(7857), 136-+. doi:10.1038/s41586-021-03412-7
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., . . . Gupta, R. K. (2021). SARS-CoV-2 evolution during treatment of chronic infection. NATURE, 592(7853), 277-+. doi:10.1038/s41586-021-03291-y
Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Salguero, J., . . . Hiscox, J. (2021). Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans. doi:10.1101/2021.03.03.433753
Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19
Salguero, F. J., White, A. D., Slack, G. S., Fotheringham, S. A., Bewley, K. R., Gooch, K. E., . . . Carroll, M. W. (2021). Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-21389-9
2020
Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom
Haldenby, S., Bronowski, C., Nelson, C., Kenny, J., Martinez-Rodriguez, C., Chaudhuri, R., . . . Winstanley, C. (2020). Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom. PLOS ONE, 15(01). doi:10.1371/journal.pone.0227535
2017
Transcriptomic and metabolic responses of <i>Calotropis procera</i> to salt and drought stress
Mutwakil, M. Z., Hajrah, N. H., Atef, A., Edris, S., Sabir, M. J., Al-Ghamdi, A. K., . . . Hall, N. (2017). Transcriptomic and metabolic responses of <i>Calotropis procera</i> to salt and drought stress. BMC PLANT BIOLOGY, 17. doi:10.1186/s12870-017-1155-7
<i>Campylobacter jejuni</i> transcriptome changes during loss of culturability in water
Bronowski, C., Mustafa, K., Goodhead, I., James, C. E., Nelson, C., Lucaci, A., . . . Winstanley, C. (2017). <i>Campylobacter jejuni</i> transcriptome changes during loss of culturability in water. PLOS ONE, 12(11). doi:10.1371/journal.pone.0188936
<i>Campylobacter jejuni</i>transcriptome changes during loss of culturability in water
A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus
Bosworth, A., Dowall, S. D., Garcia-Dorival, I., Rickett, N. Y., Bruce, C. B., Matthews, D. A., . . . Hiscox, J. A. (2017). A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus. SCIENTIFIC REPORTS, 7. doi:10.1038/srep43144
Transcriptomic analysis of salt stress responsive genes in <i>Rhazya stricta</i>
Hajrah, N. H., Obaid, A. Y., Atef, A., Ramadan, A. M., Arasappan, D., Nelson, C. A., . . . Jansen, R. K. (2017). Transcriptomic analysis of salt stress responsive genes in <i>Rhazya stricta</i>. PLOS ONE, 12(5). doi:10.1371/journal.pone.0177589