2023
Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution (Preprint)
DOI: 10.1101/2023.11.06.565769
2022
Rate of COVID-19 infection and 30 day mortality between blue and green (dedicated COVID-19 safe) pathways: Results from phase 1 and 2 of the UK foot and ankle COVID-19 national (UK-FAlCoN) audit (Journal article)
Malhotra, K., Mangwani, J., Houchen-Wollof, L., Mason, L. W., & UK, F. A. C. (2022). Rate of COVID-19 infection and 30 day mortality between blue and green (dedicated COVID-19 safe) pathways: Results from phase 1 and 2 of the UK foot and ankle COVID-19 national (UK-FAlCoN) audit. FOOT AND ANKLE SURGERY, 28(7), 1055-1063. doi:10.1016/j.fas.2022.02.017DOI: 10.1016/j.fas.2022.02.017
Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., . . . Thomson, E. C. (2022). SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (vol 7, pg 1161, 2022). NATURE MICROBIOLOGY, 7(10), 1709. doi:10.1038/s41564-022-01241-6DOI: 10.1038/s41564-022-01241-6
Wilkinson, S. A. J., Richter, A., Casey, A., Osman, H., Mirza, J. D., Stockton, J., . . . Loman, N. J. (2022). Recurrent SARS-CoV-2 mutations in immunodeficient patients.. Virus evolution, 8(2), veac050. doi:10.1093/ve/veac050DOI: 10.1093/ve/veac050
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/s41586-022-05104-2DOI: 10.1038/s41586-022-05104-2
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/s41586-022-05103-3DOI: 10.1038/s41586-022-05103-3
Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., . . . Thomson, E. C. (2022). SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. NATURE MICROBIOLOGY, 7(8), 1161-+. doi:10.1038/s41564-022-01143-7DOI: 10.1038/s41564-022-01143-7
Nickbakhsh, S., Hughes, J., Christofidis, N., Griffiths, E., Shaaban, S., Enright, J., . . . Smith-Palmer, A. (2022). Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12(1). doi:10.1038/s41598-022-15661-1DOI: 10.1038/s41598-022-15661-1
Klaser, K., Molteni, E., Graham, M., Canas, L. S., Osterdahl, M. F., Antonelli, M., . . . Duncan, E. L. (2022). COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-14016-0DOI: 10.1038/s41598-022-14016-0
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/s41586-022-04887-8DOI: 10.1038/s41586-022-04887-8
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.02408-21DOI: 10.1128/jcm.02408-21
Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., . . . Harrison, E. M. (2022). Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-28371-zDOI: 10.1038/s41467-022-28371-z
Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., . . . Consor, C. G. U. K. C. O. G. -U. K. (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-021-27942-wDOI: 10.1038/s41467-021-27942-w
2021
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-yDOI: 10.1038/s41586-021-04069-y
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.2021.103353DOI: 10.1016/j.isci.2021.103353
Ward, C. M., Aumann, R. A., Whitehead, M. A., Nikolouli, K., Leveque, G., Gouvi, G., . . . Schetelig, M. F. (2021). White pupae phenotype of tephritids is caused by parallel mutations of a MFS transporter. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-020-20680-5DOI: 10.1038/s41467-020-20680-5
2020
Darby, A. (2020). An integrated national scale SARS-CoV-2 genomic surveillance network. The Lancet Microbe. doi:10.1016/s2666-5247(20)30054-9DOI: 10.1016/s2666-5247(20)30054-9
Zhu, W., Liu, X., Hughes, M., de Crécy-Lagard, V., & Richards, N. G. J. (2020). Whole-Genome Sequence of Streptomyces kaniharaensis Shomura and Niida SF-557.. Microbiology Resource Announcements, 9(14). doi:10.1128/mra.01434-19DOI: 10.1128/mra.01434-19
Darby, A. C., Goodhead, I., Blow, F., Brownridge, P., Hughes, M., Kenny, J., . . . Beynon, R. (2020). Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microbial Genomics, 6(1), 3-15. doi:10.1099/mgen.0.000285DOI: 10.1099/mgen.0.000285
2019
Hope, W., Stone, N. R. H., Johnson, A., McEntee, L., Farrington, N., Santoro-Castelazo, A., . . . Bicanic, T. (2019). Fluconazole Monotherapy Is a Suboptimal Option for Initial Treatment of Cryptococcal Meningitis Because of Emergence of Resistance.. mBio, 10(6). doi:10.1128/mbio.02575-19DOI: 10.1128/mbio.02575-19
2018
Burgess, S. T. G., Bartley, K., Nunn, F., Wright, H. W., Hughes, M., Gemmell, M., . . . Nisbet, A. J. (2018). Draft Genome Assembly of the Poultry Red Mite, <i>Dermanyssus gallinae</i>. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 7(18). doi:10.1128/MRA.01221-18DOI: 10.1128/MRA.01221-18
Burgess, S. T. G., Bartley, K., Marr, E. J., Wright, H. W., Weaver, R. J., Prickett, J. C., . . . Nisbet, A. J. (2018). Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis.. Genome announcements, 6(16). doi:10.1128/genomeA.00265-18DOI: 10.1128/genomeA.00265-18
Gaither, M. R., Gkafas, G. A., de Jong, M., Sarigol, F., Neat, F., Regnier, T., . . . Hoelzel, A. R. (2018). Genomics of habitat choice and adaptive evolution in a deep-sea fish. NATURE ECOLOGY & EVOLUTION, 2(4), 680-687. doi:10.1038/s41559-018-0482-xDOI: 10.1038/s41559-018-0482-x
2017
Large scale and significant expression from pseudogenes in <i>Sodalis glossinidius</i> - a facultative bacterial endosymbiont (Preprint)
DOI: 10.1101/124388
D'Amore, R., Johnson, J., Haldenby, S., Hall, N., Hughes, M., Joynson, R., . . . Hall, A. (2017). SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms. BIOTECHNIQUES, 63(1), 13-20. doi:10.2144/000114565DOI: 10.2144/000114565
2016
Aljabr, W., Touzelet, O., Pollakis, G., Wu, W., Munday, D. C., Hughes, M., . . . Hiscox, J. A. (2016). Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach. JOURNAL OF VIROLOGY, 90(10), 4876-4888. doi:10.1128/JVI.02349-15DOI: 10.1128/JVI.02349-15
NGS-based assay for frequent newborn inherited diseases: from development to implementation (Preprint)
DOI: 10.1101/050419
2015
Molecular tools for studying the major malaria vector <i>Anopheles funestus</i>: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis (Journal article)
Weedall, G. D., Irving, H., Hughes, M. A., & Wondji, C. S. (2015). Molecular tools for studying the major malaria vector <i>Anopheles funestus</i>: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis. BMC GENOMICS, 16. doi:10.1186/s12864-015-2114-zDOI: 10.1186/s12864-015-2114-z
Phylogenomics of the killer whale indicates ecotype divergence in sympatry (Journal article)
Moura, A. E., Kenny, J. G., Chaudhuri, R. R., Hughes, M. A., Reisinger, R. R., de Bruyn, P. J. N., . . . Hoelzel, A. R. (2015). Phylogenomics of the killer whale indicates ecotype divergence in sympatry. HEREDITY, 114(1), 48-55. doi:10.1038/hdy.2014.67DOI: 10.1038/hdy.2014.67
2014
Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift (Journal article)
Moura, A. E., Kenny, J. G., Chaudhuri, R., Hughes, M. A., Welch, A. J., Reisinger, R. R., . . . Hoelzel, A. R. (2014). Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift. MOLECULAR ECOLOGY, 23(21), 5179-5192. doi:10.1111/mec.12929DOI: 10.1111/mec.12929
Novel Host-Related Virulence Factors Are Encoded by Squirrelpox Virus, the Main Causative Agent of Epidemic Disease in Red Squirrels in the UK (Journal article)
Darby, A. C., McInnes, C. J., Kjaer, K. H., Wood, A. R., Hughes, M., Martensen, P. M., . . . Chantrey, J. (2014). Novel Host-Related Virulence Factors Are Encoded by Squirrelpox Virus, the Main Causative Agent of Epidemic Disease in Red Squirrels in the UK. PLOS ONE, 9(7). doi:10.1371/journal.pone.0096439DOI: 10.1371/journal.pone.0096439
2013
Characterisation of the genomes of four putative vesiculoviruses: tench rhabdovirus, grass carp rhabdovirus, perch rhabdovirus and eel rhabdovirus European X (Journal article)
Stone, D. M., Kerr, R. C., Hughes, M., Radford, A. D., & Darby, A. C. (2013). Characterisation of the genomes of four putative vesiculoviruses: tench rhabdovirus, grass carp rhabdovirus, perch rhabdovirus and eel rhabdovirus European X. ARCHIVES OF VIROLOGY, 158(11), 2371-2377. doi:10.1007/s00705-013-1711-xDOI: 10.1007/s00705-013-1711-x
2012
Analysis of gene expression from the <i>Wolbachia</i> genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis (Journal article)
Darby, A. C., Armstrong, S. D., Bah, G. S., Kaur, G., Hughes, M. A., Kay, S. M., . . . Makepeace, B. L. (2012). Analysis of gene expression from the <i>Wolbachia</i> genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis. GENOME RESEARCH, 22(12), 2467-2477. doi:10.1101/gr.138420.112DOI: 10.1101/gr.138420.112
Genome Sequence for "<i>Candidatus</i> Mycoplasma haemominutum," a Low-Pathogenicity Hemoplasma Species (Journal article)
Barker, E. N., Darby, A. C., Helps, C. R., Peters, I. R., Hughes, M. A., Radford, A. D., . . . Tasker, S. (2012). Genome Sequence for "<i>Candidatus</i> Mycoplasma haemominutum," a Low-Pathogenicity Hemoplasma Species. JOURNAL OF BACTERIOLOGY, 194(4), 905-906. doi:10.1128/JB.06560-11DOI: 10.1128/JB.06560-11
2011
Molecular characterization of the uncultivatable hemotropic bacterium <i>Mycoplasma haemofelis</i> (Journal article)
Barker, E. N., Darby, A. C., Helps, C. R., Peters, I. R., Heesom, K. J., Arthur, C. J., . . . Tasker, S. (2011). Molecular characterization of the uncultivatable hemotropic bacterium <i>Mycoplasma haemofelis</i>. VETERINARY RESEARCH, 42. doi:10.1186/1297-9716-42-83DOI: 10.1186/1297-9716-42-83
A <i>De Novo</i> Expression Profiling of <i>Anopheles funestus</i>, Malaria Vector in Africa, Using 454 Pyrosequencing (Journal article)
Gregory, R., Darby, A. C., Irving, H., Coulibaly, M. B., Hughes, M., Koekemoer, L. L., . . . Wondji, C. S. (2011). A <i>De Novo</i> Expression Profiling of <i>Anopheles funestus</i>, Malaria Vector in Africa, Using 454 Pyrosequencing. PLOS ONE, 6(2). doi:10.1371/journal.pone.0017418DOI: 10.1371/journal.pone.0017418
2010
Goodhead, I., Archibald, A., Amwayi, P., Brass, A., Gibson, J., Hall, N., . . . Noyes, H. A. (2010). A Comprehensive Genetic Analysis of Candidate Genes Regulating Response to <i>Trypanosoma</i> <i>congolense</i> Infection in Mice. PLOS NEGLECTED TROPICAL DISEASES, 4(11). doi:10.1371/journal.pntd.0000880DOI: 10.1371/journal.pntd.0000880
Identification of Three Novel Superantigen-Encoding Genes in
<i>Streptococcus equi</i>
subsp.
<i>zooepidemicus</i>
,
<i>szeF</i>
,
<i>szeN</i>
, and
<i>szeP</i> (Journal article)
Paillot, R., Darby, A. C., Robinson, C., Wright, N. L., Steward, K. F., Anderson, E., . . . Waller, A. S. (2010). Identification of Three Novel Superantigen-Encoding Genes in <i>Streptococcus equi</i> subsp. <i>zooepidemicus</i> , <i>szeF</i> , <i>szeN</i> , and <i>szeP</i>. Infection and Immunity, 78(11), 4817-4827. doi:10.1128/iai.00751-10DOI: 10.1128/iai.00751-10
Identification of Three Novel Superantigen-Encoding Genes in <i>Streptococcus equi</i> subsp <i>zooepidemicus</i>, <i>szeF</i>, <i>szeN</i>, and <i>szeP</i> (Journal article)
Paillot, R., Darby, A. C., Robinson, C., Wright, N. L., Steward, K. F., Anderson, E., . . . Waller, A. S. (2010). Identification of Three Novel Superantigen-Encoding Genes in <i>Streptococcus equi</i> subsp <i>zooepidemicus</i>, <i>szeF</i>, <i>szeN</i>, and <i>szeP</i>. INFECTION AND IMMUNITY, 78(11), 4817-4827. doi:10.1128/IAI.00751-10DOI: 10.1128/IAI.00751-10
Characteristics of the genome of <i>Arsenophonus nasoniae</i>, son-killer bacterium of the wasp <i>Nasonia</i> (Journal article)
Darby, A. C., Choi, J. -H., Wilkes, T., Hughes, M. A., Werren, J. H., Hurst, G. D. D., & Colbourne, J. K. (2010). Characteristics of the genome of <i>Arsenophonus nasoniae</i>, son-killer bacterium of the wasp <i>Nasonia</i>. INSECT MOLECULAR BIOLOGY, 19, 75-89. doi:10.1111/j.1365-2583.2009.00950.xDOI: 10.1111/j.1365-2583.2009.00950.x
2009
Application of ESTs in microarray analysis. (Journal article)
Li, W., Olohan, L., Williams, D., Hughes, M., Gracey, A., & Cossins, A. (2009). Application of ESTs in microarray analysis.. Methods in molecular biology (Clifton, N.J.), 533, 289-309. doi:10.1007/978-1-60327-136-3_14DOI: 10.1007/978-1-60327-136-3_14
Expressed Sequence Tags (ESTs) (Chapter)
Parkinson, J. (Ed.) (2009). Expressed Sequence Tags (ESTs). In . Humana Press. doi:10.1007/978-1-60327-136-3DOI: 10.1007/978-1-60327-136-3
2008
Genomic resources and microarrays for the common carp <i>Cyprinus carpio </i>L. (Journal article)
Williams, D. R., Li, W., Hughes, M. A., Gonzalez, S. F., Vernon, C., Vidal, M. C., . . . Cossins, A. R. (2008). Genomic resources and microarrays for the common carp <i>Cyprinus carpio </i>L.. Journal of Fish Biology, 72(9), 2095-2117. doi:10.1111/j.1095-8649.2008.01875.xDOI: 10.1111/j.1095-8649.2008.01875.x
Genomic resources and microarrays for the common carp <i>Cyprinus carpio</i> L. (Journal article)
Williams, D. R., Li, W., Hughes, M. A., Gonzalez, S. F., Vernon, C., Vidal, M. C., . . . Cossins, A. R. (2008). Genomic resources and microarrays for the common carp <i>Cyprinus carpio</i> L.. JOURNAL OF FISH BIOLOGY, 72(9), 2095-2117. doi:10.1111/j.1095-8649.2008.01875.xDOI: 10.1111/j.1095-8649.2008.01875.x
2007
Understanding the molecular basis of environmental tolerance through transcriptomic analysis of extreme phenotypic variants (Journal article)
Cossins, A., Vernon, C., Hughes, M., & Williams, D. (2007). Understanding the molecular basis of environmental tolerance through transcriptomic analysis of extreme phenotypic variants. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 146(4), S150. doi:10.1016/j.cbpa.2007.01.303DOI: 10.1016/j.cbpa.2007.01.303
Single gene differentiation by DNA-modified carbon electrodes using an AC impedimetric approach (Journal article)
Davis, F., Hughes, M. A., Cossins, A. R., & Higson, S. P. J. (2007). Single gene differentiation by DNA-modified carbon electrodes using an AC impedimetric approach. ANALYTICAL CHEMISTRY, 79(3), 1153-1157. doi:10.1021/ac061070cDOI: 10.1021/ac061070c
Salinity adaptation and gene profiling analysis in the European eel (<i>Anguilla anguilla</i>) using microarray technology (Journal article)
Kalujnaia, S., McWilliam, I. S., Zaguinaiko, V. A., Feilen, A. L., Nicholson, J., Hazon, N., . . . Cramb, G. (2007). Salinity adaptation and gene profiling analysis in the European eel (<i>Anguilla anguilla</i>) using microarray technology. GENERAL AND COMPARATIVE ENDOCRINOLOGY, 152(2-3), 274-280. doi:10.1016/j.ygcen.2006.12.025DOI: 10.1016/j.ygcen.2006.12.025
2006
Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity (Journal article)
Cossins, A., Fraser, J., Hughes, M., & Gracey, A. (2006). Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity. JOURNAL OF EXPERIMENTAL BIOLOGY, 209(12), 2328-2336. doi:10.1242/jeb.02256DOI: 10.1242/jeb.02256
2005
Seasonally hibernating phenotype assessed through transcript screening (Journal article)
Williams, D. R., Epperson, L. E., Li, W. Z., Hughes, M. A., Taylor, R., Rogers, J., . . . Gracey, A. Y. (2005). Seasonally hibernating phenotype assessed through transcript screening. PHYSIOLOGICAL GENOMICS, 24(1), 13-22. doi:10.1152/physiolgenomics.00301.2004DOI: 10.1152/physiolgenomics.00301.2004
1997
Zebedee: a novel copia-Ty1 family of transposable elements in the genome of the medically important mosquito Aedes aegypti. (Journal article)
Warren, A. M., Hughes, M. A., & Crampton, J. M. (1997). Zebedee: a novel copia-Ty1 family of transposable elements in the genome of the medically important mosquito Aedes aegypti.. Molecular & general genetics : MGG, 254(5), 505-513. doi:10.1007/s004380050445DOI: 10.1007/s004380050445
1994
GENETIC MANIPULATION OF INSECT VECTORS AS A STRATEGY FOR THE CONTROL OF VECTOR-BORNE DISEASE (Journal article)
CRAMPTON, J. M., WARREN, A., LYCETT, G. J., HUGHES, M. A., COMLEY, I. P., & EGGLESTON, P. (1994). GENETIC MANIPULATION OF INSECT VECTORS AS A STRATEGY FOR THE CONTROL OF VECTOR-BORNE DISEASE. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY, 88(1), 3-12. doi:10.1080/00034983.1994.11812828DOI: 10.1080/00034983.1994.11812828
1992
MOLECULAR BIOLOGICAL APPROACHES TO THE STUDY OF VECTORS IN RELATION TO MALARIA CONTROL (Journal article)
CRAMPTON, J. M., COMLEY, I., EGGLESTON, P., HILL, S., HUGHES, M., KNAPP, T., . . . WARREN, A. (1992). MOLECULAR BIOLOGICAL APPROACHES TO THE STUDY OF VECTORS IN RELATION TO MALARIA CONTROL. MEMORIAS DO INSTITUTO OSWALDO CRUZ, 87, 43-49. doi:10.1590/S0074-02761992000700005DOI: 10.1590/S0074-02761992000700005
