2024
Microbiome and mitogenomics of the chigger mite Pentidionis agamae: Potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia (Preprint)
DOI: 10.21203/rs.3.rs-3837555/v1
Thoughts and perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study (Preprint)
DOI: 10.1101/2024.01.02.24300703
2023
Michael, B. D., Dunai, C., Needham, E. J., Tharmaratnam, K., Williams, R., Huang, Y., . . . Menon, D. K. (2023). Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses.. Nature communications, 14(1), 8487. doi:10.1038/s41467-023-42320-4DOI: 10.1038/s41467-023-42320-4
Cunningham-Oakes, E., Bronowski, C., Chinyama, E., Jere, K. C., Sindhu, K. N. C., Kang, G., . . . Parker, E. P. K. (2023). Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi.. BMC microbiology, 23(1), 354. doi:10.1186/s12866-023-03098-zDOI: 10.1186/s12866-023-03098-z
Martin Říhová, J., Gupta, S., Darby, A. C., Nováková, E., & Hypša, V. (2023). Arsenophonus symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance. mSystems, 8(5), e0070623. doi:10.1128/msystems.00706-23DOI: 10.1128/msystems.00706-23
Mandolo, J., Parker, E. P. K., Bronowski, C., Sindhu, K. N. C., Darby, A. C., Cunliffe, N. A., . . . Verghese, V. P. (n.d.). Association between maternal breastmilk microbiota composition and rotavirus vaccine response in African, Asian, and European infants: a prospective cohort study. The Journal of Infectious Diseases. doi:10.1093/infdis/jiad234DOI: 10.1093/infdis/jiad234
<i>Arsenophonus</i>symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance (Preprint)
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Beliavskaia, A., Tan, K. -K., Sinha, A., Husin, N. A., Lim, F. S., Loong, S. K., . . . Khoo, J. J. (2023). Metagenomics of culture isolates and insect tissue illuminate the evolution of <i>Wolbachia</i>, <i>Rickettsia</i> and <i>Bartonella</i> symbionts in <i>Ctenocephalides</i> spp. fleas.. Microbial genomics, 9(7). doi:10.1099/mgen.0.001045DOI: 10.1099/mgen.0.001045
Burnside, G., Cheyne, C. P., Leeming, G., Humann, M., Darby, A., Green, M. A., . . . Buchan, I. 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. doi:10.1177/01410768231182389DOI: 10.1177/01410768231182389
Sollazzo, G., Gouvi, G., Nikolouli, K., Aumann, R. A., Djambazian, H., Whitehead, M. A., . . . Bourtzis, K. (2023). Genomic and cytogenetic analysis of the Ceratitis capitata temperature-sensitive lethal region. G3-GENES GENOMES GENETICS, 13(6). doi:10.1093/g3journal/jkad074DOI: 10.1093/g3journal/jkad074
Labbé, F., Abdeladhim, M., Abrudan, J., Araki, A. S., Araujo, R. N., Arensburger, P., . . . McDowell, M. A. (2023). Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.. PLoS neglected tropical diseases, 17(4), e0010862. doi:10.1371/journal.pntd.0010862DOI: 10.1371/journal.pntd.0010862
Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi (Preprint)
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Goldswain, H., Dong, X., Penrice-Randal, R., Alruwaili, M., Shawli, G. T., Prince, T., . . . Hiscox, J. A. (2023). The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.. Genome biology, 24(1), 47. doi:10.1186/s13059-023-02881-5DOI: 10.1186/s13059-023-02881-5
Cotton, S., McHugh, M. P., Dewar, R., Haas, J. G., Templeton, K., & COVID-19 Genomics UK (COG-UK) Consortium. (2023). Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.. The Journal of hospital infection, 135, 28-36. doi:10.1016/j.jhin.2023.02.010DOI: 10.1016/j.jhin.2023.02.010
Panca, M., Blackstone, J., Stirrup, O., Cutino-Moguel, M. -T., Thomson, E., Peters, C., . . . Breuer, J. (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, 139, 23-32. doi:10.1016/j.jhin.2023.06.005DOI: 10.1016/j.jhin.2023.06.005
Dimitriu, T., Souissi, W., Morwool, P., Darby, A., Crickmore, N., & Raymond, B. (n.d.). Selecting for infectivity across metapopulations can increase virulence in the social microbe <i>Bacillus thuringiensis</i>. Evolutionary Applications. doi:10.1111/eva.13529DOI: 10.1111/eva.13529
Pottenger, S., Watts, A., Wedley, A., Jopson, S., Darby, A. C., & Wigley, P. (2023). Timing and delivery route effects of cecal microbiome transplants on <i>Salmonella </i>Typhimurium infections in chickens: potential for in-hatchery delivery of microbial interventions. ANIMAL MICROBIOME, 5(1). doi:10.1186/s42523-023-00232-0DOI: 10.1186/s42523-023-00232-0
Bay, V., Gillespie, A., Ganda, E., Evans, N. J., Carter, S. D., Lenzi, L., . . . Oikonomou, G. (n.d.). The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions. Microbiome, 11(1). doi:10.1186/s40168-022-01440-7DOI: 10.1186/s40168-022-01440-7
2022
Donovan-Banfield, I., Penrice-Randal, R., Goldswain, H., Rzeszutek, A. M., Pilgrim, J., Bullock, K., . . . Fletcher, T. (2022). Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-34839-9DOI: 10.1038/s41467-022-34839-9
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
Whiteford, S., Van't Hof, A. E., Krishna, R., Marubbi, T., Widdison, S., Saccheri, I. J., . . . Darby, A. C. (2022). Recovering individual haplotypes and a contiguous genome assembly from pooled long-read sequencing of the diamondback moth (Lepidoptera: Plutellidae). G3-GENES GENOMES GENETICS, 12(10). doi:10.1093/g3journal/jkac210DOI: 10.1093/g3journal/jkac210
Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., . . . Breuer, J. (2022). Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study. ELIFE, 11. doi:10.7554/eLife.78427DOI: 10.7554/eLife.78427
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
Eales, O., Page, A. J., de Oliveira Martins, L., Wang, H., Bodinier, B., Haw, D., . . . Elliott, P. (2022). SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases, 22(1). doi:10.1186/s12879-022-07628-4DOI: 10.1186/s12879-022-07628-4
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
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/giac045DOI: 10.1093/gigascience/giac045
Davison, H. R., Pilgrim, J., Wybouw, N., Parker, J., Pirro, S., Hunter-Barnett, S., . . . Siozios, S. (2022). Genomic diversity across the Rickettsia and 'Candidatus Megaira' genera and proposal of genus status for the Torix group. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-30385-6DOI: 10.1038/s41467-022-30385-6
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
The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions (Preprint)
DOI: 10.21203/rs.3.rs-650860/v2
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
Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study (Preprint)
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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
Aggarwal, D., Myers, R., Hamilton, W. L., Bharucha, T., Tumelty, N. M., Brown, C. S., . . . COVID-19 Genomics UK (COG-UK) Consortium. (2022). The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.. The Lancet. Microbe, 3(2), e151-e158. doi:10.1016/s2666-5247(21)00208-1DOI: 10.1016/s2666-5247(21)00208-1
Francis, R. V., Billam, H., Clarke, M., Yates, C., Tsoleridis, T., Berry, L., . . . COVID-19 Genomics UK (COG-UK) consortium. (2022). The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.. The Journal of infectious diseases, 225(1), 10-18. doi:10.1093/infdis/jiab483DOI: 10.1093/infdis/jiab483
Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission (Journal article)
Snell, L. B., Fisher, C. L., Taj, U., Stirrup, O., Merrick, B., Alcolea-Medina, A., . . . Awan, A. R. (2022). Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission. Clinical Microbiology and Infection, 28(1), 93-100. doi:10.1016/j.cmi.2021.07.040DOI: 10.1016/j.cmi.2021.07.040
Boshier, F. A. T., Pang, J., Penner, J., Parker, M., Alders, N., Bamford, A., . . . Breuer, J. (2022). Evolution of viral variants in remdesivir‐treated and untreated SARS‐CoV‐2‐infected pediatrics patients. Journal of Medical Virology, 94(1), 161-172. doi:10.1002/jmv.27285DOI: 10.1002/jmv.27285
2021
Elliott, P., Haw, D., Wang, H., Eales, O., Walters, C. E., Ainslie, K. E. C., . . . Riley, S. (2021). Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant. SCIENCE, 374(6574), 1463-+. doi:10.1126/science.abl9551DOI: 10.1126/science.abl9551
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
Parker, E. P. K., Bronowski, C., Sindhu, K. N. C., Babji, S., Benny, B., Carmona-Vicente, N., . . . Iturriza-Gomara, M. (2021). Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-27074-1DOI: 10.1038/s41467-021-27074-1
Mashe, T., Takawira, F. T., de Oliveira Martins, L., Gudza-Mugabe, M., Chirenda, J., Munyanyi, M., . . . SARS-CoV-2 Research Group. (2021). Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.. The Lancet. Global health, 9(12), e1658-e1666. doi:10.1016/s2214-109x(21)00434-4DOI: 10.1016/s2214-109x(21)00434-4
Davis, C., Logan, N., Tyson, G., Orton, R., Harvey, W. T., Perkins, J. S., . . . Willett, B. J. (n.d.). Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLOS Pathogens, 17(12), e1010022. doi:10.1371/journal.ppat.1010022DOI: 10.1371/journal.ppat.1010022
Boshier, F. A. T., Venturini, C., Stirrup, O., Guerra-Assunção, J. A., Alcolea-Medina, A., Becket, A. H., . . . Breuer, J. (2021). The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. Journal of Infection, 83(6), 693-700. doi:10.1016/j.jinf.2021.09.022DOI: 10.1016/j.jinf.2021.09.022
Goodfellow, L., Verwijs, M. C., Care, A., Sharp, A., Ivandic, J., Poljak, B., . . . van de Wijgert, J. H. H. M. (2021). Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control study. BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY, 128(13), 2061-2072. doi:10.1111/1471-0528.16816DOI: 10.1111/1471-0528.16816
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
Large-scale comparative genomics unravels great genomic diversity across the <i>Rickettsia</i> and <i>Ca</i>. Megaira genera and identifies Torix group as an evolutionarily distinct clade (Preprint)
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Martin, D. P., Weaver, S., Tegally, H., San, J. E., Shank, S. D., Wilkinson, E., . . . Kosakovsky Pond, S. L. (2021). The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.. Cell, 184(20), 5189-5200.e7. doi:10.1016/j.cell.2021.09.003DOI: 10.1016/j.cell.2021.09.003
Bell-Sakyi, L., Beliavskaia, A., Hartley, C. S., Jones, L., Luu, L., Haines, L. R., . . . Makepeace, B. L. (2021). Isolation in Natural Host Cell Lines of Wolbachia Strains wPip from the Mosquito Culex pipiens and wPap from the Sand Fly Phlebotomus papatasi. INSECTS, 12(10). doi:10.3390/insects12100871DOI: 10.3390/insects12100871
Stirrup, O., Boshier, F., Venturini, C., Guerra-Assunção, J. A., Alcolea-Medina, A., Beckett, A., . . . Breuer, J. (2021). SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respiratory Research, 8(1), e001029. doi:10.1136/bmjresp-2021-001029DOI: 10.1136/bmjresp-2021-001029
Lucas, E. R., Darby, A. C., Torr, S. J., & Donnelly, M. J. (2021). A gene expression panel for estimating age in males and females of the sleeping sickness vector <i>Glossina morsitans</i>. PLOS NEGLECTED TROPICAL DISEASES, 15(9). doi:10.1371/journal.pntd.0009797DOI: 10.1371/journal.pntd.0009797
Mishra, S., Mindermann, S., Sharma, M., Whittaker, C., Mellan, T. A., Wilton, T., . . . Flaxman, S. (2021). Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England. EClinicalMedicine, 39, 101064. doi:10.1016/j.eclinm.2021.101064DOI: 10.1016/j.eclinm.2021.101064
Wenlock, R. D., Tausan, M., Mann, R., Garr, W., Preston, R., Arnold, A., . . . Sargent, C. (2021). Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward.. Infection prevention in practice, 3(3), 100165. doi:10.1016/j.infpip.2021.100165DOI: 10.1016/j.infpip.2021.100165
Twohig, K. A., Nyberg, T., Zaidi, A., Thelwall, S., Sinnathamby, M. A., Aliabadi, S., . . . COVID-19 Genomics UK (COG-UK) consortium. (2021). Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study.. The Lancet. Infectious diseases, 22(1), 35-42. doi:10.1016/s1473-3099(21)00475-8DOI: 10.1016/s1473-3099(21)00475-8
Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., . . . Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889-895. doi:10.1126/science.abj0113DOI: 10.1126/science.abj0113
Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R. M., Darby, A. C., . . . Rambaut, A. (2021). Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell. doi:10.1016/j.cell.2021.08.014DOI: 10.1016/j.cell.2021.08.014
Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, A. R. J., Gerstung, M., Johnston, I., . . . Kwiatkowski, D. (2021). Patterns of within-host genetic diversity in SARS-CoV-2. eLife, 10. doi:10.7554/elife.66857DOI: 10.7554/elife.66857
Aljabr, W., Alruwaili, M., Penrice-Randal, R., Alrezaihi, A., Harrison, A. J., Ryan, Y., . . . Hiscox, J. A. (2021). Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.. mSphere, e0021921. doi:10.1128/msphere.00219-21DOI: 10.1128/msphere.00219-21
Nicholls, S. M., Poplawski, R., Bull, M. J., Underwood, A., Chapman, M., Abu-Dahab, K., . . . Loman, N. J. (2021). CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology, 22(1). doi:10.1186/s13059-021-02395-yDOI: 10.1186/s13059-021-02395-y
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., . . . Robertson, D. L. (2021). SARS-CoV-2 variants, spike mutations and immune escape.. Nature reviews. Microbiology, 19(7), 409-424. doi:10.1038/s41579-021-00573-0DOI: 10.1038/s41579-021-00573-0
The Bovine Foot Skin Microbiota is Associated with Host Genotype and the Development of Infectious Digital Dermatitis Lesions (Preprint)
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Stirrup, O., Hughes, J., Parker, M., Partridge, D. G., Shepherd, J. G., Blackstone, J., . . . Breuer, J. (n.d.). Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10. doi:10.7554/elife.65828DOI: 10.7554/elife.65828
Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., . . . Gupta, R. K. (2021). Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. CELL REPORTS, 35(13). doi:10.1016/j.celrep.2021.109292DOI: 10.1016/j.celrep.2021.109292
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A gene expression panel for estimating age in males and females of the sleeping sickness vector <i>Glossina morsitans</i> (Preprint)
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Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (Journal article)
Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., . . . Ferguson, N. M. (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. NATURE, 593(7858), 266-+. doi:10.1038/s41586-021-03470-xDOI: 10.1038/s41586-021-03470-x
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (Journal article)
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/s41586-021-03412-7DOI: 10.1038/s41586-021-03412-7
Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsaysky, T., . . . Ourselin, S. (2021). Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. LANCET PUBLIC HEALTH, 6(5), E335-E345. doi:10.1016/S2468-2667(21)00055-4DOI: 10.1016/S2468-2667(21)00055-4
Li, K. K., Woo, Y. M., Stirrup, O., Hughes, J., Ho, A., Filipe, A. D. S., . . . Mark, P. B. (2021). Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – A high risk community-hospital interface. Journal of Infection, 83(1), 96-103. doi:10.1016/j.jinf.2021.04.020DOI: 10.1016/j.jinf.2021.04.020
Lythgoe, K. A., Hall, M., Ferretti, L., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., . . . Golubchik, T. (2021). SARS-CoV-2 within-host diversity and transmission.. Science (New York, N.Y.), 372(6539), eabg0821. doi:10.1126/science.abg0821DOI: 10.1126/science.abg0821
Emary, K. R. W., Golubchik, T., Aley, P. K., Ariani, C. V., Angus, B., Bibi, S., . . . Grp, O. C. V. T. (2021). Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial. LANCET, 397(10282), 1351-1362. doi:10.1016/S0140-6736(21)00628-0DOI: 10.1016/S0140-6736(21)00628-0
Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., . . . Edmunds, W. J. (2021). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England.. Science (New York, N.Y.), 372(6538), eabg3055. doi:10.1126/science.abg3055DOI: 10.1126/science.abg3055
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-yDOI: 10.1038/s41586-021-03291-y
Hosie, M. J., Epifano, I., Herder, V., Orton, R. J., Stevenson, A., Johnson, N., . . . Weir, W. (2021). Detection of SARS‐CoV‐2 in respiratory samples from cats in the UK associated with human‐to‐cat transmission. Veterinary Record, 188(8). doi:10.1002/vetr.247DOI: 10.1002/vetr.247
Parker, M. D., Lindsey, B. B., Leary, S., Gaudieri, S., Chopra, A., Wyles, M., . . . de Silva, T. I. (2021). Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31(4), 645-658. doi:10.1101/gr.268110.120DOI: 10.1101/gr.268110.120
Staton, G. J., Clegg, S. R., Ainsworth, S., Armstrong, S., Carter, S. D., Radford, A. D., . . . Evans, N. J. (2021). Dissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms. PLOS PATHOGENS, 17(3). doi:10.1371/journal.ppat.1009464DOI: 10.1371/journal.ppat.1009464
Advanced Plaque Biofilm Modelling with Constant Depth Film Fermentation (Conference Paper)
Softley, R., Slomaka, V., Higham, S., Darby, A., & Valappil, S. (2021). Advanced Plaque Biofilm Modelling with Constant Depth Film Fermentation. In OMIG Prize meeting 2021.
Page, A. J., Mather, A. E., Le-Viet, T., Meader, E. J., Alikhan, N. -F., Kay, G. L., . . . The Covid-Genomics Uk Cog-Uk Consortium. (2021). Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.. Microbial genomics, 7(6). doi:10.1099/mgen.0.000589DOI: 10.1099/mgen.0.000589
Covid-19: variants and vaccination (Journal article)
Darby, A. C., & Hiscox, J. A. (2021). Covid-19: variants and vaccination. BMJ-BRITISH MEDICAL JOURNAL, 372. doi:10.1136/bmj.n771DOI: 10.1136/bmj.n771
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., Filipe, A. D. S., Wojcechowskyj, J. A., . . . Snell, G. (2021). Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. CELL, 184(5), 1171-+. doi:10.1016/j.cell.2021.01.037DOI: 10.1016/j.cell.2021.01.037
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Salguero, J., . . . COVID-19 Genomics UK (COG-UK) Consortium. (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:10.1101/2021.03.03.433753DOI: 10.1101/2021.03.03.433753
Hamilton, W. L., Tonkin-Hill, G., Smith, E. R., Aggarwal, D., Houldcroft, C. J., Warne, B., . . . COVID-19 Genomics Consortium UK. (2021). Genomic epidemiology of COVID-19 in care homes in the east of England.. eLife, 10, e64618. doi:10.7554/elife.64618DOI: 10.7554/elife.64618
Kelly, D., Jere, K. C., Darby, A. C., Allen, D. J., & Iturriza-Gómara, M. (2021). Complete genome characterization of human noroviruses allows comparison of minor alleles during acute and chronic infections. Access Microbiology, 3(3). doi:10.1099/acmi.0.000203DOI: 10.1099/acmi.0.000203
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/s41467-021-21389-9DOI: 10.1038/s41467-021-21389-9
du Plessis, L., McCrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutierrez, B., . . . Pybus, O. G. (2021). Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.. Science (New York, N.Y.), 371(6530), 708-712. doi:10.1126/science.abf2946DOI: 10.1126/science.abf2946
Baker, D. J., Aydin, A., Le-Viet, T., Kay, G. L., Rudder, S., de Oliveira Martins, L., . . . O'Grady, J. (2021). CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.. Genome medicine, 13(1), 21. doi:10.1186/s13073-021-00839-5DOI: 10.1186/s13073-021-00839-5
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
Goodfellow, L., Verwijs, M., Care, A., Sharp, A., Ivandic, J., Poljak, B., . . . van de Wijgert, J. H. H. M. (2021). Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control study. doi:10.1101/2021.01.14.21249680DOI: 10.1101/2021.01.14.21249680
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O'Toole, Á., . . . Connor, T. R. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.. Cell, 184(1), 64-75.e11. doi:10.1016/j.cell.2020.11.020DOI: 10.1016/j.cell.2020.11.020
CAPPABLE-SEQ REVEALS PROLIFIC NON-CANONICAL TRANSCRIPTION START SITES IN WOLBACHIA STRAINS WMELPOP-CLA AND WALBB UNDER STRESS CONDITIONS (Conference Paper)
Suliman, Y., Li, Z., Sinha, A., Dyer, P. D., Hartley, C. S., Ettwiller, L., . . . Makepeace, B. L. (2021). CAPPABLE-SEQ REVEALS PROLIFIC NON-CANONICAL TRANSCRIPTION START SITES IN WOLBACHIA STRAINS WMELPOP-CLA AND WALBB UNDER STRESS CONDITIONS. In AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Vol. 105 (pp. 153). Retrieved from https://www.webofscience.com/
CULTURE-DEPENDENT AND -INDEPENDENT METAGENOMIC ASSEMBLIES FROM MALAYSIAN CTENOCEPHALIDES SPP. FLEAS UNCOVER NEW COMPLETE GENOMES FOR BARTONELLA CLARRIDGEIAE, RICKETTSIA ASEMBONENSIS AND MULTIPLE CLADES OF WOLBACHIA (Conference Paper)
Beliavskaia, A., Khoo, J. J., Tan, K. -K., Sinha, A., Loong, S. -K., Carlow, C. K., . . . Makepeace, B. L. (2021). CULTURE-DEPENDENT AND -INDEPENDENT METAGENOMIC ASSEMBLIES FROM MALAYSIAN CTENOCEPHALIDES SPP. FLEAS UNCOVER NEW COMPLETE GENOMES FOR BARTONELLA CLARRIDGEIAE, RICKETTSIA ASEMBONENSIS AND MULTIPLE CLADES OF WOLBACHIA. In AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Vol. 105 (pp. 174). Retrieved from https://www.webofscience.com/
Leary, S., Gaudieri, S., Parker, M. D., Chopra, A., James, I., Pakala, S., . . . Mallal, S. (2021). Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level.. Pathogens & immunity, 6(2), 27-49. doi:10.20411/pai.v6i2.460DOI: 10.20411/pai.v6i2.460
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. (Journal article)
da Silva Filipe, A., Shepherd, J. G., Williams, T., Hughes, J., Aranday-Cortes, E., Asamaphan, P., . . . Thomson, E. C. (2021). Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.. Nature microbiology, 6(1), 112-122. doi:10.1038/s41564-020-00838-zDOI: 10.1038/s41564-020-00838-z
Allen, H., Vusirikala, A., Flannagan, J., Twohig, K. A., Zaidi, A., Chudasama, D., . . . Kall, M. (2021). Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study. The Lancet Regional Health - Europe, 12, 100252. doi:10.1016/j.lanepe.2021.100252DOI: 10.1016/j.lanepe.2021.100252
Frau, A., Ijaz, U. Z., Slater, R., Jonkers, D., Penders, J., Campbell, B. J., . . . Probert, C. S. J. (2021). Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach. GUT MICROBES, 13(1). doi:10.1080/19490976.2021.1930871DOI: 10.1080/19490976.2021.1930871
O'Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., . . . Kraemer, M. U. G. (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.. Wellcome open research, 6, 121. doi:10.12688/wellcomeopenres.16661.2DOI: 10.12688/wellcomeopenres.16661.2
2020
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa (Journal article)
Pulford, C., Perez-Sepulveda, B. M., Canals, R., Bevington, J. A., Bengtsson, R. J., Wenner, N., . . . Hinton, J. (2020). Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology. doi:10.1038/s41564-020-00836-1DOI: 10.1038/s41564-020-00836-1
Lefoulon, E., Clark, T., Guerrero, R., Cañizales, I., Cardenas-Callirgos, J. M., Junker, K., . . . Slatko, B. E. (2020). Diminutive, degraded but dissimilar: <i>Wolbachia</i> genomes from filarial nematodes do not conform to a single paradigm.. Microbial genomics, 6(12). doi:10.1099/mgen.0.000487DOI: 10.1099/mgen.0.000487
16282 Community relationships in the dry skin microbiome (Journal article)
Arnold, D., Cawley, A., Darby, A. C., Falciani, F., Grimshaw, S. G., Hawkins, S. S., . . . Paterson, S. (2020). 16282 Community relationships in the dry skin microbiome. Journal of the American Academy of Dermatology, 83(6), AB59. doi:10.1016/j.jaad.2020.06.322DOI: 10.1016/j.jaad.2020.06.322
Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS) (Journal article)
Aljabr, W., Alruwaili, M., Penrice-Randal, R., Alrezaihi, A., Harrison, A. J., Ryan, Y., . . . Hiscox, J. (2020). Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS). doi:10.1101/2020.11.28.400671DOI: 10.1101/2020.11.28.400671
Parker, E., Bronowski, C., Sindhu, K. N., Babji, S., Benny, B., Carmona-Vicente, N., . . . Iturriza-Gómara, M. (2020). Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants: a prospective cohort study. doi:10.1101/2020.11.02.20224576DOI: 10.1101/2020.11.02.20224576
Moore, S. C., Penrice-Randal, R., Alruwaili, M., Randle, N., Armstrong, S., Hartley, C., . . . Hiscox, J. A. (2020). Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism. VIRUSES-BASEL, 12(10). doi:10.3390/v12101164DOI: 10.3390/v12101164
Alm, E., Broberg, E. K., Connor, T., Hodcroft, E. B., Komissarov, A. B., Maurer-Stroh, S., . . . Pereyaslov, D. (2020). Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. EUROSURVEILLANCE, 25(32), 7-14. doi:10.2807/1560-7917.ES.2020.25.32.2001410DOI: 10.2807/1560-7917.ES.2020.25.32.2001410
Ladhani, S. N., Chow, J. Y., Janarthanan, R., Fok, J., Crawley-Boevey, E., Vusirikala, A., . . . Ramsay, M. E. (2020). Increased risk of SARS-CoV-2 infection in staff working across different care homes enchanced CoVID-19 outbreak investigations in London care Homes. Journal of Infection. doi:10.1016/j.jinf.2020.07.027DOI: 10.1016/j.jinf.2020.07.027
AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant <i>Achromobacter xylosoxidans</i> in a teaching hospital in Thailand (Journal article)
Pongchaikul, P., Santanirand, P., Antonyuk, S., Winstanley, C., & Darby, A. C. (2020). AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant <i>Achromobacter xylosoxidans</i> in a teaching hospital in Thailand. FEMS MICROBIOLOGY LETTERS, 367(14). doi:10.1093/femsle/fnaa109DOI: 10.1093/femsle/fnaa109
Khoo, J. J., Kurtti, T. J., Husin, N. A., Beliavskaia, A., Lim, F. S., Zulkifli, M. M. S., . . . Bell-Sakyi, L. (2020). Isolation and Propagation of Laboratory Strains and a Novel Flea-Derived Field Strain of <i>Wolbachia</i> in Tick Cell Lines.. Microorganisms, 8(7), E988. doi:10.3390/microorganisms8070988DOI: 10.3390/microorganisms8070988
Isolation and Propagation of Laboratory Strains and a Novel Flea-Derived Field Strain of Wolbachia in Tick Cell Lines (Journal article)
Khoo, J. J., Kurtti, T., Husin, N. A., Beliavskaia, A., Lim, F. S., Zulkifli, M. M. S., . . . Bell-Sakyi, L. (2020). Isolation and Propagation of Laboratory Strains and a Novel Flea-Derived Field Strain of Wolbachia in Tick Cell Lines. Microorganisms, 8(7). doi:10.3390/microorganisms8070988DOI: 10.3390/microorganisms8070988
Diminutive, degraded but dissimilar:<i>Wolbachia</i>genomes from filarial nematodes do not conform to a single paradigm (Preprint)
DOI: 10.1101/2020.06.18.160200
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
Insect—symbiont gene expression in the midgut bacteriocytes of a blood-sucking parasite (Journal article)
Husnik, F., Hypsa, V., & Darby, A. (2020). Insect-Symbiont Gene Expression in the Midgut Bacteriocytes of a Blood-Sucking Parasite.. Genome biology and evolution, 12(4), 429-442. doi:10.1093/gbe/evaa032DOI: 10.1101/572495
The Hypercomplex Genome of an Insect Reproductive Parasite Highlights the Importance of Lateral Gene Transfer in Symbiont Biology (Journal article)
Frost, C. L., Siozios, S., Nadal-Jimenez, P., Brockhurst, M. A., King, K. C., Darby, A. C., & Hurst, G. D. D. (2020). The Hypercomplex Genome of an Insect Reproductive Parasite Highlights the Importance of Lateral Gene Transfer in Symbiont Biology. mBio, 11(2). doi:10.1128/mbio.02590-19DOI: 10.1128/mbio.02590-19
van de Wijgert, J. H. H. M., Verwijs, M. C., Agaba, S. K., Bronowski, C., Mwambarangwe, L., Uwineza, M., . . . Darby, A. C. (2020). Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: A Pilot Study Incorporating Microscopy and Sequencing. Scientific Reports, 10(1). doi:10.1038/s41598-020-60671-6DOI: 10.1038/s41598-020-60671-6
van de Wijgert, J., Verwijs, M., Agaba, S., Bronowski, C., Mwambarangwe, L., Uwineza, M., . . . Darby, A. (2020). Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: Safety and Preliminary Efficacy by Microscopy and Sequencing. Scientific Reports. doi:10.1038/s41598-020-60671-6DOI: 10.1038/s41598-020-60671-6
Characterization of Circulating Clostridium difficile Strains, Host Response and Intestinal Microbiome in Hospitalized Children With Diarrhea (Journal article)
Lees, E. A., Carrol, E. D., Ellaby, N. A. F., Roberts, P., Corless, C. E., Lenzi, L., . . . Pirmohamed, M. (2020). Characterization of Circulating Clostridium difficile Strains, Host Response and Intestinal Microbiome in Hospitalized Children With Diarrhea. The Pediatric infectious disease journal, 39(3), 221-228. doi:10.1097/inf.0000000000002559DOI: 10.1097/inf.0000000000002559
Blow, F., Gioti, A., Goodhead, I. B., Kalyva, M., Kampouraki, A., Vontas, J., & Darby, A. C. (2020). Functional Genomics of a Symbiotic Community: Shared Traits in the Olive Fruit Fly Gut Microbiota. GENOME BIOLOGY AND EVOLUTION, 12(2), 3778-3791. doi:10.1093/gbe/evz258DOI: 10.1093/gbe/evz258
Verwijs, M. C., Agaba, S. K., Darby, A. C., & Van De Wijgert, J. H. H. M. (2020). Impact of Oral Metronidazole Treatment on the Vaginal Microbiota and Correlates of Treatment Failure. American Journal of Obstetrics and Gynecology, 222(2), 157.e1-157.e13. doi:10.1016/j.ajog.2019.08.008DOI: 10.1016/j.ajog.2019.08.008
Liu, Q., Lei, J., Darby, A. C., & Kadowaki, T. (2020). Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology. COMMUNICATIONS BIOLOGY, 3(1). doi:10.1038/s42003-020-0775-xDOI: 10.1038/s42003-020-0775-x
Community relationships in the dry skin microbiome (Conference Paper)
Arnold, D., Cawley, A., Darby, A. C., Falciani, F., Grimshaw, S. G., Hawkins, S. S., . . . Paterson, S. (2020). Community relationships in the dry skin microbiome. In JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY Vol. 83 (pp. AB59). Retrieved from https://www.webofscience.com/
van de Wijgert, J. H. H. M., Gill, A. C., Chikandiwa, A., Verwijs, M. C., Kelly, H. A., Omar, T., . . . Mayaud, P. (2020). Human papillomavirus infection and cervical dysplasia in HIV-positive women: potential role of the vaginal microbiota. AIDS, 34(1), 115-125. doi:10.1097/QAD.0000000000002381DOI: 10.1097/QAD.0000000000002381
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
Leng, J., Walton, G., Swann, J., Darby, A., La Ragione, R., & Proudman, C. (2020). "Bowel on the Bench": Proof of Concept of a Three-Stage, <i>In Vitro</i> Fermentation Model of the Equine Large Intestine. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 86(1). doi:10.1128/AEM.02093-19DOI: 10.1128/AEM.02093-19
Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae) (Preprint)
DOI: 10.1101/867879
Chaisiri, K., Gill, A. C., Stekolnikov, A. A., Hinjoy, S., McGarry, J. W., Darby, A. C., . . . Makepeace, B. (2019). Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand. Animal Microbiome, 1. doi:10.1186/s42523-019-0019-xDOI: 10.1186/s42523-019-0019-x
The Tick Cell Biobank: new arthropod cell lines for arbovirus research (Journal article)
Bell-Sakyi, L., Hartley, C., Darby, A., Baylis, M., & Makepeace, B. (2019). The Tick Cell Biobank: new arthropod cell lines for arbovirus research. Access Microbiology, 1(10). doi:10.1099/acmi.imav2019.po0045DOI: 10.1099/acmi.imav2019.po0045
Solano-Gonzalez, S., Darby, A. C., Cossar, D., & Caddick, M. X. (2019). High-Quality Draft Genome Sequence and Annotation of the Basidiomycete Yeast <i>Sporisorium graminicola</i> CBS10092, a Producer of Mannosylerythritol Lipids. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 8(42). doi:10.1128/MRA.00479-19DOI: 10.1128/MRA.00479-19
The draft genome of strain cCpun from biting midges establishes Cardinium as a paraphyletic group, and reveals a novel gene family expansion in a symbiont (Journal article)
Siozios, S., Pilgrim, J., Darby, A. C., Baylis, M., & Hurst, G. D. D. (2019). The draft genome of strain cCpun from biting midges establishes Cardinium as a paraphyletic group, and reveals a novel gene family expansion in a symbiont. PeerJ. doi:10.7287/peerj.preprints.27242v1DOI: 10.7287/peerj.preprints.27242v1
Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of <em>Mycobacterium ulcerans</em> and Multiple <em>Wolbachia</em> Sequence Types Revealed by Metagenomics (Preprint)
DOI: 10.20944/preprints201908.0031.v1
Hardwick, K. M., Ojwang, A. M. E., Stomeo, F., Maina, S., Bichang'a, G., Calatayud, P. -A., . . . Schaack, S. (2019). Draft Genome of <i>Busseola fusca</i>, the Maize Stalk Borer, a Major Crop Pest in Sub-Saharan Africa. GENOME BIOLOGY AND EVOLUTION, 11(8), 2203-2207. doi:10.1093/gbe/evz166DOI: 10.1093/gbe/evz166
Van de Wijgert, J., Gill, A., Darby, A., Kelly, H., Chikandiwa, A., Delany-Moretlwe, S., . . . Mayaud, P. (2019). ASSOCIATIONS OF THE VAGINAL MICROBIOTA WITH HPV INFECTION AND CERVICAL DYSPLASIA IN SOUTH AFRICAN WOMEN LIVING WITH HIV. In SEXUALLY TRANSMITTED INFECTIONS Vol. 95 (pp. A352). doi:10.1136/sextrans-2019-sti.883DOI: 10.1136/sextrans-2019-sti.883
Frau, A., Kenny, J. G., Lenzi, L., Campbell, B. J., Ijaz, U. Z., Duckworth, C. A., . . . Probert, C. S. J. (2019). DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies. SCIENTIFIC REPORTS, 9. doi:10.1038/s41598-019-44974-xDOI: 10.1038/s41598-019-44974-x
METABOLOMICS & MULTI-OMICS ANALYSIS OF CROHN'S DISEASE (Conference Paper)
Frau, A., Hough, R., Ijaz, U., Campbell, B., Kenny, J., Hall, N., . . . Probert, C. (2019). METABOLOMICS & MULTI-OMICS ANALYSIS OF CROHN'S DISEASE. In GUT Vol. 68 (pp. A68). doi:10.1136/gutjnl-2019-BSGAbstracts.131DOI: 10.1136/gutjnl-2019-BSGAbstracts.131
Blow, F., Gioti, A., Goodhead, I., Kalyva, M., Kampouraki, A., Vontas, J., & Darby, A. (2019). Functional genomics of a symbiotic community: shared traits in the olive fruit fly gut microbiota. doi:10.1101/590489DOI: 10.1101/590489
The Sodalis system and flux balance analysis as a tool for investigating insect-microbe interactions and the evolution of symbioses (Journal article)
Hall, R., Flanagan, L., Bottery, M., Springthorpe, V., Thorpe, S., Darby, A., . . . Thomas, G. (2019). The Sodalis system and flux balance analysis as a tool for investigating insect-microbe interactions and the evolution of symbioses. Access Microbiology, 1(1A). doi:10.1099/acmi.ac2019.po0057DOI: 10.1099/acmi.ac2019.po0057
Multi-omics analysis suggests an active role of fungi in Crohn's disease (Conference Paper)
Frau, A., Ijaz, U. Z., Hough, R., Campbell, B. J., Kenny, J. G., Hall, N., . . . Probert, C. S. J. (2019). Multi-omics analysis suggests an active role of fungi in Crohn's disease. In JOURNAL OF CROHNS & COLITIS Vol. 13 (pp. S545). doi:10.1093/ecco-jcc/jjy222.966DOI: 10.1093/ecco-jcc/jjy222.966
Honey bee trypanosomatid parasite dynamically changes the transcriptome during the infection of honey bee and modifies the host physiology (Preprint)
DOI: 10.1101/529321
Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand (Preprint)
DOI: 10.1101/523845
Hall, R. J., Flanagan, L. A., Bottery, M. J., Springthorpe, V., Thorpe, S., Darby, A. C., . . . Thomas, G. H. (2019). A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet.. mBio, 10(1). doi:10.1128/mbio.02106-18DOI: 10.1128/mbio.02106-18
<i>AMBLYOMMA VARIEGATUM</i>, VECTOR OF AFRICAN TICK-BITE FEVER, CONTAINS AN INTEGRATED <i>RICKETTSIA AFRICAE</i> CHROMOSOME IN ITS NUCLEAR GENOME (Conference Paper)
Darby, A. C., Al-Khafaji, A. M., Whitehead, M., Hartley, C. S., Robinson, G., Armstrong, S. D., . . . Makepeace, B. (2019). <i>AMBLYOMMA VARIEGATUM</i>, VECTOR OF AFRICAN TICK-BITE FEVER, CONTAINS AN INTEGRATED <i>RICKETTSIA AFRICAE</i> CHROMOSOME IN ITS NUCLEAR GENOME. In AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Vol. 101 (pp. 211). Retrieved from https://www.webofscience.com/
Esemu, S. N., Dong, X., Kfusi, A. J., Hartley, C. S., Ndip, R. N., Ndip, L. M., . . . Makepeace, B. L. (2019). Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of <i>Mycobacterium ulcerans</i> and Multiple <i>Wolbachia</i> Sequence Types Revealed by Metagenomics. DIVERSITY-BASEL, 11(12). doi:10.3390/d11120225DOI: 10.3390/d11120225
IMPACT OF THE GUT MICROBIOTA ON ROTAVIRUS VACCINE RESPONSE IN INDIAN, AFRICAN AND EUROPEAN INFANTS: A PROSPECTIVE COHORT STUDY (Conference Paper)
Bronowski, C., Parker, E. P. K., Sindhu, K. N. C., Praharaj, I., Babji, S., Chinyama, E., . . . Iturriza-Gomara, M. (2019). IMPACT OF THE GUT MICROBIOTA ON ROTAVIRUS VACCINE RESPONSE IN INDIAN, AFRICAN AND EUROPEAN INFANTS: A PROSPECTIVE COHORT STUDY. In TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE Vol. 113 (pp. S65-S66). Retrieved from https://www.webofscience.com/
METAGENOMICS OF CAMEROONIAN AQUATIC BUGS ASSOCIATED WITH COLONISATION BY <i>MYCOBACTERIUM</i> <i>ULCERNS</i> REVEALS <i>WOLBACHIA</i> INFECTIONS (Conference Paper)
Esemu, S. N., Dong, X., Post, R. J., Ndip, L. M., Darby, A. C., & Makepeace, B. L. (2019). METAGENOMICS OF CAMEROONIAN AQUATIC BUGS ASSOCIATED WITH COLONISATION BY <i>MYCOBACTERIUM</i> <i>ULCERNS</i> REVEALS <i>WOLBACHIA</i> INFECTIONS. In TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE Vol. 113 (pp. S256-S257). Retrieved from https://www.webofscience.com/
Al-Khafaji, A. M., Clegg, S. R., Pinder, A. C., Luu, L., Hansford, K. M., Seelig, F., . . . Makepeace, B. L. (2019). Multi-locus sequence typing of <i>Ixodes ricinus</i> and its symbiont <i>Candidatus</i> Midichloria mitochondrii across Europe reveals evidence of local co-cladogenesis in Scotland. TICKS AND TICK-BORNE DISEASES, 10(1), 52-62. doi:10.1016/j.ttbdis.2018.08.016DOI: 10.1016/j.ttbdis.2018.08.016
THE VECTOR BIOLOGY OF ECTOPARASITES ON RODENT FROM THE ASIR REGION OF SAUDI ARABIA (Conference Paper)
Alghamdi, S. Q., Alagaili, A. N., Stekolnikov, A. A., McGarry, J. W., Darby, A. C., & Makepeace, B. L. (2019). THE VECTOR BIOLOGY OF ECTOPARASITES ON RODENT FROM THE ASIR REGION OF SAUDI ARABIA. In TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE Vol. 113 (pp. S100). Retrieved from https://www.webofscience.com/
Siozios, S., Pilgrim, J., Darby, A. C., Baylis, M., & Hurst, G. D. D. (2019). The draft genome of strain <i>c</i>Cpun from biting midges confirms insect <i>Cardinium</i> are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PEERJ, 7. doi:10.7717/peerj.6448DOI: 10.7717/peerj.6448
2018
Dong, X., Chaisiri, K., Xia, D., Armstrong, S. D., Fang, Y., Donnelly, M. J., . . . Makepeace, B. L. (2018). Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism. GigaScience, 7(12), 33 pages. doi:10.1093/gigascience/giy127DOI: 10.1093/gigascience/giy127
Turner, J., Krishna, R., van’t Hof, A. E., Sutton, E. R., Matzen, K., & Darby, A. C. (2018). The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti. Parasites & Vectors, 11(1). doi:10.1186/s13071-018-3090-3DOI: 10.1186/s13071-018-3090-3
Matthews, B., Dudchenko, O., Kingan, S., Koren, S., Antoshechkin, I., Crawford, J., . . . Vosshall, L. (2018). Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control. Nature. doi:10.1038/s41586-018-0692-zDOI: 10.1038/s41586-018-0692-z
Matthews, B. J., Dudchenko, O., Kingan, S. B., Koren, S., Antoshechkin, I., Crawford, J. E., . . . Vosshall, L. B. (2018). Improved reference genome of Aedes aegypti informs arbovirus vector control. NATURE, 563(7732), 501. doi:10.1038/s41586-018-0692-zDOI: 10.1038/s41586-018-0692-z
Coates-Brown, R., Moran, J. C., Pongchaikul, P., Darby, A. C., & Horsburgh, M. J. (2018). Comparative Genomics of <i>Staphylococcus</i> Reveals Determinants of Speciation and Diversification of Antimicrobial Defense. FRONTIERS IN MICROBIOLOGY, 9. doi:10.3389/fmicb.2018.02753DOI: 10.3389/fmicb.2018.02753
The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti (Journal article)
Turner, J., Krishna, R., Van 't Hof, A., Sutton, E., Matzen, K., & Darby, A. (2018). The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti. Parasites and Vectors. doi:10.1186/s13071-018-3090-3DOI: 10.1186/s13071-018-3090-3
Abbas, A. H., Pereira, S. S., D'Archivio, S., Wickstead, B., Morrison, L. J., Hall, N., . . . Jackson, A. P. (2018). The Structure of a Conserved Telomeric Region Associated with Variant Antigen Loci in the Blood Parasite Trypanosoma congolense. Genome Biology and Evolution, 10(9), 2458-2473. doi:10.1093/gbe/evy186DOI: 10.1093/gbe/evy186
Bell-Sakyi, L., Darby, A., Baylis, M., & Makepeace, B. L. (2018). The Tick Cell Biobank: A global resource for <i>in vitro</i> research on ticks, other arthropods and the pathogens they transmit. TICKS AND TICK-BORNE DISEASES, 9(5), 1364-1371. doi:10.1016/j.ttbdis.2018.05.015DOI: 10.1016/j.ttbdis.2018.05.015
BACTERIAL AND FUNGAL COMMUNITIES IN FAECES AND BIOPSIES IN IBD (Conference Paper)
Frau, A., Ijaz, U. Z., Campbell, B., Darby, A., Kenny, J., Hall, N., & Probert, C. (2018). BACTERIAL AND FUNGAL COMMUNITIES IN FAECES AND BIOPSIES IN IBD. In GUT Vol. 67 (pp. A58-A59). doi:10.1136/gutjnl-2018-BSGAbstracts.115DOI: 10.1136/gutjnl-2018-BSGAbstracts.115
Heys, C., Lize, A., Blow, F., White, L., Darby, A., & Lewis, Z. J. (2018). The effect of gut microbiota elimination in <i>Drosophila melanogaster</i>: A how-to guide for host-microbiota studies. ECOLOGY AND EVOLUTION, 8(8), 4150-4161. doi:10.1002/ece3.3991DOI: 10.1002/ece3.3991
Comparative Genomics of <i>Staphylococcus</i> Reveals Determinants of Speciation and Diversification of Antimicrobial Defense (Preprint)
DOI: 10.1101/277400
Leng, J., Proudman, C., Darby, A., Blow, F., Townsend, N., Miller, A., & Swann, J. (2018). Exploration of the Fecal Microbiota and Biomarker Discovery in Equine Grass Sickness. JOURNAL OF PROTEOME RESEARCH, 17(3), 1120-1128. doi:10.1021/acs.jproteome.7b00784DOI: 10.1021/acs.jproteome.7b00784
Dong, X., Chaisiri, K., Xia, D., Armstrong, S., Fang, Y., Donnelly, M., . . . Makepeace, B. (2018). Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism. doi:10.1101/259044DOI: 10.1101/259044
Crohn's disease is characterised by a fungal dysbiosis (Conference Paper)
Frau, A., Jonkers, D., Penders, J., Pierik, M., Ijaz, U. Z., Campbell, B., . . . Probert, C. (2018). Crohn's disease is characterised by a fungal dysbiosis. In JOURNAL OF CROHNS & COLITIS Vol. 12 (pp. S550-S551). Retrieved from https://www.webofscience.com/
MULTI-LOCUS SEQUENCE TYPING OF THE SHEEP TICK <it>IXODES RICINUS</it> AND ITS SYMBIONT <it>CANDIDATUS</it> MIDICHLORIA MITOCHONDRII ACROSS EUROPE REVEALS EVIDENCE OF LOCAL COEVOLUTION IN SCOTLAND (Conference Paper)
Al-Khafaji, A., Clegg, S., Pinder, A., Hansford, K., Seelig, F., Dinnis, R., . . . Makepeace, B. (2018). MULTI-LOCUS SEQUENCE TYPING OF THE SHEEP TICK <it>IXODES RICINUS</it> AND ITS SYMBIONT <it>CANDIDATUS</it> MIDICHLORIA MITOCHONDRII ACROSS EUROPE REVEALS EVIDENCE OF LOCAL COEVOLUTION IN SCOTLAND. In AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Vol. 99 (pp. 481). Retrieved from https://www.webofscience.com/
2017
Yavari, C. A., Ramirez, A. S., Nicholas, R. A. J., Radford, A. D., Darby, A. C., & Bradbury, J. M. (2017). <i>Mycoplasma tullyi</i> sp nov., isolated from penguins of the genus <i>Spheniscus</i>. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 67(10), 3692-3698. doi:10.1099/ijsem.0.002052DOI: 10.1099/ijsem.0.002052
Optimised conditions for handling and transport of male Anopheles arabiensis : effects of low temperature, compaction, and ventilation on male quality (Journal article)
Culbert, N. J., Lees, R. S., Vreysen, M. J. B., Darby, A. C., & Gilles, J. R. L. (2017). Optimised conditions for handling and transport of male <i>Anopheles arabiensis</i>: effects of low temperature, compaction, and ventilation on male quality. ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, 164(3), 276-283. doi:10.1111/eea.12610DOI: 10.1111/eea.12610
Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications (vol 48, pg 130, 2016) (Journal article)
Forootan, S. S., Butler, J. M., Gardener, D., Jones, D., Baird, A. E., Dodson, A., . . . Gosden, C. M. (2017). Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications (vol 48, pg 130, 2016). INTERNATIONAL JOURNAL OF ONCOLOGY, 51(3), 997. doi:10.3892/ijo.2017.4087DOI: 10.3892/ijo.2017.4087
Large scale and significant expression from pseudogenes in <i>Sodalis glossinidius</i> - a facultative bacterial endosymbiont (Preprint)
DOI: 10.1101/124388
Doudoumis, V., Blow, F., Saridaki, A., Augustinos, A., Dyer, N. A., Goodhead, I., . . . Tsiamis, G. (2017). Challenging the <i>Wigglesworthia</i>, <i>Sodalis</i>, <i>Wolbachia</i> symbiosis dogma in tsetse flies: <i>Spiroplasma</i> is present in both laboratory and natural populations. SCIENTIFIC REPORTS, 7. doi:10.1038/s41598-017-04740-3DOI: 10.1038/s41598-017-04740-3
Blow, F., Vontas, J., & Darby, A. C. (2017). Draft Genome Sequence of <i>Chryseobacterium</i> Strain CBo1 Isolated from <i>Bactrocera oleae</i>. GENOME ANNOUNCEMENTS, 5(18). doi:10.1128/genomeA.00177-17DOI: 10.1128/genomeA.00177-17
Impact of maternal antibodies and infant gut microbiota on the immunogenicity of rotavirus vaccines in African, Indian and European infants: protocol for a prospective cohort study (Journal article)
Sindhu, K. N. C., Cunliffe, N., Peak, M., Turner, M., Darby, A., Grassly, N., . . . Kang, G. (2017). Impact of maternal antibodies and infant gut microbiota on the immunogenicity of rotavirus vaccines in African, Indian and European infants: protocol for a prospective cohort study. BMJ OPEN, 7(3). doi:10.1136/bmjopen-2017-016577DOI: 10.1136/bmjopen-2017-016577
Dong, X., Armstrong, S., Xia, D., Makepeace, B., Darby, A. C., & Kadowaki, T. (2017). Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history. GigaScience, 6(3). doi:10.1093/gigascience/gix008DOI: 10.1093/gigascience/gix008
GENOMES OF TROMBIDIOID MITES UNCOVER ADAPTATIONS TO PARASITISM IN THE SCRUB TYPHUS VECTOR, <i>LEPTOTROMBIDIUM DELIENSE</i> (Conference Paper)
Dong, X., Chaisiri, K., Donnelly, M. J., McGarry, J. W., Kadowaki, T., Darby, A. C., & Makepeace, B. L. (2017). GENOMES OF TROMBIDIOID MITES UNCOVER ADAPTATIONS TO PARASITISM IN THE SCRUB TYPHUS VECTOR, <i>LEPTOTROMBIDIUM DELIENSE</i>. In AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Vol. 97 (pp. 5). Retrieved from https://www.webofscience.com/
GLOBAL TRANSCRIPTOME ANALYSIS OF <i>WOLBACHIA</i> STRAIN <i>W</i>OO UNDER ANTIBIOTIC PRESSURE IN <i>VIVO</i> (Conference Paper)
Bah, G. S., Xia, D., Krishna, R., Tanya, V. N., Darby, A. C., & Makepeace, B. (2017). GLOBAL TRANSCRIPTOME ANALYSIS OF <i>WOLBACHIA</i> STRAIN <i>W</i>OO UNDER ANTIBIOTIC PRESSURE IN <i>VIVO</i>. In AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Vol. 97 (pp. 202-203). Retrieved from https://www.webofscience.com/
2016
Daly, K., Darby, A. C., & Shirazi-Beechey, S. P. (2016). Low calorie sweeteners and gut microbiota. PHYSIOLOGY & BEHAVIOR, 164, 494-500. doi:10.1016/j.physbeh.2016.03.014DOI: 10.1016/j.physbeh.2016.03.014
Blow, F., Vontas, J., & Darby, A. C. (2016). Draft Genome Sequence of Stenotrophomonas maltophilia SBo1 Isolated from Bactrocera oleae.. Genome Announcements, 4(5). doi:10.1128/genomea.00905-16DOI: 10.1128/genomea.00905-16
Novakova, E., Hypsa, V., Nguyen, P., Husnik, F., & Darby, A. C. (2016). Genome sequence of <i>Candidatus</i> Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly <i>Lipoptena cervi</i> (Diptera: Hippoboscidae). STANDARDS IN GENOMIC SCIENCES, 11. doi:10.1186/s40793-016-0195-1DOI: 10.1186/s40793-016-0195-1
Blow, F., Gioti, A., Starns, D., Ben-Yosef, M., Pasternak, Z., Jurkevitch, E., . . . Darby, A. C. (2016). Draft Genome Sequence of the <i>Bactrocera oleae</i> Symbiont "<i>Candidatus</i> Erwinia dacicola". GENOME ANNOUNCEMENTS, 4(5). doi:10.1128/genomeA.00896-16DOI: 10.1128/genomeA.00896-16
Gill, C., van de Wijgert, J. H. H. M., Blow, F., & Darby, A. C. (2016). Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota. PLOS ONE, 11(9). doi:10.1371/journal.pone.0163148DOI: 10.1371/journal.pone.0163148
Hof, A. E. V. T., Campagne, P., Rigden, D. J., Yung, C. J., Lingley, J., Quail, M. A., . . . Saccheri, I. J. (2016). The industrial melanism mutation in British peppered moths is a transposable element. Nature, 534(7605), 102-105. doi:10.1038/nature17951DOI: 10.1038/nature17951
Liu, L. -N., Faulkner, M., Liu, X., Huang, F., Darby, A. C., & Hall, N. (2016). Revised Genome Sequence of the Purple Photosynthetic Bacterium <i>Blastochloris viridis</i>. GENOME ANNOUNCEMENTS, 4(1). doi:10.1128/genomeA.01520-15DOI: 10.1128/genomeA.01520-15
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling (Journal article)
D'Amore, R., Ijaz, U. Z., Schirmer, M., Kenny, J. G., Gregory, R., Darby, A. C., . . . Hall, N. (2016). A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC GENOMICS, 17. doi:10.1186/s12864-015-2194-9DOI: 10.1186/s12864-015-2194-9
Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications (Journal article)
Forootan, S. S., Butler, J. M., Gardener, D., Baird, A. E., Dodson, A., Darby, A., . . . Gosden, C. M. (2016). Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications. INTERNATIONAL JOURNAL OF ONCOLOGY, 48(1), 130-144. doi:10.3892/ijo.2015.3222DOI: 10.3892/ijo.2015.3222
2015
Supergroup <i>C Wolbachia</i>, mutualist symbionts of filarial nematodes, have a distinct genome structure (Journal article)
Comandatore, F., Cordaux, R., Bandi, C., Blaxter, M., Darby, A., Makepeace, B. L., . . . Sassera, D. (2015). Supergroup <i>C Wolbachia</i>, mutualist symbionts of filarial nematodes, have a distinct genome structure. OPEN BIOLOGY, 5(12). doi:10.1098/rsob.150099DOI: 10.1098/rsob.150099
Characterisation of the faecal metabolome and microbiome of Thoroughbred racehorses (Journal article)
Proudman, C. J., Hunter, J. O., Darby, A. C., Escalona, E. E., Batty, C., & Turner, C. (2015). Characterisation of the faecal metabolome and microbiome of Thoroughbred racehorses. EQUINE VETERINARY JOURNAL, 47(5), 580-586. doi:10.1111/evj.12324DOI: 10.1111/evj.12324
Understanding Intestinal Microbiota in Equine Grass Sickness: Next Generation Sequencing of Faecal Bacterial <scp>DNA</scp> (Journal article)
Leng, J., Proudman, C., Blow, F., Darby, A., & Swann, J. (2015). Understanding Intestinal Microbiota in Equine Grass Sickness: Next Generation Sequencing of Faecal Bacterial <scp>DNA</scp>. Equine Veterinary Journal, 47(S48), 9. doi:10.1111/evj.12486_19DOI: 10.1111/evj.12486_19
Acetogenesis from H-2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist (Journal article)
Ohkuma, M., Noda, S., Hattori, S., Iida, T., Yuki, M., Starns, D., . . . Hongoh, Y. (2015). Acetogenesis from H-2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(33), 10224-10230. doi:10.1073/pnas.1423979112DOI: 10.1073/pnas.1423979112
Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus (Journal article)
Daly, K., Darby, A., Hall, N., Wilkinson, M., Pongchaikul, P., Bravo, D., & Shirazi-Beechey, S. (2015). Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus. Environmental Microbiology, 18(7), 2159-2171. doi:10.1111/1462-2920.12942DOI: 10.1111/1462-2920.12942
Complete Genome Sequence of <i>Leptospira interrogans</i> Serovar Bratislava, Strain PigK151 (Journal article)
Alt, D. P., Wilson-Welder, J. H., Bayles, D. O., Cameron, C., Adler, B., Bulach, D. M., . . . Zuerner, R. L. (2015). Complete Genome Sequence of <i>Leptospira interrogans</i> Serovar Bratislava, Strain PigK151. GENOME ANNOUNCEMENTS, 3(3). doi:10.1128/genomeA.00678-15DOI: 10.1128/genomeA.00678-15
Taking the pseudo out of pseudogenes (Journal article)
Goodhead, I., & Darby, A. C. (2015). Taking the pseudo out of pseudogenes. CURRENT OPINION IN MICROBIOLOGY, 23, 102-109. doi:10.1016/j.mib.2014.11.012DOI: 10.1016/j.mib.2014.11.012
Wright, E. A., Di Lorenzo, V., Trappetti, C., Liciardi, M., Orru, G., Viti, C., . . . Winstanley, C. (2015). Divergence of a strain of <i>Pseudomonas aeruginosa</i> during an outbreak of ovine mastitis. VETERINARY MICROBIOLOGY, 175(1), 105-113. doi:10.1016/j.vetmic.2014.11.011DOI: 10.1016/j.vetmic.2014.11.011
2014
The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction (Journal article)
Jackson, A. P., Otto, T. D., Darby, A., Ramaprasad, A., Xia, D., Echaide, I. E., . . . Pain, A. (2014). The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Research, 42(11), 7113-7131. doi:10.1093/nar/gku322DOI: 10.1093/nar/gku322
The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. (Journal article)
Jackson, A. P., Otto, T. D., Darby, A., Ramaprasad, A., Xia, D., Echaide, I. E., . . . Pain, A. (2014). The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.. Nucleic Acids Research, 42(11), 7113-7131.
Faecal Microbiome of the <scp>T</scp>horoughbred Racehorse and Its Response to Dietary Amylase Supplementation (Journal article)
Proudman, C., Darby, A., & Escalona, E. (2014). Faecal Microbiome of the <scp>T</scp>horoughbred Racehorse and Its Response to Dietary Amylase Supplementation. Equine Veterinary Journal, 46(S46), 35. doi:10.1111/evj.12267_107DOI: 10.1111/evj.12267_107
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. (Journal article)
International, G. G. I., Attardo, G. M., Abila, P. P., Auma, J. E., Baumann, A. A., Benoit, J. B., . . . al, E. (2014). Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.. Science, 344(6182), 380-386. doi:10.1126/science.1249656DOI: 10.1126/science.1249656
Darby, A. C., Gill, A. C., Armstrong, S. D., Hartley, C. S., Xia, D., Wastling, J. M., & Makepeace, B. L. (2014). Integrated transcriptomic and proteomic analysis of the global response of <i>Wolbachia</i> to doxycycline-induced stress. ISME JOURNAL, 8(4), 925-937. doi:10.1038/ismej.2013.192DOI: 10.1038/ismej.2013.192
Starns, D., Oshima, K., Suda, W., Iino, T., Yuki, M., Inoue, J. -I., . . . Ohkuma, M. (2014). Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe Isolated from Marine Mud.. Genome announcements, 2(2), e00206-e00214. doi:10.1128/genomea.00206-14DOI: 10.1128/genomea.00206-14
Compartive genomics of <i>Entrococcus faecium</i> (Conference Paper)
Shami, A., Horsburgh, M. J., & Darby, A. (2014). Compartive genomics of <i>Entrococcus faecium</i>. In FEBS JOURNAL Vol. 281 (pp. 735). Retrieved from https://www.webofscience.com/
Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance (Journal article)
Daly, K., Darby, A. C., Hall, N., Nau, A., Bravo, D., & Shirazi-Beechey, S. P. (2014). Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance. British Journal of Nutrition 111 (S1), S30-S35.
Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance. (Journal article)
Daly, K., Darby, A., Hall, N., Nau, A., Bravo, D., & Shirazi-Beechey, S. (2014). Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance.. The British Journal of Nutrition, 111(S1), S30-S35. doi:10.1017/S0007114513002274DOI: 10.1017/S0007114513002274
Gill, A. C., Darby, A. C., & Makepeace, B. L. (2014). Iron Necessity: The Secret of <i>Wolbachia</i>'s Success?. PLOS NEGLECTED TROPICAL DISEASES, 8(10). doi:10.1371/journal.pntd.0003224DOI: 10.1371/journal.pntd.0003224
2013
Phylogenomics and Analysis of Shared Genes Suggest a Single Transition to Mutualism in Wolbachia of Nematodes (Journal article)
Comandatore, F., Sassera, D., Montagna, M., Kumar, S., Koutsovoulos, G., Thomas, G., . . . Blaxter, M. (2013). Phylogenomics and Analysis of Shared Genes Suggest a Single Transition to Mutualism in Wolbachia of Nematodes. Genome Biology and Evolution, 5(9), 1668-1674. doi:10.1093/gbe/evt125DOI: 10.1093/gbe/evt125
Phylogeny and prevalence of kobuviruses in dogs and cats in the UK (Journal article)
Carmona-Vicente, N., Buesa, J., Brown, P. A., Merga, J. Y., Darby, A. C., Stavisky, J., . . . Radford, A. D. (2013). Phylogeny and prevalence of kobuviruses in dogs and cats in the UK. VETERINARY MICROBIOLOGY, 164(3-4), 246-252. doi:10.1016/j.vetmic.2013.02.014DOI: 10.1016/j.vetmic.2013.02.014
COPD Causation and Workplace Exposures: An Assessment of Agreement among Expert Clinical Raters (Journal article)
Fishwick, D., Darby, A., Hnizdo, E., Barber, C., Sumner, J., Barraclough, R., . . . Blanc, P. D. (2013). COPD Causation and Workplace Exposures: An Assessment of Agreement among Expert Clinical Raters. COPD-JOURNAL OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE, 10(2), 172-179. doi:10.3109/15412555.2012.737072DOI: 10.3109/15412555.2012.737072
Bacterial phylotypes associated with Lutzomyia sand flies sampled from 4 field sites. (Journal article)
Sant'Anna, M. R. V., Darby, A. C., Brazil, R. P., Montoya-Lerma, J., Dillon, V. M., Bates, P. A., . . . Sant'anna, M. R. (2013). Bacterial phylotypes associated with Lutzomyia sand flies sampled from 4 field sites.. Figshare, 7(8).
EVALUATING A MODIFIED INFORMED CONSENT FOR OLDER ADULTS IN CORRECTIONAL RESEARCH (Conference Paper)
Darby, A., Ahalt, C., Cenzer, I. S., Sudore, R. L., & Williams, B. (2013). EVALUATING A MODIFIED INFORMED CONSENT FOR OLDER ADULTS IN CORRECTIONAL RESEARCH. In JOURNAL OF GENERAL INTERNAL MEDICINE Vol. 28 (pp. S74). Retrieved from https://www.webofscience.com/
Phylogeny and prevalence of Kobuviruses in dogs and cats in the UK (Journal article)
Carmona-Vicente, N., Buesa, J., Brown, P. A., Merga, J. Y., Darby, A. C., Stavisky, J., . . . Radford, A. D. (2013). Phylogeny and prevalence of Kobuviruses in dogs and cats in the UK. Veterinary Microbiology, 164(3-4), 246-252. Retrieved from http://dx.doi.org/10.1016/j.vetmic.2013.02.014
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
Diversity of superantigens in Streptococcus equi and zooepidemicus populations (Journal article)
Paillot, R., Wright, N., McLean, R., Darby, A., Anderson, E., Steward, K., . . . Waller, A. (2012). Diversity of superantigens in Streptococcus equi and zooepidemicus populations. Journal of Equine Veterinary Science, 32(10), S24-S25. doi:10.1016/j.jevs.2012.08.058DOI: 10.1016/j.jevs.2012.08.058
Pili of Streptococcus equi and Streptococcus zooepidemicus (Journal article)
Steward, K. F., Robinson, C., Maskell, D. J., Holden, M. T. G., Harris, S. R., Darby, A. C., & Waller, A. S. (2012). Pili of Streptococcus equi and Streptococcus zooepidemicus. Journal of Equine Veterinary Science, 32(10), S15. doi:10.1016/j.jevs.2012.08.039DOI: 10.1016/j.jevs.2012.08.039
The population diversity of Streptococcus zooepidemicus (Journal article)
Robinson, C., Harris, S. R., Steward, K. F., Webb, K., Efstratiou, A., Darby, A., . . . Waller, A. S. (2012). The population diversity of Streptococcus zooepidemicus. Journal of Equine Veterinary Science, 32(10), S14-S15. doi:10.1016/j.jevs.2012.08.038DOI: 10.1016/j.jevs.2012.08.038
Comparative genomics of <i>Brachyspira pilosicoli</i> strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity (Journal article)
Mappley, L. J., Black, M. L., AbuOun, M., Darby, A. C., Woodward, M. J., Parkhill, J., . . . Hampson, D. J. (2012). Comparative genomics of <i>Brachyspira pilosicoli</i> strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity. BMC GENOMICS, 13. doi:10.1186/1471-2164-13-454DOI: 10.1186/1471-2164-13-454
Radford, A. D., Chapman, D., Dixon, L., Chantrey, J., Darby, A. C., & Hall, N. (2012). Application of next-generation sequencing technologies in virology. JOURNAL OF GENERAL VIROLOGY, 93, 1853-1868. doi:10.1099/vir.0.043182-0DOI: 10.1099/vir.0.043182-0
Investigation of the Bacterial Communities Associated with Females of <i>Lutzomyia</i> Sand Fly Species from South America (Journal article)
Sant'Anna, M. R. V., Darby, A. C., Brazil, R. P., Montoya-Lerma, J., Dillon, V. M., Bates, P. A., & Dillon, R. J. (2012). Investigation of the Bacterial Communities Associated with Females of <i>Lutzomyia</i> Sand Fly Species from South America. PLOS ONE, 7(8). doi:10.1371/journal.pone.0042531DOI: 10.1371/journal.pone.0042531
Comparative genomics of Shiga toxin encoding bacteriophages (Journal article)
Smith, D. L., Rooks, D. J., Fogg, P. C. M., Darby, A. C., Thomson, N. R., McCarthy, A. J., & Allison, H. E. (2012). Comparative genomics of Shiga toxin encoding bacteriophages. BMC GENOMICS, 13. doi:10.1186/1471-2164-13-311DOI: 10.1186/1471-2164-13-311
Optimization of <i>Bartonella henselae</i> multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data (Journal article)
Zhao, F., Chaloner, G., Darby, A., Song, X. -P., Li, D. -M., Birtles, R., & Liu, Q. -Y. (2012). Optimization of <i>Bartonella henselae</i> multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data. CHINESE MEDICAL JOURNAL, 125(13), 2284-2288. doi:10.3760/cma.j.issn.0366-6999.2012.13.008DOI: 10.3760/cma.j.issn.0366-6999.2012.13.008
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
Optimization of Bartonella henselae multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data (Journal article)
Zhao, F., Chaloner, G., Darby, A., Song, X. P., Li, D. M., Birtles, R., & Liu, Q. Y. (2012). Optimization of Bartonella henselae multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data. Chinese Medical Journal, 125(13), 2284-2288. Retrieved from http://www.scopus.com/
The Genus <i>Arsenophonus</i> (Chapter)
Wilkes, T. E., Duron, O., Darby, A. C., Hypsa, V., Novakova, E., & Hurst, G. D. D. (2012). The Genus <i>Arsenophonus</i>. In MANIPULATIVE TENANTS: BACTERIA ASSOCIATED WITH ARTHROPODS (pp. 225-244). Retrieved from https://www.webofscience.com/
2011
Cryptic Diversity within the Major Trypanosomiasis Vector <i>Glossina fuscipes</i> Revealed by Molecular Markers (Journal article)
Dyer, N. A., Ravel, S., Choi, K. -S., Darby, A. C., Causse, S., Kapitano, B., . . . Donnelly, M. J. (2011). Cryptic Diversity within the Major Trypanosomiasis Vector <i>Glossina fuscipes</i> Revealed by Molecular Markers. PLOS NEGLECTED TROPICAL DISEASES, 5(8). doi:10.1371/journal.pntd.0001266DOI: 10.1371/journal.pntd.0001266
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
The Genus Arsenophonus (Chapter)
The Genus Arsenophonus (2011). In Manipulative Tenants (pp. 263-282). CRC Press. doi:10.1201/b11008-17DOI: 10.1201/b11008-17
Complete Genome Sequence of <i>Mycoplasma haemofelis</i>, a Hemotropic Mycoplasma (Journal article)
Barker, E. N., Helps, C. R., Peters, I. R., Darby, A. C., Radford, A. D., & Tasker, S. (2011). Complete Genome Sequence of <i>Mycoplasma haemofelis</i>, a Hemotropic Mycoplasma. JOURNAL OF BACTERIOLOGY, 193(8), 2060-2061. doi:10.1128/JB.00076-11DOI: 10.1128/JB.00076-11
Genomic Analysis of Highly Virulent Georgia 2007/1 Isolate of African Swine Fever Virus (Journal article)
Chapman, D. A. G., Darby, A. C., Da Silva, M., Upton, C., Radford, A. D., & Dixon, L. K. (2011). Genomic Analysis of Highly Virulent Georgia 2007/1 Isolate of African Swine Fever Virus. EMERGING INFECTIOUS DISEASES, 17(4), 599-605. doi:10.3201/eid1704.101283DOI: 10.3201/eid1704.101283
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
WHOLE SHOTGUN PYROSEQUENCING OF <i>MYCOPLASMA HAEMOFELIS</i>: THROWING NEW LIGHT ON AN OLD PATHOGEN (Journal article)
Barker, E. N., Helps, C. R., Peters, I. R., Darby, A. C., & Tasker, S. (2011). WHOLE SHOTGUN PYROSEQUENCING OF <i>MYCOPLASMA HAEMOFELIS</i>: THROWING NEW LIGHT ON AN OLD PATHOGEN. JOURNAL OF VETERINARY INTERNAL MEDICINE, 25(3), 709-710. Retrieved from https://www.webofscience.com/
2010
COPD CAUSATION; AN ASSESSMENT OF AGREEMENT BETWEEN EXPERT CLINICAL RATERS (Conference Paper)
Darby, A. C., Barraclough, R., Burge, P. S., Hopkinson, N. S., Hoyle, J. L., Lawson, R. A., . . . Fishwick, D. (2010). COPD CAUSATION; AN ASSESSMENT OF AGREEMENT BETWEEN EXPERT CLINICAL RATERS. In THORAX Vol. 65 (pp. A77-A78). doi:10.1136/thx.2010.150961.3DOI: 10.1136/thx.2010.150961.3
Characterization of Pneumonia Due to <i>Streptococcus equi</i> subsp. <i>zooepidemicus</i> in Dogs (Journal article)
Priestnall, S. L., Erles, K., Brooks, H. W., Cardwell, J. M., Waller, A. S., Paillot, R., . . . Schoeniger, S. (2010). Characterization of Pneumonia Due to <i>Streptococcus equi</i> subsp. <i>zooepidemicus</i> in Dogs. CLINICAL AND VACCINE IMMUNOLOGY, 17(11), 1790-1796. doi:10.1128/CVI.00188-10DOI: 10.1128/CVI.00188-10
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
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
Amplified fragment length polymorphism (AFLP) analysis of closely related wild and captive tsetse fly (<i>Glossina morsitans morsitans</i>) populations (Journal article)
Lall, G. K., Darby, A. C., Nystedt, B., MacLeod, E. T., Bishop, R. P., & Welburn, S. C. (2010). Amplified fragment length polymorphism (AFLP) analysis of closely related wild and captive tsetse fly (<i>Glossina morsitans morsitans</i>) populations. PARASITES & VECTORS, 3. doi:10.1186/1756-3305-3-47DOI: 10.1186/1756-3305-3-47
Comparative Genomics and Transduction Potential of <i>Enterococcus faecalis</i> Temperate Bacteriophages (Journal article)
Yasmin, A., Kenny, J. G., Shankar, J., Darby, A. C., Hall, N., Edwards, C., & Horsburgh, M. J. (2010). Comparative Genomics and Transduction Potential of <i>Enterococcus faecalis</i> Temperate Bacteriophages. JOURNAL OF BACTERIOLOGY, 192(4), 1122-1130. doi:10.1128/JB.01293-09DOI: 10.1128/JB.01293-09
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
The draft genome sequence of <i>Arsenophonus nasoniae</i>, son-killer bacterium of <i>Nasonia vitripennis</i>, reveals genes associated with virulence and symbiosis (Journal article)
Wilkes, T. E., Darby, A. C., Choi, J. -H., Colbourne, J. K., Werren, J. H., & Hurst, G. D. D. (2010). The draft genome sequence of <i>Arsenophonus nasoniae</i>, son-killer bacterium of <i>Nasonia vitripennis</i>, reveals genes associated with virulence and symbiosis. INSECT MOLECULAR BIOLOGY, 19, 59-73. doi:10.1111/j.1365-2583.2009.00963.xDOI: 10.1111/j.1365-2583.2009.00963.x
Functional and Evolutionary Insights from the Genomes of Three Parasitoid <i>Nasonia</i> Species (Journal article)
Werren, J. H., Richards, S., Desjardins, C. A., Niehuis, O., Gadau, J., Colbourne, J. K., . . . Gibbs, R. A. (2010). Functional and Evolutionary Insights from the Genomes of Three Parasitoid <i>Nasonia</i> Species. SCIENCE, 327(5963), 343-348. doi:10.1126/science.1178028DOI: 10.1126/science.1178028
2009
Symbiosis Research as a Novel Strategy for Insect Pest Control (Chapter)
Darby, A. C. (2009). Symbiosis Research as a Novel Strategy for Insect Pest Control. In Biorational Control of Arthropod Pests (pp. 207-231). Springer Netherlands. doi:10.1007/978-90-481-2316-2_9DOI: 10.1007/978-90-481-2316-2_9
The inherited microbiota of arthropods, and their importance in understanding resistance and immunity (Chapter)
Hurst, G. D. D., & Darby, A. C. (2009). The inherited microbiota of arthropods, and their importance in understanding resistance and immunity. In Insect Infection and Immunity (pp. 119-136). Oxford University PressOxford. doi:10.1093/acprof:oso/9780199551354.003.0008DOI: 10.1093/acprof:oso/9780199551354.003.0008
The mosaic genome structure of the <i>Wolbachia w</i>Ri strain infecting <i>Drosophila simulans</i> (Journal article)
Klasson, L., Westberg, J., Sapountzis, P., Naesiund, K., Lutnaes, Y., Darby, A. C., . . . Andersson, S. G. E. (2009). The mosaic genome structure of the <i>Wolbachia w</i>Ri strain infecting <i>Drosophila simulans</i>. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(14), 5725-5730. doi:10.1073/pnas.0810753106DOI: 10.1073/pnas.0810753106
Symbiosis Research as a Novel Strategy for Insect Pest Control (Chapter)
Darby, A. C. (2009). Symbiosis Research as a Novel Strategy for Insect Pest Control. In BIORATIONAL CONTROL OF ARTHROPOD PESTS: APPLICATION AND RESISTANCE MANAGEMENT (pp. 207-231). doi:10.1007/978-90-481-2316-2_9DOI: 10.1007/978-90-481-2316-2_9
2008
Fast forward genetics (Journal article)
Darby, A. C., & Hall, N. (2008). Fast forward genetics. NATURE BIOTECHNOLOGY, 26(11), 1248-1249. doi:10.1038/nbt1108-1248DOI: 10.1038/nbt1108-1248
Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts (Journal article)
Tamas, I., Wernegreen, J. J., Nystedt, B., Kauppinen, S. N., Darby, A. C., Gomez-Valero, L., . . . Andersson, S. G. E. (2008). Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(39), 14934-14939. doi:10.1073/pnas.0806554105DOI: 10.1073/pnas.0806554105
Sequencing veterinary pathogens (Journal article)
Radford, A. D., Williams, N. J., Leatherbarrow, A. J. H., Hall, N., Darby, A. C., & Winstanley, C. (2008). Sequencing veterinary pathogens. VETERINARY RECORD, 163(7), 225-226. doi:10.1136/vr.163.7.225-bDOI: 10.1136/vr.163.7.225-b
Concurrent chemoradiotherapy (ConCRT) in locally advanced (LA) non-small cell Lung Cancer (NSCLC); 3-year experience at the Bank of Cyprus (BoC) oncology centre (Conference Paper)
Decatris, M. P., Charalambous, H., Darby, A., Christodoutides, G., Charalambous, C., & Katodrytis, N. (2008). Concurrent chemoradiotherapy (ConCRT) in locally advanced (LA) non-small cell Lung Cancer (NSCLC); 3-year experience at the Bank of Cyprus (BoC) oncology centre. In LUNG CANCER Vol. 60 (pp. S26). doi:10.1016/S0169-5002(08)70083-7DOI: 10.1016/S0169-5002(08)70083-7
Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction (Journal article)
Fuxelius, H. -H., Darby, A. C., Cho, N. -H., & Andersson, S. G. E. (2008). Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. GENOME BIOLOGY, 9(2). doi:10.1186/gb-2008-9-2-r42DOI: 10.1186/gb-2008-9-2-r42
Genome Analysis (Journal article)
Darby, A. C. (2008). Genome Analysis. International Journal Of Infectious Diseases, 12, E20.
2007
The genomic and metabolic diversity of <i>Rickettsia</i> (Journal article)
Fuxelius, H. -H., Darby, A., Min, C. -K., Cho, N. -H., & Andersson, S. G. E. (2007). The genomic and metabolic diversity of <i>Rickettsia</i>. RESEARCH IN MICROBIOLOGY, 158(10), 745-753. doi:10.1016/j.resmic.2007.09.008DOI: 10.1016/j.resmic.2007.09.008
Intracellular pathogens go extreme: genome evolution in the Rickettsiales (Journal article)
Darby, A. C., Cho, N. -H., Fuxelius, H. -H., Westberg, J., & Andersson, S. G. E. (2007). Intracellular pathogens go extreme: genome evolution in the Rickettsiales. TRENDS IN GENETICS, 23(10), 511-520. doi:10.1016/j.tig.2007.08.002DOI: 10.1016/j.tig.2007.08.002
Antioxidants promote establishment of trypanosome infections in tsetse (Journal article)
MacLeod, E. T., Maudlin, I., Darby, A. C., & Welburn, S. C. (2007). Antioxidants promote establishment of trypanosome infections in tsetse. PARASITOLOGY, 134, 827-831. doi:10.1017/S0031182007002247DOI: 10.1017/S0031182007002247
The <i>Orientia tsutsugamushi</i> genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes (Journal article)
Cho, N. -H., Kim, H. -R., Lee, J. -H., Kim, S. -Y., Kim, J., Cha, S., . . . Kim, I. -S. (2007). The <i>Orientia tsutsugamushi</i> genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104(19), 7981-7986. doi:10.1073/pnas.0611553104DOI: 10.1073/pnas.0611553104
Factors Affecting Trypanosome Maturation in Tsetse Flies (Journal article)
Macleod, E. T., Darby, A. C., Maudlin, I., & Welburn, S. C. (2007). Factors Affecting Trypanosome Maturation in Tsetse Flies. PLOS ONE, 2(2). doi:10.1371/journal.pone.0000239DOI: 10.1371/journal.pone.0000239
The incidence of thromboembolism in patients receiving adjuvant anthracycline based chemotherapy for early stage breast cancer (Conference Paper)
Nolan, L., Boleti, E., Darby, A., & Simmonds, P. D. (2007). The incidence of thromboembolism in patients receiving adjuvant anthracycline based chemotherapy for early stage breast cancer. In BREAST CANCER RESEARCH AND TREATMENT Vol. 106 (pp. S150). Retrieved from https://www.webofscience.com/
2006
Insect Symbiosis, Volume 2 (Chapter)
Bourtzis, K., & Miller, T. A. (Eds.) (n.d.). Insect Symbiosis, Volume 2. In . CRC Press. doi:10.1201/9781420005936DOI: 10.1201/9781420005936
2005
Aphid-symbiotic bacteria cultured in insect cell lines (Journal article)
Darby, A. C., Chandler, S. M., Welburn, S. C., & Douglas, A. E. (2005). Aphid-symbiotic bacteria cultured in insect cell lines. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 71(8), 4833-4839. doi:10.1128/AEM.71.8.4833-4839.2005DOI: 10.1128/AEM.71.8.4833-4839.2005
Extrachromosomal DNA of the symbiont <i>Sodalis glossinidius</i> (Journal article)
Darby, A. C., Lagnel, J., Matthew, C. Z., Bourtzis, K., Maudlin, I., & Welburn, S. C. (2005). Extrachromosomal DNA of the symbiont <i>Sodalis glossinidius</i>. JOURNAL OF BACTERIOLOGY, 187(14), 5003-5007. doi:10.1128/JB.187.14.5003-5007.2005DOI: 10.1128/JB.187.14.5003-5007.2005
The rapid isolation and growth dynamics of the tsetse symbiont <i>Sodalis glossinidius</i> (Journal article)
Matthew, C. Z., Darby, A. C., Young, S. A., Hume, L. H., & Welburn, S. C. (2005). The rapid isolation and growth dynamics of the tsetse symbiont <i>Sodalis glossinidius</i>. FEMS MICROBIOLOGY LETTERS, 248(1), 69-74. doi:10.1016/j.femsle.2005.05.024DOI: 10.1016/j.femsle.2005.05.024
2004
Linking the bacterial community in pea aphids with host-plant use and natural enemy resistance (Journal article)
Ferrari, J., Darby, A. C., Daniell, T. J., Godfray, H. C. J., & Douglas, A. E. (2004). Linking the bacterial community in pea aphids with host-plant use and natural enemy resistance. ECOLOGICAL ENTOMOLOGY, 29(1), 60-65. doi:10.1111/j.1365-2311.2004.00574.xDOI: 10.1111/j.1365-2311.2004.00574.x
2003
Diversity of bacteria associated with natural aphid populations (Journal article)
Haynes, S., Darby, A. C., Daniell, T. J., Webster, G., van Veen, F. J. F., Godfray, H. C. J., . . . Douglas, A. E. (2003). Diversity of bacteria associated with natural aphid populations. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 69(12), 7216-7223. doi:10.1128/AEM.69.12.7216-7223.2003DOI: 10.1128/AEM.69.12.7216-7223.2003
Elucidation of the transmission patterns of an insect-borne bacterium (Journal article)
Darby, A. C., & Douglas, A. E. (2003). Elucidation of the transmission patterns of an insect-borne bacterium. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 69(8), 4403-4407. doi:10.1128/AEM.69.8.4403-4407.2003DOI: 10.1128/AEM.69.8.4403-4407.2003
The significance of a facultative bacterium to natural populations of the pea aphid <i>Acyrthosiphon pisum</i> (Journal article)
Darby, A. C., Tosh, C. R., Walters, K. F. A., & Douglas, A. E. (2003). The significance of a facultative bacterium to natural populations of the pea aphid <i>Acyrthosiphon pisum</i>. ECOLOGICAL ENTOMOLOGY, 28(2), 145-150. doi:10.1046/j.1365-2311.2003.00492.xDOI: 10.1046/j.1365-2311.2003.00492.x
The ecological significance of symbiotic microorganisms in animals: perspectives from the microbiota of aphids (Chapter)
Douglas, A. E., Darby, A. C., Birkle., L. M., & Walters., K. F. A. (2003). The ecological significance of symbiotic microorganisms in animals: perspectives from the microbiota of aphids. In R. M. Hails, J. Berringer, & H. C. J. Godfray (Eds.), Genes in the Environment (pp. 306-325). Oxford: Blackwell Scientific Publishers,.
2001
An aphid-borne bacterium allied to the secondary symbionts of whitefly (Journal article)
Darby, A. C., Birkle, L. M., Turner, S. L., & Douglas, A. E. (2001). An aphid-borne bacterium allied to the secondary symbionts of whitefly. FEMS MICROBIOLOGY ECOLOGY, 36(1), 43-50. doi:10.1111/j.1574-6941.2001.tb00824.xDOI: 10.1111/j.1574-6941.2001.tb00824.x
An aphid-borne bacterium allied to the secondary symbionts of whitefly (Journal article)
Darby, A. (2001). An aphid-borne bacterium allied to the secondary symbionts of whitefly. FEMS Microbiology Ecology, 36(1), 43-50. doi:10.1016/s0168-6496(01)00117-9DOI: 10.1016/s0168-6496(01)00117-9
2000
Intraguild predators and the spatial distribution of a parasitoid (Journal article)
Raymond, B., Darby, A. C., & Douglas, A. E. (2000). Intraguild predators and the spatial distribution of a parasitoid. OECOLOGIA, 124(3), 367-372. doi:10.1007/s004420000396DOI: 10.1007/s004420000396
The olfactory responses of coccinellids to aphids on plants (Journal article)
Raymond, B., Darby, A. C., & Douglas, A. E. (2000). The olfactory responses of coccinellids to aphids on plants. ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, 95(1), 113-117. doi:10.1046/j.1570-7458.2000.00648.xDOI: 10.1046/j.1570-7458.2000.00648.x
The olfactory responses of coccinellids to aphids on plants. (Journal article)
Raymond, B., Darby, A. C., & Douglas, A. E. (2000). The olfactory responses of coccinellids to aphids on plants.. Entomologia experimentalis et applicata, 95(1), 113-117. doi:10.1046/j.1570-7458.2000.00648.xDOI: 10.1046/j.1570-7458.2000.00648.x
