Publications
Selected publications
- The industrial melanism mutation in British peppered moths is a transposable element. (Journal article - 2016)
- Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. (Journal article - 2014)
- Functional and Evolutionary Insights from the Genomes of Three Parasitoid <i>Nasonia</i> Species (Journal article - 2010)
- 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 - 2012)
- Integrated transcriptomic and proteomic analysis of the global response of <i>Wolbachia</i> to doxycycline-induced stress (Journal article - 2014)
2024
Genome dynamics across the evolutionary transition to endosymbiosis.
Siozios, S., Nadal-Jimenez, P., Azagi, T., Sprong, H., Frost, C. L., Parratt, S. R., . . . Hurst, G. D. D. (2024). Genome dynamics across the evolutionary transition to endosymbiosis.. Current biology : CB, S0960-9822(24)01433-7. doi:10.1016/j.cub.2024.10.044
The Drosophila adult midgut progenitor cells arise from asymmetric divisions of neuroblast-like cells
Plygawko, A. T., Stephan-Otto Attolini, C., Pitsidianaki, I., Cook, D. P., Darby, A. C., & Campbell, K. (2024). The Drosophila adult midgut progenitor cells arise from asymmetric divisions of neuroblast-like cells. Developmental Cell. doi:10.1016/j.devcel.2024.10.011
Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship
Cappable-Seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont<i>Wolbachia</i>
SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection.
Goldswain, H., Penrice-Randal, R., Donovan-Banfield, I., Duffy, C. W., Dong, X., Randle, N., . . . Emmett, S. R. (2024). SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection.. Genome medicine, 16(1), 89. doi:10.1186/s13073-024-01360-1
Emerging Variants of Canine Enteric Coronavirus Associated with Outbreaks of Gastroenteric Disease.
Cunningham-Oakes, E., Pilgrim, J., Darby, A. C., Appleton, C., Jewell, C., Rowlingson, B., . . . Radford, A. D. (2024). Emerging Variants of Canine Enteric Coronavirus Associated with Outbreaks of Gastroenteric Disease.. Emerging infectious diseases, 30(6), 1240-1244. doi:10.3201/eid3006.231184
Establishment and partial characterisation of a new cell line derived from adult tissues of the tsetse fly Glossina morsitans morsitans.
Bell-Sakyi, L., Haines, L. R., Petrucci, G., Beliavskaia, A., Hartley, C., Khoo, J. J., . . . Darby, A. C. (2024). Establishment and partial characterisation of a new cell line derived from adult tissues of the tsetse fly Glossina morsitans morsitans.. Parasites & vectors, 17(1), 231. doi:10.1186/s13071-024-06310-9
Microbial keratitis in Southern Malawi: a microbiological pilot study.
Somerville, T. F., Mdala, S., Zungu, T., Gandiwa, M., Herbert, R., Everett, D., . . . Kayange, P. C. (2024). Microbial keratitis in Southern Malawi: a microbiological pilot study.. BMJ open ophthalmology, 9(1), e001682. doi:10.1136/bmjophth-2024-001682
Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia
Alkathiry, H. A., Alghamdi, S. Q., Sinha, A., Margos, G., Stekolnikov, A. A., Alagaili, A. N., . . . Khoo, J. J. (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. BMC Genomics, 25(1). doi:10.1186/s12864-024-10301-6
Author Correction: Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses.
Michael, B. D., Dunai, C., Needham, E. J., Tharmaratnam, K., Williams, R., Huang, Y., . . . Menon, D. K. (2024). Author Correction: Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses.. Nature communications, 15(1), 2918. doi:10.1038/s41467-024-47320-6
Microbiome and mitogenomics of the chigger mite Pentidionis agamae: Potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia
Thoughts and perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study
COVID-19 risk-mitigation in reopening mass cultural events: population-based observational study for the UK Events Research Programme in Liverpool City Region
Burnside, G., Cheyne, C. P., Leeming, G., Humann, M., Darby, A., Green, M. A., . . . Buchan, I. E. (2024). 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:10.1177/01410768231182389
2023
Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses.
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/s41467-023-42320-4
Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi.
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-z
Arsenophonus symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance
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.00706-23
Association between maternal breastmilk microbiota composition and rotavirus vaccine response in African, Asian, and European infants: a prospective cohort study
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/jiad234
<i>Arsenophonus</i>symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance
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.
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.0.001045
Genomic and cytogenetic analysis of the Ceratitis capitata temperature-sensitive lethal region
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/jkad074
Genome dynamics across the evolutionary transition to endosymbiosis
The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.
Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., . . . COVID-19 Genomics UK (COG-UK) Consortium. (2023). The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.. PloS one, 18(4), e0284187. doi:10.1371/journal.pone.0284187
Enhancing Infectious Intestinal Disease diagnosis through metagenomic and metatranscriptomic sequencing of over 1000 human diarrhoeal samples
Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.
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.0010862
Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi
The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.
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/s13059-023-02881-5
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.
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.2023.02.010
Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals
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.2023.06.005
Selecting for infectivity across metapopulations can increase virulence in the social microbe <i>Bacillus thuringiensis</i>
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.13529
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
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/s42523-023-00232-0
The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions
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/s40168-022-01440-7
2022
Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial
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/s41467-022-34839-9
Genomic Analysis of Two Phlebotomine Sand Fly Vectors of<i>Leishmania</i>from the New and Old World
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (vol 7, pg 1161, 2022)
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/s41564-022-01241-6
Recovering individual haplotypes and a contiguous genome assembly from pooled long-read sequencing of the diamondback moth (Lepidoptera: Plutellidae)
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/jkac210
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study
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.78427
Recurrent SARS-CoV-2 mutations in immunodeficient patients.
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/veac050
Author Correction: SARS-CoV-2 evolution during treatment of chronic infection.
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., . . . Gupta, R. K. (2022). Author Correction: SARS-CoV-2 evolution during treatment of chronic infection.. Nature, 608(7922), E23. doi:10.1038/s41586-022-05104-2
Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., . . . Gupta, R. K. (2022). Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.. Nature, 608(7922), E24. doi:10.1038/s41586-022-05103-3
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
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/s41564-022-01143-7
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
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/s12879-022-07628-4
Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021.
Smallman-Raynor, M. R., Cliff, A. D., & COVID-19 Genomics UK (COG-UK) Consortium. (2022). Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021.. Epidemiology and infection, 150, e145. doi:10.1017/s0950268822001285
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning
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/s41598-022-15661-1
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
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/s41598-022-14016-0
Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.
Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2022). Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.. Nature, 606(7915), E18. doi:10.1038/s41586-022-04887-8
Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Donovan-Banfield, I., . . . Hiscox, J. A. (2022). Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. GIGASCIENCE, 11. doi:10.1093/gigascience/giac045
Genomic diversity across the Rickettsia and 'Candidatus Megaira' genera and proposal of genus status for the Torix group
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/s41467-022-30385-6
SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.
Ashford, F., Best, A., Dunn, S. J., Ahmed, Z., Siddiqui, H., Melville, J., . . . McNally, A. (2022). SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.. Journal of clinical microbiology, 60(4), e0240821. doi:10.1128/jcm.02408-21
Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.
Wright, D. W., Harvey, W. T., Hughes, J., Cox, M., Peacock, T. P., Colquhoun, R., . . . Carabelli, A. M. (2022). Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.. Virus evolution, 8(1), veac023. doi:10.1093/ve/veac023
The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions
Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
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-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
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
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-w
The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities
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)00208-1
The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
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/jiab483
Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission
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.2021.07.040
Evolution of viral variants in remdesivir‐treated and untreated SARS‐CoV‐2‐infected pediatrics patients
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.27285
2021
Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant
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.abl9551
Genomic reconstruction of the SARS-CoV-2 epidemic in England
Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., . . . Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), 506-511. doi:10.1038/s41586-021-04069-y
Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants
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/s41467-021-27074-1
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.
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)00434-4
Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination
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.1010022
The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study
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.2021.09.022
Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control study
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:10.1111/1471-0528.16816
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells
de, S. T. I., Liu, G., Lindsey, B. B., Dong, D., Moore, S. C., Hsu, N. S., . . . Dong, T. (2021). The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. ISCIENCE, 24(11). doi:10.1016/j.isci.2021.103353
Defining the analytical and clinical sensitivity of the ARTIC method for the detection of SARS-CoV-2
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
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.
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.2021.09.003
Isolation in Natural Host Cell Lines of Wolbachia Strains wPip from the Mosquito Culex pipiens and wPap from the Sand Fly Phlebotomus papatasi
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/insects12100871
SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study
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Dissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms
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Advanced Plaque Biofilm Modelling with Constant Depth Film Fermentation
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Genomic epidemiology of COVID-19 in care homes in the east of England.
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Complete genome characterization of human noroviruses allows comparison of minor alleles during acute and chronic infections
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Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19
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White pupae phenotype of tephritids is caused by parallel mutations of a MFS transporter
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Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control study
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Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach
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Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.
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Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
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Diminutive, degraded but dissimilar: <i>Wolbachia</i> genomes from filarial nematodes do not conform to a single paradigm.
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16282 Community relationships in the dry skin microbiome
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Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS)
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Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants: a prospective cohort study
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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
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Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
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Increased risk of SARS-CoV-2 infection in staff working across different care homes enchanced CoVID-19 outbreak investigations in London care Homes
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AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant <i>Achromobacter xylosoxidans</i> in a teaching hospital in Thailand
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/fnaa109
Isolation and Propagation of Laboratory Strains and a Novel Flea-Derived Field Strain of <i>Wolbachia</i> in Tick Cell Lines.
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Isolation and Propagation of Laboratory Strains and a Novel Flea-Derived Field Strain of Wolbachia in Tick Cell Lines
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/microorganisms8070988
Diminutive, degraded but dissimilar:<i>Wolbachia</i>genomes from filarial nematodes do not conform to a single paradigm
An integrated national scale SARS-CoV-2 genomic surveillance network
Darby, A. (2020). An integrated national scale SARS-CoV-2 genomic surveillance network. The Lancet Microbe. doi:10.1016/s2666-5247(20)30054-9
A generic white pupae sex selection phenotype for insect pest control
Insect—symbiont gene expression in the midgut bacteriocytes of a blood-sucking parasite
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/evaa032
The Hypercomplex Genome of an Insect Reproductive Parasite Highlights the Importance of Lateral Gene Transfer in Symbiont Biology
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.02590-19
Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: A Pilot Study Incorporating Microscopy and Sequencing
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/s41598-020-60671-6
Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: Safety and Preliminary Efficacy by Microscopy and Sequencing
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/s41598-020-60671-6
Characterization of Circulating Clostridium difficile Strains, Host Response and Intestinal Microbiome in Hospitalized Children With Diarrhea
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.0000000000002559
Functional Genomics of a Symbiotic Community: Shared Traits in the Olive Fruit Fly Gut Microbiota
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/evz258
Impact of Oral Metronidazole Treatment on the Vaginal Microbiota and Correlates of Treatment Failure
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.2019.08.008
Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology
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-x
Community relationships in the dry skin microbiome
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/
Human papillomavirus infection and cervical dysplasia in HIV-positive women: potential role of the vaginal microbiota
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.0000000000002381
Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont
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.0.000285
2019
"Bowel on the Bench": Proof of Concept of a Three-Stage, <i>In Vitro</i> Fermentation Model of the Equine Large Intestine
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.02093-19
Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)
Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand
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-x
The Tick Cell Biobank: new arthropod cell lines for arbovirus research
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.po0045
High-Quality Draft Genome Sequence and Annotation of the Basidiomycete Yeast <i>Sporisorium graminicola</i> CBS10092, a Producer of Mannosylerythritol Lipids
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.00479-19
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
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.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
Draft Genome of <i>Busseola fusca</i>, the Maize Stalk Borer, a Major Crop Pest in Sub-Saharan Africa
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/evz166
ASSOCIATIONS OF THE VAGINAL MICROBIOTA WITH HPV INFECTION AND CERVICAL DYSPLASIA IN SOUTH AFRICAN WOMEN LIVING WITH HIV
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.883
DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies
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-x
METABOLOMICS & MULTI-OMICS ANALYSIS OF CROHN'S DISEASE
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.131
Functional genomics of a symbiotic community: shared traits in the olive fruit fly gut microbiota
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:10.1101/590489
The Sodalis system and flux balance analysis as a tool for investigating insect-microbe interactions and the evolution of symbioses
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.po0057
Multi-omics analysis suggests an active role of fungi in Crohn's disease
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/jjy222.966
Honey bee trypanosomatid parasite dynamically changes the transcriptome during the infection of honey bee and modifies the host physiology
Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand
A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet.
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.02106-18
<i>AMBLYOMMA VARIEGATUM</i>, VECTOR OF AFRICAN TICK-BITE FEVER, CONTAINS AN INTEGRATED <i>RICKETTSIA AFRICAE</i> CHROMOSOME IN ITS NUCLEAR GENOME
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/
Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of <i>Mycobacterium ulcerans</i> and Multiple <i>Wolbachia</i> Sequence Types Revealed by Metagenomics
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/d11120225
IMPACT OF THE GUT MICROBIOTA ON ROTAVIRUS VACCINE RESPONSE IN INDIAN, AFRICAN AND EUROPEAN INFANTS: A PROSPECTIVE COHORT STUDY
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
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/
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
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.2018.08.016
THE VECTOR BIOLOGY OF ECTOPARASITES ON RODENT FROM THE ASIR REGION OF SAUDI ARABIA
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/
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
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.6448
2018
Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism
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/giy127
The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti
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/s13071-018-3090-3
Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control
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-z
Improved reference genome of Aedes aegypti informs arbovirus vector control.
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-z
Comparative Genomics of <i>Staphylococcus</i> Reveals Determinants of Speciation and Diversification of Antimicrobial Defense
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.2018.02753
The sequence of a male-specific genome region containing the sex determination switch in Aedes aegypti
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/s13071-018-3090-3
The Structure of a Conserved Telomeric Region Associated with Variant Antigen Loci in the Blood Parasite Trypanosoma congolense
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/evy186
The Tick Cell Biobank: A global resource for <i>in vitro</i> research on ticks, other arthropods and the pathogens they transmit
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.2018.05.015
BACTERIAL AND FUNGAL COMMUNITIES IN FAECES AND BIOPSIES IN IBD
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.115
The effect of gut microbiota elimination in <i>Drosophila melanogaster</i>: A how-to guide for host-microbiota studies
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/ece3.3991
Comparative Genomics of <i>Staphylococcus</i> Reveals Determinants of Speciation and Diversification of Antimicrobial Defense
Exploration of the Fecal Microbiota and Biomarker Discovery in Equine Grass Sickness
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.7b00784
Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism
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:10.1101/259044
Crohn's disease is characterised by a fungal dysbiosis
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
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
<i>Mycoplasma tullyi</i> sp nov., isolated from penguins of the genus <i>Spheniscus</i>
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.0.002052
Optimised conditions for handling and transport of male Anopheles arabiensis : effects of low temperature, compaction, and ventilation on male quality
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.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)
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.2017.4087
Large scale and significant expression from pseudogenes in <i>Sodalis glossinidius</i> - a facultative bacterial endosymbiont
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
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/s41598-017-04740-3
Draft Genome Sequence of <i>Chryseobacterium</i> Strain CBo1 Isolated from <i>Bactrocera oleae</i>
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.00177-17
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
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-2017-016577
Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history
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/gix008
GENOMES OF TROMBIDIOID MITES UNCOVER ADAPTATIONS TO PARASITISM IN THE SCRUB TYPHUS VECTOR, <i>LEPTOTROMBIDIUM DELIENSE</i>
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>
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
Low calorie sweeteners and gut microbiota
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.2016.03.014
Draft Genome Sequence of Stenotrophomonas maltophilia SBo1 Isolated from Bactrocera oleae.
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.00905-16
Genome sequence of Candidatus Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly Lipoptena cervi (Diptera: Hippoboscidae)
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/s40793-016-0195-1
Draft Genome Sequence of the <i>Bactrocera oleae</i> Symbiont "<i>Candidatus</i> Erwinia dacicola"
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.00896-16
Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota
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.0163148
The industrial melanism mutation in British peppered moths is a transposable element.
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/nature17951
Revised Genome Sequence of the Purple Photosynthetic Bacterium <i>Blastochloris viridis</i>
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.01520-15
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
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/s12864-015-2194-9
Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications
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.2015.3222
2015
Supergroup <i>C Wolbachia</i>, mutualist symbionts of filarial nematodes, have a distinct genome structure
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.150099
Characterisation of the faecal metabolome and microbiome of Thoroughbred racehorses
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.12324
Understanding Intestinal Microbiota in Equine Grass Sickness: Next Generation Sequencing of Faecal Bacterial <scp>DNA</scp>
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_19
Acetogenesis from H-2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist
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.1423979112
Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus
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:10.1111/1462-2920.12942
Complete Genome Sequence of <i>Leptospira interrogans</i> Serovar Bratislava, Strain PigK151
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.00678-15
Taking the pseudo out of pseudogenes
Goodhead, I., & Darby, A. C. (2015). Taking the pseudo out of pseudogenes. CURRENT OPINION IN MICROBIOLOGY, 23, 102-109. doi:10.1016/j.mib.2014.11.012
Divergence of a strain of <i>Pseudomonas aeruginosa</i> during an outbreak of ovine mastitis
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.2014.11.011
2014
The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction
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/gku322
The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.
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
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_107
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
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.1249656
Integrated transcriptomic and proteomic analysis of the global response of <i>Wolbachia</i> to doxycycline-induced stress
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.2013.192
Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe Isolated from Marine Mud.
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.00206-14
Compartive genomics of <i>Entrococcus faecium</i>
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
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.
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/S0007114513002274
Iron Necessity: The Secret of <i>Wolbachia</i>'s Success?
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.0003224
2013
Phylogenomics and Analysis of Shared Genes Suggest a Single Transition to Mutualism in Wolbachia of Nematodes
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/evt125
Phylogeny and prevalence of kobuviruses in dogs and cats in the UK
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.2013.02.014
Bacterial phylotypes associated with Lutzomyia sand flies sampled from 4 field sites.
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
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
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
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.138420.112
Diversity of superantigens in Streptococcus equi and zooepidemicus populations
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.2012.08.058
Pili of Streptococcus equi and Streptococcus zooepidemicus
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.2012.08.039
The population diversity of Streptococcus zooepidemicus
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.2012.08.038
Comparative genomics of <i>Brachyspira pilosicoli</i> strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity
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:10.1186/1471-2164-13-454
Application of next-generation sequencing technologies in virology
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.0.043182-0
Investigation of the Bacterial Communities Associated with Females of <i>Lutzomyia</i> Sand Fly Species from South America
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.0042531
Comparative genomics of Shiga toxin encoding bacteriophages
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:10.1186/1471-2164-13-311
Optimization of <i>Bartonella henselae</i> multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data
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.0366-6999.2012.13.008
Genome Sequence for "<i>Candidatus</i> Mycoplasma haemominutum," a Low-Pathogenicity Hemoplasma Species
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.06560-11
Optimization of Bartonella henselae multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data
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>
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
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.0001266
Molecular characterization of the uncultivatable hemotropic bacterium <i>Mycoplasma haemofelis</i>
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:10.1186/1297-9716-42-83
The Genus Arsenophonus
The Genus Arsenophonus (2011). In Manipulative Tenants (pp. 263-282). CRC Press. doi:10.1201/b11008-17
Complete Genome Sequence of <i>Mycoplasma haemofelis</i>, a Hemotropic Mycoplasma
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.00076-11
Genomic Analysis of Highly Virulent Georgia 2007/1 Isolate of African Swine Fever Virus
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/eid1704.101283
A <i>De Novo</i> Expression Profiling of <i>Anopheles funestus</i>, Malaria Vector in Africa, Using 454 Pyrosequencing
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.0017418
WHOLE SHOTGUN PYROSEQUENCING OF <i>MYCOPLASMA HAEMOFELIS</i>: THROWING NEW LIGHT ON AN OLD PATHOGEN
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
Characterization of Pneumonia Due to <i>Streptococcus equi</i> subsp. <i>zooepidemicus</i> in Dogs
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.00188-10
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>
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.00751-10
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>
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.00751-10
Amplified fragment length polymorphism (AFLP) analysis of closely related wild and captive tsetse fly (<i>Glossina morsitans morsitans</i>) populations
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:10.1186/1756-3305-3-47
Comparative Genomics and Transduction Potential of <i>Enterococcus faecalis</i> Temperate Bacteriophages
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.01293-09
Characteristics of the genome of <i>Arsenophonus nasoniae</i>, son-killer bacterium of the wasp <i>Nasonia</i>
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.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
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.x
Functional and Evolutionary Insights from the Genomes of Three Parasitoid <i>Nasonia</i> Species
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.1178028
2009
Symbiosis Research as a Novel Strategy for Insect Pest Control
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_9
The inherited microbiota of arthropods, and their importance in understanding resistance and immunity
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/9780199551354.003.0008
The mosaic genome structure of the <i>Wolbachia w</i>Ri strain infecting <i>Drosophila simulans</i>
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.0810753106
Symbiosis Research as a Novel Strategy for Insect Pest Control
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_9
2008
Fast forward genetics
Darby, A. C., & Hall, N. (2008). Fast forward genetics. NATURE BIOTECHNOLOGY, 26(11), 1248-1249. doi:10.1038/nbt1108-1248
Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts
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.0806554105
Sequencing veterinary pathogens
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-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
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)70083-7
Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction
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-r42
Genome Analysis
Darby, A. C. (2008). Genome Analysis. International Journal Of Infectious Diseases, 12, E20.
2007
The genomic and metabolic diversity of <i>Rickettsia</i>
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.2007.09.008
Intracellular pathogens go extreme: genome evolution in the Rickettsiales
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.2007.08.002
Antioxidants promote establishment of trypanosome infections in tsetse
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/S0031182007002247
The <i>Orientia tsutsugamushi</i> genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes
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.0611553104
Factors Affecting Trypanosome Maturation in Tsetse Flies
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.0000239
The incidence of thromboembolism in patients receiving adjuvant anthracycline based chemotherapy for early stage breast cancer
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
Bourtzis, K., & Miller, T. A. (Eds.) (n.d.). Insect Symbiosis, Volume 2. In . CRC Press. doi:10.1201/9781420005936
2005
Aphid-symbiotic bacteria cultured in insect cell lines
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.71.8.4833-4839.2005
Extrachromosomal DNA of the symbiont <i>Sodalis glossinidius</i>
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.187.14.5003-5007.2005
The rapid isolation and growth dynamics of the tsetse symbiont <i>Sodalis glossinidius</i>
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.2005.05.024
2004
Linking the bacterial community in pea aphids with host-plant use and natural enemy resistance
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.x
2003
Diversity of bacteria associated with natural aphid populations
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.69.12.7216-7223.2003
Elucidation of the transmission patterns of an insect-borne bacterium
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.69.8.4403-4407.2003
The significance of a facultative bacterium to natural populations of the pea aphid <i>Acyrthosiphon pisum</i>
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.x
The ecological significance of symbiotic microorganisms in animals: perspectives from the microbiota of aphids
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
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)00117-9
An aphid-borne bacterium allied to the secondary symbionts of whitefly
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.x
2000
Intraguild predators and the spatial distribution of a parasitoid
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/s004420000396
The olfactory responses of coccinellids to aphids on plants
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.x
The olfactory responses of coccinellids to aphids on plants.
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.x