Publications
2024
P2RX7 gene variants associate with altered inflammasome assembly and reduced pyroptosis in chronic nonbacterial osteomyelitis (CNO).
Charras, A., Hofmann, S. R., Cox, A., Schulze, F., Russ, S., Northey, S., . . . Hedrich, C. M. (2024). P2RX7 gene variants associate with altered inflammasome assembly and reduced pyroptosis in chronic nonbacterial osteomyelitis (CNO).. Journal of autoimmunity, 144, 103183. doi:10.1016/j.jaut.2024.103183
Corrigendum: Rapid typing of <i>Klebsiella pneumoniae</i> and <i>Pseudomonas aeruginosa</i> by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings.
Zendri, F., Schmidt, V., Mauder, N., Loeffler, A., Jepson, R. E., Isgren, C., . . . Timofte, D. (2024). Corrigendum: Rapid typing of <i>Klebsiella pneumoniae</i> and <i>Pseudomonas aeruginosa</i> by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings.. Frontiers in microbiology, 15, 1396367. doi:10.3389/fmicb.2024.1396367
Rapid typing of <i>Klebsiella pneumoniae</i> and <i>Pseudomonas aeruginosa</i> by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings.
Zendri, F., Schmidt, V., Mauder, N., Loeffler, A., Jepson, R. E., Isgren, C., . . . Timofte, D. (2024). Rapid typing of <i>Klebsiella pneumoniae</i> and <i>Pseudomonas aeruginosa</i> by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings.. Frontiers in microbiology, 15, 1334268. doi:10.3389/fmicb.2024.1334268
2023
Genotypic and Phenotypic Analyses of Two Distinct Sets of<i>Pseudomonas aeruginosa</i>Urinary Tract Isolates
Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis
Hares, M. F., Griffiths, B. E., Johnson, F., Nelson, C., Haldenby, S., Stewart, C. J., . . . Coombes, J. L. (n.d.). Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis. Animal Microbiome, 5(1). doi:10.1186/s42523-023-00265-5
Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: A metagenomic analysis
Genomic profiling of idiopathic peri-hilar cholangiocarcinoma reveals new targets and mutational pathways
Quinn, L. M., Haldenby, S., Antzcak, P., Fowler, A., Bullock, K., Kenny, J., . . . Goldring, C. (n.d.). Genomic profiling of idiopathic peri-hilar cholangiocarcinoma reveals new targets and mutational pathways. Scientific Reports, 13(1). doi:10.1038/s41598-023-33096-0
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
Panel sequencing links rare, likely damaging gene variants with distinct clinical phenotypes and outcomes in juvenile-onset SLE
Charras, A., Haldenby, S., Smith, E. M. D., Egbivwie, N., Olohan, L., Kenny, J. G., . . . Hedrich, C. M. (2023). Panel sequencing links rare, likely damaging gene variants with distinct clinical phenotypes and outcomes in juvenile-onset SLE. RHEUMATOLOGY, 62(SI2), SI210-SI225. doi:10.1093/rheumatology/keac275
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
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
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
678 Damaging variants in P2X7R associate with Chronic Nonbacterial Osteomyelitis (CNO)
Charras, A., Hofmann, S. R., Cox, A., Schulze, F., Russ, S., Hartmann, H., . . . Hedrich, C. M. (2022). 678 Damaging variants in P2X7R associate with Chronic Nonbacterial Osteomyelitis (CNO). In British Society for Rheumatology (pp. A260). BMJ Publishing Group Ltd and Royal College of Paediatrics and Child Health. doi:10.1136/archdischild-2022-rcpch.421
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
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
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
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
Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London.
Snell, L. B., Wang, W., Alcolea-Medina, A., Charalampous, T., Batra, R., de Jongh, L., . . . Curcin, V. (2022). Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London.. BMJ open, 12(2), e055474. doi:10.1136/bmjopen-2021-055474
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
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
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
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.
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)00475-8
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic
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.2021.08.014
Campylobacter Contamination at Retail of Halal Chicken Produced in the United Kingdom
Royden, A., Christley, R., Jones, T., Williams, A., Awad, F., Haldenby, S., . . . Williams, N. J. (2021). Campylobacter Contamination at Retail of Halal Chicken Produced in the United Kingdom. JOURNAL OF FOOD PROTECTION, 84(8), 1433-1445. doi:10.4315/JFP-20-428
The Bovine Foot Skin Microbiota is Associated with Host Genotype and the Development of Infectious Digital Dermatitis Lesions
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
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.2021.109292
Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
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-x
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., . . . Gupta, R. K. (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. NATURE, 593(7857), 136-+. doi:10.1038/s41586-021-03412-7
Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study
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)00055-4
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., . . . Gupta, R. K. (2021). SARS-CoV-2 evolution during treatment of chronic infection. NATURE, 592(7853), 277-+. doi:10.1038/s41586-021-03291-y
Outbreak of Severe Vomiting in Dogs Associated with a Canine Enteric Coronavirus, United Kingdom
Radford, A. D., Singleton, D. A., Jewell, C., Appleton, C., Rowlingson, B., Hale, A. C., . . . Pinchbeck, G. L. (2021). Outbreak of Severe Vomiting in Dogs Associated with a Canine Enteric Coronavirus, United Kingdom. EMERGING INFECTIOUS DISEASES, 27(2), 517-528. doi:10.3201/eid2702.202452
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.
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.2020.11.020
Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment.
Huson, K. M., Atcheson, E., Oliver, N. A. M., Best, P., Barley, J. P., Hanna, R. E. B., . . . Robinson, M. W. (2021). Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment.. Molecular & cellular proteomics : MCP, 20, 100055. doi:10.1074/mcp.ra120.002175
2020
Transcriptome and secretome analysis of intra-mammalian life-stages of the emerging helminth pathogen, Calicophoron daubneyi reveals adaptation to a unique host environment.
Huson, K. M., Atcheson, E., Oliver, N. A. M., Best, P., Barley, J. P., Hanna, R. E. B., . . . Robinson, M. W. (n.d.). Transcriptome and secretome analysis of intra-mammalian life-stages of the emerging helminth pathogen, Calicophoron daubneyi reveals adaptation to a unique host environment.. Molecular & Cellular Proteomics, mcp.RA120.002175. doi:10.1074/mcp.ra120.002175
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
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/v12101164
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
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.2020.25.32.2001410
Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma
Thornton, S., Coupland, S. E., Olohan, L., Sibbring, J. S., Kenny, J. G., Hertz-Fowler, C., . . . Kalirai, H. (2020). Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma. CANCERS, 12(4). doi:10.3390/cancers12041039
Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom
Haldenby, S., Bronowski, C., Nelson, C., Kenny, J., Martinez-Rodriguez, C., Chaudhuri, R., . . . Winstanley, C. (2020). Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom. PLOS ONE, 15(01). doi:10.1371/journal.pone.0227535
2019
Trimester-specific Zika virus infection affects placental responses in women
CD4 T-CELL HLA-U PSEUDOGENE AT BASELINE PREDICTS CLINICAL REMISSION TO ANTI-TNF AGENTS IN ULCERATIVE COLITIS
Subramanian, S., Rainbow, L., Gemmell, M., Fang, Y., Haldenby, S., Hough, R., & Probert, C. (2019). CD4 T-CELL HLA-U PSEUDOGENE AT BASELINE PREDICTS CLINICAL REMISSION TO ANTI-TNF AGENTS IN ULCERATIVE COLITIS. In GUT Vol. 68 (pp. A64-A65). doi:10.1136/gutjnl-2019-BSGAbstracts.127
CD4 T-cell transcriptome analysis at baseline predicts clinical remission to anti-TNF agents in ulcerative colitis (UC)
Subramanian, S., Rainbow, L., Gemmell, M., Hough, R., Haldenby, S., Gureviciute, A., . . . Probert, C. (2019). CD4 T-cell transcriptome analysis at baseline predicts clinical remission to anti-TNF agents in ulcerative colitis (UC). In JOURNAL OF CROHNS & COLITIS Vol. 13 (pp. S132-S133). doi:10.1093/ecco-jcc/jjy222.217
Immunological observations and transcriptomic analysis of trimester-specific full-term placentas from three Zika virus-infected women
Lum, F. -M., Narang, V., Hue, S., Chen, J., McGovern, N., Rajarethinam, R., . . . Ng, L. F. P. (n.d.). Immunological observations and transcriptomic analysis of trimester-specific full-term placentas from three Zika virus-infected women. Clinical and Translational Immunology, 8(11). doi:10.1002/cti2.1082
2018
Draft Genome Assembly of the Poultry Red Mite, <i>Dermanyssus gallinae</i>
Burgess, S. T. G., Bartley, K., Nunn, F., Wright, H. W., Hughes, M., Gemmell, M., . . . Nisbet, A. J. (2018). Draft Genome Assembly of the Poultry Red Mite, <i>Dermanyssus gallinae</i>. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 7(18). doi:10.1128/MRA.01221-18
Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis.
Burgess, S. T. G., Bartley, K., Marr, E. J., Wright, H. W., Weaver, R. J., Prickett, J. C., . . . Nisbet, A. J. (2018). Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis.. Genome announcements, 6(16). doi:10.1128/genomeA.00265-18
Genomics of habitat choice and adaptive evolution in a deep-sea fish
Gaither, M. R., Gkafas, G. A., de Jong, M., Sarigol, F., Neat, F., Regnier, T., . . . Hoelzel, A. R. (2018). Genomics of habitat choice and adaptive evolution in a deep-sea fish. NATURE ECOLOGY & EVOLUTION, 2(4), 680-687. doi:10.1038/s41559-018-0482-x
Transmission and lineage displacement drive rapid population genomic flux in cystic fibrosis airway infections of a Pseudomonas aeruginosa epidemic strain
Williams, D., Fothergill, J. L., Evans, B., Caples, J., Haldenby, S., Walshaw, M. J., . . . Paterson, S. (2018). Transmission and lineage displacement drive rapid population genomic flux in cystic fibrosis airway infections of a Pseudomonas aeruginosa epidemic strain. MICROBIAL GENOMICS, 4(3). doi:10.1099/mgen.0.000167
2017
Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut
Carroll, M. W., Haldenby, S., Rickett, N. Y., Palyi, B., Garcia-Dorival, I., Liu, X., . . . Hiscox, J. A. (2017). Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut. MSPHERE, 2(04), 19 pages. doi:10.1128/mSphereDirect.00325-17
Deep sequencing of RNA from blood and oral swab samples reveals the presence of nucleic acid from a number of pathogens in patients with acute Ebola virus disease and is consistent with bacterial translocation across the gut
Carroll, M. W., Haldenby, S., Rickett, N. Y., Pályi, B., Garcia-Dorival, I., Liu, X., . . . Hiscox, J. A. (2017). Deep sequencing of RNA from blood and oral swab samples reveals the presence of nucleic acid from a number of pathogens in patients with acute Ebola virus disease and is consistent with bacterial translocation across the gut. mSphere, 2(4). doi:10.1128/mSphereDirect.00325-17
Identification of Equid herpesvirus 2 in tissue-engineered equine tendon.
Wardle, R., Pullman, J. A., Haldenby, S., Ressel, L., Pope, M., Clegg, P. D., . . . Peffers, M. J. (2017). Identification of Equid herpesvirus 2 in tissue-engineered equine tendon.. Wellcome open research, 2, 60. doi:10.12688/wellcomeopenres.12176.2
Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity
Ransom-Jones, E., McCarthy, A. J., Haldenby, S., Doonan, J., & McDonald, J. E. (2017). Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity. mSphere, 2(4). doi:10.1128/mSphere.00300-17
Novel Sampling Method for Assessing Human-Pathogen Interactions in the Natural Environment Using Boot Socks and Citizen Scientists, with Application to Campylobacter Seasonality
Jones, N., Millman, C., van der Es, M., Hukelova, M., Forbes, K., Glover, C., . . . Lake, I. (2017). Novel Sampling Method for Assessing Human-Pathogen Interactions in the Natural Environment Using Boot Socks and Citizen Scientists, with Application to Campylobacter Seasonality. Applied and Environmental Microbiology, 83(14). doi:10.1128/AEM.00162-17
RadB acts in homologous recombination in the archaeon <i>Haloferax volcanii</i>, consistent with a role as recombination mediator
Wardell, K., Haldenby, S., Jones, N., Liddell, S., Ngo, G. H. P., & Allers, T. (2017). RadB acts in homologous recombination in the archaeon <i>Haloferax volcanii</i>, consistent with a role as recombination mediator. DNA REPAIR, 55, 7-16. doi:10.1016/j.dnarep.2017.04.005
SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms
D'Amore, R., Johnson, J., Haldenby, S., Hall, N., Hughes, M., Joynson, R., . . . Hall, A. (2017). SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms. BIOTECHNIQUES, 63(1), 13-20. doi:10.2144/000114565
Genome-Wide Association Study of Nevirapine Hypersensitivity in a sub-Saharan African HIV-infected Population
Carr, D. F., Bourgeois, S., Chaponda, M., Takeshita, L., Morris, A., Cornejo Castro, E. M., . . . Pirmohamed, M. (2017). Genome-Wide Association Study of Nevirapine Hypersensitivity in a sub-Saharan African HIV-infected Population. Journal of Antimicrobial Chemotherapy, 72(4), 1152-1162. doi:10.1093/jac/dkw545
Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
Liu, X., Speranza, E., Muñoz-Fontela, C., Haldenby, S., Rickett, N., Garcia-Dorival, I., . . . Hiscox, J. (2017). Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus. Genome Biology, 18. doi:10.1186/s13059-016-1137-3
2016
Rapid evolution of microbe-mediated protection against pathogens in a worm host
King, K. C., Brockhurst, M. A., Vasieva, O., Paterson, S., Betts, A., Ford, S. A., . . . Hurst, G. D. D. (2016). Rapid evolution of microbe-mediated protection against pathogens in a worm host. ISME Journal, 10, 1915-1924. doi:10.1038/ismej.2015.259
Temperate phages both mediate and drive adaptive evolution in pathogen biofilms
Davies, E. V., James, C. E., Williams, D., O'Brien, S., Fothergill, J. L., Haldenby, S., . . . Brockhurst, M. A. (2016). Temperate phages both mediate and drive adaptive evolution in pathogen biofilms. Proceedings of the National Academy of Sciences of the United States of America, 113(29), 8266-8271. doi:10.1073/pnas.1520056113
2015
Divergent, Coexisting Pseudomonas aeruginosa Lineages in Chronic Cystic Fibrosis Lung Infections
Williams, D., Evans, B., Haldenby, S., Walshaw, M. J., Brockhurst, M. A., Winstanley, C., & Paterson, S. (2015). Divergent, Coexisting Pseudomonas aeruginosa Lineages in Chronic Cystic Fibrosis Lung Infections. American Journal of Respiratory and Critical Care Medicine, 191(7), 775-785. doi:10.1164/rccm.201409-1646OC
Divergent, CoexistingPseudomonas aeruginosaLineages in Chronic Cystic Fibrosis Lung Infections
Williams, D., Evans, B., Haldenby, S., Walshaw, M. J., Brockhurst, M. A., Winstanley, C., & Paterson, S. (2015). Divergent, CoexistingPseudomonas aeruginosaLineages in Chronic Cystic Fibrosis Lung Infections. American Journal of Respiratory and Critical Care Medicine, 191(7), 775-785. doi:10.1164/rccm.201409-1646OC
2014
WS21.4 Use of genome sequencing to study population diversification and transmission of a Pseudomonas aeruginosa epidemic strain
Winstanley, C., Williams, D., Fothergill, J. L., Evans, B., Haldenby, S., Loman, N., . . . Paterson, S. (2014). WS21.4 Use of genome sequencing to study population diversification and transmission of a Pseudomonas aeruginosa epidemic strain. Journal of Cystic Fibrosis, 13, S41. doi:10.1016/s1569-1993(14)60129-6
NOTCH1 Mutations Occur Early during Cutaneous Squamous Cell Carcinogenesis.
South, A. P., Purdie, K. J., Watt, S. A., Haldenby, S., den Breems, N. Y., Dimon, M., . . . Leigh, I. M. (2014). NOTCH1 Mutations Occur Early during Cutaneous Squamous Cell Carcinogenesis.. J Invest Dermatol.
Temperate phage accelerate adaptation of Pseudomonas aeruginosa in a biofilm model
James, C. E., Davies, E. V., Haldenby, S., Paterson, S., Winstanley, C., & Brockhurst, M. A. (2014). Temperate phage accelerate adaptation of Pseudomonas aeruginosa in a biofilm model.
2010
The complete genome sequence of Haloferax volcanii DS2, a model archaeon.
Hartman, A. L., Norais, C., Badger, J. H., Delmas, S., Haldenby, S., Madupu, R., . . . Eisen, J. A. (2010). The complete genome sequence of Haloferax volcanii DS2, a model archaeon.. PLoS One.
2009
RecA family proteins in archaea: RadA and its cousins.
Haldenby, S., White, M. F., & Allers, T. (2009). RecA family proteins in archaea: RadA and its cousins.. Biochem Soc Trans..
2007
Genetic Analysis of RadB, a Paralogue of the Archaeal Rad51/RecA Homologue, RadA
Haldenby, S. (2007). Genetic Analysis of RadB, a Paralogue of the Archaeal Rad51/RecA Homologue, RadA. (PhD Thesis, University of Nottingham).
2006
Interactions of RadB, a DNA repair protein in archaea, with DNA and ATP.
Guy, C. P., Haldenby, S., Brindley, A., Walsh, D. A., Briggs, G. S., Warren, M. J., . . . Bolt, E. L. (2006). Interactions of RadB, a DNA repair protein in archaea, with DNA and ATP.. J Mol Biol..