Dr Sam Haldenby BSc(hons),PhD

Bioinformatician Biochemistry & Systems Biology

    Publications

    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 (Journal article)

    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

    DOI: 10.3390/v12101164

    Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma (Journal article)

    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

    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 (Journal article)

    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

    DOI: 10.1371/journal.pone.0227535

    2019

    Immunological observations and transcriptomic analysis of trimester-specific full-term placentas from three Zika virus-infected women (Journal article)

    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

    DOI: 10.1002/cti2.1082

    2018

    Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae. (Journal article)

    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, Dermanyssus gallinae.. Microbiology resource announcements, 7(18). doi:10.1128/MRA.01221-18

    DOI: 10.1128/MRA.01221-18

    Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis. (Journal article)

    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

    DOI: 10.1128/genomeA.00265-18

    Genomics of habitat choice and adaptive evolution in a deep-sea fish (Journal article)

    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

    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 (Journal article)

    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

    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 (Journal article)

    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

    DOI: 10.1128/mSphereDirect.00325-17

    Identification of Equid herpesvirus 2 in tissue-engineered equine tendon. (Journal article)

    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

    DOI: 10.12688/wellcomeopenres.12176.2

    Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity (Journal article)

    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

    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 (Journal article)

    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

    DOI: 10.1128/AEM.00162-17

    RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator (Journal article)

    Wardell, K., Haldenby, S., Jones, N., Liddell, S., Ngo, G. H. P., & Allers, T. (2017). RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator. DNA REPAIR, 55, 7-16. doi:10.1016/j.dnarep.2017.04.005

    DOI: 10.1016/j.dnarep.2017.04.005

    SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms (Journal article)

    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

    DOI: 10.2144/000114565

    Genome-Wide Association Study of Nevirapine Hypersensitivity in a sub-Saharan African HIV-infected Population (Journal article)

    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

    DOI: 10.1093/jac/dkw545

    Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus (Journal article)

    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

    DOI: 10.1186/s13059-016-1137-3

    2016

    Rapid evolution of microbe-mediated protection against pathogens in a worm host (Journal article)

    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

    DOI: 10.1038/ismej.2015.259

    Temperate phages both mediate and drive adaptive evolution in pathogen biofilms (Journal article)

    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

    DOI: 10.1073/pnas.1520056113

    2015

    Divergent, Coexisting Pseudomonas aeruginosa Lineages in Chronic Cystic Fibrosis Lung Infections (Journal article)

    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

    DOI: 10.1164/rccm.201409-1646OC

    Divergent, CoexistingPseudomonas aeruginosaLineages in Chronic Cystic Fibrosis Lung Infections (Journal article)

    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

    DOI: 10.1164/rccm.201409-1646OC

    2014

    NOTCH1 Mutations Occur Early during Cutaneous Squamous Cell Carcinogenesis. (Journal article)

    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 (Journal article)

    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. (Journal article)

    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. (Journal article)

    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 (Thesis / Dissertation)

    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. (Journal article)

    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..