2024
Fothergill, J., Kadioglu, A., & Hall, J. (2024). Exploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo. Nature Communications.
Agapov, A., Baker, K. S., Bedekar, P., Bhatia, R. P., Blower, T. R., Brockhurst, M. A., . . . Wright, R. (2024). Multi-layered genome defences in bacteria.. Current opinion in microbiology, 78, 102436. doi:10.1016/j.mib.2024.102436DOI: 10.1016/j.mib.2024.102436
Thompson, C. M. A., Hall, J. P. J., Chandra, G., Martins, C., Saalbach, G., Panturat, S., . . . Malone, J. G. (2024). Correction: Plasmids manipulate bacterial behaviour through translational regulatory crosstalk.. PLoS biology, 22(2), e3002531. doi:10.1371/journal.pbio.3002531DOI: 10.1371/journal.pbio.3002531
Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., . . . Kyrpides, N. C. (2024). IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.. Nucleic acids research, 52(D1), D164-D173. doi:10.1093/nar/gkad964DOI: 10.1093/nar/gkad964
2023
Hall, J. P. J. (2023). Microbial Musings: Spring 2023. MICROBIOLOGY-SGM, 169(7). doi:10.1099/mic.0.001379DOI: 10.1099/mic.0.001379
Horne, T., Orr, V. T., & Hall, J. P. J. (2023). How do interactions between mobile genetic elements affect horizontal gene transfer?. CURRENT OPINION IN MICROBIOLOGY, 73. doi:10.1016/j.mib.2023.102282DOI: 10.1016/j.mib.2023.102282
Bird, S. M., Ford, S., Thompson, C. M. A., Little, R., Hall, J. P. J., Jackson, R. W., . . . Brockhurst, M. A. (2023). Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities. FEMS MICROBIOLOGY ECOLOGY, 99(4). doi:10.1093/femsec/fiad027DOI: 10.1093/femsec/fiad027
Thompson, C. M. A., Hall, J. P. J., Chandra, G., Martins, C., Saalbach, G., Panturat, S., . . . Malone, J. G. (2023). Plasmids manipulate bacterial behaviour through translational regulatory crosstalk.. PLoS Biol, 21(2), e3001988. doi:10.1371/journal.pbio.3001988DOI: 10.1371/journal.pbio.3001988
2022
Coyte, K. Z., Stevenson, C., Knight, C. G., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2022). Horizontal gene transfer and ecological interactions jointly control microbiome stability.. PLoS biology, 20(11), e3001847. doi:10.1371/journal.pbio.3001847DOI: 10.1371/journal.pbio.3001847
Malaka De Silva, P., Stenhouse, G. E., Blackwell, G. A., Bengtsson, R. J., Jenkins, C., Hall, J. P. J., & Baker, K. S. (2022). A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella.. Proceedings. Biological sciences, 289(1980), 20220581. doi:10.1098/rspb.2022.0581DOI: 10.1098/rspb.2022.0581
Hall, J. P. J., Harrison, E., & Baltrus, D. A. (2022). Introduction: the secret lives of microbial mobile genetic elements. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 377(1842). doi:10.1098/rstb.2020.0460DOI: 10.1098/rstb.2020.0460
Hall, J. P. J., Botelho, J., Cazares, A., & Baltrus, D. A. (2022). What makes a megaplasmid?. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 377(1842). doi:10.1098/rstb.2020.0472DOI: 10.1098/rstb.2020.0472
2021
A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among <i>Shigella</i> (Journal article)
De Silva, M., Stenhouse, G., Blackwell, G., Bengtsson, R., Jenkins, C., Hall, J. P. J., & Baker, K. (2021). A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among <i>Shigella</i>. doi:10.1101/2021.12.17.473221DOI: 10.1101/2021.12.17.473221
Hall, J. P. J. (2021). Is the bacterial chromosome a mobile genetic element?. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-26758-yDOI: 10.1038/s41467-021-26758-y
Hall, J. P. J., Wright, R. C. T., Harrison, E., Muddiman, K. J., Wood, A. J., Paterson, S., & Brockhurst, M. A. (n.d.). Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLOS Biology, 19(10), e3001225. doi:10.1371/journal.pbio.3001225DOI: 10.1371/journal.pbio.3001225
Kottara, A., Carrilero, L., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2021). The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities.. Microbiology (Reading, England), 167(9). doi:10.1099/mic.0.001086DOI: 10.1099/mic.0.001086
Carrilero, L., Kottara, A., Guymer, D., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2021). Positive Selection Inhibits Plasmid Coexistence in Bacterial Genomes. MBIO, 12(3). doi:10.1128/mBio.00558-21DOI: 10.1128/mBio.00558-21
Kottara, A., Hall, J. P. J., & Brockhurst, M. Α. (2021). The proficiency of the original host species determines community-level plasmid dynamics.. FEMS Microbiology Ecology. doi:10.1093/femsec/fiab026DOI: 10.1093/femsec/fiab026
2020
Hall, J. P. J., Harrison, E., Parnanen, K., Virta, M., & Brockhurst, M. A. (2020). The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer. FRONTIERS IN MICROBIOLOGY, 11. doi:10.3389/fmicb.2020.01846DOI: 10.3389/fmicb.2020.01846
Cazares, A., Moore, M. P., Hall, J. P. J., Wright, L. L., Grimes, M., Emond-Rhéault, J. -G., . . . Winstanley, C. (2020). A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas.. Nature communications, 11(1). doi:10.1038/s41467-020-15081-7DOI: 10.1038/s41467-020-15081-7
Hall, J. P. J., Wright, R., Guymer, D., Harrison, E., & Brockhurst, M. (2020). Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways. Microbiology, 166(1), 56-62. doi:10.1099/mic.0.000862DOI: 10.1099/mic.0.000862
2019
Brockhurst, M. A., Harrison, E., Hall, J. P. J., Richards, T., McNally, A., & MacLean, C. (2019). The Ecology and Evolution of Pangenomes.. Current biology : CB, 29(20), R1094-R1103. doi:10.1016/j.cub.2019.08.012DOI: 10.1016/j.cub.2019.08.012
Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections (Journal article)
Jayaraman, S., Harris, C., Paxton, E., Donachie, A. -M., Vaikkinen, H., McCulloch, R., . . . Morrison, L. (2019). Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Neglected Tropical Diseases. doi:10.1371/journal.pntd.0007262DOI: 10.1371/journal.pntd.0007262
Coinfection promotes plasmid stability (Journal article)
Aguado, L. C., Hall, J. P. J., & Brockhurst, M. (2019). Coinfection promotes plasmid stability. Access Microbiology, 1(1A). doi:10.1099/acmi.ac2019.po0455DOI: 10.1099/acmi.ac2019.po0455
Zwanzig, M., Harrison, E., Brockhurst, M. A., Hall, J. P. J., Berendonk, T. U., & Berger, U. (2019). Mobile Compensatory Mutations Promote Plasmid Survival. MSYSTEMS, 4(1). doi:10.1128/mSystems.00186-18DOI: 10.1128/mSystems.00186-18
2018
Hall, J. P. J., Harrison, E., & Brockhurst, M. (2018). Competitive species interactions constrain abiotic adaptation in a bacterial soil community. Evolution Letters, 2(6), 580-589. doi:10.1002/evl3.83DOI: 10.1002/evl3.83
Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2018). Migration promotes plasmid stability under spatially heterogeneous positive selection. Proceedings of the Royal Society B: Biological Sciences, 285(1879), 20180324. doi:10.1098/rspb.2018.0324DOI: 10.1098/rspb.2018.0324
Stevenson, C., Hall, J. P. J., Brockhurst, M. A., & Harrison, E. (2018). Plasmid stability is enhanced by higher-frequency pulses of positive selection. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 285(1870). doi:10.1098/rspb.2017.2497DOI: 10.1098/rspb.2017.2497
Kottara, A., Hall, J. P. J., Harrison, E., & Brockhurst, M. A. (2018). Variable plasmid fitness effects and mobile genetic element dynamics across <i>Pseudomonas</i> species. FEMS MICROBIOLOGY ECOLOGY, 94(1). doi:10.1093/femsec/fix172DOI: 10.1093/femsec/fix172
2017
Hall, J. P. J., Brockhurst, M. A., & Harrison, E. (2017). Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 372(1735). doi:10.1098/rstb.2016.0424DOI: 10.1098/rstb.2016.0424
Hall, J. P. J., Williams, D., Paterson, S., Harrison, E., & Brockhurst, M. A. (2017). Positive selection inhibits gene mobilization and transfer in soil bacterial communities. Nature Ecology and Evolution, 1, 1348-1353. doi:10.1038/s41559-017-0250-3DOI: 10.1038/s41559-017-0250-3
Stevenson, C., Hall, J. P. J., Harrison, E., Wood, A. J., & Brockhurst, M. A. (2017). Gene mobility promotes the spread of resistance in bacterial populations. ISME JOURNAL, 11(8), 1930-1932. doi:10.1038/ismej.2017.42DOI: 10.1038/ismej.2017.42
Harrison, E., Hall, J. P. J., Paterson, S., Spiers, A. J., & Brockhurst, M. A. (2017). Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction. MOLECULAR ECOLOGY, 26(10), 2757-2764. doi:10.1111/mec.14080DOI: 10.1111/mec.14080
Hall, J. P. J., Brockhurst, M. A., Dytham, C., & Harrison, E. (2017). The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories?. PLASMID, 91, 90-95. doi:10.1016/j.plasmid.2017.04.003DOI: 10.1016/j.plasmid.2017.04.003
2016
Hall, J. P. J., & Harrison, E. (2016). Resistance is a numbers game. NATURE MICROBIOLOGY, 1(12). doi:10.1038/NMICROBIOL.2016.235DOI: 10.1038/NMICROBIOL.2016.235
Hall, J. P. J., Wood, A. J., Harrison, E., & Brockhurst, M. A. (2016). Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 113(29), 8260-8265. doi:10.1073/pnas.1600974113DOI: 10.1073/pnas.1600974113
Harrison, E., Dytham, C., Hall, J. P. J., Guymer, D., Spiers, A. J., Paterson, S., & Brockhurst, M. A. (2016). Rapid compensatory evolution promotes the survival of conjugative plasmids.. Mobile genetic elements, 6(3), e1179074. doi:10.1080/2159256x.2016.1179074DOI: 10.1080/2159256x.2016.1179074
Harvey, W. T., Benton, D. J., Gregory, V., Hall, J. P. J., Daniels, R. S., Bedford, T., . . . Reeve, R. (2016). Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses. PLoS Pathogens, 12(4). doi:10.1371/journal.ppat.1005526DOI: 10.1371/journal.ppat.1005526
Kottara, A., Hall, J. P. J., Harrison, E., & Brockhurst, M. A. (2016). Multi-host environments select for hostgeneralist conjugative plasmids. BMC EVOLUTIONARY BIOLOGY, 16. doi:10.1186/s12862-016-0642-zDOI: 10.1186/s12862-016-0642-z
2015
Hall, J. P. J., Harrison, E., Lilley, A. K., Paterson, S., Spiers, A. J., & Brockhurst, M. A. (2015). Environmentally co‐occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context‐dependent fitness effects. Environmental Microbiology, 17(12), 5008-5022. doi:10.1111/1462-2920.12901DOI: 10.1111/1462-2920.12901
DNA Recombination Strategies During Antigenic Variation in the African Trypanosome (Chapter)
McCulloch, R., Morrison, L. J., & Hall, J. P. J. (n.d.). DNA Recombination Strategies During Antigenic Variation in the African Trypanosome. In Mobile DNA III (pp. 409-435). ASM Press. doi:10.1128/9781555819217.ch19DOI: 10.1128/9781555819217.ch19
DNA Recombination Strategies During Antigenic Variation in the African Trypanosome (Journal article)
McCulloch, R., Morrison, L. J., & Hall, J. P. J. (2015). DNA Recombination Strategies During Antigenic Variation in the African Trypanosome. MICROBIOLOGY SPECTRUM, 3(2). doi:10.1128/microbiolspec.MDNA3-0016-2014DOI: 10.1128/microbiolspec.MDNA3-0016-2014
2014
Hall, J. P. J., & Plenderleith, L. (2014). Withstanding the Challenges of Host Immunity: Antigenic Variation and the Trypanosome Surface Coat. In Trypanosomes and Trypanosomiasis (pp. 61-87). Springer Vienna. doi:10.1007/978-3-7091-1556-5_3DOI: 10.1007/978-3-7091-1556-5_3
2013
Viral host-adaptation: insights from evolution experiments with phages (Journal article)
Hall, J. P. J., Harrison, E., & Brockhurst, M. A. (2013). Viral host-adaptation: insights from evolution experiments with phages. CURRENT OPINION IN VIROLOGY, 3(5), 572-577. doi:10.1016/j.coviro.2013.07.001DOI: 10.1016/j.coviro.2013.07.001
Hall, J. P. J., Wang, H., & Barry, J. D. (2013). Mosaic <i>VSGs</i> and the Scale of <i>Trypanosoma brucei</i> Antigenic Variation. PLOS PATHOGENS, 9(7). doi:10.1371/journal.ppat.1003502DOI: 10.1371/journal.ppat.1003502
2012
Genome hyperevolution and the success of a parasite (Chapter)
Barry, J. D., Hall, J. P. J., & Plenderleith, L. (2012). Genome hyperevolution and the success of a parasite. In EFFECTS OF GENOME STRUCTURE AND SEQUENCE ON VARIATION AND EVOLUTION (Vol. 1267, pp. 11-17). doi:10.1111/j.1749-6632.2012.06654.xDOI: 10.1111/j.1749-6632.2012.06654.x
