Team:Edinburgh OG/Model:References
Model: References
During the development of our model we used an extensive list of scientific literature on the topic of bacteria-phage interactions. The list presented below includes nearly all available literature on this topic up until August 2017. We hope this will serve as a good resource for anyone who wants to tap into this fascinating topic.
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Bikard, D. et al. (2014) ‘Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials’, Nature Biotechnology. Nature Publishing Group, 32(11), pp. 1146–1150. doi: 10.1038/nbt.3043.
Cairns, B. J. et al. (2009) ‘Quantitative models of in vitro bacteriophage-host dynamics and their application to phage therapy’, PLoS Pathogens, 5(1), pp. 1–10. doi: 10.1371/journal.ppat.1000253.
Campbell, A. (1961) ‘Conditions for the Existence of Bacteriophage’, Evolution. Society for the Study of Evolution, 15(2), p. 153. doi: 10.2307/2406076.
Carletti, M. (2002) ‘On the stability properties of a stochastic model for phage-bacteria interaction in open marine environment’, Mathematical Biosciences, 175(2), pp. 117–131. doi: 10.1016/S0025-5564(01)00089-X.
Carletti, M. (2007) ‘Mean-square stability of a stochastic model for bacteriophage infection with time delays’, Mathematical Biosciences, 210(2), pp. 395–414. doi: 10.1016/j.mbs.2007.05.009.
Citorik, R. J., Mimee, M. and Lu, T. K. (2014) ‘Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases’, Nature Biotechnology. Nature Publishing Group, 32(11), pp. 1141–1145. doi: 10.1038/nbt.3011.
Clokie, M. R. et al. (2011) ‘Phages in nature.’, Bacteriophage. Taylor & Francis, 1(1), pp. 31–45. doi: 10.4161/bact.1.1.14942.
Cooper, C. J., Mirzaei, M. K. and Nilsson, A. S. (2016) ‘Adapting drug approval pathways for bacteriophage-based therapeutics’, Frontiers in Microbiology. Frontiers Media SA, p. 1209. doi: 10.3389/fmicb.2016.01209.
Davies, J. and Davies, D. (2010) ‘Origins and evolution of antibiotic resistance.’, Microbiology and molecular biology reviews : MMBR. American Society for Microbiology, 74(3), pp. 417–33. doi: 10.1128/MMBR.00016-10.
Demerec, M. and Fano, U. (1945) ‘Bacteriophage-Resistant Mutants in Escherichia Coli.’, Genetics, 30(2), pp. 119–36. Available at: http://www.ncbi.nlm.nih.gov/pubmed/17247150 (Accessed: 17 August 2017).
Deng, L. et al. (2014) ‘Grazing of heterotrophic flagellates on viruses is driven by feeding behaviour’, Environmental Microbiology Reports, 6(4), pp. 325–330. doi: 10.1111/1758-2229.12119.
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Edgar, R. et al. (2012) ‘Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes.’, Applied and environmental microbiology. American Society for Microbiology, 78(3), pp. 744–51. doi: 10.1128/AEM.05741-11.
Ellis, E. L., Delbrück, M. and Delbruck, M. (1939) ‘The Growth of Bacteriophage.’, The Journal of general physiology, 22(3), pp. 365–84. doi: 10.1085/jgp.22.3.365.
Gadagkar, R. and Gopinathan, K. P. (1980) ‘Bacteriophage burst size during multiple infections’, Journal of Biosciences, 2(3), pp. 253–259. doi: 10.1007/BF02703251.
Hansen, S. R. and Hubbell, S. P. (1980) ‘Single-Nutrient Microbial Competition: Qualitative Agreement between Experimental and Theoretically Forecast Outcomes’, Science, New Series, 207(4438), pp. 1491–1493. Available at: http://links.jstor.org/sici?sici=0036-8075%2819800328%293%3A207%3A4438%3C1491%3ASMCQAB%3E2.0.CO%3B2-O (Accessed: 3 August 2017).
Howard-Varona, C. et al. (2017) ‘Lysogeny in nature: mechanisms, impact and ecology of temperate phages’, The ISME Journal. Nature Publishing Group, 11(7), pp. 1511–1520. doi: 10.1038/ismej.2017.16.
Hsu, S. B., Hubbell, S. and Waltman, P. (1977) ‘A Mathematical Theory for Single-Nutrient Competition in Continuous Cultures of Micro-Organisms’, SIAM Journal on Applied Mathematics, 32(2), pp. 366–383. doi: 10.1137/0132030.
Jones, D. A. and Smith, H. L. (2011) ‘Bacteriophage and acteria in a flow reactor’, Bulletin of Mathematical Biology. Springer-Verlag, 73(10), pp. 2357–2383. doi: 10.1007/s11538-010-9626-0.
Khairalla, A. S., Wasfi, R. and Ashour, H. M. (2017) ‘Carriage frequency, phenotypic, and genotypic characteristics of methicillin-resistant Staphylococcus aureus isolated from dental health-care personnel, patients, and environment’, Scientific Reports, 7(1), p. 7390. doi: 10.1038/s41598-017-07713-8.
Krysiak-Baltyn, K. et al. (2016) ‘Computational models of populations of bacteria and lytic phage’, Critical Reviews in Microbiology, 42(6), pp. 942–968. doi: 10.3109/1040841X.2015.1114466.
Kumada, K., Koike, K. and Fujiwara, K. (1985) ‘The Survival of Bacteria under Starvation Conditions: a Mathematical Expression of Microbial Death’, Journal of General Microbiology. Microbiology Society, 131(9), pp. 2309–2312. doi: 10.1099/00221287-131-9-2309.
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Poccia, M. E., Beccaria, A. J. and Dondo, R. G. (2014) ‘Modeling the microbial growth of two escherichia coli strains in a multi-substrate environment’, Brazilian Journal of Chemical Engineering. Associação Brasileira de Engenharia Química, 31(2), pp. 347–354. doi: 10.1590/0104-6632.20140312s00002587.
Qiu, Z. (2007) ‘The analysis and regulation for the dynamics of a temperate bacteriophage model’, Mathematical Biosciences, 209(2), pp. 417–450. doi: 10.1016/j.mbs.2007.02.005.
Rastogi, R. P. et al. (2010) ‘Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair.’, Journal of nucleic acids. Hindawi, 2010, p. 592980. doi: 10.4061/2010/592980.
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Robledo, I. E., Aquino, E. E. and Vázquez, G. J. (2011) ‘Detection of the KPC gene in Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii during a PCR-based nosocomial surveillance study in Puerto Rico’, Antimicrobial Agents and Chemotherapy. American Society for Microbiology, 55(6), pp. 2968–2970. doi: 10.1128/AAC.01633-10.
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