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Publications on microbial systems
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preprints
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Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter
F. Bull, S. Tavaddod, N. Bommer, M. Perry, C. A. Brackley and R. J. Allen
https://doi.org/10.1101/2022.10.31.514508​​
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Surface versus volume synthesis governs growth-dependent efficacy of a β-lactam antibiotic
R. Brouwers*, L. Mancini*, S. Tavaddod*, J. Biboy, M. Mauri, E. Tatham, M.-L. Enghardt, A. Zander, P. Cicuta, W. Vollmer & R. J. Allen
bioRxiv 2024.01.31.578235
https://doi.org/10.1101/2024.01.31.578235
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2025
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Spatial partitioning of a microbial population enhances collective enzymatic
defence
N. Verdon*, O. Popescu*, S. Titmuss & R. J. Allen
J. R. Soc. Interface 22 20240611 (2025)
https://doi.org/10.1098/rsif.2024.0611
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2024
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Population genetics: an introduction for physicists
A. Iglesias-Ramas, S. Pio Lipani & R. J. Allen
SciPost 89 (2024)
doi:10.21468/SciPostPhysLectNotes.89
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Bacterial aggregation triggered by low-level antibiotic-mediated lysis
S. Tavaddod, A. Dawson & R. J. Allen
npj Biofilms & Microbiomes 10 90 (2024)
https://doi.org/10.1038/s41522-024-00553-1
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2023
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Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures
G. Melaugh, V. A. Martinez, P. Baker, P. J. Hill, P. L. Howell, D. J. Wozniak and R. J. Allen
npj Biofilms & Microbiomes 9 52 (2023)
https://doi.org/10.1038/s41522-023-00412-5
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Active layer dynamics drives a transition to biofilm fingering
E. Young, G. Melaugh & R. J. Allen
npj Biofilms & Microbiomes 9 17 (2023)
https://doi.org/10.1038/s41522-023-00380-w
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A sluggish random walk with subdiffusive spread
A. Zodage, R. J. Allen, M. R. Evans & S. Majumdar
J. Stat. Mech. 033211 (2023)
https://doi.org/10.1088/1742-5468/acc4b1
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2022
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Dynamic diatom-bacteria consortia in synthetic plankton communities
Y. Deng, M. Mauri, M. Vallet, M. Staudinger, R. J. Allen and G. Pohnert
Appl. Env. Microbiol. 88 01619-22 (2022)
10.1128/aem.01619-22
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Model for quorum-sensing mediated stochastic biofilm formation
P. Sinclair, C. A. Brackley, M. Carballo-Pacheco and R. J. Allen
Physical Review Letters 129, 198102 (2022)
Reviewed in Nature Reviews Physics: "Fluctuating into a biofilm" by Zoe Budrikis (2022)
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Lineage dynamics in growing biofilms: spatial patterns of standing vs. de novo diversity
E. Young and R. J. Allen
Frontiers in Microbiology 13 915095 (2022)
Tracking the stochastic growth of bacterial populations in microfluidic droplets
Daniel Taylor, Nia Verdon, Peter Lomax, Rosalind J Allen and Simon Titmuss
Physical Biology 19, 026003 (2022)
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A computational model for microbial colonisation of an antifouling surface
P. Sinclair, J. Longyear, K. Reynolds, A. A. Finnie, C. A. Brackley, M. Carballo-Pacheco and R. J. Allen
Frontiers in Microbiology 13 920014 (2022)
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Amplification-free detection of SARS-CoV-2 using multi-valent binding
A. Roychoudhury, R. J. Allen, T. Curk, J. Farrell, G. McAllister, K. Templeton & T. T. Bachmann
ACS Sensors 7, 369203699 (2022)
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2020
Stability of beta-lactam antibiotics in bacterial growth media
R. Brouwers, H. Vass, A. Dawson, T. Squires & R. J. Allen
PLoS One 15, e0236198 (2020)
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Predictable properties of fitness landscapes induced by adaptational tradeoffs
S. G. Das, S. O. L. Direito, B. Waclaw, R. J. Allen & J. Krug
eLife 9, e55155 (2020)
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Phenotypic delay in the evolution of bacterial antibiotic resistance: Mechanistic models and their implications.
M. Carballo-Pacheco, M. D. Nicholson, E. Lilja, R. J. Allen & B. Waclaw
PLoS Computational Biology 16, e1007930 (2020)
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A roadblock-and-kill mechanism for the action of the DNA-targeting antibiotic ciprofloxacin.
N. Ojkic, E. Lilja, S. Direito, A. Dawson, R. J. Allen & B. Waclaw
Antimicrobial Agents and Chemotherapy 64, e02487-19 (2020)
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Computational design of probes to detect bacterial genomes by multivalent binding
T. Curk, C. A. Brackley, J. D. Farrell, Z. Xing, D. Joshi, S. Direito, U. Bren, S. Angioletti-Uberti, J. Dobnikar, E. Eiser, D. Frenkel and R. J. Allen
Proc. Natl. Acad. Sci. USA 117 (16) 8719-8726 (2020)
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Staff and patient perceptions of a community urinary catheter service
F. Oswald, E. Young, F. Denison, R. J. Allen & M. Perry
International Journal of Urological Nursing 1-9 (2020)
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2019
Growth-dependent drug susceptibility can prevent or enhance spatial expansion of a bacterial population
P. Sinclair, M. Carballo Pacheco* and R. J. Allen*
Physical Biology 16, 046001 (2019)
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Resource spectrum engineering by specialist species can shift the specialist-generalist balance
C. G. Mills, R. J. Allen* and R. A. Blythe*
Theoretical Ecology 13, 1-15 (2019)
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Bacterial growth: a statistical physicist's guide
R. J. Allen and B. Waclaw
Reports on Progress in Physics 82, 016601 (2019)
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A simulation study of aggregation mediated by production of cohesive molecules
G. Melaugh, D. Marenduzzo, A. Morozov and R. J. Allen
Soft Matter 15, 9120 (2019)
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2017
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Oxic-anoxic regime shifts induced by biogeochemical feedbacks in microbial communities
T. Bush, M. Diao, R. J. Allen, R. Sinnige, G. Muyzer and J. Huisman
Nature Communications 8, 789 (2017)
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Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states
E. Pagaling, K. Vassileva, C. G. Mills, T. Bush, R. A. Blythe, J. Schwarz-Linek, F. Strathdee, R. J. Allen and A. Free
Environmental Microbiology 19: 3374–3386 (2017)
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The Pseudomonas aeruginosa polysaccharide PSL is a social but non-cheatable trait in biofilms
Y. Irie, A. Roberts, K. Kragh, V. Gordon, J. Hutchison, R. Allen, G. Melaugh, T. Bjarnsholt, S. West and S. Diggle
mBio 8, e00374-17 (2017)
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P. Greulich, J. Dolezal, M. Scott, M. R. Evans & R. J. Allen
Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics
Physical Biology 14, 6 (2017)
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2016
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Challenges in microbial ecology: building predictive understanding of community function and dynamics
​​​S. Widder, R. J. Allen et al.
ISME Journal 10, 2557-2568 (2016)​​​
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Role of multicellular aggregates in biofilm formation
K. Kragh*, J. Hutchison*, G. Melaugh*, C. Rodesney, A. Roberts, Y. Irie, P. Jensen, S. Diggle, R. J. Allen**, V. D. Gordon** and T. Bjarnsholt**
mBio 7, e00237-16 (2016)
Shaping the growth behaviour of biofilms initiated from bacterial aggregates
​G. Melaugh, J. Hutchison, K. Kragh, Y. Irie, A. Roberts, T. Bjarnsholt, S. Diggle, V. Gordon and R. J. Allen
Plos One 11, e0149683 (2016)
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2015
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Redox regime shifts in microbially-mediated biogeochemical cycles
T. Bush, T. B. Butler, A. Free and R. J. Allen
Biogeosciences 12, 3717-3724 (2015)
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Competition for space during bacterial colonisation of a surface
D. P. Lloyd and R. J. Allen
J. R. Soc. Interface 12, 20150608 (2015)
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P. Greulich*, M. Scott*, M. R. Evans & R. J. Allen
Growth-dependent susceptibility to ribosome-targeting antibiotics
Molecular Systems Biology 11, 796 (2015)
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S. J. Court, B. Waclaw* & R. J. Allen*
Lower glycolysis carries a higher flux than any biochemically possible alternative
Nature Communications 6, 8427 (2015)
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2014
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The role of mechanical forces in the planar-to-bulk transition in growing Escherichia coli microcolonies
​​​M. A. A. Grant, B. Waclaw, R. J. Allen and P. Cicuta
J. R. Soc. Interface 11, 20140400 (2014)
Speed of invasion of an expanding population by a horizontally-transmitted trait
​J. Venegas-Ortiz, R. J. Allen* and M. R. Evans*
Genetics 196, 497-507 (2014)
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2013
Parasites on parasites: coupled fluctuations in stacked contact processes
​S. J. Court, R. A. Blythe and R. J. Allen
Europhys. Lett. 101, 50001 (2013)
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Selection history affects the predictability of microbial ecosystem development​​
E. Pagaling, F. Strathdee, B. Spears, M. E. Cates, R. J. Allen* and A. Free*
ISME J. 8, 19-30 (2013)
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S. L. Black, A. Dawson, F. B. Ward & R. J. Allen
Genes required for growth at high hydrostatic pressure in Escherichia coli identified by genome-wide screening
Plos One 8, e73995 (2013)
2012
Mutational pathway determines whether drug gradients accelerate evolution of drug-resistant cells
​P. Greulich*, B. Waclaw* and R. J. Allen
Phys. Rev. Lett. 109, 088101 (2012) (*=equal contribution)
Selected as editor's choice and featured in a viewpoint article "Bacteria Evolve to Go Against the Grain" by Oskar Hallatschek, Physics 5, 93 (2012)
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Oscillating microbial dynamics driven by small populations, limited nutrient supply and high death rates​
​B. S. Khatri, A. Free and R. J. Allen
J. Theor. Biol. 314, 120-129 (2012)
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A mixed population of competing TASEPs with a shared reservoir.
P. Greulich, L. Ciandrini, R. J. Allen* & M. C. Romano*
Physical Review E 85, 011142 (2012)
2011
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Effects of macromolecular crowding on genetic networks
M. J. Morelli, R. J. Allen & P. R. ten Wolde
Biophysical Journal 101, 2882 (2011)
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2010
Switching and growth for microbial populations in catastrophic responsive environments
​P. Visco, R. J. Allen, S. Majumdar and M. R. Evans
Biophys. J. 98, 1099-1108 (2010)
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Dynamical phase transition in a model for evolution with migration
​B. Waclaw, R. J. Allen and M. R. Evans
Phys. Rev. Lett. 105, 268101 (2010)
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A multi-purpose modular system for high-resolution microscopy at
high hydrostatic pressure
H. Vass, S. L. Black, E. M. Herzig, F. B. Ward, P. S. Clegg & R. J. Allen
Review of Scientific Instruments 81, 053710 (2010)
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Non-equilibrium dynamics of an active colloidal “chucker”
C. Valeriani, R. J. Allen* & D. Marenduzzo*
Journal of Chemical Physics 132, 204904 (2010)
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