Overview

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Publications

_{Copyright Notice: Any articles made available for download are for personal use only. Any other use requires prior permission of the author and the copyright holder.}

| 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1998 |

2024

• Butt L, Meyer JR, Lindsay RJ, Beardmore RE, Gudelj I. (2024) Bacterial Resistance Response and Resource Availability Mediates Viral Coexistence, J Evol Biol, DOI:10.1093/jeb/voae022. [PDF]

2023

• Wood E, Schulenburg H, Rosenstiel P, Bergmiller T, Ankrett D, Gudelj I, Beardmore R. (2023) Ribosome-binding antibiotics increase bacterial longevity and growth efficiency, Proc Natl Acad Sci U S A, volume 120, no. 40, DOI:10.1073/pnas.2221507120. [PDF]

2022

• Catalán P, Wood E, Blair JMA, Gudelj I, Iredell JR, Beardmore RE. (2022) Seeking patterns of antibiotic resistance in ATLAS, an open, raw MIC database with patient metadata, Nat Commun, volume 13, no. 1, DOI:10.1038/s41467-022-30635-7. [PDF]

2021

• Nev OA, Lindsay RJ, Jepson A, Butt L, Beardmore RE, Gudelj I. (2021) Predicting microbial growth dynamics in response to nutrient availability, PLoS Comput Biol, volume 17, no. 3, DOI:10.1371/journal.pcbi.1008817. [PDF]
• Reding C, Catalán P, Jansen G, Bergmiller T, Wood E, Rosenstiel P, Schulenberg H, Philip R, Gudelj I, Beardmore R. (2021) Antibiotic dosages of fastest resistance evolution: gene amplifications underpinning the inverted U. [PDF]

2020

• Peña-Miller R, Arnoldini M, Ackermann M, Beardmore RE. (2020) Dynamic phenotypic heterogeneity generated by delayed genetic oscillations, DOI:10.1101/2020.05.13.093831.
• Catalan P, Reding C, Blair J, Gudelj I, Iredell J, Beardmore R. (2020) Clinical Antibiotic Resistance Patterns Across 70 Countries, DOI:10.1101/2020.12.04.411504.
• Nev O, Jepson A, Butt L, Lindsay R, Beardmore R, Gudelj I. (2020) Raw growth data for the manuscript Predicting microbial growth dynamics in changing environments.
• Duxbury SJN, Bates S, Beardmore RE, Gudelj I. (2020) Evolution of drug-resistant and virulent small colonies in phenotypically diverse populations of the human fungal pathogen Candida glabrata, Proceedings of the Royal Society B: Biological Sciences, volume 287, no. 1931, pages 20200761-20200761, DOI:10.1098/rspb.2020.0761. [PDF]
• Nev OA, Jepson A, Beardmore RE, Gudelj I. (2020) Predicting community dynamics of antibiotic-sensitive and -resistant species in fluctuating environments, J R Soc Interface, volume 17, no. 166, DOI:10.1098/rsif.2019.0776. [PDF]
• Nev O, Jepson A, Beardmore R, Gudelj I. (2020) Predicting community dynamics of antibiotic sensitive and resistant species in fluctuating environments (dataset), Journal of the Royal Society Interface, DOI:10.24378/exe.2323.

2019

• Beardmore R, Hewlett M, Peña-Miller R, Reding C, Gudelj I, Meyer JR. (2019) Canonical host-pathogen tradeoffs subverted by mutations with dual benefits, DOI:10.1101/818492.
• Reding C, Catalán P, Jansen G, Bergmiller T, Rosenstiel P, Schulenburg H, Gudelj I, Beardmore R. (2019) Hotspot Dosages of Most Rapid Antibiotic Resistance Evolution, DOI:10.1101/866269.
• Reding C, Hewlett M, Bergmiller T, Gudelj I, Beardmore R. (2019) Fluorescence photography of patterns and waves of bacterial adaptation at high antibiotic doses, DOI:10.1101/806232. [PDF]
• Tonneau C. (2019) Host-pathogen-drug interactions in the context of antibiotic resistance: How host xenobiotic metabolism can affect antibiotic efficacy in a Methicillin-Resistant Staphylococcus aureus infection.

2018

• Beardmore RE, Cook E, Nilsson S, Smith AR, Tillmann A, Esquivel BD, Haynes K, Gow NAR, Brown AJP, White TC. (2018) Erratum to: Drug-mediated metabolic tipping between antibiotic resistant states in a mixed-species community (Nature Ecology & Evolution, (2018), 2, 8, (1312-1320), 10.1038/s41559-018-0582-7), Nature Ecology and Evolution, volume 2, no. 11, DOI:10.1038/s41559-018-0678-0.
• Beardmore RE, Cook E, Nilsson S, Smith AR, Tillmann A, Esquivel BD, Haynes K, Gow NAR, Brown AJP, White TC. (2018) Drug-mediated metabolic tipping between antibiotic resistant states in a mixed-species community, Nat Ecol Evol, volume 2, no. 8, pages 1312-1320, DOI:10.1038/s41559-018-0582-7. [PDF]
• Barbosa C, Beardmore R, Schulenburg H, Jansen G. (2018) Antibiotic combination efficacy (ACE) networks for a Pseudomonas aeruginosa model, PLoS Biol, volume 16, no. 4, DOI:10.1371/journal.pbio.2004356. [PDF]
• Schuetz P, Beardmore RE. (2018) Antibiotic strategies in critical care: back to square one?, Lancet Infect Dis, volume 18, no. 4, pages 360-361, DOI:10.1016/S1473-3099(18)30057-4. [PDF]

2017

• Barbosa C, Trebosc V, Kemmer C, Rosenstiel P, Beardmore R, Schulenburg H, Jansen G. (2017) Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects, Mol Biol Evol, volume 34, no. 9, pages 2229-2244, DOI:10.1093/molbev/msx158. [PDF]
• Reding-Roman C, Hewlett M, Duxbury S, Gori F, Gudelj I, Beardmore R. (2017) The unconstrained evolution of fast and efficient antibiotic-resistant bacterial genomes, Nature Ecology & Evolution, volume 1, no. 3, article no. 0050, DOI:10.1038/s41559-016-0050. [PDF]
• Beardmore RE, Peña-Miller R, Gori F, Iredell J. (2017) Antibiotic Cycling and Antibiotic Mixing: Which One Best Mitigates Antibiotic Resistance?, Mol Biol Evol, volume 34, no. 4, pages 802-817, DOI:10.1093/molbev/msw292. [PDF]

2016

• Rashkov P, Barrett IP, Beardmore RE, Bendtsen C, Gudelj I. (2016) Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle, PLoS Comput Biol, volume 12, no. 11, DOI:10.1371/journal.pcbi.1005216. [PDF]

2015

• Roemhild R, Barbosa C, Beardmore RE, Jansen G, Schulenburg H. (2015) Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa, Evolutionary Applications, volume 8, no. 10, pages 945-955, DOI:10.1111/eva.12330.
• Fuentes-Hernandez A, Plucain J, Gori F, Pena-Miller R, Reding C, Jansen G, Schulenburg H, Gudelj I, Beardmore R. (2015) Using a sequential regimen to eliminate bacteria at sublethal antibiotic dosages, PLoS Biol, volume 13, no. 4, DOI:10.1371/journal.pbio.1002104. [PDF]
• Meyer JR, Gudelj I, Beardmore R. (2015) Biophysical mechanisms that maintain biodiversity through trade-offs, Nat Commun, volume 6, DOI:10.1038/ncomms7278. [PDF]

2014

• Arnoldini M, Vizcarra IA, Peña-Miller R, Stocker N, Diard M, Vogel V, Beardmore RE, Hardt W-D, Ackermann M. (2014) Bistable expression of virulence genes in salmonella leads to the formation of an antibiotic-tolerant subpopulation, PLoS Biol, volume 12, no. 8, DOI:10.1371/journal.pbio.1001928. [PDF]
• Laehnemann D, Peña-Miller R, Rosenstiel P, Beardmore R, Jansen G, Schulenburg H. (2014) Genomics of rapid adaptation to antibiotics: convergent evolution and scalable sequence amplification, Genome Biol Evol, volume 6, no. 6, pages 1287-1301, DOI:10.1093/gbe/evu106. [PDF]
• Peña-Miller R, Fuentes-Hernandez A, Reding C, Gudelj I, Beardmore R. (2014) Testing the optimality properties of a dual antibiotic treatment in a two-locus, two-allele model, J R Soc Interface, volume 11, no. 96, DOI:10.1098/rsif.2013.1035. [PDF]

2013

• Maharjan R, Nilsson S, Sung J, Haynes K, Beardmore RE, Hurst LD, Ferenci T, Gudelj I. (2013) The form of a trade-off determines the response to competition, Ecology Letters, volume 16, no. 10, pages 1267-1276, DOI:10.1111/ele.12159.
• Maharjan R, Nilsson S, Sung J, Haynes K, Beardmore RE, Hurst LD, Ferenci T, Gudelj I. (2013) The form of a trade-off determines the response to competition, Ecol Lett, volume 16, no. 10, pages 1267-1276, DOI:10.1111/ele.12159. [PDF]
• Beardmore RE, Pena-Miller R, Laehnemann D, Jansen G, Fuentes-Hernandez A, Rosenstiel P, Schulenburg H. (2013) When the most potent combination of antibiotics selects for the greatest bacterial load: the Smile-Frown transition, PLoS Biology, volume 11, no. 4, pages 1-13, article no. e1001540, DOI:10.1371/journal.pbio.1001540. [PDF]

2012

• Peña-Miller R, Lähnemann D, Schulenburg H, Ackermann M, Beardmore R. (2012) The optimal deployment of synergistic antibiotics: a control-theoretic approach, J R Soc Interface, volume 9, no. 75, pages 2488-2502, DOI:10.1098/rsif.2012.0279. [PDF]
• Peña-Miller R, Lähnemann D, Schulenburg H, Ackermann M, Beardmore R. (2012) Selecting against antibiotic-resistant pathogens: optimal treatments in the presence of commensal bacteria, Bull Math Biol, volume 74, no. 4, pages 908-934, DOI:10.1007/s11538-011-9698-5. [PDF]

2011

• Beardmore RE, Gudelj I, Lipson DA, Hurst LD. (2011) Metabolic trade-offs and the maintenance of the fittest and the flattest, Nature, volume 472, no. 7343, pages 342-346, DOI:10.1038/nature09905. [PDF]

2010

• Peters R, Beckett N, Beardmore R, Peña-Miller R, Rockwood K, Mitnitski A, Mt-Isa S, Bulpitt C. (2010) Modelling cognitive decline in the Hypertension in the Very Elderly Trial [HYVET] and proposed risk tables for population use, PLoS One, volume 5, no. 7, DOI:10.1371/journal.pone.0011775. [PDF]
• Beardmore RE, Pena-Miller R. (2010) Antibiotic cycling versus mixing: the difficulty of using mathematical models to definitively quantify their relative merits, Math Biosci Eng, volume 7, no. 4, pages 923-933, DOI:10.3934/mbe.2010.7.923. [PDF]
• Beardmore RE, Peña-Miller R. (2010) Rotating antibiotics selects optimally against antibiotic resistance, in theory, Math Biosci Eng, volume 7, no. 3, pages 527-552, DOI:10.3934/mbe.2010.7.527. [PDF]

2008

• Beardmore R, Webster K. (2008) Normal forms, quasi-invariant manifolds, and bifurcations of nonlinear difference-algebraic equations, SIAM Journal on Mathematical Analysis, volume 40, no. 1, pages 413-441, DOI:10.1137/050638618.
• Beardmore R, Webster K. (2008) A Hopf bifurcation theorem for singular differential-algebraic equations, Mathematics and Computers in Simulation, volume 79, no. 4, pages 1383-1395, DOI:10.1016/j.matcom.2008.03.009.
• Forde SE, Beardmore RE, Gudelj I, Arkin SS, Thompson JN, Hurst LD. (2008) Understanding the limits to generalizability of experimental evolutionary models, Nature, volume 455, no. 7210, pages 220-223, DOI:10.1038/nature07152. [PDF]

2007

• Beardmore RE, Peplow A. (2007) A bifurcation analysis of the Ornstein-Zernike equation with hypernetted chain closure, Journal of Mathematical Analysis and Applications, volume 333, no. 2, pages 919-942, DOI:10.1016/j.jmaa.2006.11.045.
• Beardmore RE, Peplow AT, Bresme F. (2007) A numerical bifurcation analysis of the ornstein-zernike equation with hypernetted chain closure, SIAM Journal on Scientific Computing, volume 29, no. 6, pages 2442-2463, DOI:10.1137/060650659.
• Gudelj I, Beardmore RE, Arkin SS, MacLean RC. (2007) Constraints on microbial metabolism drive evolutionary diversification in homogeneous environments, J Evol Biol, volume 20, no. 5, pages 1882-1889, DOI:10.1111/j.1420-9101.2007.01376.x. [PDF]

2006

• Gudelj I, Coman CD, Beardmore RE. (2006) Classifying the role of trade-offs in the evolutionary diversity of pathogens, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, volume 462, no. 2065, pages 97-116, DOI:10.1098/rspa.2005.1559.
• Peplow AT, Beardmore RE, Bresme F. (2006) Algorithms for the computation of solutions of the Ornstein-Zernike equation, Phys Rev E Stat Nonlin Soft Matter Phys, volume 74, no. 4 Pt 2, DOI:10.1103/PhysRevE.74.046705. [PDF]

2005

• Beardmore RE, Peletier MA, Budd CJ, Wadee MA. (2005) Bifurcations of periodic solutions satisfying the zero-Hamiltonian constraint in reversible differential equations, SIAM Journal on Mathematical Analysis, volume 36, no. 5, pages 1461-1488, DOI:10.1137/S0036141002418637.
• Laister R, Beardmore RE. (2005) Bifurcations in degenerate elliptic equations, EQUADIFF 2003: INTERNATIONAL CONFERENCE ON DIFFERENTIAL EQUATIONS, pages 546-548, DOI:10.1142/9789812702067_0090. [PDF]

2004

• Laister R, Peplow AT, Beardmore RE. (2004) Finite time extinction in nonlinear diffusion equations, Applied Mathematics Letters, volume 17, no. 6, pages 561-567, DOI:10.1016/j.aml.2003.03.008.
• Beardmore RE, Laister R. (2004) Sequential and continuum bifurcations in degenerate elliptic equations, Proceedings of the American Mathematical Society, volume 132, no. 1, pages 165-174, DOI:10.1090/S0002-9939-03-06979-X.
• Beardmore RE, Laister R, Peplow A. (2004) Trajectories of a DAE near a pseudo-equilibrium, Nonlinearity, volume 17, no. 1, pages 253-279, DOI:10.1088/0951-7715/17/1/015.
• Laister R, Peplow AT, Beardmore RE. (2004) Finite time extinction in nonlinear diffusion equations, Applied Mathematics Letters, volume 17, no. 5, pages 561-567, DOI:10.1016/S0893-9659(04)90126-7.

2003

• Beardmore I, Beardmore R. (2003) The global structure of a spatial model of infectious disease, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, volume 459, no. 2034, pages 1427-1448, DOI:10.1098/rspa.2002.1080.
• Beardmore RE, Laister R. (2003) The flow of a DAE near a singular equilibrium, SIAM Journal on Matrix Analysis and Applications, volume 24, no. 1, pages 106-120, DOI:10.1137/S0895479800378660.
• Laister R, Beardmore RE. (2003) Transversality and separation of zeros in second order differential equations, Proceedings of the American Mathematical Society, volume 131, no. 1, pages 209-218, DOI:10.1090/S0002-9939-02-06546-2.

2002

• Beardmore RE. (2002) The singularity-induced bifurcation and its Kronecker normal form, SIAM Journal on Matrix Analysis and Applications, volume 23, no. 1, pages 126-137, DOI:10.1137/S089547989936457X.

2001

• Beardmore RE. (2001) A singularity-induced bifurcation theorem for infinite-dimensional implicit dynamical systems, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, volume 457, no. 2010, pages 1295-1305, DOI:10.1098/rspa.2000.0734.

2000

• Beardmore RE. (2000) Double singularity-induced bifurcation points and singular Hopf bifurcations, Dynamical Systems, volume 15, no. 4, pages 319-342, DOI:10.1080/713603759.

1998

• Beardmore RE, Song YH. (1998) Differential-algebraic equations: A tutorial review, International Journal of Bifurcation and Chaos in Applied Sciences and Engineering, volume 8, no. 7, pages 1399-1411, DOI:10.1142/S0218127498001091.
• Beardmore RE. (1998) Stability and bifurcation properties of index-1 DAEs, Numerical Algorithms, volume 19, no. 1-4, pages 43-53, DOI:10.1023/a:1019166725822.

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