Faculty of Health and Life Sciences

Professor Robert Beardmore

Professor Robert Beardmore

Professor of Mathematical Biosciences and EPSRC Healthcare Technology Impact Fellow

 R.E.Beardmore@exeter.ac.uk

 5839

 Living Systems Institute T05.13

 

Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD

Overview

1998 SIAM Student Prize, presented Toronto 1999
2012 Lee Segel Prize (shared), presented Arizona 2013
EPSRC Leadership Fellow, 2010-2015

EPSRC Healthcare Technology Impact Fellow, 2016-2018

Qualifications

BSc (1st Class) Edinburgh University 1990-1994
MSc Nonlinear Mathematics, Bath University 1994-1995
PhD Engineering Mathematics, Bath University 1997-2000

Career

Defence-related Project Engineer (satellite imaging), SEA Ltd, Beckington Castle, Frome, 1995-1996
Lecturer in Mathematics, Imperial College London, 2000-2005
Senior Lecturer in Mathematics, Imperial College London, 2005-2008
Reader in Mathematics, Imperial College London, 2008-2010
Professor Mathematical Biosciences, EPSRC Leadership Research Fellow 2010

EPSRC Healthcare Technology Impact Fellow 2016-2018

Links

Research group links

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Research

Research interests

  • Mathematical modelling of evolutionary datasets, particularly those relating to antibiotic resistance
  • Mathematical analysis of differential-algebraic equations
  • Applications of mathematical analysis/computation to evolutionary biology

Research projects

  • Understanding viral phage resistance in E.coli populations (with Justin Meyer)
  • Using optimisation theory as a basis to model optimal antibiotic use (with Hinrich Schulenberg)
  • Using AI to understand clinical definitions of antibiotic resistance (with Emily Wood, Jon Iredell and Pablo Catalan)
  • Understanding how death processes are mediated by antibiotics (with Emily Wood)
  • Understanding how solution paths of long-range diffusion (integro-differential) equations transition from one Banach space to another (with Robert Laister)
  • Understanding how changing the order of antibiotic use impinges rates of resistance evolution (with Emily Wood and Pablo Catalan) 
  • Developing novel hardware to interrogate microbes (with Singer Instruments)

Research networks

EPSRC-funded (now finished) Mathematical Models and Experimental Microbial Systems (www.mmems.org)

Research grants

  • 2020 EPSRC
    A collaborative hub award to research datasets and mathematical models arising in healthcare
  • 2016 EPSRC
    Award to conduct full-time research into datasets on phage and antibiotic resistance
  • 2012 EPSRC
    Developing Leaders award (value £315,000)
  • 2012 EPSRC
    Creativity @ Home award (value £20,000)
  • 2010 EPSRC
    Leadership Fellowship on the application of mathematical modelling to the study of antibiotic resistance evolution (value £1,139,110)
  • 2010 EPSRC
    Cross-Disciplinary Enhancement to Leadership Fellowship: funding to take theoretical research into the lab (value £100,000)
  • 2009 MRC
    Discipline Hopping Fellowship: Applications of Control Theory to Optimal Antibiotic Deployment (value £110,000)
  • 2002 EPSRC
    Funded Two PDRAs on the Invariant Manifolds of Differential-Algebraic Equations (value £123,000)

Links


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Publications

Journal articles

Beardmore R, Gudelj I, Hewlett M, Pena-Miller R, Meyer J (In Press). Canonical host-pathogen tradeoffs subverted by mutations with dual benefits. The American Naturalist Abstract.
Beardmore R, Gudelj I, Reding C, Wood E, Bergmiller T, Schulenberg H, Philip R, Catalan P (In Press). The Antibiotic Dosage of Fastest Resistance Evolution: gene amplifications underpinning the inverted-U. Molecular Biology and Evolution
Butt L, Meyer JR, Lindsay RJ, Beardmore RE, Gudelj I (2024). Bacterial resistance response and resource availability mediate viral coexistence. J Evol Biol, 37(4), 371-382. Abstract.  Author URL.
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, 120(40). Abstract.  Author URL.
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, 13(1). Abstract.  Author URL.
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, 17(3). Abstract.  Author URL.
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. <i>Candida glabrata</i>. Proceedings of the Royal Society B: Biological Sciences, 287(1931), 20200761-20200761. Abstract.
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, 17(166). Abstract.  Author URL.
Reding C, Hewlett M, Bergmiller T, Gudelj I, Beardmore R (2019). Fluorescence photography of patterns and waves of bacterial adaptation at high antibiotic doses. Abstract.
Barbosa C, Beardmore R, Schulenburg H, Jansen G (2018). Antibiotic combination efficacy (ACE) networks for a Pseudomonas aeruginosa model. PLoS Biol, 16(4). Abstract.  Author URL.
Schuetz P, Beardmore RE (2018). Antibiotic strategies in critical care: back to square one?. Lancet Infect Dis, 18(4), 360-361.  Author URL.
Beardmore RE, Cook E, Nilsson S, Smith AR, Tillmann A, Esquivel BD, Haynes K, Gow NAR, Brown AJP, White TC, et al (2018). Drug-mediated metabolic tipping between antibiotic resistant states in a mixed-species community. Nat Ecol Evol, 2(8), 1312-1320. Abstract.  Author URL.
Beardmore RE, Cook E, Nilsson S, Smith AR, Tillmann A, Esquivel BD, Haynes K, Gow NAR, Brown AJP, White TC, et al (2018). Erratum to: Drug-mediated metabolic tipping between antibiotic resistant states in a mixed-species community (Nature Ecology &amp; Evolution, (2018), 2, 8, (1312-1320), 10.1038/s41559-018-0582-7). Nature Ecology and Evolution, 2(11). Abstract.
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, 34(9), 2229-2244. Abstract.  Author URL.
Beardmore RE, Peña-Miller R, Gori F, Iredell J (2017). Antibiotic Cycling and Antibiotic Mixing: Which One Best Mitigates Antibiotic Resistance?. Mol Biol Evol, 34(4), 802-817. Abstract.  Author URL.
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, 1(3).
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, 12(11). Abstract.  Author URL.
Meyer JR, Gudelj I, Beardmore R (2015). Biophysical mechanisms that maintain biodiversity through trade-offs. Nat Commun, 6 Abstract.  Author URL.
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, 8(10), 945-955. Abstract.
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 Abstract.
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, 13(4). Abstract.  Author URL.
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, 12(8). Abstract.  Author URL.
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, 6(6), 1287-1301. Abstract.  Author URL.
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, 11(96). Abstract.  Author URL.
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, 16(10), 1267-1276. Abstract.
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, 16(10), 1267-1276. Abstract.  Author URL.
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, 11(4), 1-13.
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, 74(4), 908-934. Abstract.  Author URL.
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, 9(75), 2488-2502. Abstract.  Author URL.
Beardmore RE, Gudelj I, Lipson DA, Hurst LD (2011). Metabolic trade-offs and the maintenance of the fittest and the flattest. Nature, 472(7343), 342-346. Abstract.  Author URL.
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, 7(4), 923-933. Abstract.  Author URL.
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, 5(7). Abstract.  Author URL.
Beardmore RE, Peña-Miller R (2010). Rotating antibiotics selects optimally against antibiotic resistance, in theory. Math Biosci Eng, 7(3), 527-552. Abstract.  Author URL.
Beardmore R, Webster K (2008). Normal forms, quasi-invariant manifolds, and bifurcations of nonlinear difference-algebraic equations. SIAM Journal on Mathematical Analysis, 40(1), 413-441. Abstract.
Forde SE, Beardmore RE, Gudelj I, Arkin SS, Thompson JN, Hurst LD (2008). Understanding the limits to generalizability of experimental evolutionary models. Nature, 455(7210), 220-223. Abstract.  Author URL.
Beardmore RE, Peplow A (2007). A bifurcation analysis of the Ornstein-Zernike equation with hypernetted chain closure. Journal of Mathematical Analysis and Applications, 333(2), 919-942. Abstract.
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, 29(6), 2442-2463. Abstract.
Gudelj I, Beardmore RE, Arkin SS, MacLean RC (2007). Constraints on microbial metabolism drive evolutionary diversification in homogeneous environments. J Evol Biol, 20(5), 1882-1889. Abstract.  Author URL.
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, 74(4 Pt 2). Abstract.  Author URL.
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, 462(2065), 97-116. Abstract.
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, 36(5), 1461-1488. Abstract.
Laister R, Peplow AT, Beardmore RE (2004). Finite time extinction in nonlinear diffusion equations. Applied Mathematics Letters, 17(6), 561-567. Abstract.
Laister R, Peplow AT, Beardmore RE (2004). Finite time extinction in nonlinear diffusion equations. Applied Mathematics Letters, 17(5), 561-567. Abstract.
Beardmore RE, Laister R (2004). Sequential and continuum bifurcations in degenerate elliptic equations. Proceedings of the American Mathematical Society, 132(1), 165-174. Abstract.
Beardmore RE, Laister R, Peplow A (2004). Trajectories of a DAE near a pseudo-equilibrium. Nonlinearity, 17(1), 253-279. Abstract.
Beardmore RE, Laister R (2003). The flow of a DAE near a singular equilibrium. SIAM Journal on Matrix Analysis and Applications, 24(1), 106-120. Abstract.
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, 459(2034), 1427-1448. Abstract.
Laister R, Beardmore RE (2003). Transversality and separation of zeros in second order differential equations. Proceedings of the American Mathematical Society, 131(1), 209-218. Abstract.
Beardmore RE (2002). The singularity-induced bifurcation and its Kronecker normal form. SIAM Journal on Matrix Analysis and Applications, 23(1), 126-137. Abstract.
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, 457(2010), 1295-1305. Abstract.
Beardmore RE (2000). Double singularity-induced bifurcation points and singular Hopf bifurcations. Dynamical Systems, 15(4), 319-342. Abstract.
Beardmore RE, Song YH (1998). Differential-algebraic equations: a tutorial review. International Journal of Bifurcation and Chaos in Applied Sciences and Engineering, 8(7), 1399-1411. Abstract.
Beardmore RE (1998). Stability and bifurcation properties of index-1 DAEs. Numerical Algorithms, 19(1-4), 43-53. Abstract.

Conferences

Beardmore R, Webster K (2008). A Hopf bifurcation theorem for singular differential-algebraic equations. Abstract.
Laister R, Beardmore RE (2005). Bifurcations in degenerate elliptic equations.  Author URL.

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External Engagement and Impact

Awards and distinctions

1998 SIAM Student Prize, presented Toronto 1999
2012 Lee Segel Prize (shared), presented Arizona 2013

2023 Vivli Data Challenge Innovation Prize
EPSRC Leadership Fellowship, 2010-2015

EPSRC Healthcare Technologies Fellowship 2016-2018


Committee/panel activities

Member of EPSRC College, members of several panels for example:

former EPSRC Leadership Fellows Sift and Interview Panels Member in Mathematics, Doctoral Training Centres Sift and Interview Panels Chair in Healthcare Technology, Programme Grant Panel Member in Mathematics, Responsive Mode Grant Panel Member (several)

Reviewer for EPSRC, BBSRC, NSERC (Canada), Portuguese Foundation for Science and Technology (FCT), ETH Zurich Collaborative Highly Interdisciplinary Research Projects and many others...

Advisory Board Member: The Physics of Antimicrobial Resistance (grant# EPSRC EP/T002778/1) 2019-2022


Invited lectures

2008 NESCent Research Meeting, April 7-10, Duke University Campus
2008 Bifurcation Theoretic Computations for 1-d DFTs, June 24th, Imperial College
2008 17th Annual Scottish Computational Mathematics Symposium, September 10th, Heriot-Watt University, Edinburgh
2008 IEEE Seminar, Devry Institute, New Brunswick, New Jersey, US.

2009 PIMS Lecture Series (University of Alberta and UBC, Vancouver), February
2009 Analyse des Systemes et Biometrie, March, Montpellier, France
2009 One-week postgraduate lecture course: Phase Transition Tracking for Classical Density Functional Theory, April, University Carlos III, Madrid
2009 ESA, Special Session on Microbial Evolution in Ecology, June, Albuquerque, New Mexico, US
2009 Epidemiology Seminar Series, Department of Zoology, University of Oxford, October

2010 Optimal control theory & rotating or mixing antibiotics, Yale, Connecticut, US, Jan
2010 Coevolution - Rapid Reciprocal Adaptation and its Genetic Basis, `Phenotypic diversity versus resource supply for GxE and GxGxE interactions in the chemostat,' Kiel, Feb
2010 Centre for Evolutionary Genetics Seminar, September, Kiel University,
2010 Basque Center for Applied Mathematics (BCAM), December, Bilboa, Spain

2011 Centre for Evolutionary Genetics Seminar, Kiel University, September
2011 Maths for Microbes session; Society for General Microbiology, Spring Conference, Harrogate, April
2011 Departmental Seminar, Engineering Mathematics, Bristol University, December
2011 H. Lee Moffitt Cancer Center, IMO seminar, December

2012 Seminar, Harvard Medical School (Kishony Lab), Boston US, February
2012 OEB `Special Seminar' Harvard Systems Biology Seminar, Boston US, February
2012 International Conference of Numerical Analysis and Applied Mathematics, Halkidiki, Greece, September; plenary symposium on the applications of numerical analysis and scientific computation in mathematical biology
2012 Department of Systems Biology, Novo Nordisk Foundation Center for Biosustainability, Copenhagen, December

2013 Colloquium (Optimisation in Biology) ETH Zurich in Basel, January
2013 Cavendish Laboratory Seminar Series, Cambridge, February
2013 Thematic Programme on Mathematical Biology, Lyon, March, plenary talk, mathbio2013.sciencesconf.org/
2013 Departmental Seminar (Mathematical Medicine), Nottingham, October
2013 Agents against Infectious Diseases, plenary talk, University Wurzburg, November

And many others ... 


Workshops/Conferences organised

2006-2009: Imperial organiser of M4 Corridor PG Days in Numerical Analysis with Oxford, Brunel, Reading, Bath and Cardiff

2008 Bifurcation-Theoretic Computations and Classical Density Functional Theory, 24th June, Imperial College, London, approximately 20 attendees

2010 Organised the Mathematics of Microbes: Biophysical Details of the Evolving Cell, April, Imperial College, London, approximately 50 attendees

2013 Quantitative Evolutionary Dynamics (QED): microbes from cells to populations in their natural environments, April, Shaldon near Exeter University, UK, approximately 50 attendees

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Teaching

Modules

2024/25

Information not currently available


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Supervision / Group

Postdoctoral researchers

Postgraduate researchers

Alumni

  • Dr Sinan Arkin former PhD student
  • Dr Rafael Pena-Miller former PhD student & EPSRC-funded post-doc
  • Dr Andrew Peplow former EPSRC-funded PDRA
  • Dr Kevin Webster former EPSRC-funded PDRA

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