Publications

Google Scholar

2017

M. Pan, P.J. Gawthrop, J. Cursons, K. Tran, E.J. Crampin (2017). The cardiac Na+/K+ ATPase: An updated, thermodynamically consistent model
arXiv:1711.00989

K. Tran, J.-C. Han, E.J. Crampin, A.J. Taberner, D.S. Loiselle (2017). Experimental and modelling evidence of shortening heat in cardiac muscle. Journal of Physiology

P.J. Gawthrop, E.J. Crampin (2017). Energy-based Analysis of Biomolecular Pathways. Proceedings of the Royal Society A 473:20160825
arXiv:1611.02332

P.J. Gawthrop, I. Siekmann, T. Kameneva, S. Saha, M.R. Ibbotson, E.J. Crampin (2017). Bond Graph Modelling of Chemoelectrical Energy Transduction. IET Systems Biology 11 (5) 127–138
arXiv:1512.00956

J.J. Glass, L. Chen, S. Alcantara, B.E. Rolfe, E.J. Crampin, K.J. Thurecht, R. De Rose, S.J. Kent (2017). Charge has a marked influence on hyperbranched polymer nanoparticle uptake in whole human blood. ACS Macro Letters ACS 6, 586–592

J.M. Jarosz, S. Ghosh, L. Delbridge, A. Petzer, A. Hickey, E.J. Crampin, E.G. Hansen, V. Rajagopal (2017). Changes in mitochondrial morphology and organisation can enhance energy supply from mitochondrial oxidative phosphorylation in diabetic cardiomyopathy. American Journal of Physiology – Cell Physiology 312 (2) C190-C197

2016

M.C. Andrews, J. Cursons, D.G. Hurley, M. Anaka, J.S. Cebon, A. Behren, E.J. Crampin (2016). Systems analysis identifies miR-29b regulation of invasiveness in melanoma. Molecular Cancer 15:72

D.M. Budden, E.J. Crampin (2016). Distributed gene expression modelling for exploring variability in epigenetic function. BMC Bioinformatics 17:446
arXiv:1507.05720

D.M. Budden, E.J. Crampin (2016). Information theoretic inference of biological networks from continuous-valued data. BMC Systems Biology 10:89

I. Siekmann, M. Fackrell, E.J. Crampin, P. Taylor (2016). Modelling modal gating of ion channels with hierarchical Markov models. Proceedings of the Royal Society A 472: 20160122
arXiv:1602.05877

K. Tran, J.-C. Han, A. Taberner, C. Barrett, E.J. Crampin, and D. Loiselle (2016). Myocardial energetics is not compromised during compensated hypertrophy in the Dahl salt-sensitive rat model of hypertension. American Journal of Physiology – Heart and Circulatory Physiology 311 (3) H563-H571

J. Cui, M. Faria, M. Björnmalm, Y. Ju, T. Suma, S.T. Gunawan, J.J. Richardson, S. Bals, E.J. Crampin, F. Caruso (2016). A framework to account for sedimentation and diffusion in particle-cell interactions. Langmuir 32 (47), 12394-12402

P.J. Gawthrop, E.J. Crampin (2016). Modular Bond Graph Modelling and Analysis of Biomolecular Systems. IET Systems Biology 10 (5) 187-201
arXiv:1511.06482

2015

I. Siekmann, P. Cao, J. Sneyd, E.J. Crampin (2015). Data-Driven Modelling Of The Inositol-Trisphosphate Receptor (IP3R) And Its Role In IP3-Dependent Calcium-Induced Calcium Release (ICICR). In M.D. Pitta and H. Berry (Eds.), Computational Glioscience (Chapter 2). Springer

M.L. Neal, B.E. Carlson, C.T. Thompson, R.C. James, K.G. Kim, K. Tran, E.J. Crampin, D.L. Cook, J.H. Gennari (2015). Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PLoS ONE 10(12): e0145621

J. Cursons, C.E. Angel, D.G. Hurley, C.G. Print, P.R. Dunbar, M.D. Jacobs, E.J. Crampin (2015). Spatially-transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis. GigaScience.2015, 4:63
Supporting data: GigaScience Database

S. Detchokul, A. Elangovan, E.J. Crampin, M.J. Davis, A.G. Frauman (2015). Network Network analysis of an in vitro model of androgen resistance in prostate cancer. BMC Cancer 15:883

P.J. Gawthrop, J. Cursons, E.J. Crampin (2015). Hierarchical Bond Graph Modelling of Biochemical Networks. Proceedings of the Royal Society A 471: 20150642
arXiv:1503.01814

J. Cursons, J. Gao, D.G. Hurley, C.G. Print, P.R. Dunbar, M.D. Jacobs, E.J. Crampin (2015). Regulation of ERK-MAPK Signalling in Human Epidermis. BMC Systems Biology 9:41

K.T. Sharp, E.J. Crampin, J. Sneyd (2015). A spatial model of fluid recycling in the airways of the lung. Journal of Theoretical Biology 382 198-215

V. Rajagopal, G. Bass, C. Walker, D. Crossman, A. Petzer, I. Siekmann, A. Hickey, M. Hoshijima, M. Ellisman, E.J. Crampin, C. Soeller (2015). Examination of the effects of heterogeneous organization of RyR clusters, myofibrils and mitochondria on Ca2+ release patterns in cardiomyocytes. PLoS Computational Biology 11(9): e1004417

K. Tran, D. Loiselle, E.J. Crampin (2015). Regulation of cardiac cellular bioenergetics: mechanisms and consequences. Physiological Reports, 3 (7), e12464

D.M. Budden, D.G. Hurley, E.J. Crampin (2015). Modelling the conditional regulatory activity of methylated and bivalent promotors. Epigenetics & Chromatin, 8:21

J. Cursons, K.-J. Leuchowius, M. Waltham, E. Tomascovik-Crook, M. Foroutan, C. Bracken, A. Redfern, E.J. Crampin, I. Street, M.J. Davis, E.W. Thompson (2015). Stimulus-dependent differences in signalling regulate epithelial mesenchymal plasticity and change the effects of drugs in breast cancer cell lines. Cell Communication and Signaling 13:26

2014

D.M. Budden, D.G. Hurley, J. Cursons, J.F. Markham, M.J. Davis, E.J. Crampin (2014). Predicting expression: The complementary power of histone modification and transcription factor binding data. Epigenetics & Chromatin, 7:36 1-12

D.G. Hurley, D.M. Budden, E.J. Crampin (2014). Virtual reference environments: A simple way to make research reproducible. Briefings in Bioinformatics bbu043

D.G. Hurley, J. Cursons, Y. Wang, C.G. Print, E.J. Crampin (2015). NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks. Bioinformatics 31(2) 277-8

D.M. Budden, D.G. Hurley, E.J. Crampin (2015). Predictive modeling of gene expression from transcriptional regulatory elements. Briefings in Bioinformatics 16 (4): 616-628

P.J. Gawthrop, E.J. Crampin (2014). Energy-based analysis of biochemical cycles using bond graphs. Proceedings of the Royal Society A 470:20140459

J. Sneyd, E.J. Crampin, D. Yule (2014). Multiscale Modelling of Saliva Secretion. Mathematical Biosciences 257 69-79

I. Siekmann, L. Wagner, D. Yule, J. Sneyd, E.J. Crampin (2014). Statistical analysis of modal gating in ion channels. Proceedings of the Royal Society A 470:20140030

Maclaren O.J., J. Sneyd, E.J. Crampin (2014). Reply to A. E. Hill, Y. Shachar-Hill (2013) J Membr Biol 246:665–667. Journal of Membrane Biology 247:289–290

2013

Wang Y.K., Hurley D.G., Schnell S., Print C.G., E.J. Crampin (2013) Integration of Steady-State and Temporal Gene Expression Data for the Inference of Gene Regulatory Networks. PLoS ONE 8(8): e72103

Wang Y.K., Cristin Print, E.J. Crampin (2013). Biclustering reveals breast cancer tumour subgroups with common clinical features and improves prediction of disease recurrence. BMC Genomics (2013), 14:102

Maclaren O.J., J. Sneyd, E.J. Crampin (2013). What do aquaporin knockout studies tell us about fluid transport in epithelia? Journal of Membrane Biology 246:297–305

Bachtiar L.R., C.P. Unsworth, R.D. Newcomb, E.J. Crampin (2013). Multilayer Perceptron Classification of Unknown Volatile Chemicals from the Firing Rates of Insect Olfactory Sensory Neurons and Its Application to Biosensor Design. Neural Computation 25 (1), 259-287

2012

Siekmann I., J. Sneyd, E.J. Crampin (2012). MCMC can detect non-identifiable models. Biophysical Journal 103 (11) 2275-2286

Patterson K., M. Catalán, J. Melvin, D. Yule, E.J. Crampin, J. Sneyd (2012). A Quantitative Analysis of Electrolyte Exchange in the Salivary Duct. American Journal of Physiology – Gastrointestinal and Liver Physiology 

Han J.-C., Andrew Taberner, Kenneth Tran, Soyeon Goo, David Nickerson, Martyn Nash, Poul Nielsen, E.J. Crampin, and Denis Loiselle (2012). Comparison of the Gibbs and Suga Formulations of Cardiac Energetics: the Demise of “Isoefficiency”. Journal of Applied Physiology 

Han J.-C., Andrew Taberner, Kenneth Tran, David Nickerson, Martyn Nash, Poul Nielsen, E.J. Crampin, and Denis Loiselle (2012). Relating Components of Pressure-Volume Area in Suga’s Formulation of Cardiac Energetics to Components of the Stress-Time Integral. Journal of Applied Physiology 

Siekmann I., L.E. Wagner II, D. Yule, E.J. Crampin, J. Sneyd (2012). A kinetic model for type I and II IP3R accounting for mode changes. Biophysical Journal 103 (4) 658-668

Han J.-C., K Tran, AJ Taberner, DP Nickerson, RS Kirton, PMF Nielsen, M-L Ward, MP Nash, E.J. Crampin, DS Loiselle (2012). Myocardial Twitch Duration and the Dependence of Oxygen Consumption on Pressure-Volume Area: Experiments and Modelling. Journal of Physiology 590 (18) 4603-4622

Palk L., J. Sneyd, K. Patterson, T.J. Shuttleworth, D.I. Yule, O. Maclaren, E.J. Crampin (2012). Modelling the effects of calcium waves and oscillations on saliva secretion. Journal of Theoretical Biology 305, 45-53

Wang L, D. Hurley, W. Watkins, H. Araki, Y. Tamada, A. Muthukaruppan, L. Ranjard, E. Derkac, S. Imoto, S. Miyano, E.J. Crampin, C. Print (2012). Cell Cycle Gene Networks Are Associated With Melanoma Prognosis. PLoS ONE 7(4): e34247

Maclaren O., Sneyd J., E.J. Crampin (2012). Efficiency of primary saliva secretion: an analysis of parameter dependence in dynamic single-cell and acinus models, with application to aquaporin knockout studies. Journal of Membrane Biology 245(1), 29-50

Hurley D., H. Araki, Y. Tamada, B. Dunmore, D. Sanders, S. Humphreys, M. Affara, S. Imoto, K. Yasuda, Y. Tomiyasu, K. Tashiro, C. Savoie, V. Cho, S. Smith, S. Kuhara, S. Miyano, S. Charnock-Jones, E.J. Crampin, C. Print (2012). Gene Network Inference and Visualisation Tools for Biologists: Application to New Human Transcriptome Datasets. Nucleic Acids Research 40 (6) 2377-2398

2011

Bachtiar L.R., C. P. Unsworth, R. D. Newcomb, E.J. Crampin (2011). Predicting Odorant Chemical Class from Odorant Descriptor Values With an Assembly of Multi-Layer Perceptrons. 33rd Annual International IEEE EMBS Conference 2011. Contributed paper 1064, 2756 – 2759

Bachtiar L.R., C. P. Unsworth, R. D. Newcomb, E.J. Crampin (2011). Using Artificial Neural Networks to Classify Unknown Volatile Chemicals from the Firings of Insect Olfactory Sensory Neurons. 33rd Annual International IEEE EMBS Conference 2011. Contributed paper 1047, 2752 – 2755

E.J. Crampin (2011). Point: Counterpoint: Muscle lactate and H+ production do / do not have a 1:1 association in skeletal muscle. Journal of Applied Physiology 110 (5), pp. 1495, 2011. (Invited letter to the Editor)

M. A. Mourão, J. Srividhya, P.E. McSharry, E.J. Crampin, S. Schnell (2011). A Graphical User Interface for a Method to Infer Kinetics and Network Architecture (MIKANA). PLoS ONE 6(11): e27534

Araki H., D. Hurley, E.J. Crampin, C. Print, S. Kuhara (2011). Gene Network Analysis and Application. Seibutsu Butsuri (Biophysics) 51, 182-185 (in Japanese)

Siekmann I., L.E. Wagner II, D. Yule, C. Fox, D. Bryant, E.J. Crampin, J. Sneyd (2011). MCMC estimation of Markov models for ion channels. Biophysical Journal 100 (8), 1919-1929, 2011

Waltemath D., R. Adams, D. Beard, F. Bergmann, U. Bhalla, R. Britten, V. Chelliah, M. Cooling, J. Cooper, E.J. Crampin, A. Garny, S. Hoops, M. Hucka, P. Hunter, E. Klipp, C. Laibe, A. Miller, I. Moraru, D. Nickerson, P. Nielsen, M. Nikolski, S. Sahle, H. Sauro, H. Schmidt, J. Snoep, D. Tolle, O. Wolkenhauer, N. Le Novère (2011). Minimum Information About a Simulation Experiment (MIASE). PLoS Computational Biology 7(4): e1001122

Fink M., S.A. Niederer, E.M. Cherry, F.H. Fenton, J.T. Koivumaki, G. Seemann, R. Thul, H. Zhang, F.B. Sachse, D.A. Beard, E.J. Crampin, N.P. Smith (2011). Cardiac cell modelling: Observations from the heart of the cardiac physiome project. Progress in Biophysics & Molecular Biology 104 (1-3), 2-21

2010

Cursons J., D. Hurley, C.E. Angel, R. Dunbar, E.J. Crampin, M.D. Jacobs (2010). Inference of an in Situ Epidermal Intracellular Signaling Cascade. 32nd Annual International IEEE EMBS Conference 2010, Contributed Paper 906, 799 – 802

Sher A., M. Cooling, B. Bethwaite, J. Tan, T. Peachey, C. Enticott, S. Garic, D. Gavaghan, D. Noble, D. Abramson, E.J. Crampin (2010). A Global Sensitivity Tool for Cardiac Cell Modeling: Application to Ionic Current Balance and Hypertrophic Signaling. 32nd Annual International IEEE EMBS Conference 2010, Contributed Paper 1909, 1498 – 1502

Miller A.K., Print C.G., Nielsen P.M.F., E.J. Crampin (2010). A Bayesian Search for Transcriptional Motifs. PLoS ONE 5(11): e13897

Warren N.J., E.J. Crampin, M.H. Tawhai (2010). The role of airway epithelium in replenishment of evaporated airway surface liquid from the human conducting airways. Annals of Biomedical Engineering 38, 12, 3535-3549

Palk L., J. Sneyd, T.J. Shuttleworth, D.I. Yule, E.J. Crampin (2010). A dynamic model of saliva secretion. Journal of Theoretical Biology 266, 625-640

Kohl P., E.J. Crampin, T. A. Quinn, D. Noble (2010). Systems Biology: an Approach. Clinical Pharmacology and Therapeutics 88 1, 25-33

Warren N.J., M.H. Tawhai, E.J. Crampin(2010). The effect of intracellular calcium oscillations on fluid secretion in airway epithelium. Journal of Theoretical Biology 265, 270-277

Loiselle D., K. Tran, E.J. Crampin, N. Curtin (2010). Why has Reversal of the Actin-Myosin Cross-Bridge Cycle Not Been Observed Experimentally? Journal of Applied Physiology 108, 1465-1471

Tran K., N.P. Smith, D.S. Loiselle, E.J. Crampin (2010). A metabolite-sensitive, thermodynamically-constrained model of cardiac cross-bridge cycling: Implications for force development during ischemia. Biophysical Journal 98, 267-276

Srividhya J., M.A. Mourão, E.J. Crampin, S. Schnell (2010). Enzyme catalyzed reactions: from experiments to computational mechanism reconstruction. Computational Biology & Chemistry 34, 11-18

Warren N.J., M.H. Tawhai, E.J. Crampin (2010). Mathematical modelling of calcium wave propagation in airway epithelium: evidence for regenerative ATP release. Experimental Physiology 95 (1), 232-249

2009

Wimalaratne S.M., Halstead M.D.B., Lloyd C.M., Cooling M.T., E.J. Crampin, Nielsen P.F. (2009). A method for visualizing CellML models. Bioinformatics 25, 3012-3019

Wimalaratne S.M., M.D.B. Halstead, C.M. Lloyd, E.J. Crampin, P.F. Nielsen (2009). Biophysical annotation and representation of CellML models. Bioinformatics 25, 2263-2270

Warren N.J., M.H. Tawhai, E.J. Crampin (2009). A Mathematical Model of Calcium-Induced Fluid Secretion in Airway Epithelium. Journal of Theoretical Biology 259 (4), 837-849

Wimalaratne S.M., M.D.B. Halstead, C.M. Lloyd, M.T. Cooling, E.J. Crampin, P.F. Nielsen (2009). Facilitating modularity and reuse: Guidelines for structuring CellML 1.1 models by isolating common biophysical concepts. Experimental Physiology, 94 (5), 472-485

Cooling M.T., E.J. Crampin, P.J. Hunter (2009). Physiome Mark-up Languages for Systems Biology: Model Modularization and Re-use. In Systems Biomedicine, D. Lauffenburger and E. Liu (eds.), Elsevier

Cooling M.T., Hunter P.J., E.J. Crampin (2009). Sensitivity of NFAT cycling to cytosolic calcium: Implications for hypertrophic signalling in cardiac myocytes. Biophysical Journal, 96 (6) 2095-2104

Tran K., Smith N.P., Loiselle D.S., E.J. Crampin (2009). A Thermodynamic Model of the Cardiac Sarcoplasmic/ Endoplasmic Reticulum Ca2+ (SERCA) pump. Biophysical Journal, 96 (5) 2029-2042

2008

Hunter P.J., E.J. Crampin, Nielsen P.M.F. (2008). Bioinformatics and the Physiome Project. Briefings in Bioinformatics 9 (4), 333-343

Terkildsen J., Niederer S.A., E.J. Crampin, Hunter P.J., Smith N.P. (2008). Using Physiome standards to couple cellular functions for cardiac excitation-contraction. Experimental Physiology, 93 (7), 919-929

Loiselle D.S., E.J. Crampin, Niederer S.A., Smith N.P., Barclay C.J. (2008). Energetic consequences of mechanical loads. Progress in Biophysics & Molecular Biology, 97, 348-366 [correction printed vol 99 p 114]

Cooling M., Hunter P.J., E.J. Crampin (2008). Modelling biological modularity with CellML. IET Systems Biology, 2 (2), 73-79

2007

Terkildsen J., E.J. Crampin, Smith N.P. (2007). The balance between inactivation and activation of the Na+-K+ pump underlies the triphasic accumulation of extracellular K+ ions during myocardial ischemia. American Journal of Physiology – Heart and Circulatory Physiology 293, H3036-H3045

Cooling M., Hunter P.J., E.J. Crampin (2007). Modelling hypertrophic IP3 transients in the cardiac myocyte. Biophysical Journal, 93, 3421-3433

Gin E., E.J. Crampin, Brown D.A., Shuttleworth T.J., Yule D.I., Sneyd J. (2007). A mathematical model of fluid secretion from a parotid acinar cell. Journal of Theoretical Biology 248, 64-80

Smith N.P., E.J. Crampin, Niederer S.A., Bassingthwaighte J.B., Beard D.A. (2007). Computational biology of cardiac myocytes: Proposed standards for the Physiome. Journal of Experimental Biology, 210 (9), 1576-1583

Srividhya J., E.J. Crampin, McSharry P.E., Schnell S. (2007). Reconstructing biochemical pathways from time course data. Proteomics 7 (6), 828-838

2006

E.J. Crampin (2006). System Identification Challenges from Systems Biology; in Proceedings 14th IFAC Symposium on System Identification, Newcastle, Australia

Wildenhain J., E.J. Crampin (2006). Reconstructing gene regulatory networks: from random to scale-free connectivity. IEE Systems Biology 153 (4), 247-256

E.J. Crampin, Smith N.P. (2006). A dynamic model of excitation-contraction coupling during acidosis in cardiac ventricular myocytes. Biophysical Journal 90, 3074-3090

Barrass I., E.J. Crampin, Maini P.K. (2006). Mode transitions in a model reaction-diffusion system driven by domain growth and noise. Bulletin of Mathematical Biology 68 (5), 981-995

E.J. Crampin, Smith N.P., Langham A.E., Clayton R.H., Orchard C.H. (2006). Acidosis in models of cardiac ventricular myocytes. Philosophical Transactions of the Royal Society of London, Series A 364 (1842), 1171-1186

2005

Le Novere N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., E.J. Crampin, Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J., Spence H., Wanner B. (2005). Minimum information requested in the annotation of biological models (MIRIAM). Nature Biotechnology 23(12), 1509-1515

2004

E.J. Crampin, Smith N.P., Hunter P.J. (2004). Multi-scale modelling and the IUPS Physiome Project. Journal of Molecular Histology 35 (7), 707-714

E.J. Crampin, Schnell S., McSharry P.E. (2004). Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Progress in Biophysics and Molecular Biology 86 (1), 77-112

E.J. Crampin, Schnell, S. (2004). New approaches to modelling and analysis of biochemical reactions, pathways and networks. (Editorial), Progress in Biophysics & Molecular Biology, 86 (1), 1-4

Smith N.P., Nickerson D.P., E.J. Crampin, Hunter P.J. (2004). Multiscale computational modelling of the heart. Acta Numerica 13, 371-431

E.J. Crampin, McSharry P.E., Schnell S. (2004). Extracting biochemical reaction kinetics from time series data. Lecture Notes in AI 3214, 329-336

Smith N.P., E.J. Crampin (2004). Development of models of active ion transport for whole-cell modelling: Cardiac sodium-potassium pump as a case study. Progress in Biophysics & Molecular Biology 85 (2-3), 387-405

Smith N.P., E.J. Crampin (2004). Modelling cellular and tissue function. (Editorial), Progress in Biophysics & Molecular Biology, 85 (2-3), 117-119

E.J. Crampin, Halstead M., Hunter P., Nielsen P., Noble D., Smith N., Tawhai M. (2004). Computational Physiology and the Physiome Project. Experimental Physiology 89 (1), 1-26

1997 – 2003

Maini P.K., E.J. Crampin, Madzvamuse A., Wathen A.J., Thomas R.D.K. (2003). Implications of domain growth in morphogenesis; in Mathematical Modelling & Computing in Biology and Medicine, Proceedings 5th ECMTB Conference (V. Cappasso, Ed.), 67-73

P.E. McSharry, E.J. Crampin (2002). Identifying statistically significant patterns in gene expression data. (unpublished) arXiv:1606.02801

E.J. Crampin, Hackborn W.W., Maini P.K. (2002). Pattern formation in reaction-diffusion models with nonuniform domain growth. Bulletin of Mathematical Biology 64 (4), 747-769

E.J. Crampin, Gaffney E.A., Maini P.K. (2002). Mode doubling and tripling in reaction-diffusion patterns on growing domains: A piecewise linear model. Journal of Mathematical Biology 44 107-128

E.J. Crampin, Maini P.K. (2001). Reaction-diffusion models for biological pattern formation. Methods and Applications of Analysis 8 (3), 415-428

E.J. Crampin, Maini P.K. (2001). Modelling biological pattern formation: The role of domain growth. Comments on Theoretical Biology 6 (3), 229-249

E.J. Crampin (2000). Reaction-diffusion patterns on growing domains. DPhil Thesis, University of Oxford

E.J. Crampin, Gaffney E.A., Maini P.K. (1999). Reaction and diffusion on growing domains: Scenarios for robust pattern formation. Bulletin of Mathematical Biology 61 (6), 1093

Nguyen-Van-Huong C., E.J. Crampin, Laval J.-Y., Dubon A. (1997). Incorporation of silver in DyBa2Cu3O7-δ ceramics: Correlation between superconducting properties and microstructure. Superconductor Science and Technology 10 (2), 85-94