CMMB Publications

BEATTIE, K, HILL, AP, CUI, Y, VANDENBERG, JI, GAVAGHAN, DJ, DE BOER, TP and MIRAMS, GR, 2018. Sinusoidal voltage protocols for rapid characterization of ion channel kinetics The Journal of Physiology. 596(10), 1813-1828

Á BYRNE, S COOMBES and P LIDDLE, 2018. A neural mass model for abnormal beta-rebound in schizophrenia. In: Handbook of Multi-scale Models of Brain Disorders Springer.. (In Press.) 

S COOMBES, Y-M LAI, M SAYLI and R THUL, 2018.  Networks of piecewise linear neural mass models Euro. Jnl of Applied Mathematics. 22

MARTIN FALCKE, MAHSA MOEIN, AGNE TILUNAITE, RUEDIGER THUL and ALEXANDE SKUPIN, 2018. On the phase space structure of IP3 induced Ca2+ signalling and concepts for predictive modeling Chaos. (In Press.)

A GÖKÇE, D AVITABILE and S COOMBES, 2018. Neural fields: Localised states with piece-wise constant interactions In: NeuroMath, INdAM Series, Springer. (In Press.)

AYTUL GOKCE, STEPHEN COOMBES and DANIELE AVITABILE, 2018. Neural fields: Localised states with piece-wise constant interactions. In: NeuroMath, INdAM Series, (In Press.)

ELIZABETH HOLDEN, JOE COLLIS, BINDI S BROOK and REUBEN D O'DEA, 2018. A multiphase multiscale model for nutrient limited tissue growth The ANZIAM Journal. (In Press.)

JOSHI TV, AVITABILE D and OWEN MR, 2018. Capturing the Dynamics of a Hybrid Multiscale Cancer Model with a Continuum Model. Bulletin of mathematical biology. (In Press.)

SAMUEL MAILHOT-LAROUCHE, LOUIS DESCHÊNES, MORGAN GAZZOLA, KATHERINE LORTIE, CYNDI HENRY, BINDI S BROOK, MATHIEU C MORISSETTE and YNUK BOSSÉ, 2018. Repeated airway constrictions in mice do not alter respiratory function Journal of applied physiology (Bethesda, Md. : 1985). 

JAMES E MOORE JR, BINDI S BROOK and ROBERT J B NIBBS, 2018. Chemokine Transport Dynamics and Emerging Recognition of Their Role in Immune Function Current Opinion in Biomedical Engineering. 

TANVI JOSHI, DANIELE AVITABILE and DANIELE AVITABILE, 2018. Capturing the dynamics of a hybrid multiscale cancer model with a continuum model Bulletin of Mathematical Biology. 

SAMANTA, KRISHNA, MIRAMS, GARY R. and PAREKH, ANANT B., 2018. Sequential forward and reverse transport of the Na+ Ca2+ exchanger generates Ca2+ oscillations within mitochondria NATURE COMMUNICATIONS. 9,

ASTON D, CAPEL RA, FORD KL, CHRISTIAN HC, MIRAMS GR, ROG-ZIELINSKA EA, KOHL P, GALIONE A, BURTON RA and TERRAR DA, 2017. High resolution structural evidence suggests the Sarcoplasmic Reticulum forms microdomains with Acidic Stores (lysosomes) in the heart. Scientific reports. 7, 40620

DANIELE AVITABILE, MATHIEU DESROCHES and EDGAR KNOBLOCH, 2017. Spatio-temporal canards in neural field equations Physical Review E. (In Press.)

DANIELE AVITABILE and KYLE WEDGWOOD, 2017. Macroscopic coherent structures in a stochastic neural network: from interface dynamics to coarse-grained bifurcation analysis Journal of Mathematical Biology. (In Press.)

BAKER, MICHELLE, BROOK, BINDI S. and OWEN, MARKUS R., 2017. Mathematical modelling of cytokines, MMPsand fibronectin fragments in osteoarthritic cartilage JOURNAL OF MATHEMATICAL BIOLOGY. 75(4), 985-1024

M BONILLA-QUINTANA, K C A WEDGWOOD, R O'DEA and S COOMBES, 2017. An analysis of waves underlying grid cell firing in the medial enthorinal cortex Journal of Mathematical Neuroscience. 7(9), 

BYRNE, AINE, BROOKES, MATTHEW J and COOMBES, STEPHEN, 2017. A mean field model for movement induced changes in the beta rhythm. Journal of computational neuroscience. 

CHANG, KELLY C., DUTTA, SARA, MIRAMS, GARY R., BEATTIE, KYLIE A., SHENG, JIANSONG, TRAN, PHU N., WU, MIN, WU, WENDY W., COLATSKY, THOMAS, STRAUSS, DAVID G. and LI, ZHIHUA, 2017. Uncertainty Quantification Reveals the Importance of Data Variability and Experimental Design Considerations for in Silico Proarrhythmia Risk Assessment FRONTIERS IN PHYSIOLOGY. 8, 

COLLIS J, HUBBARD ME and O'DEA RD, 2017. A multiscale analysis of drug transport and response for a multiphase tumor model European Journal of Applied Mathematics. 28(3), 499-534

COLLIS, J, BROWN, DL, HUBBARD, ME and O'DEA, RD, 2017. Effective Equations Governing an Active Poroelastic Medium Proceedings of the Royal Society A. 473, 20160755

DIETRICH D, PANG L, KOBAYASHI A, FOZARD JA, BOUDOLF V, BHOSALE R, ANTONI R, NGUYEN T, HIRATSUKA S, FUJII N, MIYAZAWA Y, BAE TW, WELLS DM, OWEN MR, BAND LR, DYSON RJ, JENSEN OE, KING JR, TRACY SR, STURROCK CJ, MOONEY SJ, ROBERTS JA, BHALERAO RP, DINNENY JR, RODRIGUEZ PL, NAGATANI A, HOSOKAWA Y, BASKIN TI, PRIDMORE TP, DE VEYLDER L, TAKAHASHI H and BENNETT MJ, 2017. Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature plants. 3, 17057

JEAN-LOUIS DINH, ETIENNE FARCOT and CHARLIE HODGMAN, 2017. The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs PLoS Computational Biology. 

DUNSTER, J. L. and KING, J. R., 2017. Mathematical modelling of thrombin generation: asymptotic analysis and pathway characterization IMA JOURNAL OF APPLIED MATHEMATICS. 82(1), 60-96

ESNAOLA-ACEBES, JOSE M., ROXIN, ALEX, AVITABILE, DANIELE and MONTBRIO, ERNEST, 2017. Synchrony-induced modes of oscillation of a neural field model PHYSICAL REVIEW E. 96(5), 

FERGUSON, ALISON C., PEARCE, SIMON, BAND, LEAH R., YANG, CAIYUN, FERJENTSIKOVA, IVANA, KING, JOHN, YUAN, ZHENG, ZHANG, DABING and WILSON, ZOE A., 2017. Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis NEW PHYTOLOGIST. 213(2), 778-790

GOKCE, AYTUL, AVITABILE, DANIELE and COOMBES, STEPHEN, 2017. The Dynamics of Neural Fields on Bounded Domains: An Interface Approach for Dirichlet Boundary Conditions JOURNAL OF MATHEMATICAL NEUROSCIENCE. 7, 

HARTUNG, THOMAS, FITZGERALD, REX E., JENNINGS, PAUL, MIRAMS, GARY R., PEITSCH, MANUEL C., ROSTAMI-HODJEGAN, AMIN, SHAH, IMRAN, WILKS, MARTIN F. and STURLA, SHANA J., 2017. Systems Toxicology: Real World Applications and Opportunities CHEMICAL RESEARCH IN TOXICOLOGY. 30(4), 870-882

L. IRONS, J. COLLIS and R.D. O'DEA, 2017. Microstructural influences on growth and transport in biological tissue: a multiscale description. In: S. BECKER, ed., Microscale Transport Modelling in Biological Processes Elsevier. 

JAFARNEJAD M, ZAWIEJA DC, BROOK BS, NIBBS RJB and MOORE JE, 2017. A Novel Computational Model Predicts Key Regulators of Chemokine Gradient Formation in Lymph Nodes and Site-Specific Roles for CCL19 and ACKR4. Journal of immunology (Baltimore, Md. : 1950). (In Press.)

JOHNSTONE RH, BARDENET R, GAVAGHAN DJ and MIRAMS GR, 2017. Hierarchical Bayesian inference for ion channel screening dose-response data. Wellcome open research. 1, 6

LEI, CHON LOK, WANG, KEN, CLERX, MICHAEL, JOHNSTONE, ROSS H., HORTIGON-VINAGRE, MARIA P., ZAMORA, VICTOR, ALLAN, ANDREW, SMITH, GODFREY L., GAVAGHAN, DAVID J., MIRAMS, GARY R. and POLONCHUK, LIUDMILA, 2017. Tailoring Mathematical Models to Stem-Cell Derived Cardiomyocyte Lines Can Improve Predictions of Drug-Induced Changes to Their Electrophysiology FRONTIERS IN PHYSIOLOGY. 8, 

LIGNEAU, XAVIER, SHAH, RASHMI R., BERREBI-BERTRAND, ISABELLE, MIRAMS, GARY R., ROBERT, PHILIPPE, LANDAIS, LAURENT, MAISON-BLANCHE, PIERRE, FAIVRE, JEAN-FRANCOIS, LECOMTE, JEANNE-MARIE and SCHWARTZ, JEAN-CHARLES, 2017. Nonclinical cardiovascular safety of pitolisant: comparing International Conference on Harmonization S7B and Comprehensive in vitro Pro-arrhythmia Assay initiative studies BRITISH JOURNAL OF PHARMACOLOGY. 174(23), 4449-4463

MCMILLAN, BETH, GAVAGHAN, DAVID J. and MIRAMS, GARY R., 2017. Early afterdepolarisation tendency as a simulated pro-arrhythmic risk indicator TOXICOLOGY RESEARCH. 6(6), 912-921

KANAD MANDKE, JIL MEIER, MATTHEW J. BROOKES, REUBEN D O'DEA, PIET VAN MIEGHEM, CORNELIS J. STAM, ARJAN HILLEBRAND and PREJAAS TEWARIE, 2017. Comparing multilayer brain networks between groups: Introducing graph metrics and recommendations NeuroImage.

MELLOR, NATHAN, ADIBI, MILAD, EL-SHOWK, SEDEER, DE RYBEL, BERT, KING, JOHN, MAHONEN, ARI PEKKA, WEIJERS, DOLF and BISHOPP, ANTHONY, 2017. Theoretical approaches to understanding root vascular patterning: a consensus between recent models JOURNAL OF EXPERIMENTAL BOTANY. 68(1), 5-16

POSTMA JA, KUPPE C, OWEN MR, MELLOR N, GRIFFITHS M, BENNETT MJ, LYNCH JP and WATT M, 2017. OpenSimRoot: widening the scope and application of root architectural models. The New phytologist. 215(3), 1274-1286

RUTH SAUNDERS, HIMANSHU KAUL, RACHID BERAIR, AMISHA SINGAPURI, IGOR L CHERNYAVKSY, LATIFA CHACHI, MICHAEL BIDDLE, AMANDA SUTCLIFFE, MARIE LAURENCIN, GERALD BACHER, MICHELLE BOURNE, IAN D PAVORD, ANDREW J WARDLAW, SALMAN SIDDIQUI, RICHARD KAY, BINDI S BROOK, ROD SMALLWOOD and CHRIS E BRIGHTLING, 2017. Fevipiprant reduces airway smooth muscle mass in asthmatics via PGD2 receptor antagonism European Respiratory Journal. 50, OA283

TILŪNAITĖ A, CROFT W, RUSSELL N, BELLAMY TC and THUL R, 2017. A Bayesian approach to modelling heterogeneous calcium responses in cell populations. PLoS computational biology. 13(10), e1005794

S VISSER, R NICKS, O FAUGERAS and S COOMBES, 2017. Standing and travelling waves in a spherical brain model: the Nunez model revisited Physica D. 349, 27-45

ASHWIN, PETER, COOMBES, STEPHEN and NICKS, RACHEL, 2016. Mathematical Frameworks for Oscillatory Network Dynamics in Neuroscience. Journal of mathematical neuroscience. 6(1), 2

AVITABILE, DANIELE, SLOWI'NSKI, PIOTR, BARDY, BENOIT and TSANEVA-ATANASOVA, KRASIMIRA, 2016. Beyond in-phase and anti-phase coordination in a model of joint action Biological Cybernetics. 110(2-3), 1-16

BROWN, D. M., WILLIAMS, H., RYAN, K. J. P., WILSON, T. L., DANIEL, Z. C. T. R., MAREKO, M. H. D., EMES, R. D., HARRIS, D. W., JONES, S., WATTIS, J. A. D., DRYDEN, I. L., HODGMAN, T. C., BRAMELD, J. M. and PARR, T., 2016. Mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M) and serine biosynthetic pathway genes are co-ordinately increased during anabolic agent-induced skeletal muscle growth SCIENTIFIC REPORTS. 6, 

BROWN LE, MIDDLETON AM, KING JR and LOOSE M, 2016. Multicellular Mathematical Modelling of Mesendoderm Formation in Amphibians. Bulletin of mathematical biology. 78(3), 436-67

J. COLLIS, M.E. HUBBARD and R.D. O'DEA, 2016. Computational Modelling of Multiscale Mixture Models with Application to Tumour Growth Computer Methods in Applied Mechanics and Engineering. 309, 554–578

S COOMBES and Á BYRNE, 2016. Next generation neural mass models. In: Lecture Notes in Nonlinear Dynamics in Computational Neuroscience: from Physics and Biology to ICT Springer. (In Press.)

COOPER J, SCHARM M and MIRAMS GR, 2016. The Cardiac Electrophysiology Web Lab. Biophysical journal. 110(2), 292-300

CROFT, WAYNE, REUSCH, KATHARINA, TILUNAITE, AGNE, RUSSEL, NOAH, THUL, RÜDIGER and BELLAMY, TOMAS C., 2016. Probabilistic encoding of stimulus strength in astrocyte global calcium signals Glia. 64(4), 537–552

J.J. CROFTS, M. FORRESTER and R.D. O'DEA, 2016. Structure-function clustering in multiplex brain networks Europhysics Letters. 116(1), 18003

DAVIES MR, WANG K, MIRAMS GR, CARUSO A, NOBLE D, WALZ A, LAVÉ T, SCHULER F, SINGER T and POLONCHUK L, 2016. Recent developments in using mechanistic cardiac modelling for drug safety evaluation. Drug discovery today. 21(6), 924-38

CHRISTOPHE GODIN, EUGENIO AZPEITIA and ETIENNE FARCOT, 2016.  An introduction to modeling the initiation of the floral primordium. In: From Molecules to Living Organisms: An Interplay Between Biology and Physics 102. Oxford Scholarship. 

AP HILL, MD PERRY, N ABI-GERGES, J-P COUDEREC, B FERMINI, JC HANCOX, BC KNOLLMANN, GR MIRAMS, J SKINNER, W ZAREBA and JI VANDENBERG, 2016. Computational Cardiology and Risk Stratification for Sudden Cardiac Death: One of the Grand Challenges for Cardiology in the 21(st) Century. The Journal of physiology. 594(23), 6893-6908

J.E. HIORNS, C.M. BIDAN, O.E. JENSEN, R. GOSENS, L.E.M. KISTEMAKER, J.J. FREDBERG, J.P. BUTLER, R. KRISHNAN and B.S. BROOK, 2016. Airway and parenchymal strains during bronchoconstriction in the precision cut lung slice Frontiers in Respiratory Physiology. 

J. E. HIORNS, O.E. JENSEN and B.S. BROOK, 2016. Static and dynamic stress heterogeneity in a multiscale model of the asthmatic airway wall. Journal of Applied physiology (Bethesda, Md. : 1985). 

JOHNSTONE RH, CHANG ET, BARDENET R, DE BOER TP, GAVAGHAN DJ, PATHMANATHAN P, CLAYTON RH and MIRAMS GR, 2016. Uncertainty and variability in models of the cardiac action potential: Can we build trustworthy models? Journal of Molecular and Cellular Cardiology. 96, 49-62

KAR P, MIRAMS GR, CHRISTIAN HC and PAREKH AB, 2016. Control of NFAT Isoform Activation and NFAT-Dependent Gene Expression through Two Coincident and Spatially Segregated Intracellular Ca(2+) Signals. Molecular cell. 64(4), 746-759

MAHONEY VM, MEZZANO V, MIRAMS GR, MAASS K, LI Z, CERRONE M, VASQUEZ C, BAPAT A, DELMAR M and MORLEY GE, 2016. Connexin43 contributes to electrotonic conduction across scar tissue in the intact heart. Scientific reports. 6, 26744

MELLOR, NATHAN, BAND, LEAH R., PENCIK, ALES, NOVAK, ONDREJ, RASHED, AFAF, HOLMAN, TARA, WILSON, MICHAEL H., VOSS, UTE, BISHOPP, ANTHONY, KING, JOHN R., LJUNG, KARIN, BENNETT, MALCOLM J. and OWEN, MARKUS R., 2016. Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 113(39), 11022-11027

MELLOR N, BENNETT MJ and KING JR, 2016. GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses. Bulletin of mathematical biology. 78(2), 210-34

MENDIONDO GM, GIBBS DJ, SZURMAN-ZUBRZYCKA M, KORN A, MARQUEZ J, SZAREJKO I, MALUSZYNSKI M, KING J, AXCELL B, SMART K, CORBINEAU F and HOLDSWORTH MJ, 2016. Enhanced waterlogging tolerance in barley by manipulation of expression of the N-end rule pathway E3 ligase PROTEOLYSIS6. Plant Biotechnology Journal. 40(1), 40-50

GR MIRAMS, P PATHMANATHAN, RA GRAY, P CHALLENOR and RH CLAYTON, 2016. White paper: Uncertainty and variability in computational and mathematical models of cardiac physiology. The Journal of physiology. 594(23), 6833-6847

PEARSON T, WATTIS JA, KING JR, MACDONALD IA and MAZZATTI DJ, 2016. The Effects of Insulin Resistance on Individual Tissues: An Application of a Mathematical Model of Metabolism in Humans. Bulletin of mathematical biology. 78(6), 1189-217

REFAHI, YASSIN, BRUNOUD, GERALDINE, FARCOT, ETIENNE, JEAN-MARIE, ALAIN, PULKKINEN, MINNA, VERNOUX, TEVA and GODIN, CHRISTOPHE, 2016. A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis. eLife. 5, 

THORN GJ and KING JR, 2016. Modelling the role of CtfA/B in reverse shift continuous culture experiments of Clostridium acetobutylicum. Mathematical biosciences. 276, 101-13

THUL, RÜDIGER, COOMBES, STEPHEN and LAING, CARLO R, 2016. Neural Field Models with Threshold Noise The Journal of Mathematical Neuroscience. 6(1), 1

WOJTAK, WERONIKA, COOMBES, STEPHEN, BICHO, ESTELA and ERLHAGEN, WOLFRAM, 2016. Combining Spatial and Parametric Working Memory in a Dynamic Neural Field Model ARTIFICIAL NEURAL NETWORKS AND MACHINE LEARNING - ICANN 2016, PT I. 9886, 411-418

ZHU, HAO, OWEN, MARKUS R. and MAO, YANLAN, 2016. The spatiotemporal order of signaling events unveils the logic of development signaling Bioinformatics. 

AVITABILE, DANIELE and SCHMIDT, HELMUT, 2015. Snakes and ladders in an inhomogeneous neural field model Physica D: Nonlinear Phenomena. 294, 24-36.

BARRACK, D.S., THUL, R. and OWEN, M.R., 2015. Modelling cell cycle synchronisation in networks of coupled radial glial cells Journal of Theoretical Biology. 377, 85-97

BRAUN, WILHELM, MATTHEWS, PAUL C and THUL, RÜDIGER, 2015. First-passage times in integrate-and-fire neurons with stochastic thresholds. Physical Review E. 91(5), 052701

BREÑA-MEDINA, V F, AVITABILE, D, CHAMPNEYS, A R and WARD, M J, 2015. Stripe to Spot Transition in a Plant Root Hair Initiation Model SIAM Journal on Applied Mathematics. 75(3), 1090-1119

CAPEL RA, HERRING N, KALLA M, YAVARI A, MIRAMS GR, DOUGLAS G, BUB G, CHANNON K, PATERSON DJ, TERRAR DA and BURTON RA, 2015. Hydroxychloroquine reduces heart rate by modulating the hyperpolarization-activated current If: Novel electrophysiological insights and therapeutic potential. Heart rhythm : the official journal of the Heart Rhythm Society. 12(10), 2186-94

S COOMBES, 2015. Mathematical Neuroscience: from neurons to networks In: EDP-Normandie Proceedings of the International Conference Symposia in Applied Mathematics.

COOMBES, STEPHEN, 2015. Validating Neuro-Computational Models of Neurological and Psychiatric Disorders Foreword VALIDATING NEURO-COMPUTATIONAL MODELS OF NEUROLOGICAL AND PSYCHIATRIC DISORDERS. 14, V-V

COOPER J, SPITERI RJ and MIRAMS GR, 2015. Cellular cardiac electrophysiology modeling with Chaste and CellML. Frontiers in physiology. 5, 511

H. CROISIER, X. TAN, J. SNEYD, M.J. SANDERSON and B. S. BROOK, 2015. Ryanodine receptor sensitization results in abnormal calcium signaling in airway smooth muscle cells American Journal of Respiratory Cellular and Molecular Biology. 53, 703-711

DRAELANTS, D, AVITABILE, D and VANROOSE, W, 2015. Localized auxin peaks in concentration-based transport models of the shoot apical meristem Journal of The Royal Society Interface. 12(106), 20141407-20141407

FARCOT E, LAVEDRINE C and VERNOUX T, 2015. A modular analysis of the auxin signalling network. PloS one. 10(3), e0122231

FELLER C, FARCOT E and MAZZA C, 2015. Self-Organization of Plant Vascular Systems: Claims and Counter-Claims about the Flux-Based Auxin Transport Model. PloS one. 10(3), e0118238

HILHORST, D, KAMPMANN, J, NGUYEN, TN and VAN DER ZEE, KG, 2015.  Formal asymptotic limit of a diffuse-interface tumor-growth model. Mathematical Models and Methods in Applied Sciences. 25(6), 1011-1044.

IOSUB, RADU, AVITABILE, DANIELE, GRANT, LISA, TSANEVA-ATANASOVA, KRASIMIRA and KENNEDY, HELEN J, 2015. Calcium-Induced Calcium Release during Action Potential Firing in Developing Inner Hair Cells Biophysical Journal. 108(5), 1-10

LAVEDRINE C, FARCOT E and VERNOUX T, 2015. Modeling plant development: from signals to gene networks. Current opinion in plant biology. 27, 148-153

LAVENUS J, GOH T, GUYOMARC'H S, HILL K, LUCAS M, VOSS U, KENOBI K, WILSON M, FARCOT E, HAGEN G, GUILFOYLE T, FUKAKI H, LAPLAZE L and BENNETT MJ, 2015. Inference of the Arabidopsis lateral root gene regulatory network suggests a bifurcation mechanism that defines primordia flanking and central zones The Plant Cell. 27(5), 1368-88

O'DEA, R. D., NELSON, M. R., EL HAJ, A. J., WATERS, S. L. and BYRNE, H. M., 2015. A multiscale analysis of nutrient transport and biological tissue growth in vitro MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA. 32(3), 345-366

PARR, T., RYAN, K., WILLIAMS, H., HARRIS, D., BROWN, D., MAREKO, M., EMES, R., GILES, T., WATTIS, J., DRYDEN, I., LU, C., HODGMAN, C. and BRAMELD, J., 2015. Skeletal muscle hypertrophy in pigs is associated with an increased expression of serine biosynthetic pathway genes along with genes associated with an endoplasmic reticulum stress response PROCEEDINGS OF THE NUTRITION SOCIETY. 74(OCE5), E278-E278

PEARCE, SIMON, FERGUSON, ALISON, KING, JOHN and WILSON, ZOE A., 2015. FlowerNet: A Gene Expression Correlation Network for Anther and Pollen Development PLANT PHYSIOLOGY. 167(4), 1717-U923

PRATT, AC, WATTIS, JAD, SALTER, AM, 2015. Mathematical modelling of hepatic lipid metabolism. MathematicalBiosciences, 262, 167-181.

SAMANTA K, KAR P, MIRAMS GR and PAREKH AB, 2015. Ca(2+) Channel Re-localization to Plasma-Membrane Microdomains Strengthens Activation of Ca(2+)-Dependent Nuclear Gene Expression. Cell reports. 12(2), 203-16

THORN GJ and KING JR, 2015. The metabolic network of Clostridium acetobutylicum: Comparison of the approximate Bayesian computation via sequential Monte Carlo (ABC-SMC) and profile likelihood estimation (PLE) methods for determinability analysis. Mathematical biosciences. 271, 62-79

THUL, R, RIETDORF, K, BOOTMAN, M D and COOMBES, S, 2015. Unifying principles of calcium wave propagation - Insights from a three-dimensional model for atrial myocytes. Biochimica et Biophysica Acta. 1853(9), 2131-2143

WANG K, LEE P, MIRAMS GR, SARATHCHANDRA P, BORG TK, GAVAGHAN DJ, KOHL P and BOLLENSDORFF C, 2015. Cardiac tissue slices: preparation, handling, and successful optical mapping. American journal of physiology. Heart and circulatory physiology. 308(9), H1112-25

WILLIAMS G and MIRAMS GR, 2015. A web portal for in-silico action potential predictions. Journal of pharmacological and toxicological methods. 75, 10-6

YI-PING LO, REUBEN D O'DEA, JONATHAN J CROFTS, CHEOL E HAN and MARCUS KAISER, 2015. A geometric network model of intrinsic grey-matter connectivity of the human brain Scientific Reports. 5

BARRACK, DS, THUL, R and OWEN, MR, 2014. Modelling the coupling between intracellular calcium release and the cell cycle during cortical brain development. Journal of Theoretical Biology, 347, 17-32.

BEGITT, A, DROESCHER, M, MEYER, T, SCHMID, CD, BAKER, M, ANTUNES, F, OWEN, MR, NAUMANN, R, DECKER, T and VINKEMEIER, U, 2014. STAT1-cooperative DNA binding distinguishes type 1 from type 2 interferon signaling. Nature Immunology, 15(2), 168-176.

BESNARD, F, REFAHI, Y, MORIN, V, MARTEAUX, B, BRUNOUD, G, CHAMBRIER, P, ROZIER, F, MIRABET, V, LEGRAND, J, LAINE, S, THEVENON, E, FARCOT, E, CELLIER, C, DAS, P, BISHOPP, A, DUMAS, R, PARCY, F, HELARUITTA, Y, BOUDAOUD, A, GODIN, C, TRAAS, J, GUEDON, Y and VERNOUX, T, 2014. Cytokinin signalling inhibitory fields provide robustness to phylotaxis. Nature, 505(7483), 417-421.

BROOK, BS, 2014. Emergence of airway smooth muscle mechanical behaviour through dynamic reorganisation of contractile units and force transmission pathways. Journal of Applied Physiology. Online.

CHERNYAVSKY, IL, CROISIER, H, CHAPMAN, LAC, KIMPTON, LS, HIORNS, JE, BROOK, BS, JENSEN, OE, BILLINGTON, CK, HALL, IP and JOHNSON, SR, 2014. The role of inflammation resolution speed in airway smooth muscle mass accumulation in asthma: insight from a theoretical model. PLoS ONE 9(3), e90162.

GARG, VV, PRUDHOMME, S, VAN DER ZEE, KG and CAREY, GF, 2014. Adjoint-consistent formulations of slip models for coupled electroosmotic flow systems. Advanced Modeling and Simulation in Engineering, 2, 15.

HIORNS, JE, JENSEN, OE and BROOK, BS, 2014. Nonlinear compliance modulates dynamic bronchoconstriction in a multiscale airway model. Biophysical Journal, 107, 3030-3042.

HIRT, BV, PRESTON, S and WATTIS, JAD, 2014. Modelling the regulation of telomere length: the effects of telomerase and G-quadruplex stabilising drugs, Journal of Mathematical Biology, 68, 1521-1552.

MEIJER, HGE and COOMBES, S, 2014. Travelling waves in a neural field model with refractoriness. Journal of Mathematical Biology, 68(5), 1249-1268.

MEIJER, HGE and COOMBES, S, 2014. Travelling waves in models of neural tissue: from localised structures to periodic waves. EPJ Nonlinear Biomedical Physics, 2:3.

NOBLE, PB, PASCOE, CD, LAN, B, ITO, S, KISTEMAKER, LEM, TATLER, AL, PERA, T, BROOK, BS, GOSENS, R and WEST, AR, 2014. Airway smooth muscle in asthma: linking contraction and mechanotransduction to disease pathogenesis and remodelling. Pulmonary Pharmacology & Therapeutics. Online.

O'DEA, RD, NELSON, MR, EL HAJ, AJ, WATERS, SL and BYRNE, HM, 2014. A multiscale analysis of nutrient transport and biological tissue growth in vitro. Mathematical Medicine and Biology. Online.

PEARSON, T, KING, JR, WATTIS, JAD MACDONALD, I and MAZZATI, D, 2014. A mathematical model of the human metabolic system and metabolic flexibility. Bulletin of Mathematical Biology, 76, 2091-2121.

QI, Q, WATTIS, JAD and BYRNE, HM, 2014. Stochastic simulations of normal aging and Werner's syndrome. Bulletin of Mathematical Biology, 76, 1241-1269.

TIMOFEEVA, Y and COOMBES, S, 2014. Network response of gap junction coupled dendrites, Dendritic computations through morphology and connectivity. In The Computing Dendrite: From Structure to Function, Ed. H Cuntz, M Remme, B Torben-Nielsen, Springer.

WU, X, VAN ZWIETEN, GJ and VAN DER ZEE, KG, 2014. Stabilized second-order convex splitting schemes for Cahn–Hilliard models with application to diffuse-interface tumor-growth models. International Journal for Numerical Methods in Biomedical Engineering, 30(2), 180-203.

ZACHARIOU, M and THUL, R, 2014. Cannabinoid-mediated short-term plasticity in hippocampus. Journal of Computational Neuroscience, 37, 533-547.

BALL, F, BRITTON, T and SIRL, D,     2013.     A network with tunable clustering, degree correlation and degree distribution, and an epidemic thereon.     Journal of Mathematical Biology.     66(4-5),     979-1019.

BOKES, P, KING, JR, WOOD, ATA and LOOSE, M,     2013.     Transcriptional Bursting Diversifies the Behaviour of a Toggle Switch: Hybrid Simulation of Stochastic Gene Expression.     Bulletin of Mathematical Biology, 75,     351-371. 

BRESSLOFF, PC and COOMBES, S,     2013.     Neural ‘Bubble’ Dynamics Revisited.     Cognitive Computation,     5(3),   281-294.

BROOK, BS and JENSEN, OE,    2013.    The role of contractile unit reorganisation in force generation in airway smooth muscle.    Mathematical Medicine and Biology, (online).

CABALLERO GAUDES, C, PETRIDOU, N, FRANCIS, ST, DRYDEN, IL and GOWLAND, PA,    2013.    Paradigm free mapping with sparse regression automatically detects single-trial functional magnetic resonance imaging blood oxygenation level dependent responses.    Human Brain Mapping,    34(3),    501-18.

CHAVES, M, FARCOT, E and GOUZÉ, JL,    2013.    Probabilistic approach for predicting periodic orbits in piecewise affine differential models.    Bulletin of Mathematical Biology,    75(6),    967-987.

COOMBES, S and TIMOFEEVA, Y,    2013.    Editorial for special issue on Neurodynamics.    Journal of Mathematical Neuroscience,    3(1),    10.

CROISIER, H, TAN, X, PEREZ-ZOGHBI, JF, SANDERSON, MJ, SNEYD, J and BROOK, BS,    2013.    Activation of Store-Operated Calcium Entry in Airway Smooth Muscle Cells: Insight from a Mathematical Model.    PLoS One,    8(7),  e69598.

FARCOT, E and YUAN, Y,    2013.    Homogeneous auxin steady states and spontaneous oscillations in flux-based auxin transport models.    SIAM Journal on Applied Dynamical Systems,    12(3),    1330-1353.

FIGUEREDO, GP, JOSHI, TV, OSBORNE, JM, BYRNE, HM and OWEN, MR, 2013.  On-lattice agent-based simulation of populations of cells within the open-source Chaste framework. Interface Focus, 3(2), 2012.0081

FOZARD JA, KING JR and BENNETT MJ,     2013.     Modelling auxin efflux carrier phosphorylation and localization. Journal of Theoretical Biology,     319,     34-49.

FOZARD, JA, LUCAS, M, KING, JR and JENSEN, OE,    2013.     Vertex-element models for anisotropic growth of elongated plant organs.     Frontiers in Plant Science,     4,     233.

GUÉDON, Y, REFAHI, Y, BESNARD, F, FARCOT, E, GODIN, C and VERNOUX, T,    2013.    Pattern identification and characterization reveal permutations of organs as a key genetically controlled property of post-meristematic phyllotaxis.    Journal of Theoretical Biology,   (In Press).

HIRT, BV, WATTIS, JAD and PRESTON, SP, 2013.  Modelling the regulation of telomere length: the effects of telomerase and G-quadruplex stabilising drugs. Journal of Mathematical Biology, (online).

JABBARI S, STEINER E, HEAP JT, WINZER K, MINTON NP and KING JR,     2013.     The putative influence of the agr operon upon survival mechanisms used by Clostridium acetobutylicum.     Mathematical Biosciences,     243,     223-239.

KOUROUNIOTI, RLA, BAND, LR, FOZARD, JA, HAMPSTEAD, A, LOVRIC    S, A, MOYROUD, E, VIGNOLINI, S, KING, JR, JENSEN, OE and GLOVER, BJ,     2013.     Buckling as an origin of ordered cuticular patterns in flower petals. Journal of the Royal Society Interface,     10(80).

LEMON, G and KING, JR,     2013.     Functional Differential Equation Models for Biological Cell Sorting due to Differential Adhesion.     Mathematical Models & Methods in Applied Sciences,     23(1).

LIN KK, WEDGWOOD KCA, COOMBES S and YOUNG L,     2013.     Limitations of perturbative techniques in the analysis of rhythms and oscillations.     Journal of Mathematical Biology,     66,     139-161.

MILLAT, T, JANSSEN, H, THORN, GJ, KING, JR, BAHL, H, FISCHER, R and WOLKENHAUER, O,     2013.     A shift in the dominant phenotype governs the pH-induced metabolic switch of Clostridium acetobutylicumin phosphate-limited continuous cultures     Applied Microbiology and Biotechnology,    97(14),     6451-6466.

MURARO, D, BYRNE, HM, KING, JR and BENNETT, MJ,     2013.     The role of auxin and cytokinin signalling in specifying the root architecture of Arabidopsis thaliana,     Journal of Theoretical Biology,     317,     71-86.

MURARO, D, VOSS, U, WILSON, M, BENNETT, MJ, BYRNE, HM, DE SMET, I, HODGMAN, C and KING, JR,     2013.  Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis thalia.    IEEE-ACM Transactions on Computational Biology and Bioinformatics,    10(1),    50-60.

NELSON, MR, KING, JR and JENSEN, OE, 2013. Buckling of a growing tissue and the emergence of two-dimensional patterns. Mathematical Biosciences, 246(2), 229-241. 

O'DEA, RD, BYRNE, HM and WATERS, SL,    2013.    Continuum modelling of in vitro tissue engineering: a review.   In:  L GERIS, ed.,    Computational Modeling in Tissue Engineering    10,    Springer Berlin Heidelberg,    229-266.

O'DEA RD, CROFTS JJ and KAISER M,    2013.    Spreading dynamics on spatially constrained complex brain networks.  Journal of the Royal Society Interface,    10(81),    20130016.

O'DEA, RD and KING, JR,     2013.    The isolation of spatial patterning modes in a mathematical model of juxtacrine cell signalling.    Mathematical Medicine and Biology - A Journal of the IMA,    30(2),    95.

OLIVA, M, FARCOT, E and VERNOUX, T,    2013.    Plant hormone signaling during development: insights from computational models.    Current Opinion in Plant Biology,    16(1),    19-24.

PÉRET, B,   MIDDLETON AM, FRENCH AP, LARRIEU, A, BISHOPP, A, NJO, M, WELLS, D, PORCO, S, MELLOR, N, BAND, L, CASIMIRO, I, KLEINE-VEHN, J, VANNESTE, S, SAIRANEN, I, MALLET, R, SANDBERG, G, LJUNG, K, BEECKMAN, T, BENKOVA, E, FRIML, J, KRAMER, E, KING, JR, DE SMET, I, PRIDMORE, T, OWEN, MR and BENNETT, MJ, 2013.  Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology, 9, 699.

PICKERING, A, GORDOA, PR and WATTIS, JAD,    2013.    Behaviour of the extended Volterra lattice.    Communications in Nonlinear Science and Numerical Simulation, 19(3), 589-600.

SOLDATOS, KP, 2013.   Modelling framework for mass-growth . Mechanics Research Communications, 50, 50-57.

TAXIDIS, J, MIZUSEKI, K, MASON, R and OWEN, MR, 2013.  Influence on slow oscillation of hippocampal activity and ripples through cortico-hippocampal synaptic interactions, analyzed by a cortical-CA3-CA1 network mode. Frontiers in Computational Neuroscience, 7, 3.

THORN, GJ, KING, JR and JABBARI, S,     2013.     pH-induced gene regulation of solvent production by Clostridium acetobutylicum in continuous culture: Parameter estimation and sporulation modelling     Mathematical Biosciences,  241(2),     149-166.

TIMOFEEVA Y, COOMBES S and MICHIELETTO D,     2013.     Gap junctions, dendrites and resonances: a recipe for tuning network dynamics.     Journal of Mathematical Neuroscience,     3(1),     15    (In Press.)

VAN BOVEN, M, RUIJS, WL, WALLINGA, J, O'NEILL, PD and HAHNE, S,    2013.    Estimation of mumps vaccine efficacy and critical vaccination coverage.    Public Library of Science Computational Biology,    9(5).

WALKER, ML, FARCOT, E, TRAAS, J and GODIN, C,    2013.    The Flux-Based PIN Allocation Mechanism Can Generate Either Canalyzed or Diffuse Distribution Patterns Depending on Geometry and Boundary Conditions    PLoS ONE,    8(1),  e54802.

WEDGWOOD, KC, LIN, KK, THUL, RS and COOMBES, S, 2013.  Phase-amplitude descriptions of neural oscillator models. Journal of Mathematical Neuroscience, 3(2).

WILKINSON, RD, 2013.  Approximate Bayesian computation (ABC) gives exact results under the assumption of model error. Statistical Applications in Genetics and Molecular Biology, 12(2), 129-141.

WORBY CJ, JEYARATNAM D, ROBOTHAM JV, KYPRAIOS T, O'NEILL PD, DE ANGELIS D, FRENCH G and COOPER BS,  2013.    Estimating the effectiveness of isolation and decolonization measures in reducing transmission of methicillin-resistant Staphylococcus aureus in hospital general wards.    American Journal of Epidemiology,    177(11),    1306-13.

ZACHARIOU, M, ALEXANDER, SPH, COOMBES, S and CHRISTODOULOU, C,     2013.     A biophysical model of endocannabinoid-mediated short term depression in hippocampal inhibition.     PLoS One,     8(3),     e58926.

ZHU, H and OWEN, MR.,     2013.     Damped propagation of cell polarization explains distinct PCP phenotypes of epithelial patterning     Scientific Reports,     3, 2528.

ANBALAGAN, C, LAFAYETTE, I, ANTONIOU-KOUROUNIOTI, M, HAQUE, M, KING, JR, JOHNSEN, B, BAILLIE, D, GUTIERREZ, C, MARTIN, JAR and DE POMERAI, D, 2012.  Transgenic nematodes as biosensors for metal stress in soil pore water samples. Ecotoxicology, 21(2), 439-455.

BAKER M, DENMAN-JOHNSON S, BROOK BS, GAYWOOD I and OWEN MR, 2012. Mathematical modelling of cytokine-mediated inflammation in rheumatoid arthritis.  Mathematical Medicine and Biology: A Journal of the IMA, (online).

BAND, L.R, UBEDA-TOMAS, S, DYSON, R.J, MIDDLETON, A.M, HODGMAN, T.C, OWEN, M.R, JENSEN, O.E, BENNETT, M.J and KING, J.R, 2012.  Growth-induced hormone dilution can explain the dynamics of plant root cell elongation.   Proceedings Of The National Academy Of Sciences Of The United States Of America, 109(19), 7577-7582.

BAND LR, WELLS DM, LARRIEU A, SUN J, MIDDLETON AM, FRENCH AP, BRUNOUD G, SATO EM, WILSON MH, PÉRET B, OLIVA M, SWARUP R, SAIRANEN I, PARRY G, LJUNG K, BEECKMAN T, GARIBALDI JM, ESTELLE M, OWEN MR, VISSENBERG K, HODGMAN TC, PRIDMORE TP, KING JR, VERNOUX T and BENNETT MJ, 2012.  Root Gravitropism Is Regulated By A Transient Lateral Auxin Gradient Controlled By A Tipping-Point Mechanism. Proceedings Of The National Academy Of Sciences Of The United States Of America, 109(12), 4668-4673.

BOOTMAN, MD and THUL, R, 2012.  Calcium: Local and Global Cell Messenger. In UVERSKY, VN, KRETSINGER, RH and PERMYAKOV, EA (eds.) Encyclopedia of Metalloproteins (to appear).

BRIDGE, LJ, MIRAMS, GR, KIEFFER, ML, KING, JR and KEPINKSI, S, 2012.  Distinguishing possible mechanisms for auxin-mediated developmental control in Arabidopsis: Models with two Aux/IAA and ARF proteins, and two target gene-sets. Mathematical Biosciences, 235(1), 32-44.

COOMBES, S, SCHMIDT, H and BOJAK, I, 2012.  Interface dynamics in planar neural field models. Journal of Mathematical Neuroscience, 2(9).

COOMBES, S, THUL, R, LAUDANSKI, J, PALMER, A.R. and SUMNER, C.J., 2012.  Neuronal spike-train responses in the presence of threshold noise. Frontiers in Life Sciences, 5(3-4), 91-105.

HIRT, BV, WATTIS, JAD, PRESTON, SP and LAUGHTON, CA, 2012.  The effects of a telomere destabilizing agent on cancer cell-cycle dynamics-Integrated modelling and experiments. Journal of Theoretical Biology,295, 9-22.

HOYLE, RB, AVITABILE, D and KIERZEK, AM, 2012.  Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. PLoS Computational Biology 8(6): e1002396. 

JABBARI, S, KING, JR and WILLIAMS, P, 2012.  Cross-strain quorum sensing inhibition by staphylococcus aureus - Part 1: a spatially homogeneous model. Bulletin of Mathematical Biology, 74, 1292-1325.

JABBARI, S, KING, JR and WILLIAMS, P, 2012.  Cross-strain quorum sensing inhibition by staphylococcus aureus - Part 2: a spatially inhomogeneous model. Bulletin of Mathematical Biology, 74, 1326-1353.

MIDDLETON AM, FARCOT E, OWEN MR and VERNOUX T, 2012.  Modeling regulatory networks to understand plant development: small is beautiful.  The Plant Cell, 24, 3876-3891.

MIDDLETON AM, UBEDA-TOMÁS S, GRIFFITHS J, HOLMAN T, HEDDEN P, THOMAS SG, PHILLIPS AL, HOLDSWORTH MJ, BENNETT MJ, KING JR and OWEN MR, 2012.  Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling. Proceedings Of The National Academy Of Sciences Of The United States Of America, 109(19), 7571-7576.

MILLER, CE, BATRA, R, COOPER, BS, PATEL, AK, KLEIN, J, OTTER, JA, KYPRAIOS, T, FRENCH, GL, TOSAS, O and EDGEWORTH, JD, 2012.  An Association Between Bacterial Genotype Combined With a High-Vancomycin Minimum Inhibitory Concentration and Risk of Endocarditis in Methicillin-Resistant Staphylococcus aureus Bloodstream Infection. Clinical Infectious Diseases, 54(5), 591-600.

NELSON, MR, BAND, LR, DYSON, RJ, LESSINES, T, WELLS, DM, YANG, C, EVERITT, NM, JENSEN, OE and WILSON, ZA, 2012.  A biomechanical model of anther opening reveals the roles of dehydration and secondary thickening. New Phytologist 196(4), 1030-1037.

O'DEA, R and KING, JR, 2012.  Continuum limits of pattern formation in hexagonal-cell monolayers. Journal of Mathematical Biology, 64(3), 579-610.

PELLIS, L, BALL, F and TRAPMAN, P, 2012.  Reproduction numbers for epidemic models with households and other social structures. I. Definition and calculation of R-0. Mathematical Biosciences, 235(1), 85-97.

SCHENDEL, T, THUL, R, SNEYD, J and FALCKE, M, 2012.  How does the ryanodine receptor in the ventricular myocyte wake up: by a single or by multiple open L-type Ca(2+) channels? European Biophysics Journal with Biophysics Letters, 41(1), 27-39.

SVENSSON, CM, COOMBES, S and PIERCE, JW, 2012.  Using evolutionary algorithms for fitting high-dimensional models to neuronal data. Neuroinformatics, 10, 199-218.

TAXIDIS, S, Coombes, S, MASON, R and OWEN, MR, 2012.  Modeling sharp wave-ripple complexes through a CA3-CA1 network model with chemical synapses. Hippocampus, 22, 995–1017.

THUL, R, 2012. Translating intracellular calcium signalling into models. Cold Spring Harbor Protocols (to appear).

THUL, R, COOMBES, S and BOOTMAN, MD.  Persistence of pro-arrhythmic spatio-temporal calcium patterns in atrial myocytes: a computational study of ping waves. Frontiers in Computational Physiology and Medicine, 3, 279.

THUL, R, COOMBES, S, RODERICK, HL and BOOTMAN, MD, 2012.  Subcellular calcium dynamics in a whole-cell model of an atrial myocyte. Proceedings of the National Academy of Sciences USA, 109(6), 2150-2155.

ALLEN, E, MOING, A, WATTIS, JAD, LARSON, T, MAUCOURT, M, GRAHAM, IA, ROLIN, D, HOOKS, MA, 2011.  Evidence that ACN1 (acetate non-utilizing 1) prevents carbon leakage from peroxisomes during lipid mobilization in Arabidopsis seedlings. Biochemical Journal, 437, 505-513.

BALL, F, BRITTON, T and SIRL, D, 2011.  Household epidemic models with varying infection response. Journal of Mathematical Biology, 63(2), 309-337.

BENíTEZ, M, MONK, N. A. M. AND ALVAREZ-BUYLLA, E. R., 2011.  Epidermal patterning in Arabidopsis: Models make a difference. Journal of Experimental Zoology B: Molecular and Developmental Evolution, 316B(4), 241-253.

BOOTMAN, MARTIN D, SMYRNIAS, IOANNIS, THUL, RüDIGER, COOMBES, STEPHEN and RODERICK, H LLEWELYN, 2011.  Atrial cardiomyocyte calcium signalling. Biochimica et Biophysica Acta, 1813, 922-934.

BRITTON, T, KYPRAIOS, T AND O'NEILL, P.D, 2011.  Inference for epidemics with three levels of mixing: methodology and application to a measles outbreak. Scandinavian Journal of Statistics, 38(3), 578-599.

BROOK, B.S., KOHL, P and KING, J.R., 2011.  Towards the virtual physiological human: mathematical and computational case studies (preface). Philosophical Transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences, 369(1954), 4145-4148.

CHERNYAVSKY, I.L., LEACH, L., DRYDEN, I.L. and JENSEN, O.E., 2011.  Transport in the placenta: homogenizing haemodynamics in a disordered medium. Philosophical Transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences, 369(1954), 4162-4182.

COOMBES, S and LAING, C R, 2011.  Pulsating fronts in periodically modulated neural field models. Physical review. E, Statistical, nonlinear, and soft matter physics, 83(1-1), 011912.

DUDUIALA, CI, WATTIS, JAD and LAUGHTON, CA, 2011.  Self-organised criticality in base-pair breathing in DNA with a defect. Physica D, 240(16), 1254-1261.

FINK, MARTIN, NIEDERER, STEVEN A, CHERRY, ELIZABETH M, FENTON, FLAVIO H, KOIVUMäKI, JUSSI T, SEEMANN, GUNNAR, THUL, RüDIGER, ZHANG, HENGGUI, SACHSE, FRANK B, BEARD, DAN, CRAMPIN, EDMUND J and SMITH, NP, 2011.  Cardiac cell modelling: Observations from the heart of the cardiac physiome project. Progress in biophysics and molecular biology, 104, 2-21.

FOZARD, JA, KIRKHAM, GR, BUTTERY, LDK, KING, JR, JENSEN, OE and BYRNE, HM, 2011.  Techniques for analysing pattern formation in populations of stem cells and their progeny. BMC Bioinformatics, 12, 396.

GRAEBER, K, LINKIES, A, WOOD, ATA and LEUBNER-METZGER, M, 2011.  A Guideline to Family-Wide Comparative State-of-the-Art Quantitative RT-PCR Analysis Exemplified with a Brassicaceae Cross-Species Seed Germination Case Study. Plant Cell, 23(6), 2045-2063.

HAQUE, M, KING, JR, LOOSE, M and de POMERAI, D, 2011.  Modelling of the Metallothionein Gene Network in Caenorhabditis elegans: Mathematical Models, Predictions and Laboratory Experiments. ATLA-alternatives to laboratory animals, 39(1), 81-81.

HAUS, S, JABBARI, S, MILLAT, T, JANSSEN, H, FISCHER, RJ, BAHL, H, KING, JR and WOLKENHAUER, O, 2011.  A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture. BMC Systems Biology, 5, 10.

JABBARI, S., HEAP, J. T. and KING, J. R., 2011.  Mathematical Modelling of the Sporulation-Initiation Network in Bacillus Subtilis Revealing the Dual Role of the Putative Quorum-Sensing Signal Molecule PhrA. Bulletin of Mathematical Biology, 73(1), 181-211.

KING, J.R., 2011.  Mathematical modelling of eukaryotic stress-response networks. ATLA-alternatives to laboratory animals, 39(1), 73-73. 

KUWABARA, A, BACKHAUS, A, MALINOWSKI, R, BAUCH, M, HUNT, L, NAGATA, T, MONK, N, SANGUINETTI, G and FLEMING, A, 2011.  A shift towards smaller cell size via manipulation of cell cycle gene expression acts to smoothen aridopsis leaf shape. Plant Physiology, 156(4), 2196-2206.

KYPRAIOS, T, O'NEILL, P.D., JONES, D.E., WARE, J, BATRA, R, EDGEWORTH, J.D. and COOPER, B.S., 2011.  Effect of systemic antibiotics and topical chlorhexidine on meticillin-resistant Staphylococcus aureus carriage in intensive care unit patients. Journal of Hopsital Infection, 79(3), 222-226.

LEMON, G., HOWARD, D., ROSE, F. R. A. J. and KING, J. R., 2011.  Individual-based modelling of angiogenesis inside three-dimensional porous biomaterials. Biosystems, 103(3), 372-383.

LEMON, G., HOWARD, D., YANG, H., RATCHEV, S.M., SEGAL, J.I., ROSE, F.R.A.J., JENSEN, O.E., WATERS, S.L. and KING, J.R., 2011.  Growth of the chorioallantoic membrane into a rapid-prototyped model pore system: experiments and mathematical model. Biomechanics and Modeling in Mechanobiology, 10(4), 539-558.

NELSON, M.R., HOWARD, D., JENSEN, O.E., KING, J.R., ROSE, F.R.A.J. and WATERS, S.L., 2011.  Growth-induced buckling of an epithelial layer. Biomechanics and Modeling in Mechanobiology, 10(6), 883-900.

O'DEA, R.D., KING, J.R., 2011.  Multiscale analysis of pattern formation via intercellular signalling. Mathematical Biosciences, 231(2), 172-185.

OWEN, MARKUS R, STAMPER, I JOHANNA, MUTHANA, MUNITTA, RICHARDSON, GILES W, DOBSON, JON, LEWIS, CLAIRE E and BYRNE, HELEN M, 2011.  Mathematical Modeling Predicts Synergistic Antitumor Effects of Combining a Macrophage-Based, Hypoxia-Targeted Gene Therapy with Chemotherapy. Cancer research, 71(8), 2826-2837.

PERFAHL, H, BYRNE, HM, CHEN, TG, ESTRELLA, V, ALARCON, T, LAPIN, A, GATENBY, RA, GILLIES, RJ, LLOYD, MC, MAINI, PK, REUSS, M and OWEN, MR, 2011.   Multiscale Modelling of Vascular Tumour Growth in 3D: The Roles of Domain Size and Boundary Conditions. PLOS ONE, 6(4), e14790.

SARWARDI, S, HAQUE, M and VENTURINO, E, 2011.  Global stability and persistence in LG-Holling type II diseased predator ecosystems. Journal of Biological Physics, 37(1), 91-106.

SPENCER, S.E.F., O'NEILL, P.D., 2011.  The probability of containment for multitype branching process models for emerging epidemics. Journal of Applied Probability, 48(1), 173-188.

WATERS, S.L., ALASTRUEY, J., BEARD, D.A., BOVENDEERD, P.H.M., DAVIES, P.F., JAYARAMAN, G., JENSEN, O.E., LEE, J., PARKER, K.H., POPEL, A.S., SECOMB, T.W., SHERWIN, S.J., SHIPLEY, R.J., SIEBES, M, SMITH, NP and VAN DE VOSSE, FN, 2011.  Theoretical models for coronary vascular biomechanics: progress and challenges. Progress in Biophysical and Molecular Biology, 104, 49-76.

WILKINSON, RD, STEIPER, ME, SOLIGO, C, MARTIN, RD, YANG, ZH and TAVARE, S, 2011.  Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data. Systematic Biology, 60(1), 16-31.