CellML publications listing

Below is a list of peer-reviewed publications which relate to CellML. If you think there are CellML-related articles missing from the list below, please feel free to contact us with the publication details and we will add the article for you.

• Cooling, M.T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J. and Wipat, A. Standard Virtual Biological Parts: A Repository of Modular Modeling Components for Synthetic Biology. Bioinformatics. Advance Access published 2010 Feb 16.
• Wimalaratne, S.M., Halstead, M.D., Lloyd, C.M., Cooling, M.T., Crampin, E.J. and Nielsen, P.F. A method for visualizing CellML models. Bioinformatics. 2009 Nov;25(22):3012-3019.
• Wimalaratne, S.M., Halstead, M.D., Lloyd, C.M., M.T., Crampin, E.J. and Nielsen, P.F. Biophysical annotation and representation of CellML models. Bioinformatics. 2009 Sept;25(17):2263-2270.
• Matos E.E., Campos F., Braga R. and Palazzi D. CelOWS: An ontology based framework for the provision of semantic web services related to biological models. Journal of Biological Informatics. 2009 Aug 18. [Epub ahead of print]
• Cooper J. Automatic Validation and Optimisation of Biological Models University of Oxford 2009 doctoral thesis.
• Nickerson, D.P. and Buist, M. A physiome standards-based model publication paradigm. Philosophical Transactions of the Royal Society A. 2009 May;367(1895):1823-1844.
• Garny, A., Noble, D., Hunter, P.J. and Kohl, P. Cellular Open Resource (COR): current status and future directions. Philosophical Transactions of the Royal Society A. 2009 May;367(1895):1885-1905.
• Beard, D.A., Britten, R., Cooling, M.T., Garny, A., Halstead, M.D.B., Hunter, P.J., Lawson, J., Lloyd, C.M., Marsh, J., Miller, A., Nickerson, D.P., Nielsen, P.F., Nomura, T., Subramanium, S., Wimalaratne, S.M. and Yu, T. CellML metadata standards, associated tools and repositories. Philosophical Transactions of the Royal Society A. 2009 May;367(1895):1845-1867.
• Wimalaratne, S.M., Halstead, M.D.B., Lloyd, C.M., Cooling, M.T., Crampin, E.J. and Nielsen, P.F. Facilitating modularity and reuse: guidelines for structuring CellML 1.1 models by isolating common biophysical concepts. Experimental Physiology. 2009 May;94(5):472-485.
• Suzuki, Y., Asai, Y., Kawazu, T., Nakanishi, M., Taniguchi, Y., Heien, E., Hagihara, K., Kurachi, Y., and Nomira, T. A platform for in silico modeling of physiological systems II. CellML compatibility and other extended capabilities.  Conference Proceedings: 30th Annual International Conference of the IEEE Engineering in Medicine and Biology. 2008;2008:573-576.
• Lloyd, C.M., Lawson, J.L., Hunter, P.J. and Nielsen, P.F. The CellML Model Repository. Bioinformatics. 2008 September;24(18):2122-2123.
• Nickerson, D.P. and Buist, M.L. Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model. Progress in Biophysics and Molecular Biology. 2008;98:38-51.
• Garny, A., Nickerson, D., Cooper, J., Weber dos Santos, R., Miller, A.K., McKeever, S., Nielsen, P. and Hunter, P.J. CellML and associated tools and techniques. Philosophical Transactions of the Royal Society A. 2008 September;366(1878):3017-3043.
• Cooper, J., McKeever, S. A model-driven approach to automatic conversion of physical units Software: Practice and Experience 2008 Apr. 38(4):337-359.
• Nickerson, D.P., Corrias, A. and Buist, M.L. Reference descriptions of cellular electrophysiology models. Bioinformatics. 2008 April;24(8):1112-1114.
• Terkildsen, J.R., Niederer, S.A., Crampin, E.J., Hunter, P.J. and Smith, N.P. Using Physiome standards to couple cellular functions for cardiac excitation contraction. Experimental Physiology. 2008 March.
• Cooling, M., Hunter, P. and Crampin, E.J. Modeling biological modularity with CellML. IET Systems Biology. 2008 March;2(2):73-79.
• Cooper, J., McKeever, S. Experience Report: A Haskell interpreter for CellML ICFP '07: Proceedings of the 2007 ACM SIGPLAN international conference on Functional programming 2007 Oct 247—250. ACM Press.
• Hui, B.B., Dokos, S. and Lovell, N.H. Parameter identifiability of cardiac ionic models using a novel CellML least squares optimization tool. Conference Proceedings: 29th Annual International Conference of the IEEE Engineering in Medicine and Biology. 2007;2007:5307-5310.
• Nickerson, D., Nash, M., Nielsen, P., Smith, N. and Hunter, P. Computational multiscale modeling in the IUPS Physiome Project: modeling cardiac electromechanics. IBM Journal of Research and Development. 2006 November;50(6):617-630.
• Schilstra, M.J., Li. L., Matthews, J., Finney, A., Hucka, M. and Le Novère, N. CellML2SBML: conversion of CellML into SBML. Bioinformatics. 2006 April 15;22(8):1018-1020.
• Hunter, P.J. Modeling human physiology: the IUPS/EMBS Physiome Project. Proceedings of the IEEE. 2006 April;94(4):678-691.
• Nickerson, D.P. and Hunter, P.J. The Noble cardiac ventricular electrophysiology models in CellML. Progress in Biophysics and Molecular Biology. 2006 Jan-April;90(1-3):346-359.
• Cooper, J., McKeever, S., Garny, A. On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations PEPM '06: Proceedings of the 2006 ACM SIGPLAN symposium on Partial evaluation and semantics-based program manipulation. 2006 Jan, pp. 12-20, DOI: 10.1145/1111542.1111546
• Hunter, P.J. and Nielsen, P.M.F. A strategy for integrative computational physiology. Physiology. 2005 Oct;20(5):316-325.
• Nickerson, D. and Hunter, P. Using CellML in Computational Models of Multiscale Physiology. Conference Proceedings: 27th Annual International Conference of the IEEE Engineering in Medicine and Biology. 2005 Sept; 6096-6099.
• Le Novère, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D. and Wanner, B.L. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology. 2005 Dec;23(12):1509-1515.
• Crampin, E.J., Halstead, M.D.B., Hunter, P.J., Nielsen, P.M.F., Noble, D., Smith, N.P. and Tawhai, M. Computational physiology and the Physiome Project. Experimental Physiology: Translation and Integration. 2004 Jan;89(1):1-26.
• Lloyd, C.M., Halstead, M.D.B. and Nielsen, P.F. CellML: its future, present and past. Progress in Biophysics and Molecular Biology. 2004 Jun-Jul;85(2-3):433-450.
• Nielsen, P.F. and Halstead, M.D. The Evolution of CellML. Conference Proceedings: 26th Annual International Conference of the IEEE Engineering in Medicine and Biology. 2004;7:5411-5414.
• Cuellar, A.A., Lloyd, C.M., Nielsen, P.F., Bullivant, D.P., Nickerson, D.P. and Hunter, P.J. An overview of CellML 1.1, a biological model description language. SIMULATION: Transactions of The Society for Modeling and Simulation International. 2003 Dec;79(12):740-747.
• Cuellar, A.A., Nielsen, P.F., Bullivant, D.P. and Hunter, P.J. CellML 1.1 for the Definition and Exchange of Biological Models. Conf. Proc. 2003 IFAC Symposium on Modelling and Control in Biomedical Systems. 2003 Nov; 451-456.
• Bullivant, D.P., Hedley, W.J., Hunter, P.J., Nelson, M.R. and Nielsen, P.F. Languages for the Definition and Exchange of Biological Models. Proc. of the Physiological Society of New Zealand. Volume 20, August 2001.
• Hedley W.J., Nelson, M.R., Nielsen, P.F., Bullivant, D.P. and Hunter, P.J. XML Languages for Describing Biological Models. Proceedings of the Physiological Society of New Zealand. Vol 19. December 2000.