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.

• Miller A.K., Marsh, J., Reeve, A., Garny, A., Britten, R., Halstead, M., Cooper, J., Nickerson, D.P. and  Nielsen, P.F., An overview of the CellML API and its implementation. BMC Bioinformatics, 2010, 11:178.
• Miller, A.K., Yu, T., Britten, R., Cooling, M.T., Lawson, J., Cowan, D., Garny, A., Halstead, M.D., Hunter, P.J., Nickerson, D.P., Nunns, G., Wimalaratne, S.M., Nielsen, P.M.,  Revision history aware repositories of computational models of biological systems. BMC Bioinformatics, 2011, 12:22.
• Yu, T., Lloyd, C.M., Nickerson, D.P., Cooling, M.T., Miller, A.K., Garny, A., Terkildsen, J.R., Lawson, J., Britten, R.D., Hunter, P.J., Nielsen, P.M., The Physiome Model Repository 2. Bioinformatics. Advance Access published 2011 Jan 08.
• Cooling, Mike. A Primer on Modular Mass-Action Modelling with CellML. Systems Biology, 2010, Volume 1, Part 4, 721-750
• 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.