Scientific Publications

• Proceedings of IEEE 2006 will publish a special issue on computer modeling in medicine: The Physiome: In-Silico Living Human. Editors are Dr. James B. Bassingthwaighte, University of Washington, Seattle, WA, USA and Dr. Jean-Louis Coatrieux, Université de Rennes, Rennes, France.

• Hunter, P., Smith, N., Fernandez, J. and Tawhai, M., Integration from proteins to organs: the IUPS Physiome Project, Mech. Ageing Dev., 126(1), 187-192, 2005

• Fernandez, J., Mithraratne, P., Thrupp, S., Tawhai, M. H. and Hunter, P. J., Anatomically based geometric modelling of the musculo-skeletal system and other organs, Biomechan. Model. Mechanobiol., 2(3), 139-155, 2004

• Lloyd, C., Halstead, M. and Nielsen, P., CellML:Its future, present and past, Prog. Biophys. Molec. Biol., 85(2-3), 433-450, 2004

• Crampin, E., Halstead, M., Hunter, P., Nielsen, P., Noble, D., Smith, N. and Tawhai, M., Computational physiology and the physiome project, Experimental Physiology, 89(1), 1-26, 2004

• Crampin, E., Smith, N. and Hunter, P., Multi-scale modelling and the IUPS Physiome Project, J. Mol. His., 35(7), 707-714, 2004

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

• Bassingthwaighte, J. B. and Vinnakota, K. C., The Computational Integrated Myocyte A view into the heart, Ann. N. Y. Acad. Sci., 1015(1), 391-404, 2004

• Hunter, P., The IUPS physiome project: a framework for computational physiology, Prog. Biophys. Molec. Biol., 85(2-3), 551-569, 2004

• Bassingthwaighte JB. The macro-ethics of genomics to health: The Physiome Project. Comptes Rendus de l'Academie francaise, 326: 1105-1110, 2003.

• Cuellar, A., Lloyd, C., Nielsen, P., Halstead, M., Bullivant, D., Nickerson, D. and Hunter, P., An Overview of CellML 1.1, a biological model description language, Trans Soc Model Sim Int, 79(12), 740-747, 2003

• Anderson, K. E. and Jackson S P, , Class I phosphoinositide 3-kinases, Int. J. Biochem & Cell Bio., 35, 1028-1033, 2003

• Hunter, P. J. and Borg, T., Integration from Proteins to Organs: The Physiome Project, Nature, 4(3), 237-243, 2003

• Hucka, M., Bolouri, H., Finney, A., Sauro, H. M., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cuellar, A., Dronov, S., Ginkel, M., Gor, V., Goryanin, I. I., Hedley, W., Hodgman, T. C., Hunter, P. J., Juty, N. S., Kasberger, J. L., Kremling, A., Kummer, U., LeNovere, N., Loew, L. M., Lucio, D., Mendes, P., Mjolsness, E. D., Nakayama, Y., Nelson, M. R., Nielsen, P., Sakurada, T., Schaff, J. C., Shapiro, B. E., Shimizu, T. S., Spence, H. D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J. and Wang, J., The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models, Bioinformatics, 19, 524-531, 2003

• Bock, G. and Goode, J. A., Integrative biological modelling in silico: in 'In silico' simulation of biological processes, Bock, G. and Goode, J. (eds), Wiley, 2002

• Hunter, P. J., Robbins, P. and Noble, D., The IUPS Human Physiome Project, Eur. J. Physiol., 445(1), 1-9, 2002

• Bassingthwaighte, J. B., The modelling of a primative "sustainable" conservative cell, Phil. Trans. R. Soc. Lond. A, 359(1783), 1055-1072, 2001

• Kohl, P., Noble, D., Winslow, R. L. and Hunter, P. J., Computational Modelling of Biological System: Tools and Visions, Phil. Trans. R. Soc. Lond. A, 358(1766), 579-610, 2000

• Bassingthwaighte JB.  Strategies for the Physiome Project. Ann Biomed Eng 28:1043-1058, 2000.

• Rudy, Y., From Genome To Physiome: Integrative Models of Cardiac Excitation, Ann. Biomed. Eng., 28(8), 945-950, 2000

• McCulloch, A., Modeling the human cardiome in silico, J. Nucl. Cardiol., 7(5), 496-499, 2000

• Bassingthwaighte, J. B., Stategies for the Physiome Project, Ann. Biomed. Eng., 28(8), 1043-1058, 2000

• Bassingthwaighte, J. B., Qian, H. and Li, Z., The Cardiome Project: An integrated view of cardiac metabolism and regional mechanical function, Adv. Exp. Med. Biol., 471, 541-553, 1999

• McCulloch, A., Bassingthwaighte, J. B., Hunter, P. J. and Noble, D., Computational Biology of the Heart: From Structure to Function, Prog. Biophys. Molec. Biol., 69(2-3), 151-572, 1998

• Bassingthwaighte JB, Goresky CA, and Linehan JH (Editors). Whole organ approaches to cellular metabolism. Capillary permeation, cellular uptake and product formation. New York: Springer Verlag, 1998.

• Bassingthwaighte JB, Li Z, and Qian H. Blood Flows and Metabolic Components of the Cardiome. Prog Biophys Mol Biol 69:445-461, 1998.

• Bassingthwaighte JB. Toward modeling the human physionome. In: Molecular and Subcellular Cardiology: Effects on Structure and Function. Sideman S, and Beyar R (Editors). New York: Adv Exp Med Biol Vol 382, Plenum Press, 1995.

• Boyd CAR and Noble D (Editors). The Logic of Life: The Challenge of Integrative Physiology. New York: Oxford University Press, 1993.

• Bassingthwaighte JB. Fractal vascular growth patterns. Acta Stereol. 11 (Suppl. 1): 305-319, 1992.

• Glass L, Hunter P, and McCulloch A. Theory of Heart: Biomechanics, Biophysics, and Nonlinear Dynamics of Cardiac Function. New York: Springer-Verlag, 1991.

• Glass L and Hunter P. There is a theory of heart. Physica D 43: 1-16, 1990.

• Bassingthwaighte JB, Noodleman L, Eakin RT, and King RB. Integrated phenomenology of transport, permeation, and metabolic reactions in the heart. In: Activation, Metabolism and Perfusion of the Heart. Simulation and Experimental Models.  Sideman S and Beyar R (Editors). Dordrecht: Martinus Nijhoff, 1987.

News Publications

• The doctor will see your prototype now. Wired, February 13, 2005.
• Anonymous. The heart of the matter. The Economist Technology Quarterly, December 8, 2001, p. 21-23.

Reports

• White RJ, Bassingthwaighte JB, Charles JB, Kushmerick MJ, and Newman DJ. Issues of exploration: Human health and well being during a mission to Mars. COSPAR, 2000.

• Higgins G, Athey B, Bassingthwaighte JB, Burgess J, Champion H, Cleary K, Dev P, Duncan J, Hopmeier M, Jenkins D, Johnson C, Kelly H, Leitch R, Lorensen W, Metaxas D, Spitzer V, Vaidehi N, Vosburgh K, and Winslow R. Modeling and simulation in medicine: Toward an integrated framework. July 20-21, 2000, National Library of Medicine, National Institutes of Health, Bethesda, Maryland. Comput Aided Surg 6: 32-39, 2001.

• Bassingthwaighte JB. Developing efficiency in characterizing drug and substrate reaction schemes. In: Advances in the use of computer simulation and in vitro techniques reducing the use of whole animals in testing: IBC USA Conferences Inc, 1991, p. 1-10.

• Bassingthwaighte JB, Friesner R, Honig B, Starmer CF, and Marmarelis VZ. Modeling and Simulation. Bethesda MD: NIH/NCRR Workshop on Technologies for the Future: Biomedical Computing for Visualization, Modeling and Decision Support, April 12-13, 1991, p. 1-15.