1. Welcome to the NSR Physiome Project!
  2. Refereed research and JSim related publications

Refereed research and JSim related publications

Recent:

  • Christmas KM and Bassingthwaighte JB. Equations for O2 and CO2 solubilities in saline and plasma: Combining temperature and density dependences. J Appl Physiol Vol:122, no. 5, 1313-1320 DOI: 10.1152/japplphysiol.01124.2016 2017.
  • Jardine B, Raymond GM, and Bassingthwaighte JB. Semi-automated modular program constructor for physiological modeling: Building Cell and organ models. F1000 Research 4: 1461 (doi: 10.12688/f1000research.7476.3) 12pp., 2016.
  • van Beek JHGM, Kirkwood TBL, and Bassingthwaighte JB. Understanding the physiology of the ageing individual: computational modeling of changes in metabolism and endurance. Interface Focus 6: 20150079,1-17 (2016).
  • Yipintsoi T, Kroll K, and Bassingthwaighte JB. Fractal regional myocardial blood flows pattern according to metabolism, not vascular anatomy. Am J Physiol Heart Circ Physiol 310: 351-364, DOI: 10.1152/ajpheart.00632.2015. 2016
  • Dash, R.K., Korman, B. & Bassingthwaighte, J.B. Simple accurate mathematical models of blood HbO2 and HbCO2 dissociation curves at varied physiological conditions: evaluation and comparison with other models. Eur J Appl Physiol (2016) 116: 97. doi:10.1007/s00421-015-3228-3
  • Arts T, Reneman RS, Bassingthwaighte JB, van der Vusse GJ (2015) Modeling Fatty Acid Transfer from Artery to Cardiomyocyte. PLoS Comput Biol 11(12): e1004666. doi:10.1371/journal.pcbi.1004666
  • Raymond,GM, Bassingthwaighte JB, Diverse data sets can yield reliable information through mechanistic modeling: salicylic acid clearance, Brit J. Pharmacol. Res.(2015),7(6): 457-473, DOI: 10.9734/BJPR/2015/19156
  • Vicini, Paolo, Bassingthwaighte, James B., Blood-tissue exchange modeling. Chapter 17, Modelling Methodology for Physiology and Medicine, 2nd Ed., ed: Carson E, Cobelli C, Elsevier, London, 2014,382-415, DOI: http://dx.doi.org/10.1016/B978-0-12-411557-6.00017-3
  • Butterworth E, Jardine BE, Raymond GM, Neal ML, Bassingthwaighte JB (2013) JSim, an open-source modeling system for data analysis [v3; ref status: indexed],. F1000Research 2: 288 (19pp) (doi: 10.12688/f1000research.2-288.v3), 2014
  • Smith L, Butterworth E, Bassingthwaighte JBB, Sauro H, SBML and CellML Translation in Antimony and JSim, Bioinformatics (2013) doi: 10.1093/bioinformatics/btt641, First published online: November 8, 2013
  • Jardine B, Bassingthwaighte JB, Modeling serotonin uptake in the lung shows endothelial tranporters dominate over cleft permeation, Am J Physiol Lung Cell Mol Physiol 305: L42-L55, 2013, PMID:23645496


Previous:

  • Bassingthwaighte JB and Chinn TM. Re-examining Michaelis-Menten enzyme kinetics for xanthine oxidase. Adv Physiol Educ, 37: 37-48, 2013.
  • Bassingthwaighte JB, Butterworth E, Jardine B, and Raymond G. Compartmental modeling in the analysis of biological systems. In: Computational Toxicology (Methods in Molecular Biology Series), edited by Brad Reisfeld and Arthur N Mayeno. New York NY: Springer Science+Business Media LLC, 2012, Vol. 929, pp 391-438.
  • Bassingthwaighte JB, Beard DA, Carlson BE, Dash RK, and Vinnakota K. Modeling to link regional myocardial work, metabolism and blood flows. Ann Biomed Eng. 2012 Nov;40(11):2379-98. doi: 10.1007/s10439-012-0613-5. PMCID: PMC3471663
  • Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE. Multi-scale modeling and data integration in the Virtual Physiological Rat Project. Ann Biomed Eng. 2012 Nov;40(11):2365-78. doi: 10.1007/s10439-012-0611-7, PMCID: PMC3463790
  • Alessio AM, Butterworth E, Caldwell JH, and Bassingthwaighte JB. Quantitative imaging of coronary blood flow. Nano Reviews 1: 5110 - DOI: 10.3402/nano.v1i0 .5110: 1-13, PMC3215216, 2010
  • Bassingthwaighte JB, Raymond GM, Butterworth E, Alessio A, and Caldwell JH Multiscale modeling of metabolism, flows, and exchanges in heterogeneous organs. edited by Beyar R and Landesberg A. New York: Analysis of Cardiac Development from Embryo to Old Age. Ann. New York Acad Sci 1188: pp 111- 120. DOI: 10.1111/j.1749-6632.2009.05090.x PMC2849657, 2010
  • Bassingthwaighte JB. Predictive Modeling and Integrative Physiology: The Physiome Projects. TOPETJ (The Open Pacing, Electrophysiology, and Therapy Journal) 3: 66-74, DOI: 10.2174/1876536X01003010066, 2010
  • Dash RK and Bassingthwaighte JB. Erratum to: Blood HbO2 and HbCO2 dissociation curves at varied O2, CO2, pH, 2,3-DPG and Temperature Levels. Ann Biomed Eng 38(4): 1683-1701, DOI: 10.1007/s10439-010-9948-y PMC2862600, 2010
  • Bassingthwaighte James B., Noble Denis, Hunter Peter J., The Cardiac Physiome: perspectives for the future, Experimental Physiology , 94.5, (597-605}, 2009
  • Chizeck Howard Jay, Butterworth Erik, Bassingthwaighte James B., Error detection and unit conversion. Automated unit balancing in modeling interface systems, IEEE Eng Med Biol, 28(3), (50-58}, 2009
  • Bassingthwaighte J. B., Linking cellular energetics to local flow regulation in the heart, Control and Regulation of Transport Phenomena in the Cardiac System., Ed: Sideman, S.; Beyar, R.; Landesberg, A., , (126-133}, 2008
  • Carlson Brian E., Anderson Joseph C., Raymond Gary R., Dash Ranjan K., Bassingthwaighte J. B., Modeling oxygen and carbon dioxide transport and exchange using a closed loop circulatory system, Oxygen Transport to Tissue XXIX, Ed: Kang, K. A.;Harrison, D. K.;Bruley, D. F., Springer, (353-360}, 2008
  • Bassingthwaighte James B., Microcirculation and the Physiome Projects, Microcirculation, 15, (835-839}, 2008
  • Bassingthwaighte James B., Chizeck Howard J., The Physiome Projects and multiscale modeling, IEEE Signal Processing, 25(2), (121-123,144}, 2008
  • Kerckhoffs Roy C. P., Neal Maxwell L., Gu Quan, Bassingthwaighte James B., Omens Jeff H., McCulloch Andrew D., Coupling of a 3D finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonary circulation, Ann. Biomed. Eng., 35, (1-18}, 2007
  • Smith Nicolas A., Crampin Edmund J., Niederer Steven A., Bassingthwaighte James B., Beard Daniel A., Computational biology of the cardiac myocyte: proposed standards for the physiome, J Exper Biol, 210, (1576-1583}, 2007
  • Neal Maxwell L., Bassingthwaighte J. B., Subject-specific model estimation of cardiac output and blood volume during hemorrhage, Cardiovascular Eng., 7, (97-120}, 2007
  • Anderson Joseph Clark, Bassingthwaighte James B., Tracers in physiological systems modeling, Mathematical Modeling in Nutrition and Agriculture. Proc 9th Internat Conf, Ed: Mark D. Hanigan, Janet Novotny, and Casey L. Marsteller, Virginia Polytechnic Institute and State University Blacksburg, VA, (125-159}, 2007
  • Proceedings of IEEE: The Physiome and Beyond. Eds.: Dr. James B. Bassingthwaighte, University of Washington, Seattle, WA, USA, Dr. Jean-Louis Coatrieux, Université de Rennes, Rennes, France, 94, 2006.
  • Hunter P, Smith N, Fernandez J and Tawhai M. Integration from proteins to organs: the IUPS Physiome Project. Mech Ageing Dev 126: 187-192, 2005.
  • Crampin EJ, Halstead M, Hunter P, Nielson P, Noble D, Smith N, and Tawhai M. Computational physiology and the physiome project. Exp Physiol 89: 1-26, 2004.
  • Bassingthwaighte JB. The macro-ethics of genomics to health: The Physiome Project. Comptes  Rendus de l'Academie francaise, 326: 1105-1110, 2003.
  • Bassingthwaighte JB. The modeling of a primative "sustainable" conservative cell. Phil Trans Roy Soc Lond A 359: 1055-1072, 2001.
    Bassingthwaighte JB.  Strategies for the Physiome Project. Ann Biomed Eng 28:1043-1058, 2000.
  • Bassingthwaighte JB, 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.
  • 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.
  • McCulloch A, Bassingthwaighte JB, Hunter P, and Noble D. Editorial: Computational biology of the heart: from structure to function. Prog Biophys Mol Biol 69:153-155, 1998.
  • McCulloch A, Bassingthwaighte JB, Hunter P, and Noble D. Computational Biology of the Heart: From Structure to Function Progress in Biophysics and Molecular Biology Volume 69, 151-572: Elsevier/Pergamon, 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.

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.
    PDF62.38 KB
  • 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.

Model development and archiving support at https://www.imagwiki.nibib.nih.gov/physiome provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.