Systems Biology References

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Contents

Books

  • Akay, M. and A. Marsh (ed.s), 2001, Information Technologies in Medicine, Volume 1, Medical Simulation and Education, Wiley- IEEE Computer Society PR.
  • Brown, J.H.U. and D. S. Gann, (ed.s), 1973, Engineering Principles in Physiology, Academic Press, New York and London.
  • Cannon, W.B., 1932, The Wisdom of the Body, W. W. Norton, New York.
  • Carson, E.R., C. Cobelli and L. Finkelstein, 1983, The Mathematical Modeling of Metabolic and Endocrine Systems: Model Formulation, Identification, and Validation, New York: Wiley.
  • Guyton, A.C. and J.E. Hall., 2000, Textbook of Medical Physiology, Philadelphia: W.B. Saunders Company.
  • Hargrove, J.L., 1998, Dynamic Modeling in the Health Sciences (Modeling Dynamic Systems), Springer Verlag.
  • Kimko, Hui C., Stephen B. Duffull, K. Kimko, 2003, Simulation for Designing Clinical Trials, Marcel Dekker Inc.
  • Koeppen, B., B. Stanton, 2001, Renal Physiology, The Mosby Physiology Monograph Series.
  • Mitchison, J. M., The Biology of the Cell Cycle, 1971, Cambridge University Press.
  • Northrop, R. B., 2000, Endogenous and exogenous regulation and control of physiological systems, Chapman & Hall / CRC Press.
  • Pollard, J. H., 1973, Mathematical models for the growth of human populations, Cambridge University Press.
  • Reeve, E.B, and A.C. Guyton (eds.), 1967, Physical Bases of Circulatory Transport: Regulation and Exchange,Philadelphia: W.B. Saunders Company.
  • Rideout, V.C, 1991, Mathematical and Computer Modeling of Physiological Systems, Englewood Cliffs, N.J.: Prentice Hall.
  • Riggs, D.S, 1970, Control Theory and Physiological Feedback Mechanisms, Baltimore: Williams and Wilkins.
  • Strogatz, Steven H., 2001, Nonlinear Dynamics and Chaos, Westview Press.

Journal Articles

  • Bush, James W., Allan M. Schneider, L. Wachtel, John E. Brimm, "Fluid therapy in acute large area burns: a system dynamics model", Syst. Dyn. Rev., Vol: 1. Nr.1.
  • Gallaher, E. J., 1996, "Biological system dynamics: from personal discovery to universal application", Simulation, Vol: 66, pp. 243-257.
  • Hansen, Jan E. and Peter Bie, 1987, "Distribution of body fluids, plasma protein, and sodium in dogs: a system dynamics model", Syst. Dyn. Rev., Vol: 3. Nr.2.


Renal and Circulatory Physiology

Models

  • Flood, R. L, 1985, Quantitative Modelling of the Fluid-Electrolyte, Acid-Base Balance for Clinical Application, Ph. D. Thesis , The City University, Department of Systems Science.
  • Guyton, A.C., T.G. Coleman, 1967, “Long Term Regulation of the Circulation: Interrelationships with Body Fluid Volumes”. In: Physical Bases of Circulatory Transport: Regulation and Exchange, edited by E.B. Reeve, and A.C. Guyton. Philadelphia: W.B. Saunders Company.
  • Karaaslan, F., 2004, Modeling and Analysis of the Interaction Between Renal Symphathetic Nerve Activity, Arterial Pressure and Sodium Excretion, PhD Thesis, Bogazici University.
  • Kofranek, J., L.D.Vu, H. Snaselova, R. Kerekes, T. Velan, 2001, “GOLEM—multimedia simulator for medical education”, Medinfo, Vol. 10, No: 2, pp. 1042-1046.
  • Reeve, E.B. and L. Kulhanek, 1967, "Regulation of Body Water Content: A Preliminary Analysis", in: Physical Bases of Circulatory Transport: Regulation and Exchange, edited by E.B. Reeve, and A.C. Guyton. Philadelphia: W.B. Saunders Company.
  • Roman, R. J. and F. R. Sias, 1985, “Network Computer Analysis of the Human Kidney”, Mathematical Modelling, Vol: 7, pp. 1045-1069.
  • Sagawa, K., 1975, "Critique of a large-scale organ system model: the Guytonian cardiovascular model", Annals of Biomedical Engineering.
  • Toates, F.M. and K. Oatley, 1970, “Computer Simulation of Thirst and Water Balance”, Medical and Biological Engineering, Vol: 8, pp.71-87.
  • Toates, F.M. and K. Qatley, 1977, “Control of Water Excretion by Antidiuretic Hormone: Some Aspects of Modelling the System”, Medical and Biological Engineering and Computing, Vol: 15, No: 6, pp.579-588.
  • Uttamsingh, R. J., 1981, A Systems Approach to Renal Dialysis, PhD. Thesis, The City University, Department of Systems Science.
  • Uttamsingh, R. J., M.S. Leaning, J.A. Bushman, E.R. Carson and L. Finkelstein, 1985, “Mathematical Model of the Human Renal System”, Medical and Biological Engineering and Computing, Vol: 23, pp. 525-536.

Other Studies


Endocrine Physiology

Models

  • Katzper, M., "Adrenal Dynamics and Corticosteroids", Proceedings of the 2003 International Symposium on Health Sciences Simulation, pp.93-96.

Other Studies

  • Northrop, R.B., 2000, "Hormonal Regulation of Sodium, Potassium, Calcium and Magnesium Ions", in: Endogeneous and Exogeneous Regulation and Control of Physiological Systems, Boca Raton, Fla.: Chapman & Hall/CRC, c2000.
  • Sturis, J., Van Cauter E., Blackman J.D., Polonsky K.S., 1991 "Entrainment of pulsatile insulin secretion by oscillatory glucose infusion", J. Clin. Invest., Vol: 87, pp. 439-445.

Immunology

Models

  • Bernard, S., L. Pujo-Menjouet and M. C. Mackey, 2003, “Analysis of Cell Kinetics Using a Cell Division Marker: Mathetical Modeling of Experimental Data”, Biophysical Journal, Vol: 84, pp. 3414-3424.
  • Bonhoeffer, S., H. Mohri, D. Ho and A. Perelson, 2000, “Quantification of cell turnover kinetics using 5-Bromo-2-deoxyyuridine”, The Journal of Immunology, Vol: 164, pp. 5049-5054.
  • DeBoer, R. J., V. V. Ganusov, D. Milutinovic, P. D. Hodgkin and A. Perelson, 2006, “Estimating lymphocyte division and death rates from CFSE data”, Bulletin of Mathematical Biology, Vol: 68, pp. 1011-31.
  • DeBoer, R.J., A.A. Freitas and A. Perelson, “Resource Competition Determines Selection of B Cell Repertoires”, Journal of Theoretical Biology, Vol: 212, pp. 333-343.
  • Haurie, C., D. C. Dale and M. C. Mackey, 1998, “Cyclical Neutropenia and Other Periodic Hematological Disorders: A Review of Mechanisms & Math. Models”, Blood, Vol: 92, pp. 2629-2640
  • Kalet Leon et al, 2004, “A general mathematical framework to model generation structure in a population of asynchronously dividing cells”, Journal of Theoretical Biology, Vol: 229, pp. 455-476.
  • Macallan et al., 2003, Measurement and modeling of human T cell kinetics”, European Journal of Immunology, Vol: 33, pp. 2316-2326.
  • Mackey, M. C., 2000, “Cell kinetic status of haemotopoietic stem cells”, Cell Proliferation, Vol: 34, pp 71-83.
  • Mackey, M.C., A.A. Aprikyan and D.C. Dale, 2003, “The rate of apoptosis in post mitotic neutrophil precursors of normal and neutropenic humans”, Cell Proliferation, Vol: 36, pp. 27-34.
  • Mackey, M. C. and P. Dörmer, 1982, “Continuous maturation of proliferating erythroid precursors”, Cell Tissue Kinetics, Vol: 15, pp. 381-392.
  • Mackey, M. C. and P. Dörmer, 1981, “Enigmatic Hemapoiesis”, Biomathematics and Cell Kinetics, pp. 87-103.
  • McLean, A.R., M.M. Rosado, F. Agenes, R. Vasconcellos and A. A. Freitas, “Resource competition as a mechanism for B cell homeostasis”, Immunology, Vol: 94, pp. 5792-5797.
  • Mehr, R., A. Perelson, M. Fridkis-Hareli and A. Globerson, 1996, “Feedback regulation of T cell development in the thymus”, Journal of Theoretical Biology, Vol: 181, pp. 157-167.
  • Mehr, R., A. Perelson, M. Fridkis-Hareli and A. Globerson, 1997, “Regulatory feedback pathways in the thymus”, Immunology Today, Vol: 18, pp. 581-585.
  • Mehr, R., A. Globerson and A. Perelson, 1995, “Modeling Positive and Negative Selection and Differentiation Processes in the Thymus”, Journal of Theoretical Biology, Vol: 175, pp. 103-126.
  • Mehr, M., L. Abel, P. Ubezio, A. Globerson and Z. Agur, 1993, “A mathematical model of the effect of aging on bone marrow cells colonizing the thymus”, Mechanisms of Ageing and Development, Vol: 67, pp. 159-172.
  • Mehr, R., G. Shahaf, A. Sah and M Cancro, 2003, “Asynchronus differentiation models explain BM labeling kinetics and predict reflux btw the pre-and immature B cell pools”, International Immunology, Vol: 15, pp. 301-312.
  • Rubinow, S. I. and J. L. Lebowitz, 1975, “A mathematical model of neutrophil production and control in normal man”, Journal of Mathematical Biology, Vol: 1, pp. 187-225.
  • Shahaf, G. D. Allman, M. P. Cancro and R. Mehr, 2004, “Screening of alternative models for transitional B cell maturation”, International Immunology, Vol: 16, pp. 1081-1090.
  • Srivastava, B., R. C. Lindsley, N. Nikbakht and D. Allman, “Models for peripheral B cell development and homeostasis”, Seminars in Immunology, Vol: 17, pp. 175-182.

Other Studies

  • Novak, J.P. and E. Necas, 1994, “Proliferation-differentiation pathways of murine haemopoiesis: correlation of lineage fluxes”, Cell Prolif., Vol: 27, pp. 597-633
  • Tanchot, C. and B. Rocha, 1998, “The organization of mature T-cell pools”, Immunology Today, Vol: 19, pp. 575-579.
  • Tanchot, C., M. M. Rosado, F. Agenes, A. A. Freitas and B. Rocha, 1997, “Lymphocyte homeostasis”, Seminars in Immunology, Vol: 9, pp. 331-337.

Conference Papers

  • Asami, K. and T. Kitamura, "A Diagnostic Support System for a Circulatory Model based on Structural Modeling and Path Tracking", Proc. of the 2001 IEEE Systems, Man, and Cybernetics Conference.
  • Fisher, Diana M. et al., "How Drugs Work in the Human Body, Analysis of a Modeling Unit Used in a Second Year Algebra Class", ISDC, 2002?
  • George, A. and R. Taylor, "A Systems Theory of Small-Cell Lung Cancer", ISDC, 2006.
  • Hirsch, G.B., "A Generic Model of Contagious Disease and Its Application to Human-to-Human Transmission of Avian Influenza", ISDC, 2006.
  • Homer, J. et. al., "The CDC's Diabetes Systems Modeling Project: Developing a New Tool for Chronic Disease Prevention and Control", ISDC, 2004.
  • Homer, J. and B. Milstein et. al., "Obesity Population Dynamics: Exploring Historical Growth and Plausible Futures in the U.S.", ISDC, 2006.
  • McDonnell, G. and J. Dewdney, "Exploring the Political and Economic Dynamics of Health Policy", ISDC, 2006.
  • Miller, R.L. et. al., "Recruiting clients to a community-based HIV-prevention program: A dynamic model", ISDC, 2006.
  • Rees, D., "System Dynamics Modelling as a Tool in Healthcare Planning", ISDC, 2006.
  • Toussaint, P. and G. McDonnell, "Modeling the Communications Dimension of Clinical Work and Medication Errors", ISDC, 2006.
  • Azar, A, Mohamed, Abdalla S.A and Wahba, K., Analyzing the Dynamic Implications For Improving Hemodialysis Session Performance By System Dynamics Approach”, ISDC, 2006
  • Wahba, K., F. Ahmed and A. Mohamed, "Modelling the Glucose Regulatory Feedback System -- Understand the Mechanism Underlying Ultradian Oscillations", ISDC, 2006.

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Systems Biology has a large scale research agenda for Modeling Cellular Systems and linking cell component structure and interaction networks to overall component and cellular macroscopic dynamics, involving multilevel models of spatial and temporal scales.

Acknowledgement

  • These references were initially collected by Ozge Karanfil for the HPSIG
Questions & Comments to Geoff McDonnell
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