Systems Biology References
From SystemsWiki
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.
 Beuter, A., L. Glass, M.C. Mackey, M.S. Titcombe (ed.s), 2003, Nonlinear Dynamics in Physiology and Medicine (Interdisciplinary Applied Mathematics, V.25). Springer Verlag.
 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.
 Carson, Ewart R. and C. Cobelli, 2000, Modeling Methodology for Physiology and Medicine (Academic Press Biomedical Engineering Series),Academic Press.
 Carson, Ewart R. and Derek G. Cramp (eds), 1985, Computers and Control in Clinical Medicine,Springer.
 Charlesworth, B., 1994, Evolution of AgeStructured Populations, Cambridge Studies in Mathematical Biology.
 Finkelstein, Ludwik and Ewart R. Carson, 1985, Mathematical Modeling of Dynamic Biological Systems,Research Studies Press.
 Ford, A., 1999, Modeling the Environment: An Introduction to System Dynamics Modeling of Environmental Systems, Island Press, Washington.
 Grossman, Stanley I. and James E. Turner, 1974,Mathematics for the Biological Sciences,Macmillan Publishing Co.
 Guyton, A.C. and J.E. Hall., 2000, Textbook of Medical Physiology, Philadelphia: W.B. Saunders Company.
 Hannon, B. and M. Ruth, 1997, Modeling Dynamic Biological Systems, ISBN 0387948503 Springer.
 Hargrove, J.L., 1998, Dynamic Modeling in the Health Sciences (Modeling Dynamic Systems), Springer Verlag.
 Iyengar, S. Sitharama (eds.), 1992, Structuring Biological Systems: A Computer Modeling Approach,CRC Press.
 Keener, J., J. Sneyd, 1998, Mathematical Physiology, SpringerVerlag.
 Khoo, M.C.K., 1999, Physiological Control Systems: Analysis, Simulation, and Estimation. WileyIEEE Computer Society Pr.
 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.
 Kreyszig, E., 2005, Advanced Engineering Mathematics, Wiley.
 Marmarelis, Vasilis Z., 2004, Nonlinear Dynamic Modeling of Physiological Systems, WileyIEEE Press.
 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
 AbdelHamid, Tarek K., 2002, "Modeling the Dynamics of Human Energy Regulation and its Implications for Obesity Treatment", Syst. Dyn. Rev., Vol: 18, pp. 431471.
 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.
 Carson, Ewart R., 1998, "Decision support systems in diabetes: a systems perspective", Computer Methods and Programs in Biomedicine Vol:56, pp. 77–91.
 Dangerfield, B. and C. Roberts, 2001, "Modelbased scenarios for the epidemiology of HIV/AIDS: The consequences of highly active antiretroviral therapy,Syst. Dyn. Rev., Vol:17, pp.119150.
 Finkelstein, A. et al., 2004,"Computational Challenges of Systems Biology", IEEE Computer, Vol: 37, No:5, pp. 2633.
 Gallaher, E. J., 1996, "Biological system dynamics: from personal discovery to universal application", Simulation, Vol: 66, pp. 243257.
 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.
 Heydrich, J.G., 1999, "Using ‘off the shelf’, computer programs to mine additional insights from published data: diurnal variation in potency of ACTH stimulation of cortisol secretion revealed", Computer Methods and Programs in Biomedicine, Vol: 58, pp. 227–238.
 Homer, J.et. al, 2000, "Toward a Dynamic Theory of Antibiotic Resistance", Syst. Dyn. Rev. 16, 287–319.
 Kofráneka, J., 2001, "GOLEM  Multimedia Simulator for Medical Education", MEDINFO, Vol: 10, pp.10426.
 Kofráneka, J., S. Svacina, 2000, "From obesity to diabetes  a multimedia simulation guide", Diabetes Research and Clinical Practice, Vol:50, Suppl:1, pp.245.
Renal and Circulatory Physiology
Models
 Bigelow, J.H, J.C. DeHaven and M.L. Shapley, 1973, “Systems Analysis of the Renal Function”, Journal of Theoretical Biology, Vol: 41, pp. 287322.
 Cameron, W. H., 1977, "A Model Framework for Computer Simulation of Overall Renal Function", Journal of Theoretical Biology, Vol: 66, pp. 551572.
 Coleman, T.G. and J. E. Hall, 1992, "A Mathematical Model of Renal Hemodynamics and Excretory Function", in Structuring Biological Systems A Computer Modeling Approach, edited by S. Sitharama Iyengar, CRC Press.
 DeHaven J.C., N.Z. Shapiro, 1967, "On the control of urine formation", Nephron, Vol: 4:Suppl 4, pp. 163.
 Dehaven, J. C. and N. Z. Shapiro, "Simulation of the renal effects of antidiuretic hormone (ADH) in man", Journal of Theoretical Biology, Vol: 28, pp. 261286.
 Flood, R. L, 1985, Quantitative Modelling of the FluidElectrolyte, AcidBase Balance for Clinical Application, Ph. D. Thesis , The City University, Department of Systems Science.
 Goldstein, L.J. and E.B. Rypins, 1992, "A Computer Model of the Kidney", Computer Methods and Programs in Biomedicine.
 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.
 Guyton, A. C., T. G. Coleman, and H. J. Granger, 1972, "Circulation: overall regulation", Annu. Rev. Physiol.,Vol: 34, pp. 1346.
 Gyenge, C.C., B.D. Bowen, R.K. Reed, J.L. Bert, 2003, "Mathematical model of renal elimination of fluid and small ions during hyper and hypovolemic conditions", Acta Anaesthesiol. Scand. Vol: pp. 12237.
 Ikeda N., Marumo F., Shirataka M., Sato T.,1979, "A model of overall regulation of body fluids", Annals of Biomedical Engineering, Vol: 7, pp. 13566.
 Karaaslan, F., 2004, Modeling and Analysis of the Interaction Between Renal Symphathetic Nerve Activity, Arterial Pressure and Sodium Excretion, PhD Thesis, Bogazici University.
 Karanfil, Ö., 2005, A Dynamic Simulator for the Management of Disorders of the Body water Metabolism, MSc. 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. 10421046.
 Koushanpour, E. and Gordon K. Stipp, 1982, "Mathematical simulation of the body fluid regulating system in dog", Journal of Theoretical Biology, Vol:99, pp.203235.
 Leaning M.S., R.L. Flood, D.G. Cramp, E.R. Carson, 1985, “A System of Models for FluidElectrolyte Dynamics”, IEEE Trans Biomed Eng., Vol: 32, No: 10, pp. 856864.
 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. 10451069.
 Sagawa, K., 1975, "Critique of a largescale 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.7187.
 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.579588.
 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. 525536.
Other Studies
 Bagby, S.P. and W. M. Bennett, 1998, “Differentiating Disorders of ECF Volume/ Na Content Regulation versus Disorders of Total Body Fluid Osmolarity/ Water Regulation”, Advances in Physiology Education, Vol. 20, No: 1, pp. 169184.
 Granger, Joey P., 1998, "Regulation of Extracellular Fluid Volume by Integrated Control of Sodium Excretion", Adv. Physiol. Educ., Vol: 275, pp. 157168.
 Guyton, A. C., T.G. Coleman, D.B. Young, T.E.Lohmeier, and J. W. DeClue, 1980, "Salt Balance and LongTerm Blood Pressure Control", Ann. Rev. Med., Vol: 31, pp. 1527.
 AC Guyton, 1987, "Renal function curvea key to understanding the pathogenesis of hypertension", Hypertension, Vol: 10, pp.16.
 Halperin, M.L and D. Bohn, 2002, “Clinical Approach to Disorders of Salt and Water Balance; Emphasis on Integrative Physiology”, Critical Care Clinics, Vol: 18, No: 2, pp. 249272.
 Halperin M.L., 2002, “Body Compartment Volumes and Composition After Giving a Vasopressin Antagonist”, Nephrol. Dial. Transplant, Vol: 17, No: 2, pp. 300303.
 Verbalis, J.G., 1992, “Pathogenesis of Hyponatremia in an Experimental Model of the Syndrome of Inappropriate Antidiuresis”, American Journal of Physiology, Vol: 267, pp. 16171625.
 Verbalis, J.G., 2003, “Disorders of Body Water Homeostasis”, Best Practice & Research Clinical Endocrinology & Metabolism, Vol. 17, No. 4, pp. 471–503.
 Weir, M.R., V.J. Dzau, 1999, “The ReninAngiotensinAldosterone System: a Specific Target for Hypertension Management”, American Journal of Hypertension, Vol: 12, pp. 205213.
 Wong, L.L. and J.G. Verbalis, 2002, “Systemic Diseases Associated with Disorders of Water Homeostasis”, Endocrinology and Metabolism Clinics of North America, Vol: 31, No: 1, pp. 121140.
Endocrine Physiology
Models
 GonzalezHeydrich J., Steingard R.J., and Kohane I.,"Hypothalamicpituitaryadrenal Axis Modeling".
 Katzper, M., "Adrenal Dynamics and Corticosteroids", Proceedings of the 2003 International Symposium on Health Sciences Simulation, pp.9396.
 Otero, Jay Michael and Hans B. Sieburg, "Emergent Patterns of HPA Hormone Pulsatility and Diurnal Variability in silico".
 Stear, Edwin B., 1975, "Application of control theory to endocrine regulation and control", Journal Annals of Biomedical Engineering, Vol: 3, pp. 439455.
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. 439445.
Immunology
Models
 Bernard, S., L. PujoMenjouet and M. C. Mackey, 2003, “Analysis of Cell Kinetics Using a Cell Division Marker: Mathetical Modeling of Experimental Data”, Biophysical Journal, Vol: 84, pp. 34143424.
 Bonhoeffer, S., H. Mohri, D. Ho and A. Perelson, 2000, “Quantification of cell turnover kinetics using 5Bromo2deoxyyuridine”, The Journal of Immunology, Vol: 164, pp. 50495054.
 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. 101131.
 DeBoer, R.J., A.A. Freitas and A. Perelson, “Resource Competition Determines Selection of B Cell Repertoires”, Journal of Theoretical Biology, Vol: 212, pp. 333343.
 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. 26292640
 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. 455476.
 Macallan et al., 2003, Measurement and modeling of human T cell kinetics”, European Journal of Immunology, Vol: 33, pp. 23162326.
 Mackey, M. C., 2000, “Cell kinetic status of haemotopoietic stem cells”, Cell Proliferation, Vol: 34, pp 7183.
 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. 2734.
 Mackey, M. C. and P. Dörmer, 1982, “Continuous maturation of proliferating erythroid precursors”, Cell Tissue Kinetics, Vol: 15, pp. 381392.
 Mackey, M. C. and P. Dörmer, 1981, “Enigmatic Hemapoiesis”, Biomathematics and Cell Kinetics, pp. 87103.
 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. 57925797.
 Mehr, R., A. Perelson, M. FridkisHareli and A. Globerson, 1996, “Feedback regulation of T cell development in the thymus”, Journal of Theoretical Biology, Vol: 181, pp. 157167.
 Mehr, R., A. Perelson, M. FridkisHareli and A. Globerson, 1997, “Regulatory feedback pathways in the thymus”, Immunology Today, Vol: 18, pp. 581585.
 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. 103126.
 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. 159172.
 Mehr, R., G. Shahaf, A. Sah and M Cancro, 2003, “Asynchronus differentiation models explain BM labeling kinetics and predict reflux btw the preand immature B cell pools”, International Immunology, Vol: 15, pp. 301312.
 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. 187225.
 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. 10811090.
 Srivastava, B., R. C. Lindsley, N. Nikbakht and D. Allman, “Models for peripheral B cell development and homeostasis”, Seminars in Immunology, Vol: 17, pp. 175182.
Other Studies
 Novak, J.P. and E. Necas, 1994, “Proliferationdifferentiation pathways of murine haemopoiesis: correlation of lineage fluxes”, Cell Prolif., Vol: 27, pp. 597633
 Tanchot, C. and B. Rocha, 1998, “The organization of mature Tcell pools”, Immunology Today, Vol: 19, pp. 575579.
 Tanchot, C., M. M. Rosado, F. Agenes, A. A. Freitas and B. Rocha, 1997, “Lymphocyte homeostasis”, Seminars in Immunology, Vol: 9, pp. 331337.
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 SmallCell Lung Cancer", ISDC, 2006.
 Hirsch, G.B., "A Generic Model of Contagious Disease and Its Application to HumantoHuman 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.
 Katzper, M., "Baroreceptor Dynamics", Health Sciences Conference, 2004.
 Karanfil, Ö., "A Dynamic Simulator for the Management of Disorders of the Body Water Metabolism", 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 communitybased HIVprevention 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.
Useful Links
 WHO  World Health Organization
 NSR Physiome Project
 Physiome Project Websites
 PhysioNet Simulation and Computation
 Medical Informatics Sites in US
 The Games for Health Project
 MITACS Project Website
 Medical Encyclopedia
 Medical Dictionaries
 Centers for Disease Control and Prevention
 National Center for Health Statistics
 Frequently Accessed Databases
 Link to Canadian and American universities
 Book Sources
Physiology Resources
 Anatomy
 Essentials of Human Physiology]
Software
Opening Models
Models listed here can be opened by downloading and installing the appropriate player/viewer or demo version.
 Anylogic (*.ALP) Healthcare Demonstrations
 iThink (*.ITM) iSee Player,iThink or Stella Trial
 Powersim Studio (*.SIP and *.SIM) Trial or Player (Player will only view models developed in * Powersim Studio Enterprise)
 Vensim (*.MDL) Vensim PLE
Miscellaneous
 Powers of 10
 People who think about biodiversity
 Debunking third world myths about global health using statistics
 The inner life of the cell: probably a white blood cell:)
 System Dynamics Modeling: Population Flows, Feedback Loops and Health NIH, given by Jack Homer and George Richardson
 Diane Finegood Challenges of Obesity
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.
 B.P. Tu et al., "Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes," Science,310:11528 ,Nov. 18, 2005. This paper examines oscillation in metabolic and cellcycle processes.
 O. Brandman et al., "Interlinked fast and slow positive feedback loops drive reliable cell decisions," Science, 310:4968, Oct. 21, 2005. This paper explores positive feedback loops in various cell types and (it appears) loop dominance.
 Nature Reviews on Molecular Cell Biology March 2006 Web focus on Modelling Cellular Systems http://www.nature.com/nrm/focus/modelling/index.html for a review (accessed March 1.2006)
 Systems Biology Research Group UCSD
 Biomodels Database
 Systems Biology Markup Language
 CellDesigner Software
 MIRIAM Bringing quality control to systems biology modeling (Accessed March 4.2006)
Acknowledgement
 These references were initially collected by Ozge Karanfil for the HPSIG
