A methodology for performing global uncertainty and sensitivity analysis in systems biology
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Anderson, 2003
Apostolakis, 1990, The concept of probability in safety assessments of technological systems, Science, 250, 1359, 10.1126/science.2255906
Blower, 1994, Sensitivity and uncertainty analysis of complex-models of disease transmission—an HIV model, as an example, Int. Stat. Rev., 62, 229, 10.2307/1403510
Cacuci, 2004, A comparative review of sensitivity and uncertainty analysis of large-scale systems—II: statistical methods, Nucl. Sci. Eng., 147, 204, 10.13182/04-54CR
Chang, S.T., Linderman, J.J., Kirschner, D.E., 2008. Multiple polymorphisms on antigen presentation and susceptilbity to M. tuberculosis infection. Infect. Immun., doi:10.1128/IAI.01677-07.
Collins, 1994, An evaluation with the Fourier amplitude sensitivity test (FAST) of which land-surface parameters are of greatest importance in atmospheric modeling, J. Climate, 7, 681, 10.1175/1520-0442(1994)007<0681:AEWTFA>2.0.CO;2
Cooke, 1991
Cukier, 1973, Study of sensitivity of coupled reaction systems to uncertainties in rate coefficients 1. Theory, J. Chem. Phys., 59, 3873, 10.1063/1.1680571
Draper, 1995, Assessment and propagation of model uncertainty, J. R. Stat. Soc. B—Methodological, 57, 45
Evans, 1994, Use of probabilistic expert judgment in uncertainty analysis of carcinogenic potency, Regul. Toxicol. Pharmacol., 20, 15, 10.1006/rtph.1994.1034
Helton, 1993, Uncertainty and sensitivity analysis techniques for use in performance assessment for radioactive-waste disposal, Reliab. Eng. Syst. Saf., 42, 327, 10.1016/0951-8320(93)90097-I
Helton, 1997, Uncertainty and sensitivity analysis in the presence of stochastic and subjective uncertainty, J. Stat. Comput. Simulation, 57, 3, 10.1080/00949659708811803
Helton, 1999, Uncertainty and sensitivity analysis in performance assessment for the waste isolation pilot plant, Comput. Phys. Commun., 117, 156, 10.1016/S0010-4655(98)00171-4
Helton, 1993, Calculation of reactor accident safety goals, Reliab. Eng. Syst. Saf., 39, 129, 10.1016/0951-8320(93)90038-Z
Helton, 2002, Illustration of sampling-based methods for uncertainty and sensitivity analysis, Risk Anal., 22, 591, 10.1111/0272-4332.00041
Helton, 2003, Latin hypercube sampling and the propagation of uncertainty in analyses of complex systems, Reliab. Eng. Syst. Saf., 81, 23, 10.1016/S0951-8320(03)00058-9
Helton, 1995, Uncertainty and sensitivity analysis of early exposure results with the Maccs reactor accident consequence model, Reliab. Eng. Syst. Saf., 48, 91, 10.1016/0951-8320(95)00002-J
Helton, 2000, Characterization of subjective uncertainty in the 1996 performance assessment for the waste isolation pilot plant, Reliab. Eng. Syst. Saf., 69, 191, 10.1016/S0951-8320(00)00032-6
Helton, 2006, Survey of sampling-based methods for uncertainty and sensitivity analysis, Reliab. Eng. Syst. Saf., 91, 1175, 10.1016/j.ress.2005.11.017
Helton, 2007, A sampling-based computational strategy for the representation of epistemic uncertainty in model predictions with evidence theory, Comput. Methods Appl. Mech. Eng., 196, 3980, 10.1016/j.cma.2006.10.049
Hoare, 2008, Sampling and sensitivity analyses tools (SaSat) for computational modeling, Theor. Biol. Med. Model., 5, 4, 10.1186/1742-4682-5-4
Hora, 2003, A distribution-free test for the relationship between model input and output when using Latin hypercube sampling, Reliab. Eng. Syst. Saf., 79, 333, 10.1016/S0951-8320(02)00240-5
Hora, 1989, Expert opinion in risk analysis—the Nureg-1150 methodology, Nucl. Sci. Eng., 102, 323, 10.13182/NSE89-A23645
Iman, 1980, Small sample sensitivity analysis techniques for computer-models, with an application to risk assessment, Commun. Stat. A—Theory Methods, 9, 1749, 10.1080/03610928008827996
Iman, 1982, A distribution-free approach to inducing rank correlation among input variables, Commun. Stat. B—Simulation Comput., 11, 311, 10.1080/03610918208812265
Iman, 1987, A measure of top-down correlation, Technometrics, 29, 351
Iman, 1982, Rank correlation plots for use with correlated input variables, Commun. Stat. B—Simulation Comput., 11, 335, 10.1080/03610918208812266
Iman, 1988, An investigation of uncertainty and sensitivity analysis techniques for computer models, Risk Anal., 8, 71, 10.1111/j.1539-6924.1988.tb01155.x
Kirschner, 2007, Toward a multiscale model of antigen presentation in immunity, Immunol. Rev., 216, 93, 10.1111/j.1600-065X.2007.00490.x
Kleijnen, 1999, Statistical analyses of scatterplots to identify important factors in large-scale simulations, 1: review and comparison of techniques, Reliab. Eng. Syst. Saf., 65, 147, 10.1016/S0951-8320(98)00091-X
Lotka, 1925
Marino, 2004, The human immune response to Mycobacterium tuberculosis in lung and lymph node, J. Theor. Biol., 227, 463, 10.1016/j.jtbi.2003.11.023
Marino, 2004, Dendritic cell trafficking and antigen presentation in the human immune response to Mycobacterium tuberculosis, J. Immunol., 173, 494, 10.4049/jimmunol.173.1.494
Marino, 2007, The role of delays in innate and adaptive immunity to intracellular bacteria infection, Math. Biosci. Eng., 4, 261, 10.3934/mbe.2007.4.261
McKay, 2000, Critique of and limitations on the use of expert judgements in accident consequence uncertainty analysis, Radiat. Prot. Dosim., 90, 325, 10.1093/oxfordjournals.rpd.a033155
Mckay, 1979, Comparison of 3 methods for selecting values of input variables in the analysis of output from a computer code, Technometrics, 21, 239
Morris, 1991, Factorial sampling plans for preliminary computational experiments, Technometrics, 33, 161, 10.1080/00401706.1991.10484804
Morris, 2000, Three technometrics experimental design classics, Technometrics, 42, 26
Parry, 1981, Characterization and evaluation of uncertainty in probabilistic risk analysis, Nucl. Saf., 22, 28
Pate’-Cornell, 1996, Uncertainties in risk analysis: six levels of treatment, Reliab. Eng. Syst. Saf., 54, 95, 10.1016/S0951-8320(96)00067-1
Perelson, 1993, Dynamics of HIV infection of CD4+ T cells, Math. Biosci., 114, 81, 10.1016/0025-5564(93)90043-A
Ratto, 2007, State dependent parameter metamodelling and sensitivity analysis, Comput. Phys. Commun., 177, 863, 10.1016/j.cpc.2007.07.011
Riggs, 2008, A comparison of random vs. chemotaxis-driven contacts of T cells with dendritic cells during repertoire scanning, J. Theor. Biol., 250, 732, 10.1016/j.jtbi.2007.10.015
Saltelli, 2002, Making best use of model evaluations to compute sensitivity indices, Comput. Phys. Commun., 145, 280, 10.1016/S0010-4655(02)00280-1
Saltelli, 2004
Saltelli, 1998, An alternative way to compute Fourier amplitude sensitivity test (FAST), Comput. Stat. Data Anal., 26, 445, 10.1016/S0167-9473(97)00043-1
Saltelli, 1990, Nonparametric statistics in sensitivity analysis for model output—a comparison of selected techniques, Reliab. Eng. Syst. Saf., 28, 229, 10.1016/0951-8320(90)90065-U
Saltelli, 1999, A quantitative model-independent method for global sensitivity analysis of model output, Technometrics, 41, 39, 10.1080/00401706.1999.10485594
Saltelli, 2000
Savage, 1956, Contributions to the theory of rank order-statistics—the 2-sample case, Ann. Math. Stat., 27, 590, 10.1214/aoms/1177728170
Schaibly, 1973, Study of sensitivity of coupled reaction systems to uncertainties in rate coefficients 2. Applications, J. Chem. Phys., 59, 3879, 10.1063/1.1680572
Segovia-Juarez, 2004, Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model, J. Theor. Biol., 231, 357, 10.1016/j.jtbi.2004.06.031
SimLab. 2006. Distributed under the SimLab Software License, Version 1.0 〈http://simlab.jrc.ec.europa.eu/〉.
Storlie, 2008, Multiple predictor smoothing methods for sensitivity analysis: description of techniques, Reliab. Eng. Syst. Saf., 93, 28, 10.1016/j.ress.2006.10.012
Storlie, 2008, Multiple predictor smoothing methods for sensitivity analysis: example results, Reliab. Eng. Syst. Saf., 93, 55, 10.1016/j.ress.2006.10.013
Tarantola, 2006, Random balance designs for the estimation of first order global sensitivity indices, Reliab. Eng. Syst. Saf., 91, 717, 10.1016/j.ress.2005.06.003
Volterra, V., 1926. Variazioni e fluttuazioni del numero d’individui in specie animali conviventi. Mem. R. Accad. Naz. dei Lincei. Ser. VI, vol. 2 (English version can be found in Animal Ecology. McGraw-Hill, 1931. Translated from 1926 edition by R.N. Chapman. Title “Variations and fluctuations of the number of individuals in animal species living together.”).