Literature DB >> 21785515

ON IDENTIFIABILITY OF NONLINEAR ODE MODELS AND APPLICATIONS IN VIRAL DYNAMICS.

Hongyu Miao1, Xiaohua Xia, Alan S Perelson, Hulin Wu.   

Abstract

Ordinary differential equations (ODE) are a powerful tool for modeling dynamic processes with wide applications in a variety of scientific fields. Over the last 2 decades, ODEs have also emerged as a prevailing tool in various biomedical research fields, especially in infectious disease modeling. In practice, it is important and necessary to determine unknown parameters in ODE models based on experimental data. Identifiability analysis is the first step in determing unknown parameters in ODE models and such analysis techniques for nonlinear ODE models are still under development. In this article, we review identifiability analysis methodologies for nonlinear ODE models developed in the past one to two decades, including structural identifiability analysis, practical identifiability analysis and sensitivity-based identifiability analysis. Some advanced topics and ongoing research are also briefly reviewed. Finally, some examples from modeling viral dynamics of HIV, influenza and hepatitis viruses are given to illustrate how to apply these identifiability analysis methods in practice.

Entities:  

Year:  2011        PMID: 21785515      PMCID: PMC3140286          DOI: 10.1137/090757009

Source DB:  PubMed          Journal:  SIAM Rev Soc Ind Appl Math        ISSN: 0036-1445            Impact factor:   10.780


  37 in total

Review 1.  Modelling viral and immune system dynamics.

Authors:  Alan S Perelson
Journal:  Nat Rev Immunol       Date:  2002-01       Impact factor: 53.106

2.  Mathematical analysis of delay differential equation models of HIV-1 infection.

Authors:  Patrick W Nelson; Alan S Perelson
Journal:  Math Biosci       Date:  2002 Jul-Aug       Impact factor: 2.144

3.  Structural identifiability of the parameters of a nonlinear batch reactor model.

Authors:  M J Chappell; K R Godfrey
Journal:  Math Biosci       Date:  1992-03       Impact factor: 2.144

4.  Practical identifiability of HIV dynamics models.

Authors:  J Guedj; R Thiébaut; D Commenges
Journal:  Bull Math Biol       Date:  2007-06-08       Impact factor: 1.758

5.  Parameter identifiability and estimation of HIV/AIDS dynamic models.

Authors:  Hulin Wu; Haihong Zhu; Hongyu Miao; Alan S Perelson
Journal:  Bull Math Biol       Date:  2008-02-05       Impact factor: 1.758

6.  A delay-differential equation model of HIV infection of CD4(+) T-cells.

Authors:  R V Culshaw; S Ruan
Journal:  Math Biosci       Date:  2000-05       Impact factor: 2.144

7.  A dynamical model of human immune response to influenza A virus infection.

Authors:  Baris Hancioglu; David Swigon; Gilles Clermont
Journal:  J Theor Biol       Date:  2006-12-19       Impact factor: 2.691

8.  Modeling and estimation of kinetic parameters and replicative fitness of HIV-1 from flow-cytometry-based growth competition experiments.

Authors:  Hongyu Miao; Carrie Dykes; Lisa M Demeter; James Cavenaugh; Sung Yong Park; Alan S Perelson; Hulin Wu
Journal:  Bull Math Biol       Date:  2008-07-22       Impact factor: 1.758

9.  Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems.

Authors:  Maria Rodriguez-Fernandez; Jose A Egea; Julio R Banga
Journal:  BMC Bioinformatics       Date:  2006-11-02       Impact factor: 3.169

10.  Systematic identifiability testing for unambiguous mechanistic modeling--application to JAK-STAT, MAP kinase, and NF-kappaB signaling pathway models.

Authors:  Tom Quaiser; Martin Mönnigmann
Journal:  BMC Syst Biol       Date:  2009-05-09
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  111 in total

1.  Inverse problems from biomedicine: inference of putative disease mechanisms and robust therapeutic strategies.

Authors:  James Lu; Elias August; Heinz Koeppl
Journal:  J Math Biol       Date:  2012-04-18       Impact factor: 2.259

2.  The core control system of intracellular iron homeostasis: a mathematical model.

Authors:  J Chifman; A Kniss; P Neupane; I Williams; B Leung; Z Deng; P Mendes; V Hower; F M Torti; S A Akman; S V Torti; R Laubenbacher
Journal:  J Theor Biol       Date:  2012-01-23       Impact factor: 2.691

3.  A general model-based design of experiments approach to achieve practical identifiability of pharmacokinetic and pharmacodynamic models.

Authors:  Federico Galvanin; Carlo C Ballan; Massimiliano Barolo; Fabrizio Bezzo
Journal:  J Pharmacokinet Pharmacodyn       Date:  2013-06-04       Impact factor: 2.745

4.  A confidence building exercise in data and identifiability: Modeling cancer chemotherapy as a case study.

Authors:  Marisa C Eisenberg; Harsh V Jain
Journal:  J Theor Biol       Date:  2017-07-19       Impact factor: 2.691

5.  The inflammatory response to influenza A virus (H1N1): An experimental and mathematical study.

Authors:  Ian Price; Ericka D Mochan-Keef; David Swigon; G Bard Ermentrout; Sarah Lukens; Franklin R Toapanta; Ted M Ross; Gilles Clermont
Journal:  J Theor Biol       Date:  2015-04-03       Impact factor: 2.691

6.  Nonparametric inference of interaction laws in systems of agents from trajectory data.

Authors:  Fei Lu; Ming Zhong; Sui Tang; Mauro Maggioni
Journal:  Proc Natl Acad Sci U S A       Date:  2019-06-28       Impact factor: 11.205

7.  Identifiability analysis for stochastic differential equation models in systems biology.

Authors:  Alexander P Browning; David J Warne; Kevin Burrage; Ruth E Baker; Matthew J Simpson
Journal:  J R Soc Interface       Date:  2020-12-16       Impact factor: 4.118

8.  Structural and practical identifiability of dual-input kinetic modeling in dynamic PET of liver inflammation.

Authors:  Yang Zuo; Souvik Sarkar; Michael T Corwin; Kristin Olson; Ramsey D Badawi; Guobao Wang
Journal:  Phys Med Biol       Date:  2019-09-05       Impact factor: 3.609

9.  Representing Sudden Shifts in Intensive Dyadic Interaction Data Using Differential Equation Models with Regime Switching.

Authors:  Sy-Miin Chow; Lu Ou; Arridhana Ciptadi; Emily B Prince; Dongjun You; Michael D Hunter; James M Rehg; Agata Rozga; Daniel S Messinger
Journal:  Psychometrika       Date:  2018-03-19       Impact factor: 2.500

10.  Identifying Spatial Invasion of Pandemics on Metapopulation Networks Via Anatomizing Arrival History.

Authors:  Jian-Bo Wang; Lin Wang; Xiang Li
Journal:  IEEE Trans Cybern       Date:  2015-11-09       Impact factor: 11.448

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