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Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments

N. A.W. van Riel
2006 Briefings in Bioinformatics  
Mathematical models of biochemical networks can look very different.  ...  It is shown how these methods can be applied in the design of model-based experiments which iteratively yield models that are decreasingly wrong and increasingly gain predictive power.  ...  Acknowledgements The author wishes to thank Mark Musters for his helpful comments and Ad Damen and Paul van den Bosch for useful discussions.  ... 
doi:10.1093/bib/bbl040 pmid:17107967 fatcat:seoscbai2bblfd37izrnu2jnb4

Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics

Irina Surovtsova, Natalia Simus, Katrin Hübner, Sven Sahle, Ursula Kummer
2012 BMC Systems Biology  
Results: We have developed a strategy based on the Computational Singular Perturbation (CSP) method which can be used to perform a "biochemically-driven" model reduction of even large and complex kinetic  ...  system and a full-scale model of yeast glycolysis.  ...  Authors' contributions IS conceived the procedure for CSP based model reduction, performed the CSP analysis and drafted the initial manuscript.  ... 
doi:10.1186/1752-0509-6-14 pmid:22390191 pmcid:PMC3349553 fatcat:uhw5lwp42jcmbgopwxufqh3mpe

Modeling Cell Signaling Networks

N EUNGDAMRONG
2004 Biology of the Cell  
Analysis of signaling networks requires a combination of experimental and theoretical approaches including the development and analysis of models.  ...  Different mathematical approaches that are currently used to model signaling networks are described, and future challenges including the need for databases as well as enhanced computing environments are  ...  While modeling signaling network with reaction-diffusion equations affords a more realistic approach for the analysis of spatially restricted biochemical reactions, the mathematical challenges involved  ... 
doi:10.1016/j.biolcel.2004.03.004 pmid:15207904 pmcid:PMC3620715 fatcat:xsvheghhszerhcp5bwuf4aozby

Biochemical and statistical network models for systems biology

Nathan D Price, Ilya Shmulevich
2007 Current Opinion in Biotechnology  
PBNs, which are stochastic rule-based models, bear a close relationship to dynamic Bayesian networks [43] -a popular model class for representing the dynamics of gene expression.  ...  Genome-scale models based on biochemical networks provide a comprehensive, yet concise, description of cellular functions.  ...  Comparison of Network Analysis Approaches There are fundamental differences between the biochemical and statistical classes of network modeling described herein.  ... 
doi:10.1016/j.copbio.2007.07.009 pmid:17681779 pmcid:PMC2034526 fatcat:bpdls7rhbvdwjkoedgnkdzd5ci

Regulatory Networks & Systems Biology - I

2008 Biophysical Journal  
Traditionally 50 -1500 mg of protein has been consumed to complete an ITC experiment and completing each experiment could require two hours or more.  ...  lack of sufficient quantities of protein during those early stages and the time required to perform the ITC experiments on large numbers of potential ligands (or protein constructs) of interest.  ...  Stochastic dynamical analysis with adaptive landscape potential functions is used to study the dynamics of such a molecular and cellular endogenous interaction network.  ... 
doi:10.1016/s0006-3495(08)79197-5 fatcat:2vtd6p7rbzdhtnuwmbrp7buvgy

Bipartite Network Analysis of (bio)CHEMICAL Reaction Systems

Craig C. Jolley, Trevor Douglas
2011 Biophysical Journal  
In this study, we use a computational method called cellGPS (cell global pattern simulator) to study the dynamic process of proliferating epithelia based on a mechanical off-lattice cellular model.  ...  The work fills the missing gap between studies on intramolecular and network dynamics. 913-Pos Board B713 Theoretical Modeling of Bi-Connected Elementary Biochemical Reaction Cycles Tatsunori Nishimura  ...  In this study, we use a computational method called cellGPS (cell global pattern simulator) to study the dynamic process of proliferating epithelia based on a mechanical off-lattice cellular model.  ... 
doi:10.1016/j.bpj.2010.12.1127 fatcat:6uybrte6o5crrd7rjjvq6resjq

Modeling Signaling Networks

2005 Science  
Here we review current approaches to the development of computational models of biochemical networks and describe the insights gained from models that integrate experimental data, using three examples  ...  The development of computational models and the integration of these models with experiments provide valuable insight into these complex systems-level behaviors.  ...  Theoretical analysis of biochemical networks has a long history, and has been successfully applied to the analysis of metabolic pathways and physiological processes.  ... 
doi:10.1126/science.308.5721.464a fatcat:i5et3vg4ovdsjl4dn7jjsupp4a

Interactive Multiresolution Visualization of Cellular Network Processes [article]

Oscar O. Ortega, Carlos F Lopez
2019 biorxiv/medrxiv   pre-print
Visualization plays a central role in the analysis of biochemical network processes to identify patterns that arise from model dynamics and perform model exploratory analysis.  ...  Here, we present PyViPR, a visualization tool that provides researchers static and dynamic representations of biochemical network processes within a Python-based Literate Programming environment.  ...  of increasingly large networks; (2) generate intuitive dynamic network visualizations of model simulations; and (3) facilitate the integration of visualizations into model building and analysis pipelines  ... 
doi:10.1101/659367 fatcat:bh57bwif2ndavkaz7ut2sxluhi

Mathematical Modelling of Gene Regulatory Networks [chapter]

Ana Tuek, elimir Kurtanjek
2012 Applied Biological Engineering - Principles and Practice  
It is very import to understand and explain the dynamic of gene regulatory networks. To explain and understand those complex biochemical systems different mathematical models have been developed.  ...  ., 2004 apart sequence-based method, few others approaches can be used: (i) analysis of temporal, spatial and physiological proteins regulation, (ii) analysis of protein interactions, (iii) analysis of  ...  Mathematical Modelling of Gene Regulatory Networks, Applied Biological Engineering -Principles and Practice, Dr. Ganesh R.  ... 
doi:10.5772/31388 fatcat:vbvytqbmnra7ndxtnb6fjofye4

Interactive Multiresolution Visualization of Cellular Network Processes

Oscar O. Ortega, Carlos F. Lopez
2019 iScience  
Visualization plays a central role in the analysis of biochemical network models to identify patterns that arise from reaction dynamics and perform model exploratory analysis.  ...  To facilitate these analyses, we developed PyViPR, a visualization tool that generates static and dynamic representations of biochemical network processes within a Python-based environment.  ...  of increasingly large networks; (2) generate intuitive dynamic network visualizations of model simulations; and (3) facilitate the integration of visualizations into model building and analysis pipelines  ... 
doi:10.1016/j.isci.2019.100748 pmid:31884165 pmcid:PMC6941861 fatcat:pqtsyx6tzbgm5mzuvmnbyk457u

Complexity Reduction of Biochemical Networks

Ravishankar Vallabhajosyula, Herbert Sauro
2006 Proceedings of the 2006 Winter Simulation Conference  
This enables complex networks to be rationalized as a series of hierarchical modules and greatly simplifies our ability to understand the dynamics of complex networks.  ...  This paper discusses two broad approaches for reducing the complexity of large cellular network models.  ...  However, this is guided by experience, and often based on knowledge of the system being studied, and does not lend itself to automation.  ... 
doi:10.1109/wsc.2006.322944 dblp:conf/wsc/VallabhajosyulaS06 fatcat:njvpspk5zrbybg57cf2opstczi

Boolean Modeling of Biochemical Networks

Helikar Tomás
2011 The Open Bioinformatics Journal  
The use of modeling to observe and analyze the mechanisms of complex biochemical network function is becoming an important methodological tool in the systems biology era.  ...  Number of different approaches to model these networks have been utilized--they range from analysis of static connection graphs to dynamical models based on kinetic interaction data.  ...  EMERGENT PROPERTIES IN CELLS; BOOLEAN STUDIES OF GLOBAL CELLULAR DYNAMICS While modeling is useful for modeling specific mechanisms of biochemical function, the real promise of modeling lies in the development  ... 
doi:10.2174/1875036201105010016 fatcat:ehlqcj7pijdhnnnm2wzind7cvu

Deciphering the Mechanical Network of Chronic Atrophic Gastritis: A Urinary Time-Dependent Metabonomics-Based Network Pharmacology Study

YueTao Liu, WenQian Xu, XueMei Qin
2019 Frontiers in Physiology  
Deciphering its mechanical network is of significant importance for its diagnosis and treatment.  ...  In the present work, 1H NMR-based dynamic metabonomics was firstly performed to analyze the urinary metabolic features of CAG coupled with ANOVA-simultaneous component analysis (ASCA).  ...  ACKNOWLEDGMENTS We thank Scientific Instrument Center of Shanxi University for the NMR analysis.  ... 
doi:10.3389/fphys.2019.01004 pmid:31447694 pmcid:PMC6691169 fatcat:7dcvjeytrffkbpr4yoqmigoayi

Extracting Mechanistic Insight from Large Biochemical Networks via Statistical Analysis

Michael Dworkin, Sayak Mukherjee, Ciriyam Jayaprakash, Jayajit Das
2011 Biophysical Journal  
In this study, we use a computational method called cellGPS (cell global pattern simulator) to study the dynamic process of proliferating epithelia based on a mechanical off-lattice cellular model.  ...  The work fills the missing gap between studies on intramolecular and network dynamics. 913-Pos Board B713 Theoretical Modeling of Bi-Connected Elementary Biochemical Reaction Cycles Tatsunori Nishimura  ...  In this study, we use a computational method called cellGPS (cell global pattern simulator) to study the dynamic process of proliferating epithelia based on a mechanical off-lattice cellular model.  ... 
doi:10.1016/j.bpj.2010.12.1128 fatcat:sxih4yg3pzd55l47j4i2tkuxcq

Modeling of signaling networks

Susana R. Neves, Ravi Iyengar
2002 Bioessays  
Here we review current approaches to the development of computational models of biochemical networks and describe the insights gained from models that integrate experimental data, using three examples  ...  The development of computational models and the integration of these models with experiments provide valuable insight into these complex systems-level behaviors.  ...  Theoretical analysis of biochemical networks has a long history, and has been successfully applied to the analysis of metabolic pathways and physiological processes.  ... 
doi:10.1002/bies.1154 pmid:12447976 fatcat:ttc4qfbir5achazqhxymz2w7oq
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