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Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
2006
Briefings in Bioinformatics
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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
2012
BMC Systems Biology
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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
2004
Biology of the Cell
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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
2007
Current Opinion in Biotechnology
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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
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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
2011
Biophysical Journal
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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
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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]
2019
biorxiv/medrxiv
pre-print
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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]
2012
Applied Biological Engineering - Principles and Practice
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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
2019
iScience
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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
2006
Proceedings of the 2006 Winter Simulation Conference
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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
2011
The Open Bioinformatics Journal
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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
2019
Frontiers in Physiology
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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
2011
Biophysical Journal
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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
2002
Bioessays
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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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