Biochemical systems theory: a review (Q355964): Difference between revisions

Summary: Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools that facilitate the analysis of dynamic biological systems. This paper depicts major developments in BST up to the current state of the art in 2012. It discusses its rationale, describes the typical strategies and methods of designing, diagnosing, analyzing, and utilizing BST models, and reviews areas of applications. The paper is intended as a guide for investigators entering the fascinating field of biological systems analysis and as a resource for practitioners and experts.

@@ Property / cites work @@
+Q4182306
@@ Property / cites work: Q4182306 / rank @@
+Normal rank
@@ Property / cites work @@
+Q4003916
@@ Property / cites work: Q4003916 / rank @@
+Normal rank
@@ Property / cites work @@
+Q4787527
@@ Property / cites work: Q4787527 / rank @@
+Normal rank
@@ Property / cites work @@
+Q3682286
@@ Property / cites work: Q3682286 / rank @@
+Normal rank
@@ Property / cites work @@
+Models-of-data and models-of-processes in the post-genomic era
+Normal rank
@@ Property / cites work @@
+Q4877856
@@ Property / cites work: Q4877856 / rank @@
+Normal rank
@@ Property / cites work @@
+Design principles for elementary gene circuits: Elements, methods, and examples
+Normal rank
@@ Property / cites work @@
+Biochemical systems theory and metabolic control theory: I. Fundamental similarities and differences
+Normal rank
@@ Property / cites work @@
+Biochemical systems theory and metabolic control theory: II. The role of summation and connectivity relationships
+Normal rank
@@ Property / cites work @@
+Strategies for representing metabolic pathways within biochemical systems theory: Reversible pathways
+Normal rank
@@ Property / cites work @@
+A comparison of variant theories of intact biochemical systems. II: Flux- oriented and metabolic control theories
+Normal rank
@@ Property / cites work @@
+A comparison of variant theories of intact biochemical systems. I: Enzyme-enzyme interactions and biochemical systems theory
+Normal rank
@@ Property / cites work @@
+Recent developments in parameter estimation and structure identification of biochemical and genomic systems
+Normal rank
@@ Property / cites work @@
+Design principles and operating principles: the Yin and Yang of optimal functioning
+Normal rank
@@ Property / cites work @@
+Tutorial:<i>S</i>-system analysis of continuous univariate probability distributions
+Normal rank
@@ Property / cites work @@
+Efficient Solution of Nonlinear Ordinary Differential Equations Expressed in S-system Canonical Form
+Normal rank
@@ Property / cites work @@
+A Taylor-series solution in Cartesian space to GMA-system equations and its application to initial-value problems
+Normal rank
@@ Property / cites work @@
+Recasting nonlinear differential equations as S-systems: a canonical nonlinear form
+Normal rank
@@ Property / cites work @@
+Concordant chemical reaction networks
@@ Property / cites work: Concordant chemical reaction networks / rank @@
+Normal rank
@@ Property / cites work @@
+Solution of a two-point boundary value model of immobilized enzyme reactions, using an \(S\)-system-based root-finding method
+Normal rank
@@ Property / cites work @@
+A simple and highly accurate numerical differentiation method for sensitivity analysis of large-scale metabolic reaction systems
+Normal rank
@@ Property / cites work @@
+An efficient method for calculation of dynamic logarithmic gains in biochemical systems theory
+Normal rank
@@ Property / cites work @@
+Computation and analysis of time-dependent sensitivities in generalized mass action systems
+Normal rank
@@ Property / cites work @@
+A reliable Taylor series-based computational method for the calculation of dynamic sensitivities in large-scale metabolic reaction systems: algorithm and software evaluation
+Normal rank
@@ Property / cites work @@
+Growth of complex systems can be related to the properties of their underlying determinants
+Normal rank
@@ Property / cites work @@
+Q5562204
@@ Property / cites work: Q5562204 / rank @@
+Normal rank
@@ Property / cites work @@
+Q3696908
@@ Property / cites work: Q3696908 / rank @@
+Normal rank
@@ Property / cites work @@
+Equivalence between S-systems and Volterra systems
+Normal rank
@@ Property / cites work @@
+Coexistence and chaos in complex ecologies
@@ Property / cites work: Coexistence and chaos in complex ecologies / rank @@
+Normal rank
@@ Property / cites work @@
+Chaos in low-dimensional Lotka–Volterra models of competition
+Normal rank
@@ Property / cites work @@
+Graph-theoretic description of the interplay between non-linearity and connectivity in biological systems
+Normal rank
@@ Property / cites work @@
+Lotka-Volterra representation of general nonlinear systems
+Normal rank
@@ Property / cites work @@
+Simple evaluation of Casimir invariants in finite-dimensional Poisson systems
+Normal rank
@@ Property / cites work @@
+Hamiltonian structure and Darboux theorem for families of generalized Lotka–Volterra systems
+Normal rank
@@ Property / cites work @@
+Algebraic recasting of nonlinear systems of ODEs into universal formats
+Normal rank
@@ Property / cites work @@
+Renormalization group approach to power-law modeling of complex metabolic networks
+Normal rank
@@ Property / cites work @@
+Metabolic engineering with power-law and linear-logarithmic systems
+Normal rank
@@ Property / cites work @@
+Calculation errors of time-varying flux control coefficients obtained from elasticity coefficients by means of summation and connectivity theorems in metabolic control analysis
+Normal rank
@@ Property / cites work @@
+A comparison of the monomial method and the S-system method for solving systems of algebraic equations
+Normal rank
@@ Property / cites work @@
+Finding multiple roots of nonlinear algebraic equations using S-system methodology
+Normal rank
@@ Property / cites work @@
+Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: Model definition and nomenclature
+Normal rank
@@ Property / cites work @@
+Mathematical models of purine metabolism in man
@@ Property / cites work: Mathematical models of purine metabolism in man / rank @@
+Normal rank
@@ Property / cites work @@
+Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models
+Normal rank
@@ Property / cites work @@
+Power-law modeling based on least-squares minimization criteria
+Normal rank
@@ Property / cites work @@
+Power-law modeling based on least-squares criteria: Consequences for system analysis and simulation
+Normal rank
@@ Property / cites work @@
+Simplified method for the computation of parameters of power-law rate equations from time-series
+Normal rank
@@ Property / cites work @@
+Q4877859
@@ Property / cites work: Q4877859 / rank @@
+Normal rank
@@ Property / cites work @@
+A Spline Least Squares Method for Numerical Parameter Estimation in Differential Equations
+Normal rank
@@ Property / cites work @@
+Parameter estimation of ODE's via nonparametric estimators
+Normal rank
@@ Property / cites work @@
+\(\sqrt{n}\)-consistent parameter estimation for systems of ordinary differential equations: bypassing numerical integration via smoothing
+Normal rank
@@ Property / cites work @@
+Inference of \(S\)-system models of genetic networks by solving one-dimensional function optimization problems
+Normal rank
@@ Property / cites work @@
+Method for inferring and extracting reliable genetic interactions from time-series profile of gene expression
+Normal rank
@@ Property / cites work @@
+An effective method to increase solvability in biochemical systems using S-system
+Normal rank
@@ Property / cites work @@
+Estimating parameters for generalized mass action models using constraint propagation
+Normal rank
@@ Property / cites work @@
+Parameter reconstruction for biochemical networks using interval analysis
+Normal rank
@@ Property / cites work @@
+Q3645264
@@ Property / cites work: Q3645264 / rank @@
+Normal rank
@@ Property / cites work @@
+Parameter estimation in modulated, unbranched reaction chains within biochemical systems
+Normal rank
@@ Property / cites work @@
+A modified collocation method for solving differential-algebraic equations
+Normal rank
@@ Property / cites work @@
+Q4486927
@@ Property / cites work: Q4486927 / rank @@
+Normal rank
@@ Property / cites work @@
+Evolutionary Multi-Criterion Optimization
@@ Property / cites work: Evolutionary Multi-Criterion Optimization / rank @@
+Normal rank
@@ Property / cites work @@
+Characterizability of metabolic pathway systems from time series data
+Normal rank
@@ Property / cites work @@
+Structural identifiability of polynomial and rational systems
+Normal rank
@@ Property / cites work @@
+Nash manifolds
@@ Property / cites work: Nash manifolds / rank @@
+Normal rank
@@ Property / cites work @@
+A systems-theoretical framework for health and disease: inflammation and preconditioning from an abstract modeling point of view
+Normal rank
@@ Property / cites work @@
+Analysis of operating principles with S-system models
+Normal rank
@@ Property / cites work @@
+Approximation of dynamical systems using s-systems theory
+Normal rank
@@ Property / cites work @@
+Alternative designs for a genetic switch: Analysis of switching times using the piecewise power-law representation
+Normal rank
@@ Property / cites work @@
+Synergism analysis of biochemical systems. II: Tensor formulation and treatment of stoichiometric constraints
+Normal rank
@@ Property / cites work @@
+Synergism analysis of biochemical systems. I: Conceptual framework
+Normal rank
@@ Property / cites work @@
+Robust filtering circuit design for stochastic gene networks under intrinsic and extrinsic molecular noises
+Normal rank
@@ Property / cites work @@
+On the interplay between entropy and robustness of gene regulatory networks
+Normal rank
@@ Property / cites work @@
+Dynamic sensitivities in chaotic dynamical systems
+Normal rank
@@ Property / cites work @@
+Q5843611
@@ Property / cites work: Q5843611 / rank @@
+Normal rank
@@ Property / cites work @@
+Q4692840
@@ Property / cites work: Q4692840 / rank @@
+Normal rank
@@ Property / cites work @@
+CONSTRUCTION AND CUSTOMIZATION OF STABLE OSCILLATION MODELS IN BIOLOGY
+Normal rank
@@ Property / cites work @@
+Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics
+Normal rank
@@ Property / cites work @@
+Analytical solutions to a generalized growth equation
+Normal rank
@@ Property / cites work @@
+Q4417547
@@ Property / cites work: Q4417547 / rank @@
+Normal rank
@@ Property / cites work @@
+Q4417490
@@ Property / cites work: Q4417490 / rank @@
+Normal rank
@@ Property / cites work @@
+Q5456737
@@ Property / cites work: Q5456737 / rank @@
+Normal rank
@@ Property / cites work @@
+Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice
+Normal rank
@@ Property / cites work @@
+Algebraic Systems Biology: Theses and Hypotheses
@@ Property / cites work: Algebraic Systems Biology: Theses and Hypotheses / rank @@
+Normal rank
@@ Property / cites work @@
+Q4413206
@@ Property / cites work: Q4413206 / rank @@
+Normal rank
@@ Property / cites work @@
+Hybrid Automata in Systems Biology: How Far Can We Go?
+Normal rank
@@ Property / cites work @@
+Design of the lac gene circuit revisited
@@ Property / cites work: Design of the lac gene circuit revisited / rank @@
+Normal rank
@@ Property / cites work @@
+Q3491370
@@ Property / cites work: Q3491370 / rank @@
+Normal rank
@@ Property / cites work @@
+Methods for and results from the study of design principles in molecular systems
+Normal rank
@@ Property / cites work @@
+Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis
+Normal rank
@@ Property / cites work @@
+Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: Steady-state analysis
+Normal rank
@@ Property / cites work @@
+Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: Model validation and dynamic behavior
+Normal rank
@@ Property / cites work @@
+Bi-objective optimization of biochemical systems by linear programming
+Normal rank
@@ Property / cites work @@
+Model based optimization of biochemical systems using multiple objectives: a comparison of several solution strategies
+Normal rank
@@ Property / cites work @@
+Mathematical modelling and assessment of the ph homeostasis mechanisms in \textit{Aspergillus niger} while in citric acid producing conditions
+Normal rank
@@ Property / cites work @@
+A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis
+Normal rank
@@ Property / cites work @@
+Requirement for multiple activation signals by anti-inflammatory feedback in macrophages
+Normal rank
@@ Property / cites work @@
+The potential for signal integration and processing in interacting MAP kinase cascades
+Normal rank
@@ Property / cites work @@
+Dynamic Trends in Distributions
@@ Property / cites work: Dynamic Trends in Distributions / rank @@
+Normal rank
@@ Property / cites work @@
+Mathematical modeling of monolignol biosynthesis in populus xylem
+Normal rank
@@ Property / cites work @@
+Bioeconomic dynamics of a fishery modeled as an S-system
+Normal rank
@@ Property / cites work @@
+Controllability of non-linear biochemical systems
@@ Property / cites work: Controllability of non-linear biochemical systems / rank @@
+Normal rank
@@ Property / cites work @@
+The Power-Law Formalism as a Tool for Modeling Hormonal Systems
+Normal rank
@@ Property / cites work @@
+A pharmacodynamic model for the action of the antibiotic imipenem on Pseudomonas aeruginosa populations in vitro
+Normal rank
@@ Property / cites work @@
+S-system modelling of endemic infections
@@ Property / cites work: S-system modelling of endemic infections / rank @@
+Normal rank
@@ Property / cites work @@
+Mechanistic simulations of inflammation: current state and future prospects
+Normal rank
@@ Property / cites work @@
+Optimization of biochemical systems by linear programming and general mass action model representations
+Normal rank
@@ Property / cites work @@
+Investigation of the performance of fermentation processes using a mathematical model including effects of metabolic bottleneck and toxic product on cells
+Normal rank
@@ Property / cites work @@
+Optimization of biochemical systems through mathematical programming: methods and applications
+Normal rank
@@ Property / cites work @@
+Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase
+Normal rank
@@ Property / cites work @@
+Mathematical analysis of models for reaction kinetics in intracellular environments
+Normal rank
@@ Property / cites work @@
+Approximation of delays in biochemical systems
@@ Property / cites work: Approximation of delays in biochemical systems / rank @@
+Normal rank
@@ Property / cites work @@
+Analysis of dynamic labeling data
@@ Property / cites work: Analysis of dynamic labeling data / rank @@
+Normal rank
@@ Property / cites work @@
+Comparison of isoeffect relationships in radiotherapy
+Normal rank
@@ Property / cites work @@
+Q3992491
@@ Property / cites work: Q3992491 / rank @@
+Normal rank
@@ Property / cites work @@
+Allometric morphogenesis of complex systems: Derivation of the basic equations from first principles
+Normal rank
@@ Property / cites work @@
+Growth equations: A general equation and a survey of special cases
+Normal rank
@@ Property / cites work @@
+Regenerative growth curves
@@ Property / cites work: Regenerative growth curves / rank @@
+Normal rank
@@ Property / cites work @@
+Universal formats for nonlinear ordinary differential systems
+Normal rank
@@ Property / cites work @@
+Analysis of Non-polynomial Systems Using the Sum of Squares Decomposition
+Normal rank
@@ Property / cites work @@
+Q4877860
@@ Property / cites work: Q4877860 / rank @@
+Normal rank
@@ Property / cites work @@
+Symmetries of \(S\)-systems
@@ Property / cites work: Symmetries of \(S\)-systems / rank @@
+Normal rank
@@ Property / cites work @@
+A Suprasystem of Probability Distributions
@@ Property / cites work: A Suprasystem of Probability Distributions / rank @@
+Normal rank
@@ Property / cites work @@
+Evaluation of the Noncentral t Distribution with S-Systems
+Normal rank
@@ Property / cites work @@
+Q2708454
@@ Property / cites work: Q2708454 / rank @@
+Normal rank
@@ Property / cites work @@
+Computing the noncentral beta distribution with S-system.
+Normal rank
@@ Property / cites work @@
+On the statistical computation of the sample multiple correlation moefficient
+Normal rank
@@ Property / cites work @@
+Computing the Distribution of the Squared Sample Multiple Correlation Coefficient with S-Systems
+Normal rank
@@ Property / cites work @@
+The S-system computation of non-central gamma distribution
+Normal rank
@@ Property / cites work @@
+TheS-Distribution A Tool for Approximation and Classification of Univariate, Unimodal Probability Distributions
+Normal rank
@@ Property / cites work @@
+The S‐Distribution: Approximation of Discrete Distributions
+Normal rank
@@ Property / cites work @@
+A Simple, Flexible Failure Model
@@ Property / cites work: A Simple, Flexible Failure Model / rank @@
+Normal rank
@@ Property / cites work @@
+Q4218219
@@ Property / cites work: Q4218219 / rank @@
+Normal rank
@@ Property / cites work @@
+Estimation and completion of survival data with piecewise linear models and<i>S</i>-distributions
+Normal rank
@@ Property / cites work @@
+Analytical Quantile Solution for the S-distribution, Random Number Generation and Statistical Data Modeling
+Normal rank
@@ Property / cites work @@
+Scalability Properties of the S-Distribution
@@ Property / cites work: Scalability Properties of the S-Distribution / rank @@
+Normal rank
@@ Property / cites work @@
+A Maximum Likelihood Estimator for Shape Parameters of S-Distributions
+Normal rank
@@ Property / cites work @@
+Construction of bivariate S-distributions with copulas
+Normal rank
@@ Property / cites work @@
+GS-distributions: a new family of distributions for continuous unimodal variables
+Normal rank
@@ Property / cites work @@
+Q3645261
@@ Property / cites work: Q3645261 / rank @@
+Normal rank

Biochemical systems theory: a review (Q355964): Difference between revisions

Latest revision as of 15:51, 6 July 2024

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Mathematics(1 entry)