Energy balance for analysis of complex metabolic networks

scientific article

Energy balance for analysis of complex metabolic networks is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1016/S0006-3495(02)75150-3
P932PMC publication ID1302128
P698PubMed publication ID12080101
P5875ResearchGate publication ID11295269

P2093author name stringHong Qian
Daniel A Beard
Shou-dan Liang
P2860cites workMetabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletionsQ21284379
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilitiesQ24655269
From molecular to modular cell biologyQ29547493
The large-scale organization of metabolic networksQ29547498
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental dataQ29618471
Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraintsQ31920157
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.Q33543834
Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.Q33651317
The underlying pathway structure of biochemical reaction networksQ36465790
Equilibrium compositions of solutions of biochemical species and heats of biochemical reactionsQ37481841
Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirementsQ45108799
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systemsQ46109374
Robustness analysis of the Escherichia coli metabolic networkQ46731594
Metabolic flux analysis of hybridoma cells in different culture media using mass balancesQ47863678
Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensationQ52048127
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical UseQ56773460
P433issue1
P407language of work or nameEnglishQ1860
P921main subjectmetabolic networkQ2263094
P304page(s)79-86
P577publication date2002-07-01
P1433published inBiophysical JournalQ2032955
P1476titleEnergy balance for analysis of complex metabolic networks
P478volume83

Reverse relations

cites work (P2860)
Q28480577A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks
Q26778643A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease
Q29615371A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
Q50520702A model-based method for investigating bioenergetic processes in autotrophically growing eukaryotic microalgae: application to the green algae Chlamydomonas reinhardtii
Q36277163A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems
Q34475028A proof for loop-law constraints in stoichiometric metabolic networks.
Q35261034A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks
Q81157263Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry
Q28658520An efficient graph theory based method to identify every minimal reaction set in a metabolic network
Q90442733An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment
Q33830486An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data
Q97643842An upper limit on Gibbs energy dissipation governs cellular metabolism
Q51114019Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
Q34180306Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices
Q38775834Application of theoretical methods to increase succinate production in engineered strains.
Q37892104Bacterial growth rate reflects a bottleneck in resource allocation
Q39776363Bayesian flux balance analysis applied to a skeletal muscle metabolic model.
Q89436058Bond graph modelling of the cardiac action potential: implications for drift and non-unique steady states
Q42983671Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
Q31085868Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data
Q33252676Building the power house: recent advances in mitochondrial studies through proteomics and systems biology
Q28545184CONSTRICTOR: constraint modification provides insight into design of biochemical networks
Q34601005Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.
Q28474249Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis
Q43234569Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling
Q51924640Combining flux and energy balance analysis to model large-scale biochemical networks.
Q24803776Computation of elementary modes: a unifying framework and the new binary approach
Q26859964Computational approaches for understanding energy metabolism
Q41994185Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks
Q28551270Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach
Q34257056Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
Q28485363Construction and Analysis of the Model of Energy Metabolism in E. coli
Q41779480Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks
Q91763183Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Q47674753CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions
Q33415709Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation
Q54995027Development of network-based pathway definitions: the need to analyze real metabolic networks
Q54326315Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis.
Q35605218Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity
Q30441717Dynamic analysis of integrated signaling, metabolic, and regulatory networks
Q51014328Energy-based analysis of biochemical cycles using bond graphs
Q42709039Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures
Q36349637Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
Q25257616Evolutionary programming as a platform for in silico metabolic engineering
Q33350707Exhaustive identification of steady state cycles in large stoichiometric networks
Q37585376Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs.
Q42476494Exploring the gap between dynamic and constraint-based models of metabolism.
Q43122158Extreme pathways and Kirchhoff's second law.
Q42686494Fast thermodynamically constrained flux variability analysis.
Q39331953Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models
Q36336618Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach
Q39968205Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.
Q35101082Genome-scale microbial in silico models: the constraints-based approach.
Q33391538Genome-scale models of bacterial metabolism: reconstruction and applications
Q29616789Genome-scale models of microbial cells: evaluating the consequences of constraints
Q42155867Genome-scale thermodynamic analysis of Escherichia coli metabolism
Q51952432Grand canonical Markov model: a stochastic theory for open nonequilibrium biochemical networks.
Q26781584Heading in the right direction: thermodynamics-based network analysis and pathway engineering
Q36286169How important is thermodynamics for identifying elementary flux modes?
Q51320677Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis
Q28474725Identification of potential pathway mediation targets in Toll-like receptor signaling
Q21202794Impact of the solvent capacity constraint on E. coli metabolism
Q33286434Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks
Q28752237Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
Q35921620Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.
Q40328686Kinetic constraints for formation of steady states in biochemical networks
Q33935470Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation
Q90093259Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
Q33334972Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory
Q34464555MC3: a steady-state model and constraint consistency checker for biochemical networks
Q37849847Mathematical models of cell factories: moving towards the core of industrial biotechnology
Q38048435Mathematical optimization applications in metabolic networks
Q28469032Matrix formalism to describe functional states of transcriptional regulatory systems
Q43704553MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis
Q33849784Metabolic Network-Based Interpretation of Gene Expression Data Elucidates Human Cellular Metabolism
Q57797074Metabolic determinants of enzyme evolution in a genome-scale bacterial metabolic network
Q28473577Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multi-scale, top-down integrated model
Q36380207Metabolic flux analysis of heterotrophic growth in Chlamydomonas reinhardtii
Q51577942Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos
Q39344014Metabolomics-on-a-chip and metabolic flux analysis for label-free modeling of the internal metabolism of HepG2/C3A cells.
Q33917819Model-based dietary optimization for late-stage, levodopa-treated, Parkinson's disease patients
Q41591729Model-driven elucidation of the inherent capacity of Geobacter sulfurreducens for electricity generation.
Q38374438Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Q50502346Network reduction in metabolic pathway analysis: elucidation of the key pathways involved in the photoautotrophic growth of the green alga Chlamydomonas reinhardtii
Q28212164Network-based analysis of metabolic regulation in the human red blood cell
Q33236264Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition
Q37901403Non-invasive tools for measuring metabolism and biophysical analyte transport: self-referencing physiological sensing
Q30943969Nutritional systems biology modeling: from molecular mechanisms to physiology
Q35749937Obstructions to Sampling Qualitative Properties
Q39822152Parameter balancing in kinetic models of cell metabolism
Q38118241Parameter identification of in vivo kinetic models: Limitations and challenges
Q92876480Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio
Q37196179Predicting metabolic biomarkers of human inborn errors of metabolism
Q48238418Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
Q38968451Promise and reality in the expanding field of network interaction analysis: metabolic networks
Q28766251Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
Q34205663Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures
Q37023365Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models
Q35895080Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.
Q46083927Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum
Q57971640Reply to "Challenges in modeling the human gut microbiome"
Q43190784Reply to "Do genome-scale models need exact solvers or clearer standards?".
Q46614710Reverse engineering the cancer metabolic network using flux analysis to understand drivers of human disease
Q37086464Role of NADH/NAD+ transport activity and glycogen store on skeletal muscle energy metabolism during exercise: in silico studies
Q38748541Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling.
Q38154674Software platforms to facilitate reconstructing genome-scale metabolic networks
Q35005596Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load
Q59049845Steady-state robustness of qualitative gene regulation networks
Q33264473Systematic assignment of thermodynamic constraints in metabolic network models
Q30479887Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
Q37929450Systems approaches to modelling pathways and networks
Q42647472The Influence of Crowding Conditions on the Thermodynamic Feasibility of Metabolic Pathways
Q36182002The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
Q34181787The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools
Q28681370The cost of efficiency in energy metabolism
Q29616019The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
Q34352367The geometry of the flux cone of a metabolic network
Q34785166The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
Q35905293The systems biology of glycosylation
Q38632109Thermodynamic Constraints Improve Metabolic Networks
Q40648189Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling
Q51806019Thermodynamic and Probabilistic Metabolic Control Analysis of Riboflavin (Vitamin B₂) Biosynthesis in Bacteria
Q34306900Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks
Q45126764Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism
Q51661914Thermodynamically based constraints for rate coefficients of large biochemical networks
Q30479408Thermodynamically feasible kinetic models of reaction networks
Q35683444Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community
Q43474233Thermodynamics of biochemical networks and duality theorems
Q41874839Thermodynamics-based metabolic flux analysis
Q35109629Thirteen years of building constraint-based in silico models of Escherichia coli
Q33563265Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design
Q37751917Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators.
Q27499038Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Q34372537Yeast dynamic metabolic flux measurement in nutrient-rich media by HPLC and accelerator mass spectrometry
Q39788095ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks
Q38670060redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Search more.