Amigo

Baldazzi

Beard

Benyamini

Blank

Boggy

Burgard

Christian

Dauner

Ebenh  h

Edwards

Feist

Fell

Fleming

Garfinkel

Gianchandani

Goodwin

Handorf

Heinrich

Hoppe

Hucka

Jerby

Jevremovic

Kacser

Klamt

Locke

Lotka

Murabito

Nov  re

Pfeiffer

Poolman

Ramakrishna

Rapoport

Raymond

Ruppin

Samal

Schilling

Schuster

Schutte

Sel'kov

Ullah

Briefings in Functional Genomics

English

Pfau, Thomas

Christian, Nils

Ebenhöh, Oliver

The Open University

A genome-scale metabolic model accurately predicts uxes in central carbon metabolism under stress conditions. Plant Physiol

A genomescale metabolic model of Arabidopsis and some of its properties. Plant Physiol

A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an eector.

A linear steady-state treatment of enzymatic chains. General properties, control and eector strength.

A mechanistic model of PCR for accurate quanti of quantitative PCR data. PLoS One

A review on molecular topology: applying graph theory to drug discovery and design.

An environmental perspective on metabolism.

An integrative approach towards completing genome-scale metabolic networks.

Analysis of optimality in natural and perturbed metabolic networks.

Analytical note on certain rhythmic relations in organic systems.

Building and analysing genome-scale metabolic models. Biochem Soc Trans

Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics

Capturing the essence of a metabolic network: A ux balance analysis approach.

Combinatorial complexity of pathway analysis in metabolic networks.

Comparing ux balance analysis to network expansion: producibility, sustainability and the scope of compounds. Genome Inform

Computational reconstruction of tissue-speci metabolic models: application to human liver metabolism. Mol Syst Biol

Computing the shortest elementary ux modes in genome-scale metabolic networks. Bioinformatics

Detection of elementary ux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol

Determining all extreme semipositive conservation relations in chemical reaction systems: a test criterion for conservativity.

Energy balance for analysis of complex metabolic networks.

Expanding metabolic networks: scopes of compounds, robustness, and evolution.

Experimental validation of a predicted feedback loop in the multioscillator clock of Arabidopsis thaliana. Mol Syst Biol

Flux balance analysis accounting for metabolite dilution. Genome Biol

Fluxbalance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.

Functional classi of genome-scale metabolic networks.

Generalized concept of minimal cut sets in biochemical networks. Biosystems

Genome-scale metabolic model of Helicobacter pylori 26695.

Geometric Algorithms and Combinatorial Optimization,

Including metabolite concentrations into ux balance analysis: thermodynamic realizability as a constraint on ux distributions in metabolic networks.

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.

Integrating quantitative proteomics and metabolomics with a genomescale metabolic network model. Bioinformatics

KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2010), 38(Database issue),

Large-scale 13Cux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol

Metabolic control mechanisms. VII.A detailed computer model of the glycolytic pathway in Ascites cells.

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks.

Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics

MetaPath Online: a web server implementation of the network expansion algorithm.

Metatool: for studying metabolic networks. Bioinformatics

Minimal cut sets in biochemical reaction networks. Bioinformatics

Modeling the complex dynamics of enzyme-pathway coevolution. Chaos

Modular decomposition of metabolic systems via null-space analysis.

Notes on Linear Programming: Part I: The Generalized Simplex Method for Minimizing a Linear Form Under Linear Inequality Restraints.

Notice sur la loi que la population poursuit dans son accroissement. Correspondance mathmatique et physique (1838),

On algebraic properties of extreme pathways in metabolic networks.

On elementary ux modes in biochemical reaction systems at steady state.

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.

Oscillatory behavior in enzymatic control processes. Adv Enzyme Regul

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

Probabilistic Linguistics, chapter 5: Probability in Language Change,

Re algorithm and computer program for calculating all non-negative uxes admissible in steady states of biochemical reaction systems with or without some ux rates  Comput Appl Biosci

Recursive MILP model for  all the alternate optima in LP models for metabolic networks.

Regulatory on/o minimization of metabolic ux changes after genetic perturbations.

Self-oscillations in glycolysis. 1. A simple kinetic model.

Stochastic approaches in systems biology. Wiley Interdiscip Rev Syst Biol Med

Stoichiometric growth model for ribo avin-producing Bacillus subtilis. Biotechnol Bioeng

Structural analysis of expanding metabolic networks. Genome Inform

Systems approach to re genome annotation.

The application of ux balance analysis in systems biology. Wiley Interdiscip Rev Syst Biol Med

The biomass objective function.

The carbon assimilation network in escherichia coli is densely connected and largely sign-determined by directions of metabolic uxes. PLoS Comput Biol

The control of ux. Symp Soc Exp Biol

The eect of oxygen on biochemical networks and the evolution of complex life.

The Escherichia coli MG1655 in silico metabolic genotype: its de characteristics, and capabilities.

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2010), 38(Database issue),

The growing scope of applications of genome-scale metabolic reconstructions using escherichia coli. Nat Biotechnol

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

The origin and evolutoin of predator-prey theory. Ecology

The Regulation of Cellular Systems.

The regulatory network of E. coli metabolism as a boolean dynamical system exhibits both homeostasis and exibility of response.

The regulatory principles of glycolysis in erythrocytes in vivo and in vitro.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics

Theory for the systemic de of metabolic pathways and their use in interpreting metabolic function from a pathwayoriented perspective.

Thermodynamics-based metabolic ux analysis.

Variazioni e uttuazioni del numero dindividui in specie animali conviventi.

What is life?

Systems approaches to modelling pathways and networks.

peer reviewedIt has become commonly accepted that systems approaches to biology are of outstanding importance to gain understanding from the vast amount of data which is presently being generated by advancing high-throughput technologies. The diversity of methods to model pathways and networks has significantly expanded over the past two decades. Modern and traditional approaches are equally important and recent activities aim at integrating the advantages of both. While traditional methods, based on differential equations, are useful to study the dynamics of small systems, modern constraint-based models can be applied to genome-scale systems, but are not able to capture dynamic features. Integrating different approaches is important to develop consistent theoretical descriptions encompassing various scales of biological information. The rapid progress of the field of theoretical systems biology, however, demonstrates how our fundamental theoretical understanding of biology is gaining momentum. The scientific community has apparently accepted the challenge to truly understand the principles of life

Systems approaches to modelling pathways and networks.

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