(Q38529047)

3 September 2017

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title

Genome scale models of yeast: towards standardized evaluation and consistent omic integration (English)

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3 September 2017

2

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3 September 2017

Benjamín J Sánchez

1

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publication date

1 August 2015

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3 September 2017

number of pages

13

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based on heuristic

inferred from page(s)

published in

Integrative Biology

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3 September 2017

volume

7

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3 September 2017

issue

8

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3 September 2017

page(s)

846-858

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Yeast as a model organism

3 September 2017

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The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

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What is flux balance analysis?

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Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

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Regulatory on/off minimization of metabolic flux changes after genetic perturbations

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Functional profiling of the Saccharomyces cerevisiae genome

21 January 2018

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Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

21 January 2018

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Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

21 January 2018

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Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

21 January 2018

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Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

21 January 2018

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Recent advances in the reconstruction of metabolic models and integration of omics data

21 January 2018

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Integration of expression data in genome-scale metabolic network reconstructions

21 January 2018

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What mRNA Abundances Can Tell us about Metabolism

21 January 2018

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Integration of gene expression data into genome-scale metabolic models

21 January 2018

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Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae.

21 January 2018

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Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations.

21 January 2018

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Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies

21 January 2018

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Inferring metabolic states in uncharacterized environments using gene-expression measurements

21 January 2018

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Prediction of metabolic flux distribution from gene expression data based on the flux minimization principle

21 January 2018

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Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

21 January 2018

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TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

21 January 2018

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Metabolic constraint-based refinement of transcriptional regulatory networks

21 January 2018

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Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism

21 January 2018

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Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools

21 January 2018

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Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious

21 January 2018

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Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

21 January 2018

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Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism

21 January 2018

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Uncovering transcriptional regulation of metabolism by using metabolic network topology

21 January 2018

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Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

21 January 2018

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Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation

21 January 2018

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A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae.

21 January 2018

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Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.

21 January 2018

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Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

21 January 2018

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Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast.

21 January 2018

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Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast

21 January 2018

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AMBIENT: Active Modules for Bipartite Networks--using high-throughput transcriptomic data to dissect metabolic response

21 January 2018

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Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae

21 January 2018

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Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae

21 January 2018

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Filling gaps in a metabolic network using expression information

21 January 2018

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Identifying metabolic enzymes with multiple types of association evidence

21 January 2018

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Thermodynamic analysis of fermentation and anaerobic growth of baker's yeast for ethanol production

21 January 2018

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Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

21 January 2018

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Epistatic interaction maps relative to multiple metabolic phenotypes

21 January 2018

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Plasticity of genetic interactions in metabolic networks of yeast

21 January 2018

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An integrated approach to characterize genetic interaction networks in yeast metabolism

21 January 2018

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Dynamic epistasis for different alleles of the same gene

21 January 2018

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Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks

21 January 2018

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Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

21 January 2018

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Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways

21 January 2018

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Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

21 January 2018

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anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

21 January 2018

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System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes

21 January 2018

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Network thermodynamic curation of human and yeast genome-scale metabolic models.

21 January 2018

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Systematic construction of kinetic models from genome-scale metabolic networks

21 January 2018

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From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

21 January 2018

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Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures

21 January 2018

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Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture

21 January 2018

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Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae

21 January 2018

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Quantitative modeling of triacylglycerol homeostasis in yeast--metabolic requirement for lipolysis to promote membrane lipid synthesis and cellular growth

21 January 2018

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Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures.

21 January 2018

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Expanding a dynamic flux balance model of yeast fermentation to genome-scale

21 January 2018

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Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures

21 January 2018

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Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis

21 January 2018

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Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

21 January 2018

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A reliable simulator for dynamic flux balance analysis

21 January 2018

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DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

21 January 2018

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Dynamic model-based analysis of furfural and HMF detoxification by pure and mixed batch cultures of S. cerevisiae and S. stipitis

21 January 2018

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Dynamic flux balance analysis of batch fermentation: effect of genetic manipulations on ethanol production

21 January 2018

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MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis

21 January 2018

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k-OptForce: integrating kinetics with flux balance analysis for strain design

21 January 2018

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Towards a genome-scale kinetic model of cellular metabolism

21 January 2018

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BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

21 January 2018

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Dynamic flux balance analysis of diauxic growth in Escherichia coli

21 January 2018

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Modelling dynamic processes in yeast.

21 January 2018

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Metabolic control theory: a structural approach.

21 January 2018

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Production of biofuels and biochemicals: in need of an ORACLE.

21 January 2018

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Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.

21 January 2018

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Redox balance is key to explaining full vs. partial switching to low-yield metabolism

21 January 2018

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Yeast cells with impaired drug resistance accumulate glycerol and glucose.

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Yeast dynamic metabolic flux measurement in nutrient-rich media by HPLC and accelerator mass spectrometry

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export.

21 January 2018

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Integration of metabolome data with metabolic networks reveals reporter reactions

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Flux coupling analysis of genome-scale metabolic network reconstructions.

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Metabolic networks in motion: 13C-based flux analysis

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC5IB00083A

Improving collaboration by standardization efforts in systems biology.

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

21 January 2018

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SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

21 January 2018

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The European Bioinformatics Institute's data resources: towards systems biology

21 January 2018

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Enhancement of the chemical semantic web through the use of InChI identifiers

21 January 2018

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MIPS: curated databases and comprehensive secondary data resources in 2010

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC5IB00083A

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC5IB00083A

Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect in Saccharomyces cerevisiae and explaining evolutionary trade-offs of adaptation to galactose through systems biology

21 January 2018

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https://api.crossref.org/works/10.1039%2FC5IB00083A

The integrated response of primary metabolites to gene deletions and the environment

21 January 2018

1 reference

24 October 2022

https://opencitations.net/index/coci/api/v1/citations/10.1039/C2MB25423A

Identifiers

DOI

10.1039/C5IB00083A

1 reference

3 September 2017

1 reference