Software applications for flux balance analysis (Q26824185)

G. Koh

series ordinal

2

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B. K. S. Chung

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3

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D.-Y. Lee

series ordinal

4

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language of work or name

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January 2014

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Briefings in Bioinformatics

published in

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volume

15

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issue

1

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page(s)

108-22

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What is flux balance analysis?

cites work

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Flux balance analysis of biological systems: applications and challenges.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Metabolic modeling of a mutualistic microbial community.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Genome‐scale metabolic modeling of a clostridial co‐culture for consolidated bioprocessing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Emergent cooperation in microbial metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Advances in flux balance analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

VANTED: a system for advanced data analysis and visualization in the context of biological networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

OptFlux: an open-source software platform for in silico metabolic engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

The Systems Biology Research Tool: evolvable open-source software

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

BioMet Toolbox: genome-wide analysis of metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

FASIMU: flexible software for flux-balance computation series in large metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Structural and functional analysis of cellular networks with CellNetAnalyzer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

SNA--a toolbox for the stoichiometric analysis of metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

FBA-SimVis: interactive visualization of constraint-based metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Construction and completion of flux balance models from pathway databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

CycSim--an online tool for exploring and experimenting with genome-scale metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

High-throughput generation, optimization and analysis of genome-scale metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

FAME, the Flux Analysis and Modeling Environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Analysis of optimality in natural and perturbed metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Evolutionary programming as a platform for in silico metabolic engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Context-specific metabolic networks are consistent with experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

KEGG: Kyoto Encyclopedia of Genes and Genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

BRENDA, enzyme data and metabolic information

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

A protocol for generating a high-quality genome-scale metabolic reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

The RAST Server: rapid annotations using subsystems technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Optimization based automated curation of metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

MFAML: a standard data structure for representing and exchanging metabolic flux models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

CellML: its future, present and past

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

METATOOL: for studying metabolic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

GrowMatch: an automated method for reconciling in silico/in vivo growth predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Expert system for predicting protein localization sites in gram-negative bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Accelerating the reconstruction of genome-scale metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Transcriptional regulation in constraints-based metabolic models of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Functional integration of a metabolic network model and expression data without arbitrary thresholding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Predicting selective drug targets in cancer through metabolic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Large-scale bi-level strain design approaches and mixed-integer programming solution techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Constraints-based genome-scale metabolic simulation for systems metabolic engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

Network-based prediction of human tissue-specific metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

inferred from DOI database lookup

7 January 2021

based on heuristic

iMAT: an integrative metabolic analysis tool

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS069

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1093/BIB/BBS069

1 reference

Consolidated OpenCitations Corpus – April 2017

journals/bib/LakshmananKCL14

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

Consolidated OpenCitations Corpus – April 2017

PubMed publication ID

23131418

1 reference

Consolidated OpenCitations Corpus – April 2017