Applications of genome-scale metabolic network model in metabolic engineering

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

(2014) Miguel A. Campodonico et al.   METABOLIC ENGINEERING

Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production

(2014) Justyna Nocon et al.   METABOLIC ENGINEERING

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation

(2013) Nicolas A. L. Flahaut et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

Metabolic engineering ofEscherichia colifor the production of fumaric acid

(2013) Chan Woo Song et al.   BIOTECHNOLOGY AND BIOENGINEERING

Flux-coupled genes and their use in metabolic flux analysis

(2013) Hyun Uk Kim et al.   Biotechnology Journal

Computational evaluation ofSynechococcussp. PCC 7002 metabolism for chemical production

(2013) Trang T. Vu et al.   Biotechnology Journal

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering

(2013) Cameron Cotten et al.   Biotechnology Journal

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

(2013) Tobias Österlund et al.   BMC Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

(2013) Sergio Rossell et al.   PLoS Computational Biology

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

COFACTOR MODIFICATION ANALYSIS: A COMPUTATIONAL FRAMEWORK TO IDENTIFY COFACTOR SPECIFICITY ENGINEERING TARGETS FOR STRAIN IMPROVEMENT

(2013) MEIYAPPAN LAKSHMANAN et al.   Journal of Bioinformatics and Computational Biology

Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture

(2012) Suresh Selvarasu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

(2012) Nadine Töpfer et al.   BMC Systems Biology

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

(2012) Benjamin D Heavner et al.   BMC Systems Biology

Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

(2012) Ali Navid et al.   BMC Systems Biology

Flux variability scanning based on enforced objective flux for identifying gene amplification targets

(2012) Jong Park et al.   BMC Systems Biology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

(2012) Aarash Bordbar et al.   Molecular Systems Biology

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

(2012) Aaron Brandes et al.   PLoS One

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Temporal Expression-based Analysis of Metabolism

(2012) Sara B. Collins et al.   PLoS Computational Biology

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

(2012) Joonhoon Kim et al.   GENOME BIOLOGY

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

(2011) Pablo Carbonell et al.   BMC Systems Biology

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

(2011) Paul A Jensen et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

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

(2011) Jan Schellenberger et al.   Nature Protocols

GLAMM: Genome-Linked Application for Metabolic Maps

(2011) J. T. Bates et al.   NUCLEIC ACIDS RESEARCH

In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production

(2010) H. S. Choi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Microbial 1-butanol production: Identification of non-native production routes andin silicoengineering interventions

(2010) Sridhar Ranganathan et al.   Biotechnology Journal

Genome-scale metabolic model of methylotrophic yeastPichia pastorisand its use forin silicoanalysis of heterologous protein production

(2010) Seung Bum Sohn et al.   Biotechnology Journal

Prediction of novel synthetic pathways for the production of desired chemicals

(2010) Ayoun Cho et al.   BMC Systems Biology

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

(2010) Isabel Rocha et al.   BMC Systems Biology

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

CASOP: A Computational Approach for Strain Optimization aiming at high Productivity

(2010) Oliver Hädicke et al.   JOURNAL OF BIOTECHNOLOGY

The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies

(2010) Kyung Lee et al.   Microbial Cell Factories

Improved vanillin production in baker's yeast through in silico design

(2010) Ana Brochado et al.   Microbial Cell Factories

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

(2010) Livnat Jerby et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

PathPred: an enzyme-catalyzed metabolic pathway prediction server

(2010) Y. Moriya et al.   NUCLEIC ACIDS RESEARCH

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

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

(2009) N. Tepper et al.   BIOINFORMATICS

Metabolic engineering ofEscherichia colifor the production of polylactic acid and its copolymers

(2009) Yu Kyung Jung et al.   BIOTECHNOLOGY AND BIOENGINEERING

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

(2009) Bevan Chung et al.   BMC Systems Biology

Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties

(2009) Guido Melzer et al.   BMC Systems Biology

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

(2009) Rogier J P van Berlo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

(2009) Yohei Shinfuku et al.   Microbial Cell Factories

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Integration of Metabolic Modeling and Phenotypic Data in Evaluation and Improvement of Ethanol Production Using Respiration-Deficient Mutants of Saccharomyces cerevisiae

(2008) D. Dikicioglu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

(2008) Joungmin Lee et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

DESHARKY: automatic design of metabolic pathways for optimal cell growth

(2008) Guillermo Rodrigo et al.   BIOINFORMATICS

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology