Genome-scale metabolic network models: from first-generation to next-generation

A genome‐scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures

(2021) Song‐Min Schinn et al.   BIOTECHNOLOGY AND BIOENGINEERING

Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism

(2021) Christopher Pries et al.   Scientific Reports

Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance

(2021) Joshua E. Lewis et al.   Nature Communications

Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava

(2021) Ratchaprapa Kamsen et al.   Scientific Reports

A multi-objective hybrid machine learning approach-based optimization for enhanced biomass and bioactive phycobiliproteins production in Nostoc sp. CCC-403

(2021) Dinesh Kumar Saini et al.   BIORESOURCE TECHNOLOGY

Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice

(2021) Yu-Te Lin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Integrated knowledge mining, genome-scale modeling, and machine learning for predicting Yarrowia lipolytica bioproduction

(2021) Jeffrey J. Czajka et al.   METABOLIC ENGINEERING

Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models

(2021) Xue Yang et al.   METABOLIC ENGINEERING

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

(2021) Omid Oftadeh et al.   Nature Communications

A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation

(2021) David Henriques et al.   mSystems

Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms

(2021) Nicole Pearcy et al.   mSystems

Comprehensive understanding of Saccharomyces cerevisiae phenotypes with whole‐cell model WM_S288C

(2020) Chao Ye et al.   BIOTECHNOLOGY AND BIOENGINEERING

Improving lysine production through construction of an Escherichia coli enzyme‐constrained model

(2020) Chao Ye et al.   BIOTECHNOLOGY AND BIOENGINEERING

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

(2020) Fernando Cruz et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

(2019) Ilaria Massaiu et al.   Microbial Cell Factories

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

Pan-cancer analysis of the metabolic reaction network

(2019) F. Gatto et al.   METABOLIC ENGINEERING

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Genome scale metabolic models as tools for drug design and personalized medicine

(2018) Vytautas Raškevičius et al.   PLoS One

Towards predicting the environmental metabolome from metagenomics with a mechanistic model

(2018) Daniel R. Garza et al.   Nature Microbiology

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

(2018) Yara Seif et al.   Nature Communications

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

(2018) Hao Wang et al.   PLoS Computational Biology

Genome-scale metabolic modelling common cofactors metabolism in microorganisms

(2017) Nan Xu et al.   JOURNAL OF BIOTECHNOLOGY

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models

(2017) Chao Ye et al.   Scientific Reports

IdealKnock: A framework for efficiently identifying knockout strategies leading to targeted overproduction

(2016) Deqing Gu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Comparative genome-scale modelling ofStaphylococcus aureusstrains identifies strain-specific metabolic capabilities linked to pathogenicity

(2016) Emanuele Bosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

(2016) Ali Khodayari et al.   Nature Communications

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina

(2015) Chao Ye et al.   BMC Systems Biology

Cancer biomarker detection: recent achievements and challenges

(2015) Li Wu et al.   CHEMICAL SOCIETY REVIEWS

The principles of whole-cell modeling

(2015) Jonathan R Karr et al.   CURRENT OPINION IN MICROBIOLOGY

Deep learning

(2015) Yann LeCun et al.   NATURE

Reconstructing genome-scale metabolic models with merlin

(2015) Oscar Dias et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

(2015) Shuyi Ma et al.   PLoS Computational Biology

The future of whole-cell modeling

(2014) Derek N Macklin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production

(2014) Chao Ye et al.   JOURNAL OF BIOTECHNOLOGY

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

(2014) J. Carrera et al.   Molecular Systems Biology

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

(2014) R. Agren et al.   Molecular Systems Biology

Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model

(2014) M. Simons et al.   PLANT PHYSIOLOGY

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

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

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints

(2013) Shaogang Ren et al.   BMC BIOINFORMATICS

Development of a minimal chemically defined medium for Ketogulonicigenium vulgare WSH001 based on its genome-scale metabolic model

(2013) Shicun Fan et al.   JOURNAL OF BIOTECHNOLOGY

Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis

(2013) Xueyang Feng et al.   Microbial Cell Factories

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

(2013) Zixiang Xu et al.   PLoS One

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

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective

(2013) Graham Rockwell et al.   PLoS Computational Biology

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

(2012) Yuliang Wang et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

An integrated computational and experimental study for overproducing fatty acids in Escherichia coli

(2012) Sridhar Ranganathan et al.   METABOLIC ENGINEERING

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

(2012) Steven M. Kelk et al.   Scientific Reports

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

(2011) Jan Schellenberger et al.   Nature Protocols

Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques

(2011) Joonhoon Kim et al.   PLoS One

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

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

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

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

Functional Characterization of Alternate Optimal Solutions of Escherichia coli's Transcriptional and Translational Machinery

(2010) Ines Thiele et al.   BIOPHYSICAL JOURNAL

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

(2010) Fahimeh Salimi et al.   Biotechnology Journal

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

(2010) Joonhoon Kim et al.   BMC Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

What are biomarkers?

(2010) Kyle Strimbu et al.   Current Opinion in HIV and AIDS

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

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

Flux balance analysis accounting for metabolite dilution

(2010) Tomer Benyamini et al.   GENOME BIOLOGY

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

(2009) N. Tepper et al.   BIOINFORMATICS

Flux balance analysis: A geometric perspective

(2009) Kieran Smallbone et al.   JOURNAL OF THEORETICAL BIOLOGY

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

(2008) Markus W. Covert et al.   BIOINFORMATICS

Context-Specific Metabolic Networks Are Consistent with Experiments

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