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

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

(2020) Matthew L. Jenior et al.   PLoS Computational Biology

OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling

(2019) Fangzhou Shen et al.   PLoS Computational Biology

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

(2019) Laurent Heirendt et al.   Nature Protocols

iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6

(2019) Oscar Dias et al.   Frontiers in Microbiology

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

(2018) Emanuel Gonçalves et al.   METABOLIC ENGINEERING

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

(2018) Colton J. Lloyd et al.   PLoS Computational Biology

The Genome-Scale Integrated Networks in Microorganisms

(2018) Tong Hao et al.   Frontiers in Microbiology

Methods for automated genome-scale metabolic model reconstruction

(2018) José P. Faria et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

(2018) Alberto Santos-Zavaleta et al.   BMC BIOLOGY

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

(2018) Ye Gao et al.   NUCLEIC ACIDS RESEARCH

A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints

(2018) Sara Barbosa et al.   BIOSYSTEMS

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

(2018) Elizabeth Brunk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

(2017) Miguel C Teixeira et al.   NUCLEIC ACIDS RESEARCH

Global transcriptional regulatory network forEscherichia colirobustly connects gene expression to transcription factor activities

(2017) Xin Fang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

(2017) Zhuo Wang et al.   PLoS Computational Biology

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models

(2016) R.P. Vivek-Ananth et al.   BIOSYSTEMS

Multiplex methods provide effective integration of multi-omic data in genome-scale models

(2016) Claudio Angione et al.   BMC BIOINFORMATICS

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data

(2016) José P. Faria et al.   Frontiers in Microbiology

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

(2015) Dawn Thompson et al.   Annual Review of Cell and Developmental Biology

CoRegNet: reconstruction and integrated analysis of co-regulatory networks: Fig. 1.

(2015) Rémy Nicolle et al.   BIOINFORMATICS

FlexFlux: combining metabolic flux and regulatory network analyses

(2015) Lucas Marmiesse et al.   BMC Systems Biology

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

High-throughput bacterial functional genomics in the sequencing era

(2015) Andrew N Gray et al.   CURRENT OPINION IN MICROBIOLOGY

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

(2015) M. L. Arrieta-Ortiz et al.   Molecular Systems Biology

Reconstructing genome-scale metabolic models with merlin

(2015) Oscar Dias et al.   NUCLEIC ACIDS RESEARCH

Predictive analytics of environmental adaptability in multi-omic network models

(2015) Claudio Angione et al.   Scientific Reports

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

(2015) Shuyi Ma et al.   PLoS Computational Biology

Data-driven integration of genome-scale regulatory and metabolic network models

(2015) Saheed Imam et al.   Frontiers in Microbiology

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis

(2015) Serdar Turkarslan et al.   Scientific Data

iOD907, the first genome-scale metabolic model for the milk yeastKluyveromyces lactis

(2014) Oscar Dias et al.   Biotechnology Journal

Refining metabolic models and accounting for regulatory effects

(2014) Joonhoon Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

A system-level model for the microbial regulatory genome

(2014) A. N. Brooks et al.   Molecular Systems Biology

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Daniel Machado et al.   PLoS Computational Biology

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

(2013) Brian J. Schmidt et al.   BIOINFORMATICS

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

(2013) Claudine Chaouiya et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

(2013) J. P. Faria et al.   BRIEFINGS IN BIOINFORMATICS

Somewhat in control—the role of transcription in regulating microbial metabolic fluxes

(2013) Karl Kochanowski et al.   CURRENT OPINION IN BIOTECHNOLOGY

The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk

(2013) Anne de Jong et al.   PLoS One

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

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

(2013) Dmitry A. Rodionov et al.   Frontiers in Microbiology

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

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

(2012) Ali Navid 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

Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor–DNA Interactions with Expression Data: An Entropy-Based Approach

(2012) Guy Karlebach et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

(2012) P. S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

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

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

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Temporal Expression-based Analysis of Metabolism

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

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

(2012) Xin Fang et al.   PLoS Computational Biology

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

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

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

Using the reconstructed genome-scale human metabolic network to study physiology and pathology

(2011) A. Bordbar et al.   JOURNAL OF INTERNAL MEDICINE

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

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

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

(2010) Paul A. Jensen et al.   BIOINFORMATICS

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information

(2010) Paulo Vilaça et al.   BIOSYSTEMS

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

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

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

(2010) P. S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

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

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

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

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Towards environmental systems biology of Shewanella

(2008) James K. Fredrickson et al.   NATURE REVIEWS MICROBIOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

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