Reconstructing organisms in silico: genome-scale models and their emerging applications

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

(2020) Chao Ye et al.   BIOTECHNOLOGY AND BIOENGINEERING

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

(2020) Pierre Salvy et al.   Nature Communications

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

(2020) Gregory L. Medlock et al.   Cell Systems

Computational Modeling of the Human Microbiome

(2020) Shomeek Chowdhury et al.   Microorganisms

A biochemically-interpretable machine learning classifier for microbial GWAS

(2020) Erol S. Kavvas et al.   Nature Communications

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

(2020) David Heckmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen

(2019) Joanne K. Liu et al.   PLoS Computational Biology

Coupling S-adenosylmethionine–dependent methylation to growth: Design and uses

(2019) Hao Luo et al.   PLOS BIOLOGY

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

(2019) Sankha Ghatak et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Laurent Heirendt et al.   Nature Protocols

Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates

(2019) Charles J. Norsigian et al.   Frontiers in Cellular and Infection Microbiology

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

(2019) Laurence Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modelling approaches for studying the microbiome

(2019) Manish Kumar et al.   Nature Microbiology

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

(2019) Juan Nogales et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenomic Analysis Reveals the Evolutionary Route of Resistant Genes in Staphylococcus aureus

(2019) Jiffy John et al.   Genome Biology and Evolution

Expanding the uses of genome‐scale models with protein structures

(2019) Nathan Mih et al.   Molecular Systems Biology

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

(2019) Hongzhong Lu et al.   Nature Communications

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

(2019) Cristal Zuñiga et al.   Nature Microbiology

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

(2019) Charles J. Norsigian et al.   Nature Protocols

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

(2019) Bin Du et al.   PLoS Computational Biology

ssbio: a Python framework for structural systems biology

(2018) Nathan Mih et al.   BIOINFORMATICS

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

(2018) Xin Fang et al.   BMC Systems Biology

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

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

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

(2018) Charles J. Norsigian et al.   Frontiers in Genetics

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

(2018) Yara Seif et al.   Nature Communications

Pan-genomic analysis provides novel insights into the association of E.coli with human host and its minimal genome

(2018) Zhi-Kai Yang et al.   BIOINFORMATICS

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann 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

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

(2018) Xin Fang et al.   Frontiers in Microbiology

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

BioModels: expanding horizons to include more modelling approaches and formats

(2017) Mihai Glont et al.   NUCLEIC ACIDS RESEARCH

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

(2017) Ke Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities

(2017) Ali R. Zomorrodi et al.   Nature Communications

Metabolic Models of Protein Allocation Call for the Kinetome

(2017) Avlant Nilsson et al.   Cell Systems

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

(2017) Sjoerd Opdam et al.   Cell Systems

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

(2016) Joseph R. Peterson et al.   BMC GENOMICS

Systems biology of the structural proteome

(2016) Elizabeth Brunk et al.   BMC Systems Biology

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

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

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

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

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

(2016) Derrick E. Fouts et al.   PLoS Neglected Tropical Diseases

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

(2016) Hooman Hefzi et al.   Cell Systems

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

(2015) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

(2015) Laurence Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-driven discovery of underground metabolic functions inEscherichia coli

(2015) Gabriela I. Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

(2015) Kathryn E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

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

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

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

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

(2014) Adil Mardinoglu et al.   Nature Communications

MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data

(2014) Stephan Pabinger et al.   Database-The Journal of Biological Databases and Curation

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

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

(2013) D. McCloskey et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions

(2013) C. Y. Maurice Cheung et al.   PLANT JOURNAL

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

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

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

(2012) Michael J McAnulty 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

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Plant genome-scale metabolic reconstruction and modelling

(2012) Cristiana Gomes de Oliveira Dal’Molin et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

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

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

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

(2011) Colin T Archer et al.   BMC GENOMICS

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

(2011) Vinay Satish Kumar et al.   BMC Systems Biology

Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A

(2011) M. N. Benedict et al.   JOURNAL OF BACTERIOLOGY

Systems medicine and metabolic modelling

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

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

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

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

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim 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

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

(2011) S. Mintz-Oron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

(2010) Arnau Montagud et al.   BMC Systems Biology

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2010) Kai Zhuang et al.   ISME Journal

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

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

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

(2010) Radhakrishnan Mahadevan et al.   NATURE REVIEWS MICROBIOLOGY

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Metabolic Network Model of a Human Oral Pathogen

(2008) V. Mazumdar et al.   JOURNAL OF BACTERIOLOGY

Predicting synthetic rescues in metabolic networks

(2008) Adilson E Motter et al.   Molecular Systems Biology

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Modeling Hybridoma Cell Metabolism Using a Generic Genome-Scale Metabolic Model of Mus musculus

(2005) Kashif Sheikh et al.   BIOTECHNOLOGY PROGRESS