The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water

(2019) Héctor Alejandro Ruiz-Moreno et al.   ECOLOGICAL MODELLING

Experimental testing of a spatiotemporal metabolic model for carbon monoxide fermentation with Clostridium autoethanogenum

(2018) Jin Chen et al.   BIOCHEMICAL ENGINEERING JOURNAL

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

PlantSEED Enables Automated Annotation and Reconstruction of Plant Primary Metabolism with Improved Compartmentalization and Comparative Consistency

(2018) Samuel M. D. Seaver et al.   PLANT JOURNAL

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling

(2018) Cheng Zhang et al.   Frontiers in Physiology

Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Improvement

(2018) Jian Li et al.   Genes

Combining multiple functional annotation tools increases coverage of metabolic annotation

(2018) Marc Griesemer et al.   BMC GENOMICS

Reframing gene essentiality in terms of adaptive flexibility

(2018) Gabriela I. Guzmán et al.   BMC Systems Biology

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

(2018) Joana C. Xavier et al.   PLoS Computational Biology

A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

(2018) Christian Lieven et al.   Frontiers in Microbiology

Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus

(2017) Junhua Wang et al.   Microbial Cell Factories

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

(2017) Sebastián N. Mendoza et al.   Frontiers in Microbiology

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

(2017) Aarash Bordbar et al.   Scientific Reports

Metabolic Reconstruction and Modeling Microbial Electrosynthesis

(2017) Christopher W. Marshall et al.   Scientific Reports

Modeling central metabolism and energy biosynthesis across microbial life

(2016) Janaka N. Edirisinghe et al.   BMC GENOMICS

Network-based metabolic analysis and microbial community modeling

(2016) Cesar Cardona et al.   CURRENT OPINION IN MICROBIOLOGY

Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen

(2016) Esteban Marcellin et al.   GREEN CHEMISTRY

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation

(2016) Jin Chen et al.   METABOLIC ENGINEERING

Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli

(2016) Björn-Johannes Harder et al.   METABOLIC ENGINEERING

Rewriting yeast central carbon metabolism for industrial isoprenoid production

(2016) Adam L. Meadows et al.   NATURE

Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions

(2016) Cristal Zuñiga et al.   PLANT PHYSIOLOGY

Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments

(2016) Tong Ding et al.   PLoS One

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

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

(2016) George C. diCenzo et al.   Nature Communications

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

(2016) Ali Khodayari et al.   Nature Communications

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets

(2016) Daniel Hartleb et al.   PLoS Computational Biology

Improving prediction fidelity of cellular metabolism with kinetic descriptions

(2015) Anupam Chowdhury et al.   CURRENT OPINION IN BIOTECHNOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa 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

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

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

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

(2015) James G Jeffryes et al.   Journal of Cheminformatics

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

(2015) Samuel M. D. Seaver et al.   Frontiers in Plant Science

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Long-term phenotypic evolution of bacteria

(2014) Germán Plata et al.   NATURE

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves

(2014) C. Y. M. Cheung et al.   PLANT PHYSIOLOGY

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

(2014) Samuel M. D. Seaver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

(2013) M. Ganter et al.   BIOINFORMATICS

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

In silico aided metabolic engineering of Klebsiella oxytoca and fermentation optimization for enhanced 2,3-butanediol production

(2013) Jong Myoung Park et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford et al.   PLoS One

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

(2012) Elad Noor et al.   BIOINFORMATICS

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

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

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 multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC 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

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

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL

ExplorEnz: the primary source of the IUBMB enzyme list

(2008) A. G. McDonald et al.   NUCLEIC ACIDS RESEARCH