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Article
Open AccessGenome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation
Pseudomonas aeruginosa is one of the leading causes of hospital-acquired infections. To decipher the metabolic mechanisms associated with virulence and antibiotic resistance, we have developed an updated genome-s...
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Article
Open AccessAn updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism
Mucins are present in mucosal membranes throughout the body and play a key role in the microbe clearance and infection prevention. Understanding the metabolic responses of pathogens to mucins will further enab...
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Article
Open AccessCurating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus
Staphylococcus aureus is a high-priority pathogen causing severe infections with high morbidity and mortality worldwide. Many S. aureus strains are methicillin-resistant (MRSA) or even multi-drug resistant. It is...
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Protocol
Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications
Genome-scale metabolic modeling is and will continue to play a central role in computational systems metabolic engineering and synthetic biology applications for the productions of chemicals and antibiotics. T...
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Article
Open AccessAuthor Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Open AccessVisualizing metabolic network dynamics through time-series metabolomic data
New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring t...
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Article
Open AccessCOVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
Researchers around the world join forces to reconstruct the molecular processes of the virus-host interactions aiming to combat the cause of the ongoing pandemic.
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Article
Open AccessPublisher Correction: MEMOTE for standardized genome-scale metabolic model testing
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
MEMOTE for standardized genome-scale metabolic model testing
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Article
Open AccessThe 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes
The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was “Methods, tools and platforms for Personalised Medicine in the Big Data Era”, bu...
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Protocol
Insights into Dynamic Network States Using Metabolomic Data
Metabolomic data is the youngest of the high-throughput data types; however, it is potentially one of the most informative, as it provides a direct, quantitative biochemical phenotype. There are a number of wa...
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Article
Recon3D enables a three-dimensional view of gene variation in human metabolism
Large-scale integration of metabolite and protein structural data with existing networks of human metabolism provides insights into gene function and how drugs affect metabolic response.
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Article
Open AccessEvaluation of rate law approximations in bottom-up kinetic models of metabolism
The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often address...
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Article
Open AccessSBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks
The size and complexity of published biochemical network reconstructions are steadily increasing, expanding the potential scale of derived computational models. However, the construction of large biochemical n...
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Article
Open AccessSBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not re...
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Article
Open AccessParkinson’s disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein
Parkinson’s disease is an age-related disease whose pathogenesis is not completely known. Animal models exist for investigating the disease but not all results can be easily transferred to humans. Therefore, m...
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Article
Open AccessPath2Models: large-scale generation of computational models from biochemical pathway maps
Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature...
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Article
Open AccessThe systems biology simulation core algorithm
With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems...
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Article
Open AccessPrecise generation of systems biology models from KEGG pathways
The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, th...
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Chapter
Automating Mathematical Modeling of Biochemical Reaction Networks
In this chapter we introduce a five-step modeling pipeline that ultimately leads to a mathematical description of a biochemical reaction system. We discuss how to automate each individual step and how to put t...
