ArticlePlant physiology2014
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803.
Article in Plant physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A quantitative description of light-limited cyanobacterial growth using flux balance analysis.PLoS computational biology · 2024Article
- Channeling Anabolic Side Products toward the Production of Nonessential Metabolites: Stable Malate Production inACS synthetic biology · 2021Article
- Article
- Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield.PLoS computational biology · 2018Article
- Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth.Biotechnology for biofuels · 2018Article
- Model-based quantification of metabolic interactions from dynamic microbial-community data.PloS one · 2017Article
- Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects.Life (Basel, Switzerland) · 2016Review
- Different strategies of metabolic regulation in cyanobacteria: from transcriptional to biochemical control.Scientific reports · 2016Article
- Chirality Matters: Synthesis and Consumption of the d-Enantiomer of Lactic Acid by Synechocystis sp. Strain PCC6803.Applied and environmental microbiology · 2016Article
- Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.Frontiers in microbiology · 2016Review
- Slr1670 from Synechocystis sp. PCC 6803 Is Required for the Re-assimilation of the Osmolyte Glucosylglycerol.Frontiers in microbiology · 2016Article
- Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach.Frontiers in bioengineering and biotechnology · 2016Review
- Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models.PLoS computational biology · 2015Article
- Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure.Frontiers in microbiology · 2015Article
- BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.Nucleic acids research · 2014Article
- Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria.Frontiers in genetics · 2014Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Data integration is a central activity in systems biology. The integration of genomic, transcript, protein, metabolite, flux, and computational data yields unprecedented information about the system level functioning of organisms. Often, data integration is done purely computationally, leaving the user with little insight in addition to statistical information. In this article, we present a visualization tool for the metabolic network of Synechocystis sp. PCC 6803, an important model cyanobacterium for sustainable biofuel production. We illustrate how this metabolic map can be used to integrate experimental and computational data for Synechocystis sp. PCC 6803 systems biology and metabolic engineering studies. Additionally, we discuss how this map, and the software infrastructure that we supply with it, can be used in the development of other organism-specific metabolic network visualizations. In addition to the Python console package VoNDA (http://vonda.sf.net), we provide a working demonstration of the interactive metabolic map and the associated Synechocystis sp. PCC 6803 genome-scale stoichiometric model, as well as various ready-to-visualize microarray data sets, at http://f-a-m-e.org/synechocytis.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.