ArticleNucleic acids research2020
Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.Biology · 2026Article
- NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks.Bioinformatics (Oxford, England) · 2026Article
- Comparing metabolic engineering scenarios using simulated design-build-test-learn-cycles.Frontiers in bioengineering and biotechnology · 2026Article
- Article
- MicroMap: a network visualisation resource for human microbiome metabolism.NPJ biofilms and microbiomes · 2025Article
- GBA Solver: a user-friendly web server for growth balance analysis.Bioinformatics (Oxford, England) · 2025Article
- Article
- Identification of essential genes by transposon insertion sequencing and genome-scale metabolic model construction inMicrobiology spectrum · 2025Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Article
- ScyNet: Visualizing interactions in community metabolic models.Bioinformatics advances · 2024Article
- State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs.Microorganisms · 2023Review
- Metabolism-associated molecular classification of cervical cancer.BMC women's health · 2023Article
- Disease-specific loss of microbial cross-feeding interactions in the human gut.Nature communications · 2023Article
- Unveiling metabolic pathways involved in the extreme desiccation tolerance of an Atacama cyanobacterium.Scientific reports · 2023Article
- Adapting modeling and simulation credibility standards to computational systems biology.Journal of translational medicine · 2023Review
- FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data.Nucleic acids research · 2023Article
- CAVE: a cloud-based platform for analysis and visualization of metabolic pathways.Nucleic acids research · 2023Article
- Supplementation of Sulfide or Acetate and 2-Mercaptoethane Sulfonate Restores Growth of theMicroorganisms · 2023Article
- Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism?PloS one · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing has paved the way for the reconstruction of genome-scale metabolic networks as a powerful tool for understanding metabolic circuits in any organism. However, the visualization and extraction of knowledge from these large networks comprising thousands of reactions and metabolites is a current challenge in need of user-friendly tools. Here we present Fluxer (https://fluxer.umbc.edu), a free and open-access novel web application for the computation and visualization of genome-scale metabolic flux networks. Any genome-scale model based on the Systems Biology Markup Language can be uploaded to the tool, which automatically performs Flux Balance Analysis and computes different flux graphs for visualization and analysis. The major metabolic pathways for biomass growth or for biosynthesis of any metabolite can be interactively knocked-out, analyzed and visualized as a spanning tree, dendrogram or complete graph using different layouts. In addition, Fluxer can compute and visualize the k-shortest metabolic paths between any two metabolites or reactions to identify the main metabolic routes between two compounds of interest. The web application includes >80 whole-genome metabolic reconstructions of diverse organisms from bacteria to human, readily available for exploration. Fluxer enables the efficient analysis and visualization of genome-scale metabolic models toward the discovery of key metabolic pathways.
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Registered trials
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 Socratic graph.