ArticleBMC systems biology2013
Sybil--efficient constraint-based modelling in R.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 1 of them a synthesis that pooled it.
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Who cites it
79 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Leveraging genome-scale metabolic models to understand aerobic methanotrophs.The ISME journal · 2024Pooled it
- Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome.Gut microbes · 2026Article
- Dietary patterns influence the in silico GABA production capacity of Bifidobacterium adolescentis HD17T2H and other human gut bacteria.Scientific reports · 2026Article
- Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.mSystems · 2026Article
- Comparative phenotypic and genomic analysis of the methanogen Methanomethylovorans thermophila L2FAW and its phylogenomic placement within the Genome Taxonomy Database.Access microbiology · 2026Article
- Cross-species engraftment biases and metabolic divergence in gnotobiotic mice humanized with ulcerative colitis microbiota.Gut microbes · 2025Article
- A multi-omic characterization of the physiological responses to salt stress in Scenedesmus obliquus UTEX393.Communications biology · 2025Article
- Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.Nature communications · 2025Article
- Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota.Molecular systems biology · 2025Article
- Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.Nature microbiology · 2025Article
- Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes.Computational and structural biotechnology journal · 2025Article
- pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.Genome biology · 2024Article
- Genome and Compound Analysis of Sioxanthin-Producing Marine Actinobacterium Micromonospora sp. nov. Strain SH-82 Isolated from Sponge Scopalina hapalia.Current microbiology · 2024Article
- Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy.Life science alliance · 2024Article
- Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.Microbiology spectrum · 2024Article
- Changes in Bacterial Gut Composition in Parkinson's Disease and Their Metabolic Contribution to Disease Development: A Gut Community Reconstruction Approach.Microorganisms · 2024Article
- Prediction of Response to Systemic Corticosteroids in Active UC by Microbial Composition-A Prospective Multicenter Study.Inflammatory bowel diseases · 2024Article
- Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO.Microbiology spectrum · 2023Article
- Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability.The ISME journal · 2023Article
- Optimal density of bacterial cells.PLoS computational biology · 2023Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundConstraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the automated search for model improvements. Furthermore, available implementations cannot easily be extended or adapted by users.
resultsHere, we present sybil, an open source software library for constraint-based analyses in R; R is a free, platform-independent environment for statistical computing and graphics that is widely used in bioinformatics. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), MOMA, and ROOM that are about ten times faster than previous implementations when calculating the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic model.
conclusionsDue to the object-oriented architecture of sybil, users can easily build analysis pipelines in R or even implement their own constraint-based algorithms. Based on its highly efficient communication with different mathematical optimisation programs, sybil facilitates the exploration of high-dimensional optimisation problems on small time scales. Sybil and all its dependencies are open source. Sybil and its documentation are available for download from the comprehensive R archive network (CRAN).
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