ArticleNucleic acids research2020
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.
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 162 papers.
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Who cites it
162 citing papers in PubMed.
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- Metabolic Modelling Facilitates the Design of Synthetic Communities by Simplifying Natural Microbial Communities.Environmental microbiology · 2026Article
- MechAInistic: A Reviewer-Supervised Multi-Agent LLM System for Auditable Mechanistic Drug-Hypothesis Generation.bioRxiv : the preprint server for biology · 2026Article
- Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.Science advances · 2026Article
- Heterologous production of a plant biostimulant in Streptomyces albidoflavus.Applied microbiology and biotechnology · 2026Article
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- Model-based inference of enzyme inhibitions from perturbation-induced metabolic dynamics.bioRxiv : the preprint server for biology · 2026Article
- Enumeration of Autocatalytic Subsystems in Large Chemical Reaction Networks.Journal of chemical theory and computation · 2026Article
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
- Article
- NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks.Bioinformatics (Oxford, England) · 2026Article
- Defining metabolic niches for marine microbial heterotrophs.Science advances · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Reconstruction of human metabolic models with large language models.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The return of metabolism: biochemistry and physiology of glycolysis.Biological reviews of the Cambridge Philosophical Society · 2026Review
- Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
- In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.Microbiome · 2026Article
102 more citing papers are in PubMed but not listed here.
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models.
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