ReviewBriefings in bioinformatics2021
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
122 citing papers in PubMed.
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- Genome Database for Vaccinium: a knowledgebase for genetics, genomics, and breeding research.Genetics · 2026Article
- Identification of specific metabolic capacities associated with major extraintestinal pathogenicJournal of bacteriology · 2026Article
- Magnetoreception in a freshwater ciliate arises from endosymbiosis.Nature communications · 2026Article
- Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy.The Plant cell · 2026Article
- DMEM and EMEM as alternate growth media for pathogenic Leptospira.PLoS neglected tropical diseases · 2026Article
- Persistent effects of early-life arsenic exposure inEnvironmental science. Processes & impacts · 2026Article
- LumbriCyc: towards metabolic modelling of earthworms.NPJ systems biology and applications · 2026Article
- Sequencing and Analysis of Chicken Segmented Filamentous Bacteria Genome Revealed Unique Avian-Specific Features.Microorganisms · 2026Article
- Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- MagnetotacticISME communications · 2026Article
- Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with thePeerJ · 2026Article
- Impaired antioxidant defense associated with flavonoid biosynthesis reprogramming in the mangroveFrontiers in plant science · 2026Article
- Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivatedISME communications · 2026Article
- Blood metabolites mediate causal inference studies on the effect of gut microbiota on the risk of vascular calcification.Journal of advanced research · 2026Article
- Substrate complexity and species number jointly shift the balance between competition and facilitation in a chitin-degrading bacterial consortium.ISME communications · 2026Article
- The genome-scale sugar metabolic model fromCurrent research in microbial sciences · 2026Article
62 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
motivationBiological systems function through dynamic interactions among genes and their products, regulatory circuits and metabolic networks. Our development of the Pathway Tools software was motivated by the need to construct biological knowledge resources that combine these many types of data, and that enable users to find and comprehend data of interest as quickly as possible through query and visualization tools. Further, we sought to support the development of metabolic flux models from pathway databases, and to use pathway information to leverage the interpretation of high-throughput data sets.
resultsIn the past 4 years we have enhanced the already extensive Pathway Tools software in several respects. It can now support metabolic-model execution through the Web, it provides a more accurate gap filler for metabolic models; it supports development of models for organism communities distributed across a spatial grid; and model results may be visualized graphically. Pathway Tools supports several new omics-data analysis tools including the Omics Dashboard, multi-pathway diagrams called pathway collages, a pathway-covering algorithm for metabolomics data analysis and an algorithm for generating mechanistic explanations of multi-omics data. We have also improved the core pathway/genome databases management capabilities of the software, providing new multi-organism search tools for organism communities, improved graphics rendering, faster performance and re-designed gene and metabolite pages. AVAILABILITY: The software is free for academic use; a fee is required for commercial use. See http://pathwaytools.com. CONTACT: pkarp@ai.sri.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Briefings in Bioinformatics online.
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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.