ArticleBriefings in bioinformatics2016
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.
Article in Briefings in bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 154 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
154 citing papers in PubMed.
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- The EcoCyc database (2025).EcoSal Plus · 2025Review
- Identifying Modulators of the Post-Antibiotic Effect.ACS infectious diseases · 2025Article
- Proteomic profiling of zinc homeostasis mechanisms in Pseudomonas aeruginosa through data-dependent and data-independent acquisition mass spectrometry.Metallomics : integrated biometal science · 2025Article
- Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.npj antimicrobials and resistance · 2025Article
- Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways.PLoS computational biology · 2025Article
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.eLife · 2025Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Interspecies interactions mediated by arginine metabolism enhance the stress tolerance ofMicrobiology spectrum · 2025Article
- Proteomic profiling of zinc homeostasis mechanisms inbioRxiv : the preprint server for biology · 2025Article
- Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens.Nature microbiology · 2025Article
- Isolation and characterization of aApplied and environmental microbiology · 2024Article
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- Unveiling biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2.BMC genomics · 2024Article
- The Comparative Genome Dashboard.bioRxiv : the preprint server for biology · 2024Article
- Strategies for tailoring functional microbial synthetic communities.The ISME journal · 2024Review
- RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.Nucleic acids research · 2024Article
- The Comparative Genome Dashboard.Frontiers in microbiology · 2024Article
- The EcoCyc Database (2023).EcoSal Plus · 2023Review
94 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
14 authors.
Funding
Abstract
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.
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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 OpenQuestion graph.