ArticleBriefings in bioinformatics2010
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Article in Briefings in bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 248 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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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.
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Who cites it
248 citing papers in PubMed.
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- Proteomic profiling of zinc homeostasis mechanisms inbioRxiv : the preprint server for biology · 2025Article
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- The differential gut microbiota and their MetaCyc pathways in IBRV infected Angus calves.Frontiers in microbiology · 2025Article
- An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.Nature microbiology · 2024Article
- Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms.Scientific data · 2024Article
- Longitudinal Transcriptomic, Proteomic, and Metabolomic Response ofJournal of proteome research · 2024Article
- A deep learning architecture for metabolic pathway prediction.Bioinformatics (Oxford, England) · 2024Article
- Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative.Molecular ecology resources · 2024Article
- A multi-omics approach to unravel the interaction between heat and drought stress in theFrontiers in plant science · 2024Article
- A multi-omics insight on the interplay between iron deficiency and N forms in tomato.Frontiers in plant science · 2024Article
- Insights into the differences related to the resistance mechanisms to the highly toxic fruitFrontiers in physiology · 2024Article
- Review
- CuGenDBv2: an updated database for cucurbit genomics.Nucleic acids research · 2023Article
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- Biochemical Insights into the Ability ofPlants (Basel, Switzerland) · 2022Article
188 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 production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry.
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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.