Bioinformatics publications
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Evaluation of reaction gap-filling accuracy by randomization
We report on computational experiments of reaction gap filling in which we generated degraded versions of the EcoCyc-20.0-GEM model by randomly removing flux-carrying reactions from a growing model.
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How accurate is automated gap filling of metabolic models?
Here we compare the results of applying an automated likelihood-based gap filler within the Pathway Tools software with the results of manually gap filling the same metabolic model.
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The MetaCyc database of metabolic pathways and enzymes
This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
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The Omics Dashboard for interactive exploration of gene-expression data
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets.
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Update notifications for the BioCyc collection of databases
The BioCyc update notifications service is a new mechanism to keep researchers informed of the latest developments in their areas of interest.
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The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12
New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.
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The BioCyc collection of microbial genomes and metabolic pathways
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by…
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life.
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Can we replace curation with information extraction software?
Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are…
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Representation and inference of cellular architecture for metabolic reconstruction and modeling
We developed a tool for inferring cellular architectures across many domains of life and extended our Cell Component Ontology to enable representation of the inferred architectures.
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Pathway collages: personalized multi-pathway diagrams
We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts.
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How Much Does Curation Cost?
Here we calculate the cost of biocuration of articles for the EcoCyc database as $219 per article over a 5-year period.