Bioinformatics publications
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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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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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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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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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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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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.
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How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research.
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Crowd-sourcing and author submission as alternatives to professional curation
This perspective considers the significant experience accumulated by the bioinformatics community with these two alternatives to professional curation in the last 20 years...
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The Time Is Right to Focus on Model Organism Metabolomes
We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to…
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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.