Bioinformatics publications
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The Multiple Scientific Disciplines Served By EcoCyc
The EcoCyc database integrates information about theĀ E. coliĀ genome, its metabolic pathways, and its regulatory network. EcoCyc is in use by scientists from a variety of disciplines.
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Biowarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats
BioWarehouse is an open-source project for integrating bioinformatics databases within a relational database warehouse. It has multiple databases can be queried together within a single common schema.
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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
An updated genome-scale reconstruction of the metabolic network inĀ Escherichia coliĀ K-12 MG1655 is presented.
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Multidimensional annotation of the Escherichia coli K-12 genome
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations.
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Using genome context data to identify specific types of functional associations in pathway/genome databases
Genome-context methods have proved useful in providing clues about functional annotations for many proteins. They detect many biological types of functional associations, and do not identify which type of functional…
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A Survey of Orphan Enzyme Activities
Here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities.
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Using the MetaCyc pathway database and the BioCyc database collection
The MetaCyc database ( http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the literature by manual curation.
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BioWarehouse: a bioinformatics database warehouse toolkit
We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes
MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments.
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Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests
Using the completedĀ V.choleraeĀ genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium.
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The Outcomes of Pathway Database Computations Depend on Pathway Ontology
Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations.
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The Pathway Tools Cellular Overview Diagram and Omics Viewer
Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram and a software component called the Omics Viewer.