Author: Peter Karp
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Optimal Metabolic Route Search Based on Atom Mappings
We present the algorithm used in the new RouteSearch tool within the Pathway Tools software.
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The EcoCyc Database
This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
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A Framework for Application of Metabolic Modeling in Yeast to Predict the Effects of Nssnv in Human Orthologs
Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV.
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A Genome-Scale Metabolic Flux Model of Escherichia coli K-12 Derived from the EcoCyc Database
We present EcoCyc–18.0–GEM, a genome-scale model of the E. coli K–12 MG1655 metabolic network.
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Curation Accuracy of Model Organism Databases
We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions.
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Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the Ecocyc Database
We have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database.
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PortEco: A Resource for Exploring Bacterial Biology through High-Throughput Data and Analysis Tools
PortEco ( http://porteco.org) aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli.
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The Metacyc Database of Metabolic Pathways and Enzymes and the Biocyc Collection of Pathway/Genome Databases
MetaCyc (MetaCyc.org) is a universal database of metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are curated from the primary scientific literature, and are experimentally determined small-molecule metabolic pathways.
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The EcoCyc Database
The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level under-standing of E. coli.
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Addition of Escherichia coli K–12 Growth-Observation and Gene Essentiality Data to the EcoCyc database
We have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database.
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Metabolic Reconstruction Databases and Their Application to Metabolomics Research
This chapter describes the MetaCyc family of Pathway/Genome Databases (PGDBs).
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Dead End Metabolites – Defining the Known Unknowns of the E. coli Metabolic Network
We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their production or consumption within the metabolic network.