Author: Peter Karp
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A Systematic Study of Genome Context Methods: Calibration, Normalization and Combination
We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor.
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Creation of a Genome-Wide Metabolic Pathway Database for Populus Trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
We developed a general approach for reconstructing metabolic pathway complements of plant genomes.
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Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB).
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality…
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An advanced web query interface for biological databases
We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists.
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The Metacyc Database of Metabolic Pathways and Enzymes and the Biocyc Collection of Pathway/Genome Databases
Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database.
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What We Can Learn About Escherichia Coli Through Application of Gene Ontology
Gene Ontology (GO) is one of the most successful systems for classifying biological function. Although GO is widely used for eukaryotic genomics, it has not yet been widely used for bacterial systems.
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The Multiple Scientific Disciplines Served By EcoCyc
The EcoCyc database integrates information about the E. coli 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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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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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 in Escherichia coli 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.