Author: Peter Karp
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The complete genome sequence of Francisella tularensis, the causative agent of tularemia
We report the complete genome sequence of a highly virulent isolate of F. tularensis. The sequence uncovers previously uncharacterized genes encoding type IV pili, a surface polysaccharide and iron-acquisition systems.
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EcoCyc: a comprehensive database resource for Escherichia coli
The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli.
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Querying and Computing with BioCyc Databases
We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases.
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Expansion of the BioCyc Collection of Pathway/Genome Databases to 160 Genomes
This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways.
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Computational Prediction of Human Metabolic Pathways from the Complete Human Genome
We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways.
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The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database
No longer restricted to metabolic pathways, this curated database includes data on genomics, molecular biology, and more.
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An Evidence Ontology for use in Pathway/Genome Databases
This paper presents an ontology for encoding the type of support and the degree of support for DB assertions, and for encoding the literature source in which that support is reported.
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Call for an enzyme genomics initiative
I propose an Enzyme Genomics Initiative, the goal of which is to obtain at least one protein sequence for each enzyme that has previously been characterized biochemically.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes
In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper.
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Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
We have constructed PlasmoCyc, a PGDB for Plasmodium falciparum 3D7, using its annotated genomic sequence. We also add 956 additional annotations to proteins annotated as “hypothetical” using the GeneQuiz annotation system.
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Using Functional and Organizational Information to Improve Genome-Wide Computational Prediction of Transcription Units on Pathway/Genome Databases
We implemented a TU predictor that uses only intergenic distance and functional classification of genes to predict TU boundaries, and applied it to EcoCyc, our PGDB of Escherichia coli.
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A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases.