Bioinformatics publications
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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.
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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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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…
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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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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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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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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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The Pathway Tools software and its Role in Anti-Microbial Drug Discovery
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HpyCyc: Helicobacter pylori Pathway/Genome Database
A Pathway/Genome Database for Helicobacter pylori is available at URL BioCyc.org. The database integrates the full genome of H. pylori with its computationally predicted metabolic pathways.
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PseudoCyc, a Pathway/Genome Database for Pseudomonas aeruginosa
Our PathoLogic software can generate a PGDB from an annotated genome of an organism, predicting the metabolic reactions and pathways corresponding to the enzymes present in the annotation.
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Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO.
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The MetaCyc Metabolic Pathway Database