Bioinformatics publications
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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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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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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
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Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway…
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The Pathway Tools Software
The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB).
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The MetaCyc Database
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms.
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The past, present and future of genome-wide re-annotation
We define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches.