Bioinformatics publications

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…

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.

We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases.

We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways.

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…

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.

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.

No longer restricted to metabolic pathways, this curated database includes data on genomics, molecular biology, and more.

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.

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.

In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO.