Bioinformatics publications
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The Pathway Tools Cellular Overview Diagram and Omics Viewer
Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram and a software component called the Omics Viewer.
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MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research
In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome.
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Identifying Candidate Genes Using The BioWarehouse: A Case Study
The BioWarehouse is an open source data warehousing environment focused on supporting bioinformatics databases (DBs). BioWarehouse integrates public source DBs such as Swiss-Prot and GenBank into a unified normalized schema…
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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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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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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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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…
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Genome Annotation Errors in Pathway Databases Due to Semantic Ambiguity in Partial EC Numbers
We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as ‘1.1.1.-’.
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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.