Bioinformatics publications
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Groups: Knowledge Spreadsheets for Symbolic Biocomputing
‘Groups’ is an implementation of Knowledge Spreadsheets (KSs) within the Pathway Tools system.
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The Challenge of Constructing, Classifying, and Representing Metabolic Pathways
This review describes the criteria that need to be considered, and the rules that have been developed by MetaCyc curators as they make decisions regarding the representation and classification of…
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A Systematic Comparison of the MetaCyc and Kegg Pathway Databases
We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012...
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Data Mining in the Metacyc Family of Pathway Databases
The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB).
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Dead End Metabolites — Defining the Known Unknowns of the E. coli Metabolic Network
We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their…
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A systematic comparison of the MetaCyc and KEGG pathway databases
We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their…
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Groups: Knowledge Spreadsheets for symbolic biocomputing
Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database.
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EcoCyc: Fusing Model Organism Databases with Systems Biology
Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and…
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Construction and completion of flux balance models from pathway databases
We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP).
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Metabolomics Reveals Amino Acids Contribute to Variation in Response to Simvastatin Treatment
We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism.
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Regulatory Network Operations in the Pathway Tools Software
Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism’s genome and metabolic network.
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Accurate Atom-Mapping Computation for Biochemical Reactions
We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric.