Bioinformatics publications
-
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.
-
Accurate Atom-Mapping Computation for Biochemical Reactions
We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric.
-
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).
-
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.
-
Browsing Metabolic and Regulatory Networks with BioCyc
The BioCyc database collection at BioCyc.org integrates genome and cellular network information for more than 1,100 organisms.
-
A Survey of Metabolic Databases Emphasizing the Metacyc Family
The main families are the MetaCyc, KEGG, Reactome, Model SEED, and BiGG families. We survey these database families, as well as important individual metabolic databases, including multiple human metabolic databases.
-
Metabolic Pathway Databases for 1,000 Organisms
-
The Pathway Tools Pathway Prediction Algorithm
The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes.
-
BioCyc: Microbial Genomes and Cellular Networks
-
A Systematic Study of Genome Context Methods: Calibration, Normalization and Combination
We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor.
-
Creation of a Genome-Wide Metabolic Pathway Database for Populus Trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
We developed a general approach for reconstructing metabolic pathway complements of plant genomes.
-
An advanced web query interface for biological databases
We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough…