Author: Peter Karp

We show that alternative pathway definitions can alter enrichment p -values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichment p -values by only two orders of magnitude.

We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains, imposing several quality-control filters to reduce the chances of introducing errors.

We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network.

This document compares SRI’s Pathway Tools (PTools) software with the Reactome software. Both software systems serve the pathway bioinformatics area, including representation and analysis of metabolic pathways and signaling pathways.

This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1.

We describe the MultiOmics Explainer, a new tool within the Pathway Tools software suite that leverages what is known about an organism’s metabolic and regulatory network to suggest explanations for the results of omics experiments.

We developed an efficient software tool to search for metabolic routes that include metabolic reactions from multiple organisms.

This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs.