Bioinformatics Resources

Our lab has developed popular, open source user-friendly tools for use by biologists and bioinformaticians. These encompass Network/Systems Biology approaches to analyzing large mammalian omic (particularly transcriptomic) data sets (NetworkAnalyst and InnateDB), a protein:protein interactions database, InnateDB, that is curated for immune system interactions but also incorporates all known experimentally verified and predicted interactions, and the genome database.
NetworkAnalyst Logo


A fast, comprehensive web-based tool that couples statistical procedures with state-of-the-art data network visualization techniques, to enable researchers to easily navigate large complex gene expression datasets to determine important features, functions, and interconnections, leading to the generation of new biological hypotheses.

InnateDB logo


A popular (6 million hits per year) manually-curated database and systems biology analysis platform of all of the genes, proteins, interactions, pathways, and signaling responses involved in human, mouse and bovine innate immunity.


A user-friendly tool which facilitates the integration of metabolomics with other omics data types, using data from MetaCyc & KEGG to map input metabolites to genes through pathways and reactions.


A Shiny app which gives easy access to manually curated sepsis signatures from over 100 publications, and allows the user to analyze their own data with these sepsis signatures.

Pseudomonas Genome Database

A popular (6 million hits annually) database with high quality updates to the PAO1 genome annotation.