19Helicobacter pylori is a gram-negative bacterium that establishes life-long infections by inducing 20 immunoregulatory responses. We have developed a novel ex vivo H. pylori co-culture system to 21 identify new regulatory genes based on expression kinetics overlapping with that of genes with known 22 regulatory functions. Using this novel experimental platform, in combination with global transcriptomic 23 analysis, we have identified five lead candidates, validated them using mouse models of H. pylori 24 infection and in vitro co-cultures under pro-inflammatory conditions. Plexin domain containing 2 25 (Plxdc2) was selected as the top lead immunoregulatory target. Gene silencing and ligand-induced 26 activation studies confirmed its predicted regulatory function. Our integrated bioinformatics analyses 27 and experimental validation platform has enabled the discovery of new immunoregulatory genes. This 28 pipeline can be used for the identification of genes with therapeutic applications for treating infectious, 29 inflammatory, and autoimmune diseases.