The innate immune system is the body's first line of defense to protect us from disease-causing microbes in our environment. However, the innate immune system can also generate other unintended and serious effects such as prolonged – and sometimes fatal – inflammation. The study of human systems such as the innate immune system is assisted by examining similar systems in other organisms, known as model organisms. Researchers link equivalent genes in the model organism to human genes, so that knowledge can be transferred from the model organism to humans. However, identifying equivalent genes between species can be a difficult task. The Brinkman laboratory at Simon Fraser University has developed a software program called Ortholuge that can detect pairs of genes that are likely to be “orthologs” – genes in different species that are similar to each other because they originated from a common ancestor. Orthologs are of significant interest when inferring function in humans based on different species, or when linking equivalent genes between species for large scale comparative analyses. Matthew Whiteside is working to improve the accuracy and speed of Ortholuge, adding functionality to the program that will resolve some of the more complex gene relationships. He will then use the software to perform a large-scale study of the innate immune system in humans, mice and animals important in agriculture, such as cattle. Whiteside’s work will be the first large-scale cross-species comparative analysis of the innate immune system. He hopes that this study will provide fundamental new insights regarding the evolution of innate immune system. This analysis may also highlight important innate immunity genes that are conserved between the species, with potential for identifying new therapeutic targets for immune diseases.