Martin's main interest is in the interaction of trypanosomes with the mammalian host, including the acquisition of essential micronutrients such as vitamins and minerals. He is currently investigating micronutrient salvage pathways and iron utiisation in T. brucei and T. cruzi.

He is also investigating the local immunological response to infected cells in the chronic stage of T. cruzi infection in the mouse model using dual reporter parasite lines. He is particularly interested in immune evasion in Chagas disease and the role of the immune system in disease pathogenesis.

He is  involved in the creation of models for drug development in Stage II African trypanosomiasis, Chagas disease and Leishmaniasis. This has involved the engineering of parasite lines expressing very high levels of firefly luciferase. Use of  red-shifted luciferase has led to a highly sensitive infection model which is being used to streamline in vivo drug development for these neglected tropical diseases. He has developed a combined bioluminescence/fluorescence model for investigating the pathogenesis and immunology of Chagas disease which allows the investigation of host-parasite interactions within the chronic stage. He is currently extending this system to Leishmaniasis (both visceral and cutaneous forms).

Martin has also developed a tetracycline based inducible expression system for T. cruzi which is now being used in several laboratories worldwide. He is currently developing RNA/protein level knockdown systems for Trypanosoma cruzi which lacks conventional RNA interference machinery and an improved inducible expression system for this organism.