Lilly's current research is focussed on Neolithic subsistence practices and transfer of pottery technology by using techniques from analytical chemistry and radiocarbon dating.

Imbedded in the Passage Tomb People project, based at University College Dublin - Lilly's PhD-project aims to shed light on subsistence strategies and social structures in the Middle and Late Neolithic in Ireland, Wales and Orkney. In this period, funerary structures are well known, but settlement structures are underrepresented in the archaeological record.  Characterising the molecules entrapped in the ceramics walls as well as their isotopic composition can increase our knowledge about the palaeodiet, subsistence practices and how pottery was incorporated into everyday life and funerary practices. Compound-specific radiocarbon dating of the major fatty acids extracted from potsherds further helps refining the chronology of the passage tomb phenomenon and comparing developments in different areas.