He is noted for his efforts to place religious disagreements on a rational historical footing, for his advocacy of a liberal form of Protestantism, and for his endeavours as an educator, librarian, and scholar in Irish history.

He began publishing in earnest, including papers on John Wycliffe, church history, and the religious questions of his day.

He was Donnellan Lecturer in 1838 and 1839, publishing works related to the Antichrist in which he opposed the views of the more extreme of his co-religionists who applied this term to the Roman Catholicism and the Pope.

In 1852 he was appointed Librarian, and working alongside John O'Donovan and Eugene O'Curry, he classified and arranged the collection of manuscripts.

Alongside Charles Graves he presented a proposal to the British government which led to the formation of the Brehon Law Commission in December 1852.