In 1982 he was appointed chairman of the Department of Molecular Biology, then five years later assumed the directorship. In 1991, when the TSRI was established as a nonprofit entity, Lerner became its first president.
From 1982 to 1987, he held the position of chairman in the Molecular Biology Department; subsequently, in 1991, after TSRI became a nonprofit institution, Lerner took on the role of its inaugural president.