Teaming up with Stuart Schreiber from Harvard University, they began to study the calcium-calcineurin-NFAT pathway essential to function of the immune system and vertebrate development including neural and heart development.
He joined the research group of Robert B. Woodward and after Woodward's death continued his studies under the supervision of Yoshito Kishi.
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Clardy, in collaboration with Stuart Schreiber and colleagues, obtained the crystal structure for both the FK506/FKBP12 and rapamycin/FKBP12 complexes.