Zhilin earned his B.S. in Biomedical Engineering from Columbia University after completing a bachelor's degree in Biochemistry at Brandeis University through the 3+2 program. Prior to starting his PhD, he joined Dr. Timothy Street's lab at Brandeis to study the enzymatic mechanisms of molecular chaperones. He also worked in Dr. Anthony Fitzpatrick's lab at Columbia's Zuckerman Institute, where he used cryo-EM to study the molecular and structural basis of neurodegeneration and memory.