In September 2001, at the urging of Academia Sinica president Lee Yuan-tseh, Chen, who was at the time chief of the Division of Medical Genetics in the Department of Pediatrics at the Duke University Medical Center, returned to Taiwan to take the position of director of the Institute of Biomedical Sciences at Academia Sinica.
2001 年 9 月，原任職美國杜克大學醫學中心遺傳系主任的陳垣崇，也在中研院院長李遠哲的力邀下，毅然由美國返台接任中研院生醫所所長。