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After graduation, Thangaraj became ARCH's CFO. During this time, Thangaraj participated in the firm's early growth from a small technology transfer organization to a well-respected venture capital firm. In 1996, Thangaraj left ARCH and helped form Integrated Telemanagement, a telecommunications services company, where he served as CEO until its merger with a public company.

Thangaraj joined Essex Woodlands Health Ventures, a private venture capital firm that invests exclusively in health care, in 1998. By 2003, he was one of four managing directors of the firm and one of seven investment professionals. He also served as the firm's senior administrative partner. During this same period, Essex increased in committed capital five-fold, making it one of the largest health care venture capital firms in the country; its investment performance consistency placed it among the top-tier firms of the venture capital industry.

Thangaraj has served at Chicago Booth as a LEAD Challenge judge, a SAGE program mentor, and an Admission Alliance volunteer.