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From 1984-1986, Dr. Harden was on the staff of the National Institute of Allergy and Infectious Diseases (NIAID), researching and writing Rocky Mountain Spotted Fever: History of a Twentieth-Century DiseasDisease (Johns Hopkins, 1990). It won the 1991 Henry Adams prize of the Society for History in the Federal Government for the best book published in 1990 about the history of the federal government.

In 1989 and 1993 she organized conferences on the history of AIDS. The proceedings were published as as AIDS and the Historian (IOS Press, 1991) and AIDS and the Public Debate: Historical and Contemporary Perspectives (IOS Press, 1995). In June 2001, she launched a website commemorating the twentieth anniversary of the first publication about AIDS: In Their Own Words: NIH Researchers Recall the Early Years of AIDS. In 2012, she published AIDS at 30: A History, an overview of the epidemic emphasizing the response of the medical community—physicians and nurses, public health officials, and biomedical researchers—to AIDS.