Shotwell is best known for her contributions to the research of mycotoxins, especially to the study of aflatoxin, a carcinogen produced by mold that grows on rice and corn.[22][23] Byproducts of corn production fed to cattle can cause cancer, stunted growth, and congenital malformations.[23][24] In the late 1980s she was appointed the Research Leader of the Mycotoxin Research Unit still within the Agricultural Research Service of the USDA.[4] She instructed the Federal Drug Administration on how to detect contaminated feed grain using ultraviolet light.[25] As a member of the American Society of Oil Chemists she helped decide the standards of purity for the grain storage industry.[6] In 1980 she received the USDA's Distinguished Service Award for "contributing to the protection of human health by developing identification standards and analytical methods essential to excluding mold toxins from cereal foods, milk and animal feed."[7]