Woodruff returned to Northwestern University as a faculty member in 1995 to study inhibin and activin actions and interactions within the pituitary-gonadal axis, characterizing the regulation of subunit assembly and ligand processing in the ovary, the ligands’ role in paracrine regulation of folliculogenesis, and their signal transduction pathways in the regulation of follicle-stimulating hormone (FSH). In collaboration with Theodore Jardetzky, she solved the crystal structures of activin with its receptor and with its bioneutralizing binding protein follistatin. In 2015, her lab used in silico methods to design small molecule activin antagonists based on the structure of activin bound to its receptor.