Eaton began her research career working on immunoglobulin heavy chain genes at University of California, Los Angeles, in the laboratory of Kathryn Calame.[1] In 1988, Eaton switched fields to developmental biology, investigating how cells obtain their tissue identities in the fruit fly, Drosophila melanogaster, while in the group of Thomas B. Kornberg at University of California, San Francisco.[2][5] Eaton moved to Germany in 1993 to work at the European Molecular Biology Laboratory in Heidelberg in the group of Kai Simons, where she combined her expertise in microbiology and developmental biology to investigate how the cytoskeleton helps cells attain their polarity in tissues, using the fruit fly as a model system.[3][5][6] In 2000, Eaton became one of the founding group leaders at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, where her group investigated how signalling molecules and mechanical properties of cells act together to shape tissues in the fruit fly.[2][6][7] In 2015, she became professor of developmental cell biology of invertebrates at the TU Dresden.[5]