Professor Clarke's major contribution is to understanding the mechanism of cell-cell recognition in plants. She investigated the basis of cell-cell recognition in two systems, fertilization and fungal disease. As part of the strategy to understand these systems, she established structures of the complex surface carbohydrates of the cells in contact during recognition. A major contribution is the molecular cloning of a cDNA encoding a protein from the female sexual tissues which is probably the product of the gene controlling self-fertilization. This forms the foundation for understanding the genetic basis of self- and non-self recognition in plants.