[9] RNA folding was also introduced to allow for a non-linear genotype to phenotype mapping to study evolution on complex fitness landscapes .
[10][11] The first phase-phase trajectory of a chaotic attractor in an ecological food-chain model of three differential equations appeared long before chaos became popular.
[15][16] This CPM approach is now used for modeling in various areas of developmental biology, and the migration of immune cells in lymphoid tissues.
In recent years, Hogeweg has continued her research on co-evolutionary dynamics and morphogenesis, to expand on “adaptive genomics” and to study the interface between gene regulation and evolution in cellular organisms.
Also, her research is focused on evolvability at the level of genome organization and regulatory networks, and has shown RNA increase in complexity as the result of interactions of secondary structure and spatial pattern formation.
Her contribution varies from developing computational methods such as algorithm for tree based multiple sequence alignment which has become a standard practice.