Fig. 1.

Timeline of selected phylogenetic profiling advances with a focus on eukaryotes. Since Pellegrini et al.’s pioneering paper, advances in phylogenetic profiling have been made in terms of method development (and in particular profile representation), size of the datasets processed, and the kinds of systems studied—from genome-wide enrichment of known associations to reconstructing complex systems such as protein complexes and interaction networks. Novel milestones in terms of profiler, size, and system are depicted where applicable. Owing to space limitations, this list is necessarily incomplete and subjective; we apologize to authors whose valuable work is not included.