YVdP’s lab is considered a center of excellence in three areas of research: a) gene prediction and genome annotation, b) comparative and evolutionary genomics, and c) top-down systems biology. As stated above, regarding gene prediction and genome annotation, YVdP was involved in numerous genome projects, from plants to fungi and animals. His group, in close collaboration with researchers from the University of Toulouse (France), developed a gene prediction and genome annotation platform named ‘Eugene’, which combines both intrinsic and extrinsic methods for gene prediction. To improve intrinsic gene prediction (of splice sites and coding potential, for instance), YVdP and his team developed (and are still developing) several new machine learning approaches. His team also developed novel algorithms to unveil synteny and collinearity between and within genomes. For instance, sophisticated methods that can detect homology in the so-called twilight zone of homology were developed based on the construction of genomic profiles combining gene order and content information of multiple mutually homologous genomic segments. These profiles can then be used to scan one or more genomes for detecting segments that show significant collinearity with the entire profile but not necessarily with individual segments. Regarding top-down systems biology, YVdP and his team have developed several approaches to reverse-engineer gene regulatory networks. By analyzing large amounts of transcriptome data, transcriptional modules can be identified that explain the expression of genes and their regulators. These newly developed methods have been successfully applied to several datasets and biological problems.
YVdP was the first to show that the Arabidopsis genome had undergone three whole-genome dupli-cations (WGDs) in its evolutionary past. Furthermore, his group was one of the first to develop mathematical models to show that gene retention following whole genome duplications is considerably different from gene retention following small scale gene duplications and is highly biased with respect to gene function. Also, YVdP has been the first to link whole genome duplications with the origin of the angiosperms, coined ‘an abominable mystery’ by Charles Darwin, and more recently, he has provided evidence that whole genome duplications probably have been instrumental in organisms avoiding extinction. Most flowering plants are ancient polyploids which have undergone one or more whole genome duplications early in their evolution. Importantly, YVdP dated these youngest duplication events through sophisticated phylogenetic tree inference methods and could show that a majority of these independent genome duplications are clustered in time and seem to coincide with the Cretaceous–Paleogene (K/Pg) boundary. Following this result, YVdP proposed that polyploidization may have contributed to the survival and propagation of several plant lineages during or following the K/Pg extinction event. This hypothesis is now gaining wide support and several (plant) researchers are building on this and have begun to put forward additional new theories on how WGDs can explain the survival of major mass extinctions. YVdP is now planning to use both evolutionary experiments with unicellular green algae and duckweed, as well as evolutionary robotics and modeling, to gain more insights into the mechanisms and adaptive capabilities of polyploid organisms in dynamically changing environments.