Yves Van de Peer (YVdP) obtained his PhD in 1996 at the University of Antwerp, Belgium. After a postdoctoral fellowship with Axel Meyer at the University of Konstanz, Germany, he was hired at Ghent University (BE) as Group Leader of VIB (Department of Plant Systems Biology) in 2000 and as an Associate Professor at Ghent University in 2001, and promoted to Full Professor in 2008. YVdP’s research group is considered a genome analysis powerhouse specialized in the study of the structure and evolution of (plant) genomes. Because of their unique expertise and experience in gene prediction, genome annotation, and genome analysis, his research group has been, and still is, involved in many international genome projects.
YVdP is particularly interested in the study of gene and genome duplications as well as in the evolution of novel gene functions after duplication. YVdP published more than 450 papers, many of which in high-profile journals such as Nature, Nature Genetics, Nature Reviews Genetics, Science, PNAS, Genome Research, and The Plant Cell. YVdP has an H-index > 100 and his work has been cited more than 60,000 times. For many consecutive years, YVdP has been a Highly Cited Researcher. In 2013, YVdP received an ERC Advanced Grant entitled “DOUBLE-UP: The evolutionary significance of genome duplications for natural and artificial organism populations”, and in 2018 another one entitled “DOUBLE-TROUBLE: Replaying the ‘genome duplication’ tape of life: the adaptive potential of polyploidy in a stressful or changing environment”. YVdP is Organizer and Chair of the bi-annual international Current Opinion Conference on Plant Genome Evolution. This meeting was held in 2011, 2013, 2015, 2017, and 2019. In 2019, YVdP also organized the triannual International Conference on Polyploidy, Ghent, Belgium. YVdP is a member of the Royal Flemish Academy of Belgium for Science and the Arts (KVAB; since 2012) and serves on the Editorial Boards of five international journals (The Plant Journal, PeerJ, Genome Biology and Evolution, Current Plant Biology, Frontiers in Genetics). YVdP is also part-time professor at the Department of Biochemistry, Genetics and Microbiology, at the University of Pretoria, South Africa, and at the College of Horticulture at Nanjing Agricultural University, China.
Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.
syntenet is available on Bioconductor (https://bioconductor.org/packages/syntenet), and the source code is available on a GitHub repository (https://github.com/almeidasilvaf/syntenet).
Supplementary data are available at Bioinformatics online.