Cuppen Group

Genome biology

Technological innovations soon make it possible to read the complete genetic code of an individual for an affordable price (1,000 dollar genome). However, understanding such personal genomes and the biological consequences of the enclosed genetic variation remains a large challenge. The Cuppen group studies the general mechanisms underlying genotype-phenotype relationships using systematic genomics approaches in rat genetic model systems. A diversity of high-throughput techniques and bioinformatic tools, including next-generation sequencing approaches, are employed to systematically discover and study genetic variation (SNPs, structural variation) and functional genomic elements.

About the research

Key publications
Linsen,, S.E.V., de Wit, E., Janssens, G., Heater, S., Chapman, L., Parkin, R.K., Fritz, B., Wyman, S.K., de Bruijn, E., Voest, E.E., Kuersten, S., Tewari, M., Cuppen, E. (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nat. Meth. 6:474-476.

Guryev, V., Saar, K., Adamovic, T., Verheul, M., van Heesch, S., Cook, S., Pravenec, M., Aitman, T., Jacob, H., Shull, JD., Hubner, N., Cuppen, E. (2008) Distribution and functional impact of DNA copy number variation in the rat. Nat. Genet. 40: 538-545.

Cuppen, E., Gort, E., Hazendonk, E., Mudde, J., van de Belt, J., Nijman, I.J., Guryev, V., Plasterk, R.H.A. (2007) Efficient target-selected mutagenesis in Caenorhabditis elegans: towards a knockout for every gene. Genome Res. 17: 649-658.

Guryev, V., Smits, B.M.G., van de Belt, J., Verheul, M., Hubner, N., Cuppen, E. (2006) Haplotype block structure Is conserved 
across mammals. PLoS Genet. 2: e121.

Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R.H.A., Cuppen, E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.

Publication list