Comparative (pan)genomics
My research aims to contribute to our understanding of the genotype-phenotype relationship through comparative genomics. We use high-throughput measurements at various omics levels (genome, transcriptome, proteome, metabolome) to understand the causal chain leading to the observed variation in phenotype.
Since we are dealing with big data, we need computational tools for the analysis. In my work, both the application and development of computational tools for comparative omics are important aspects. I am particularly interested in early incorporation of biological knowledge in computational analyses.
The focus of my work has been on the evolution of complex eukaryotic genomes. To perform comparative analyses high-quality ingredients are essential. Therefore I am involved in several genome projects, aiming to deliver high-quality reference genomes. Often these are connected to interesting phenotypes, where one species can do a particular trick, while a close relative cannot. Typical questions are: which genetic loci influence the phenotype, how did this trait evolve?
Publications
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Operophtera brumata RefSeq Genome
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Wolbachia endosymbiont of Operophtera brumata strain:Ob_Wba Genome sequencing and assembly
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Operophtera brumata isolate:WM2013NL Genome sequencing and assembly
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Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome
G3 : Genes Genomes Genetics (2014), Volume: 4, Issue: 8 - ISSN 2160-1836 - p. 1395-1405. -
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
The Plant Journal (2014), Volume: 80, Issue: 1 - ISSN 0960-7412 - p. 136-148. -
Using fluorescence in situ hybridization (FISH) to improve the assembly of the tomato genome
Tomato Genetics Cooperative Report (2013), Volume: 63 - ISSN 0495-8306 - p. 5-14. -
RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs
RNA-A Publication of the RNA Society (2012), Volume: 18, Issue: 7 - ISSN 1355-8382 - p. 1319-1327. -
Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum × Solanum pennellii introgression lines
Theoretical and Applied Genetics (2012), Volume: 124, Issue: 5 - ISSN 0040-5752 - p. 947-956. -
The tomato genome sequence provides insights into fleshy fruit evolution
Nature (2012), Volume: 485 - ISSN 0028-0836 - p. 635-641.