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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Computational pan-genomics: status, promises and challenges
Briefings in Bioinformatics (2018), Volume: 19, Issue: 1 - ISSN 1467-5463 - p. 118-135. -
Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia
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NCBI-compliant genome submissions: tips and tricks to save time and money
Briefings in Bioinformatics (2017), Volume: 18, Issue: 2 - ISSN 1467-5463 - p. 179-182. -
Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan
Genome Announcements (2016), Volume: 4, Issue: 3 - ISSN 2169-8287 -
Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta
Genome Biology and Evolution (2016), Volume: 8, Issue: 7 - ISSN 1759-6653 - p. 2106-2117. -
PanTools: representation, storage and exploration of pan-genomic data
Bioinformatics (2016), Volume: 32, Issue: 17 - ISSN 1367-4803 - p. i487-i493. -
Beauveria bassiana Genome sequencing and assembly
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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