Dirk is involved in the "BWT Read Server" project which aims at efficient storage in and fast retrieval of genome sequencing reads from a compact data structure. This includes testing the data structure for its applicability for common analyses in genomics and population genetics and exploring new ways of data analysis only possible with this technology.
I am interested in all fields that try to decipher what could be called the "source code of life" which includes:
- Genomics (e.g. genome structure and composition, genomic variation)
- Genetics (e.g. gene structure and function)
- Transcriptomics and (post-) transcriptional regulation (e.g. enhancer/promoter function and interaction and its effect on spatiotemporal gene expression)
- Evolutionary and developmental biology (e.g. changes in the regulatory network and their effect on the development of organisms)
... and others!
For this I mainly apply bioinformatic techniques that help to address these questions on a larger scale but always with the firm interest in tracing each finding all the way to its biological impact.
Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.
G3 (Bethesda, Md.) 2014;4;3;433-45
Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis.
Cell reports 2015;10;9;1544-1556
A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets.
Genes & development 2011;25;9;930-45
Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor.
Nature genetics 2011;43;4;379-86
The light responsive transcriptome of the zebrafish: function and regulation.
PloS one 2011;6;2;e17080
NPC-db, a Niemann-Pick type C disease gene variation database.
Human mutation 2008;29;3;345-50