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18
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Introduction
I am a bioinformatician with a particular interest in developing fast, scalable & reproducible workflows and web applications facilitating integrative and interactive analysis of large biological datasets.
My current work is predominantly focused on the characterization of crop mutants and the development of scientific software for the study of gene family evolution.
Current institution
Publications
Publications (18)
Sequence-indexed insertional libraries in maize (Zea mays L.) are fundamental resources for functional genetics studies. Here, we constructed a Mutator (Mu) insertional library in the B73 inbred background designated BonnMu. A total of 1,152 Mu-tagged F2-families were sequenced using the Mu-seq approach. We detected 225,936 genomic Mu insertion sit...
Motivation
Insertional mutagenesis allows for the creation of loss-of-function mutations on a genome-wide scale. In theory, every gene can be “knocked out” via the insertion of an additional DNA sequence. Resources of sequence-indexed mutants of plant and animal model organisms are instrumental for functional genomics studies. Such repositories sig...
Populus is a valuable and fast‐growing tree species commonly cultivated for economic and scientific purposes. But most of the poplar species are sensitive to drought and salt stress. Thus, we compared the physiological effects of osmotic stress (PEG8000) and salt treatment (NaCl) on poplar roots to identify potential strategies for future breeding...
Background: Plants differ in their ability to cope with external stresses (e.g., drought tolerance). Genome duplications are an important mechanism to enable plant adaptation. This leads to characteristic footprints in the genome, such as protein family expansion. We explore genetic diversity and uncover evolutionary adaptation to stresses by explo...
Significance
To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 ( EGT2 ) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth angle regulation in response to gr...
The BonnMu resource is a transposon tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator ( Mu ) stock with dent (B73, Co125) and flint (DK105, EP1, and F7) germplasm, resulting in the generation of 8064 mutagenized BonnMu F 2 ‐families. Sequencing of these Mu ‐tagged famil...
We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GHGA). In this effort, we developed NCBench, a continuous benchmarking platform for the evaluation of small genom...
Mutator ( Mu ) transposons facilitate untargeted insertional mutagenesis in maize by moving within the genome and disrupting genes. Such an approach has been used to generate collections such as the BonnMu resource, a Mu- tagged maize population for functional genomics studies. Mutant-Seq (Mu-Seq) is a sequencing-based method for the high-throughpu...
The BonnMu resource represents a tagged collection of maize ( Zea mays L.) Mutator ( Mu ) transposon-induced mutants, designed for functional genomics studies. Here, we describe the use of the BonnMu collection for identifying and characterizing mutations. Specifically, we describe workflows for use in both reverse and forward genetics strategies i...
Cold stress during early development limits maize (Zea mays L.) production in temperate zones. Low temperatures restrict root growth and reprogram gene expression. Here, we provide a systematic transcriptomic landscape of maize primary roots, their tissues, and cell types in response to cold stress. The epidermis exhibited a unique transcriptomic c...
The BonnMu resource is a transposon-tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator ( Mu ) line with dent (B73, Co125) and flint (DK105, EP1 and F7) germplasm, resulting in the generation of 8,064 mutagenized BonnMu F 2 -families. Sequencing of these Mu -tagged famili...
The precise functions of suberized apoplastic barriers in root water and nutrient transport physiology have not fully been elucidated. While lots of research has been performed with mutants of Arabidopsis , little to no data are available for mutants of agricultural crop or tree species.
By employing a combined set of physiological, histochemical,...
This study focuses on the role of the qualitative leaf wax composition in modulating the cuticular water loss using a Populus × canescens cer6 mutant line, which accumulates C34–C46 wax ester dimers and is reduced in wax monomers >C24. The two literature‐based hypotheses to be tested were the importance of the amount of wax esters and the weighted...
We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GHGA).
In this effort, we developed NCBench, a continuous benchmarking platform for the evaluation of small genom...
The cuticle is a protective layer covering aerial plant organs. We studied the function of waxes for the establishment of the cuticular barrier in barley (Hordeum vulgare). The barley eceriferum mutants cer‐za.227 and cer‐ye.267 display reduced wax loads, but the genes affected, and the consequences of the wax changes for the barrier function remai...
Background: Plants differ in their ability to cope with external stresses (e.g., drought tolerance). Genome duplications are an important mechanism to enable plant adaptation. This leads to characteristic footprints in the genome, such as protein family expansion. We explore genetic diversity and uncover evolutionary adaptation to stresses by explo...
Background
The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant mo...
The root growth angle defines how roots grow towards the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience and as a consequence yield of crop plants. We demonstrated that the egt2 ( enhanced gravitropism 2 ) mutant of barley exhibits...
