About me

I am lecturer in the department of Biodiversity headed by Jens Boenigk at the University of Duisburg-Essen, Germany. I am working as a bioinformatician with a focus on next-generation sequencing analysis in biodiversity research. This includes metagenome and -transcriptome studies for freshwater habitats, transcriptome and genome assemblies of protist model species (Chrysophyceae) and the assessment of their molecular reactions and responses to environmental stressors. Before, I have worked as a postdoctoral researcher in the department of Genome Informatics headed by Sven Rahmann at the University Clinics in Essen. Former projects included the detection of structural variants in damaged genomes, functional and taxonomic assessment in metatranscriptome sequencing data and the analysis of new pathogens by assembling the genome and transcriptome. During my PhD I worked on methods for integrated network analysis using different *omics datasets in conjunction with biological networks.

Staff and (co-) supervised students

Postdocs and Technical staff

  • Ken Dreger (current): Data management and integration (CRC 1439 - Z-INF)
  • Benjamin Meyer (starting July): Data management and integration (CRC 1439 - Z-INF)

PhD students

  • Aman Deep (current): The roles of bacteria and fungi for CPOM degradation during stressor increase and release: A metatranscriptomic approach (CRC 1439 - A04)
  • Annemie Doliwa (current): Degradation and recovery of protistan parasite communities under multiple stressors (CRC 1439 - A07)
  • Manan Shah (current): Differential potential of metabarcoding, metatranscriptomics, and metagenomics for the assessment of lake water quality (Bauer-Stiftung und Stemmler-Stiftung)
  • Julia Nuy (finished 2020): The effects of the environment on microbial freshwater communities investigated using high-throughput sequencing
  • Stephan Majda (finished 2020): Evolution in Chrysophyceae regarding the nutritional mode and intraspecific variation based on comparative genomics
  • Nadine Graupner (finished 2018): Molecular insights into the functional diversity of protists

Master students

  • Sandra Roeser (2020): Transcriptional responses of aquatic and terrestrial protistan communities to flooding events
  • Marius Welzel (2018): Development of an Amplicon Snakemake Workflow including a Novel K-Mer Based Detection Method for Chimeric Sequences

Bachelor students

  • Nico Kreuder (2020): Who prefers what? Indicator OTUs for groups of fresh water samples across Europe
  • Josefa Welling (2019): Zellzyklus assoziierte Gene in Chrysophyceae
  • Luise Franke (2018): Comparative pigment analysis of Chrysophyceae
  • Sonja Amri (2018): Isolation of chrysophytes from soil samples
  • Benedict Schubert (2017): Systematische Evaluation von k-mer-basierten phylogenetischen Baumrekonstruktionsalgorithmen

Internships

  • Sarah Olberg (current)
  • Nico Kreuder (2019)
  • Marius Weltzel (2018)
  • Judith Blömer (2017)
  • Philipp Heidelbach (2013)