In 2018, we formed a bioinformatics team focusing on microbial transcriptomics and metagenomics in collaboration with the RNA Bioinformatics group at the FSU Jena.

With Martin’s move to the bioinformatics department of the Robert Koch Institute in 2020, the team will no longer exist in its original form, but the science will continue at the RKI.

We develop novel tools and workflows for handling large amounts of sequence data. We apply computational methods to automate de novo (meta-)genome and transcriptome assembly, analysis and annotation of RNA-Seq data, identification and characterization of pathogens such as viruses and bacteria from environmental samples and (more recently) molecular monitoring of infectious diseases.

We strive to combine well-established and novel computational approaches into reproducible workflows to analyze and visualize large amounts of short- and long-read sequencing data.

Research interests

  • Microbial bioinformatics
  • de novo assembly & annotation
  • Transcriptomics & comparative genomics
  • Metagenomics & -transcriptomics
  • Real-time nanopore sequencing
  • Workflow management & reproducibility
  • Automation & visualization

ONT hybrid MAGs


11. April 2021

Our chromosome-level hybrid genome assembly with RNA-Seq-improved annotation of the oleaginous yeast Rhodotorula toruloides is out as a preprint! Great collaboration w/ the Swedish University of Agricultural Sciences, Uppsala (SLU)!

05. April 2021

Finally! Together with great colleagues from ANSES in France (among others) we describe a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae isolated from flamingo! The bioinformatics part actually started with Fabien visiting us in 2016 and 2017 to learn about assembly and finally found its successful conclusion with the analysis of nanopore data and high-quality genomes.

06. March 2021

Questions about the characteristics, spread and significance of mutated variants of SARS-CoV-2 play a major role in the progress of the pandemic. Here, we summarize in the "Deutsches Ärzteblatt International" (in German) how molecular surveillance using whole genome sequencing is carried out at the Robert Koch Institute.

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