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


09. June 2021

Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done! In the latest preprint, we investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data.

08. May 2021

Many laboratories have ramped up nanopore sequencing for SARS-CoV-2 surveillance, but are in dire need of bioinformatics support. Here we present poreCov, a high-throughput software pipeline for reliable genotyping and reference-based genome reconstruction of SARS-CoV-2 samples based on nanopore tiled amplicon sequencing focused around the ARTIC protocol. On GitHub! Big kudos @CaSe Group Jena!

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)!

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