Welcome

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







News

06. December 2020

RNA-Seq workflows are a dime a dozen. Nevertheless, we are happy to present RNAflow as an easy to use pipeline for gene expression calculation with less configuration effort. Made possible by Nextflow and most importantly Marie ;) !

14. November 2020

Genomic surveillance is limited not only by the speed at which genomes can be shared, but also by the speed at which they reach the right person or algorithm to analyze them. DarkQ is a proof-of-concept on how we might share data for genomic surveillance in the future.

10. November 2020

Very happy that this is finally out, a review on workflows and tools that have been developed by the virus bioinformatics community as a rapid reaction to the COVID-19 pandemic! Including a comprehensive (yet incomplete) collection of tools and resources for virus detection, annotation, tracking and drug design.

... see all News