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


01. September 2020

Welcome Kunaphas! For his bioinformatics research internship at the FU Berlin he joins the team to work on the detection of antimicrobial peptides from large collections of publicly available RNA-Seq data.

26. August 2020

The in-depth characterization of model species is important to advance the field of molecular biology. So I'm more than happy that this study about a marine Chlamydomonas sp. as an algal model system is finally accepted in the Journal of Phycology (will add a link asap)!

13. August 2020

Yeah, our joint study (CRC AquaDiva) on hybrid metagenome assembly is out at Environmental Microbiology! We show how including nanopore long reads improves the recovery of microbial and viral genomes from a complex groundwater sample. A great cooperation w/ the Küsel Lab, thx all, and special kudos to Will Overholt for all the hard work!

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