Welcome

We are a bioinformatics team at the FSU Jena focusing on transcriptomics and metagenomics using short and long reads.

We develope tools and workflows to handle large sequencing data sets. We apply our computational methods to de novo genome and transcriptome assembly, the comprehensive analysis of RNA-Seq data, and the identification and characterization of pathogens such as viruses and bacteria from environmental samples.

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

We work closely with the RNA Bioinformatics/High-Throughput group of Manja Marz and we are a member of the European Virus Bioinformatics Center.


Research Interests

  • Bioinformatics
  • Transcriptomics & comparative genomics
  • de novo assembly & annotation
  • Microbes & viruses
  • Metagenomics & -transcriptomics
  • Oxford Nanopore Sequencing
  • Non-coding RNA & RNA secondary structure
  • Automation & visualization

ONT hybrid MAGs







News

24. May 2020

I am very happy to be able to contribute to this review on workflows and tools that have been developed by the virus bioinformatics community as a rapid reaction to the COVID19 pandemic! Also check this comprehensive (yet incomplete) collection of tools and resources for virus detection, annotation, tracking and drug design.

22. May 2020

I am happy to announce that PoSeiDon, a pipeline to detect significantly positive selected sites and possible recombination events in an alignment of multiple protein-coding sequences, is now available as a Nextflow w/ Dockers! And a small preprint is also out.

21. May 2020

You really like Prokka to annotate your bacterial genomes? But sometimes there are so many hypothetical proteins? Try out our small tool HyPro where we extend hypothetical protein annotations from Prokka using additional homology searches against larger databases.

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