Bioinformatics & Systems Biology
Today, massively parallel DNA sequencing or hybridization approaches allow the identification of not only the gene repertoire but also the gene regulatory networks of an organism. The huge amounts of data acquired from such experiments can only be handled with intensive bioinformatics support that has to provide an adequate infrastructure for storing and analyzing these data. Thus, bioinformatics has to deliver efficient data analysis algorithms, user-friendly tools and software applications, as well as extensive hardware infrastructure for answering such questions.
As part of the Bielefeld-Giessen Resource Center for Microbial Bioinformatics (BiGi), a service unit of the 'German Network for Bioinformatics Infrastructure – de.NBI', the group is focused on data management for genome and post-genome research projects that require new software solutions for systematic data acquisition, secure data storage of structured information, and high-throughput data analysis. Bioinformatics training and education and the cooperation within the German bioinformatics community is a main scope of the group.
- Recent publications
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identificationA high-quality regional and functional annotation of bacterial genomes plays a crucial role in modern microbiology, as it is the basis for many downstream analyses. Here, we present a new method and CLI / web software tool for the comprehensive but rapid annotation of bacterial genomes, plasmids and metagenome-assembled genomes.
Single cell RNA-seq (scRNA-seq) enables analysis of cellular transcriptomes in an unprecedented resolution, allowing e.g., the identification of previously undiscovered rare cell populations with corresponding marker genes, detection of heterogeneity between cells of the same type or to follow transcriptional programs of cells during differentiation. Current high-throughput sequencing techniques yield enormous amounts of data that need to be analyzed. Hence, there is need for bioinformatic analysis solutions adapted to the specific challenges deriving from scRNA-seq data. Our software WASP is designed for the management, analysis and interpretation of scRNA-seq high-throughput data. The software addresses all aspects from initial quality control, demultiplexing and reference alignment to downstream statistical evaluation. Furthermore, it provides an automated workflow suitable for both non-bioinformaticians as well as experts. The software is available via a web-based interface and supports deployment to local as well as cloud-based compute infrastructures.