Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data. Previous benchmarks focused on isoform …
*Motivation*Disease module mining methods (DMMMs) extract subgraphs that constitute candidate disease mechanisms from molecular interaction networks such as protein–protein interaction (PPI) networks. Irrespective of the employed models, DMMMs …
De novo pathway enrichment is a systems biology approach in which OMICS data are projected onto a molecular interaction network to identify subnetworks representing condition-specific functional modules and molecular pathways. Compared to classical …
Background: 16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows for studying microbial diversity, taxonomic profiling, phylogenetics, functional and network analysis. While a plethora of tools have …
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. …
Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance …
Process amplicon data and study microbial diversity across the globe.