microbiome

Namco: A microbiome explorer

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 …

KeyPathwayMineR: de novo pathway enrichment in the R ecosystem

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 …

Alternative splicing analysis benchmark with DICAST

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 …

Robust disease module mining via enumeration of diverse prize-collecting Steiner trees

*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 …

Network analysis methods for studying microbial communities: A mini review

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. …

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes

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 …

BioAtlas

Process amplicon data and study microbial diversity across the globe.