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On the limits of 16S rRNA gene-based metagenome prediction and functional profiling

Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to …

Inference of differential gene regulatory networks using boosted differential trees

Diseases can be caused by molecular perturbations that induce specific changes in regulatory interactions and their coordinated expression, also referred to as network rewiring. However, the detection of complex changes in regulatory connections …

Fake paper identification in the pool of withdrawn and rejected manuscripts submitted to Naunyn–Schmiedeberg’s Archives of Pharmacology

Honesty of publications is fundamental in science. Unfortunately, science has an increasing fake paper problem with multiple cases having surfaced in recent years, even in renowned journals. There are companies, the so-called paper mills, which …

Alternative splicing impacts microRNA regulation within coding regions

MicroRNAs (miRNAs) are small non-coding RNA molecules that bind to target sites in different gene regions and regulate post-transcriptional gene expression. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the …

Independent Tissue-Based Biomarkers in Endometrioid Endometrial Cancer: Tumor Budding in Microsatellite Instability and WHO Grading in Copy-Number-Low Patients

The molecular characterization of endometrial endometrioid adenocarcinomas has provided major advances in its prognostic stratification. However, risk assessment of microsatellite instability (MSI) and copy-number (CN)-low cases remains a challenge. …

The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach

*Background:* Machine learning and artificial intelligence have shown promising results in many areas and are driven by the increasing amount of available data. However, these data are often distributed across different institutions and cannot be …

Should Artificial Intelligence be used to support clinical ethical decision-making? A systematic review of reasons

Background Healthcare providers have to make ethically complex clinical decisions which may be a source of stress. Researchers have recently introduced Artificial Intelligence (AI)-based applications to assist in clinical ethical decision-making. …

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 …

Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond

A long-term objective of network medicine is to replace our current, mainly phenotype-based disease definitions by subtypes of health conditions corresponding to distinct pathomechanisms. For this, molecular and health data are modeled as networks …