Stefan Janssen

This study evaluates YOLOv8 and Mask R-CNN for detecting TADs in bulk Hi-C data by converting Hi-C matrices into images and comparing their performance against reference TADs.

The paper shows that matching microbial communities with their environment in tree crowns improves plant performance.

TEMPTED improves analysis of longitudinal microbiome data by incorporating time as a continuous variable, achieving high accuracy in phenotype classification and identifying microbial markers linked to birth outcomes.

The paper investigates how host genetics shape microbiome composition across generations, finding that host genotype has a stronger influence than maternal legacy after the first generation.

This study shows that FLASH irradiation with carbon ions spares normal tissue and maintains tumor control in mice, similar to conventional dose-rate treatments.

The authors reanalyze their pan-cancer microbiome findings using decontaminated data to address concerns about contamination, batch effects, and machine learning approaches.

The paper predicts structures and annotates functions for diverse microbial protein sequences, identifying novel folds and highlighting the saturation of structural space.

EMPress provides an interactive tool for visualizing phylogenetic trees alongside multi-omic data, enabling exploratory analyses of microbiome and metabolome datasets.

OPAL is a software package for benchmarking taxonomic metagenome profilers using performance metrics and visualizations, demonstrating its application on CAMI challenge datasets.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.