Bernhard Dumoulin

UTOPIA quantifies confidence in virtual spatial transcriptomics predictions across scales, improving reliability and preventing false conclusions.

Pixel2Gene improves spatial gene expression reconstruction and prediction by integrating histology images with spatial transcriptomics data.

HistoSweep improves tissue quality control in gigapixel images by removing artifacts and preserving biologically relevant structures, enhancing analysis accuracy in digital pathology and spatial omics.

The paper identifies splicing variants in human kidney tissue associated with kidney function and cardiovascular-kidney-metabolic syndrome traits using long-read RNA sequencing and QTL analysis.

Nephrobase Cell+ is a kidney-specific foundation model that outperforms existing models in single-cell analysis, cross-species transfer, and batch effect correction.

The paper maps human kidney development using single-cell RNA sequencing and spatial transcriptomics, revealing fate decisions influenced by the local microenvironment.

Multi-omic and spatial profiling of 81 human kidney samples resolves four tissue microenvironments; the fibrotic one's gene signature is reported to beat histopathology at predicting outcome.