Author

Marcel H. Schulz

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Open access Oct 2026

Dual-Foundation-Model Ensemble Predicts Gene Expression in Muscle-Invasive Bladder Cancer for Patient Outcome Stratification.

Muscle-invasive bladder cancer (MIBC) exhibits significant heterogeneity in clinical outcomes and treatment responses. While gene expression profiling has provided important biological and prognostic insight, transcriptomic assays are not routinely incorporated into standard clinical practice, in part due to cost. AI m...

I. F. Mathisen, F. Koll, R. Mayer et al. · Modern Pathology · 0 citations

Open access Jul 2026

AtlasLens: Metadata-centric exploration and analysis of single-cell atlases

AtlasLens is developed, an open-source R/Shiny application for interactive exploration of scRNA-seq datasets and integrated cellular atlases that integrates interactive visualization, differential expression analysis, Gene Ontology enrichment with redundancy reduction, temporal expression analysis, and context-dependen...

Shamim Ashrafiyan, Iaroslav Kosaretskii, Marcel H. Schulz · bioRxiv · 0 citations

Open access Jul 2026

Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies

This work provides a foundation for applications that link epigenome variation to gene expression in human cells, by benchmarking methods on a per-gene basis, illustrating their use in a disease context and making trained models available to the community.

Fatemeh Behjati Ardakani, Shamim Ashrafiyan, Laura Rumpf et al. · Genome Biology · 0 citations