Stefan Fröhling

scIRES-seq reveals multimodal molecular heterogeneity in CTCs from small cell cervical cancer

This study introduces scIRES-seq to analyze CTCs from cervical cancer, revealing multimodal molecular heterogeneity through integrated genetic, epigenomic, and transcriptomic profiling.

TOPAS: phosphoproteome data analysis and decision support platform for molecular tumor boards

TOPAS converts phosphoproteomic data into patient-specific reports for molecular tumor boards, focusing on clinically relevant signaling and therapeutic targets.

Hierarchical classification of hematologic malignancies using epigenetic and genetic information

The paper develops a hierarchical classification framework combining epigenetic and genetic data with machine learning to improve diagnosis and risk stratification in hematologic malignancies.

Knowledge Connector: Decision support system for multiomics-based precision oncology

The paper introduces Knowledge Connector, a decision support system that integrates multiomics data with clinical information to aid in precision oncology decision-making.

Digital Spatial Pathway Mapping Reveals Prognostic Tumor States in Head and Neck Cancer

This paper introduces a method to infer signaling pathway activities from H&E slides in HNSCC, revealing two prognostic tumor states.

Selective targeting of TBXT with DARPins identifies regulatory networks and therapeutic vulnerabilities in chordoma

This study uses T-DARPins to inhibit TBXT in chordoma cells, revealing its regulome and identifying therapeutic vulnerabilities, including sensitivity to JAK2 inhibitors.

Conserved programs and specificities of T cells targeting hematological malignancies

This study identifies rare tumor-reactive T cells and conserved antigen repertoires in multiple myeloma and acute myeloid leukemia, developing a TCR fitness model to predict immunotherapy response.

CD38 biallelic loss is a recurrent mechanism of resistance to anti-CD38 antibodies in multiple myeloma.

This study identifies biallelic CD38 loss as a mechanism of resistance to anti-CD38 antibodies in multiple myeloma, with specific mutations affecting antibody efficacy.

End-to-end deep learning versus machine learning for biomarker discovery in cancer genomes

This study compares deep learning and machine learning for biomarker prediction in cancer genomes, finding DL performs better in cross-assay and data-sparse settings.

Exploiting WEE1 kinase activity as FUS::DDIT3-dependent therapeutic vulnerability in myxoid liposarcoma

This study identifies WEE1 kinase activity as a therapeutic target in FUS::DDIT3-driven myxoid liposarcoma by showing its role in replication stress tolerance and cell survival.

ZygosityPredictor

ZygosityPredictor evaluates the number of gene copies affected by mutations in sequencing data, providing confidence measures for precision oncology applications.

Dynamic DNA methylation reveals novel cis-regulatory elements in murine hematopoiesis

The paper develops a computational framework for analyzing DNA methylation data in mouse hematopoiesis, identifying novel cis-regulatory elements associated with gene expression during differentiation.