Jan‐Philipp Mallm

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

This paper introduces Split-flow, a pipeline that uses concordance between demultiplexing methods to classify cell quality in multiplexed single-cell data, revealing structured quality gradients.

The paper shows that inflammatory injury leads to polyploid pancreatic acinar cells with CIN and STING loss, contributing to tissue repair and cancer risk.

The paper uses single-cell RNA sequencing to analyze somatic mutations in HSCs and finds age-related clonal expansion and transcriptional divergence.

The paper identifies two chromatin modules, ACs and DCs, that regulate proinflammatory gene expression through distinct mechanisms in human endothelial cells.

This study identifies oncofetal reprogramming in juvenile myelomonocytic leukemia, linking RAS-pathway activation to fetal gene expression and revealing CD52 as a therapeutic target.

This study integrates spatial and multi-omic data from bladder cancer patients to show L1 retrotransposition drives genomic instability, ecDNA formation, and a viral mimicry response.

This study compares four spatial transcriptomics technologies for analyzing medulloblastoma cryosections, highlighting their strengths and providing guidance for method selection.

The paper compares CCR8+ Treg cells in tumor and tumor-free tissues using chromatin accessibility and DNA methylation, finding high similarity suggesting tumor microenvironment activation of tissue Treg cells.

The paper uses single-cell technologies to show that large-scale chromosomal aberrations drive medulloblastoma initiation, while single-gene oncogenic events like MYC contribute to progression and therapy resistance.

This study identifies cell-state plasticity as a driver of heterogeneity in Group 3/4 medulloblastomas, showing that transcription factor perturbation can redirect tumor cells along different differentiation trajectories.

This paper improves scATAC-seq by increasing Tn5 transposase activity and integrates chromatin and transcriptome data from the same cell.

This study identifies changes in nucleosome positioning and packing in chronic lymphocytic leukaemia, linking them to epigenetic mechanisms and patient stratification.

The paper identifies epigenetic features that regulate cell type-specific interferon beta responses in mouse cells by analyzing chromatin and gene expression changes.

This study integrates phospho-proteogenomic and single-cell transcriptomic data to subtype meningiomas and identify subtype-specific immune infiltration patterns.

The paper introduces pheno-seq, a method that links morphological features to gene expression in 3D cell cultures, showing its ability to identify morphology-specific genes and regulatory states not captured by scRNA-seq.

The paper identifies HMGB2 loss as an early event in senescence that disrupts chromatin organization by inducing CTCF clustering across multiple human cell types.