Jan‐Philipp Mallm

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.

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

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.

Inflammatory injury drives CIN and STING loss in polyploidpancreatic acinar cells

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

A divergent mutational and clonal landscape in aged HSCs is not linked to aging-associated clonal hematopoiesis

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

Two distinct chromatin modules regulate proinflammatory gene expression

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

Integrative spatial and multi-omic profiling in bladder cancer links L1 retrotransposition to extrachromosomal DNA, genomic instability, and viral mimicry response

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.

Comparison of spatial transcriptomics technologies used for tumor cryosections

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

Single-cell chromatin landscape and DNA methylation patterns reveal shared molecular programs in human tumor and non-tumor tissue CCR8+ Treg cells

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.

Medulloblastoma oncogene aberrations are not involved in tumor initiation, but essential for disease progression and therapy resistance

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.

Cell-state plasticity drives heterogeneity in Group 3/4 medulloblastoma

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.

Enhancing sensitivity and versatility of Tn5 based single cell omics

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

Nucleosome repositioning in chronic lymphocytic leukaemia

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

Epigenetic signals that direct cell type specific interferon beta response in mouse cells

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

Integrated phospho-proteogenomic and single-cell transcriptomic analysis of meningiomas establishes robust subtyping and reveals subtype-specific immune invasion

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

pheno-seq - linking morphological features to gene expression in 3D cell culture systems

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.

Topological Demarcation By HMGB2 Is Disrupted Early Upon Senescence Entry Across Cell Types And Induces CTCF Clustering

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