Karsten Rippe

The paper uses super-resolution microscopy to show that single-stranded telomeric repeats are spatially segregated within ALT-associated PML bodies.

The paper investigates how HP1 binding represses transcription at chromocenters and persists during decondensation, using a 1D lattice model to explain chromatin state transitions.

The paper identifies genomic and transcriptomic features of telomere maintenance mechanisms in complex karyotype sarcomas, linking ALT status to therapeutic vulnerabilities.

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

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.

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

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.

The paper develops a chromatin hierarchical lattice framework to predict heterochromatin nanodomains and identifies DNA sequence and protein binding factors that determine their formation and boundaries.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

The paper improves the MIPRIP method to identify common and cancer-type specific TERT regulators across 19 cancers using human and mouse regulatory networks.

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.

This study identifies ALT markers and mechanisms in pediatric glioblastoma using genomic and telomere features, revealing non-canonical ALT and a reliable classification scheme.

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

TelomereHunter estimates and characterizes telomere content from whole genome sequencing data in cancer studies.