Hendrik G. Stunnenberg

This study examines how different transplantation platforms affect the clonal and transcriptional changes in αβ and γδT cells over time, finding that graft engineering has a lasting impact on βTCR clonality, while viral reactivation mainly drives expansion without altering repertoire structure.

This paper presents an integrative multimodal atlas of pediatric-type diffuse high-grade gliomas, identifying cancer-myeloid cell programs and distinct cancer cell states across multiple patients.

This paper develops a human brainstem organoid model of H3.3K27M-altered DMG to study GD2 CAR T cell function and identify therapeutic targets.

The paper develops a γδT-omics pipeline to analyze compartmentalization of Vδ1⁺ T cell migration, tumor-reactivity, and clonality in human colorectal cancer, revealing distinct functional and transcriptional features across tumor compartments.

The paper uses single-cell spatial analysis to identify SPP1+/GPNMB+ myeloid cells in pediatric high-grade gliomas that suppress CD8+ T cells and promote tumor growth.

This study investigates DNA methylation changes in SetDB1-deficient mouse ESCs, revealing its role in silencing retrotransposons and imprinted regions through coordination with H3K9me3.

This paper introduces a microfluidic platform for standardized, sensitive ChIP-Seq on low-input samples, enabling high-throughput and reproducible epigenetic profiling.

This study examines 3D genome architecture changes during B cell differentiation and in B cell neoplasias using Hi-C and multi-omic data, revealing dynamic compartment shifts and tumor-specific chromatin reorganization.

This study shows that P53 regulates G1-phase progression in ground state ESCs by controlling RB expression, and its inactivation leads to loss of RB and uncontrolled proliferation.

The paper identifies novel long non-coding RNAs and circular RNAs in hematopoietic cells using BLUEPRINT consortium data, highlighting their cell type specificity.

The paper introduces RAID, a method to analyze both transcriptomes and intracellular phosphoproteins from fixed single cells, showing its ability to detect heterogeneity in cellular responses.

This study investigates how p63 mutations alter the enhancer landscape in epidermal keratinocytes, affecting cell identity through changes in gene regulation.

The paper identifies DNA methylation oscillations as a marker for enhancer classification, showing high predictive power compared to other methods.

The paper introduces ID-seq, a technology that measures multiple molecular and cellular phenotypes in parallel, and uses it to study kinase inhibitor effects on human epidermal stem cells.

The paper maps the epigenomic and functional changes during human neutrophil differentiation from bone marrow progenitors to mature cells, revealing key regulatory mechanisms.

This study compares the epigenomes of neutrophils and monocytes to identify regulatory elements and chromatin states, revealing differences in enhancer activity and DNA methylation.

The paper tracks the transition of mouse embryonic stem cells from ground state pluripotency to a formative phase, showing acute exit from naive status and transcriptome changes similar to early post-implantation epiblast.

The paper measures and compares transcriptional and epigenetic variability across immune cell types and finds neutrophils exhibit higher variability linked to immune pathways and environmental exposure.