Holger Heyn

The paper compares gene regulatory networks in mouse and pig limb development to reveal conserved and divergent regulatory programs and mechanisms of developmental robustness.

This study identifies MET signaling as a targetable vulnerability in rhabdoid tumors through integrated single-cell multi-omic and spatial transcriptomics analyses.

HARP integrates PBMC data from multiple studies to create a reference atlas with consensus annotations and identifies age, sex, and disease-related cellular modules.

This study identifies C1q from C1q+ tumor-associated myeloid cells as a key immunosuppressive factor in glioblastoma that impairs T-cell engagers and CAR T-cell efficacy, induced by LIF and glucocorticoids.

The paper identifies tissue-specific entry factors for SARS-CoV-2 in human tissues using single-cell analysis and functional validation.

This study presents the first comprehensive single-cell and multi-omic atlas of pleural effusions, revealing disease-specific immune landscapes and tumor heterogeneity.

The paper develops spFBA to analyze spatial metabolic differences in cancer, revealing metastatic mimicking and lactate-consuming cells in colorectal tumors.

This paper constructs a single-cell atlas of circulating immune cells to understand inflammation across diseases and develops a classifier for inflammatory diseases.

The paper uses spatial molecular imaging data to map human tonsil architecture and provides an analytical framework for Spatial Immunology.

The paper identifies age-related dysregulation of transcription networks in oligodendrocyte differentiation using single-nucleus RNA and ATAC sequencing in mice, with parallels in MS lesions.

The paper constructs a single-cell multiomics atlas of the human pancreas across development, health, and T2D, identifying plastic cell states and lineage trajectories.

This paper adapts copy number variation inference to image-based spatial transcriptomics data to map malignant clones and tumor microenvironment at single-cell resolution.

This paper traces colorectal cancer progression by integrating spatial transcriptomics, single-nucleus RNA-sequencing, and histopathology to map cellular and molecular changes across tumor stages.

STAMP enables low-cost, high-throughput single-cell analysis by integrating transcriptomics and proteomics imaging, supporting both single and multimodal profiling of diverse cell types.

This study tracks T cell dynamics in a pediatric cancer patient post-ICI therapy to identify tumor-reactive TCRs for personalized TCR-T cell therapy.

This paper benchmarks multimodal single-cell data integration methods to improve kidney reference atlas quality by identifying adaptive states and rare cell types.

The paper uses single-cell sequencing and spatial transcriptomics to compare immune responses in leptomeningeal disease with other CNS disorders, identifying disease-specific immune environments and progression mechanisms.

This study integrates single-cell multi-omics data from CAR-T cells to identify factors influencing immunotherapy response in B-cell neoplasias.

FixNCut is a reversible fixation and dissociation method that preserves RNA integrity and cellular composition in human and mouse tissues, enabling robust single-cell and spatial analyses.

scDrugPrio uses single-cell RNA sequencing to prioritize drugs for immune-mediated inflammatory diseases, showing personalized drug response variations across patients.

This study evaluates background noise in single-cell RNA-seq data and assesses methods for its removal, finding that CellBender performs best for marker gene detection.

This study investigates X-chromosome inactivation and reactivation dynamics in female mouse PGCLCs, showing that a precise temporal sequence is critical for meiotic potential.

This study identifies HASTER, a lncRNA that stabilizes HNF1A expression through cis-regulatory mechanisms, and shows its disruption leads to diabetes.

This study analyzes the transcriptomes of human oocytes at different maturation stages and finds that age affects specific gene pathways in matured oocytes.

SPOTlight integrates spatial transcriptomics with single-cell RNA-seq to deconvolute cell types and states in tissues, showing accurate predictions in mouse brain and human pancreatic cancer.

The paper models TBX5 haploinsufficiency in iPSC-derived cardiomyocytes to identify gene regulatory network imbalances linked to congenital heart disease.

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

The paper benchmarks bulk functional genomics tools on scRNA-seq data, showing comparable performance to bulk data and suggesting their applicability over dedicated single-cell tools.

The paper identifies sampling artifacts in single-cell genomics and proposes solutions to mitigate them in cohort studies.

The paper identifies a human accelerated region in Chromosome 14q12 that enhances forebrain expansion through increased enhancer activity in transgenic mice and organoids.