Holger Heyn

Network inference at single-cell resolution reveals morphoregulatory divergence and multilayered buffering in limb evolution

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

MET inhibition exploits conserved regulatory dependencies in malignant rhabdoid tumors

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

A Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease

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

C1q from C1q+ tumor-associated myeloid cells promotes resistance to T-cell engagers and CAR T-cells and is induced by LIF and glucocorticoids

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.

Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

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

Multi-omic profiling of pleural effusions: a reservoir-incubator for non-invasive insights into tumor heterogeneity

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

Spatial Flux Balance Analysis reveals region-specific cancer metabolic rewiring and metastatic mimicking

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

A transcriptional map of human tonsil architecture:beyond the sum of (single cell) parts

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

Dysregulation of transcription networks regulating oligodendrogenesis in age-related decline in CNS remyelination

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.

Latent plasticity of the human pancreas across development, health, and disease.

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

In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics

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

Tracing colorectal malignancy transformation from cell to tissue scale

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: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

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.

Spatio-temporal T cell tracking for personalized TCR-T designs in childhood cancer

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.

Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.

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

Decoding the immune response in leptomeningeal disease through single-cell sequencing of cerebrospinal fluid

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.

FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

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.

The effect of background noise and its removal on the analysis of single-cell expression data

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.

A temporally controlled sequence of X-chromosomeinactivation and reactivation defines female mouse in vitro germ cells with meiotic potential

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

HASTER is a transcriptional stabilizer of HNF1A

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

Single cell analysis reveals the impact of age and maturation stage on the human oocyte transcriptome

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

SPOTlight:Seeded NMF regression to Deconvolute Spatial Transcriptomics Spots with Single-Cell Transcriptomes

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.

Modeling human TBX5 haploinsufficiency predicts regulatory networks for congenital heart disease

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

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

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

Robustness and applicability of functional genomics tools on scRNA-seq data

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.

Sampling artifacts in single-cell genomics cohort studies

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

A Human Accelerated Region participates in early human forebrain patterning and expansion

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

Single-Cell Transcriptomics Unveils Gene Regulatory Network Plasticity

This study develops a framework to infer global regulatory networks from scRNA-seq data, revealing gene regulatory changes missed by traditional methods.

Single cell expression analysis uncouples transdifferentiation and reprogramming

The paper uses single cell transcriptomics to show that transdifferentiation and reprogramming can be uncoupled in pre-B cells based on their intrinsic plasticity.

Comparison of single-cell whole-genome amplification strategies

This study compares six single-cell whole-genome amplification methods using human cells, finding that REPLIg performs best in DNA yield and uniformity while Ampli1 shows fewer technical artifacts.