Martijn C. Nawijn

The paper identifies a novel asthma-associated epithelial differentiation trajectory involving KRT14+ basal cells and hillock-like cells that contributes to airway inflammation and remodelling in childhood-onset asthma.

LongOmicsTraj provides a topology-based framework to represent and query longitudinal omics trajectories, identifying corticosteroid response genes with temporal patterns across treatment groups.

UnBlender enables cell type deconvolution in respiratory bulk RNA-seq data and provides routine validation of deconvolution accuracy.

The paper performs a federated cis-eQTL meta-analysis across single-cell datasets to identify cell-type-specific genetic effects and link them to disease mechanisms.

This study shows RANKL promotes alveolar epithelial cell expansion in mice and humans, suggesting RANKL/RANK signaling as a conserved pathway for lung tissue repair.

The paper uses single-cell RNA sequencing to identify myeloid cell retention and differentiation in extracorporeal membrane oxygenators of ARDS patients, linking it to potential MO dysfunction.

The paper creates a regulon atlas mapping TF activity across human cell types and uses it to link disease signatures to cell types and TFs, improving disease risk locus analysis.

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.

FastCAR corrects ambient RNA contamination in scRNA-Seq data, improving the accuracy of differential gene expression analysis by reducing false positives.

RNA sequencing in bronchial biopsies from wheezing infants and children < 2 years shows evidence for an airway epithelial hillock-to-squamous differentiation pathway that marks the development of asthma.

This study identifies genetic variants associated with sputum mucin concentrations and links one variant to COPD phenotypes like chronic bronchitis and acute exacerbations.

This study examines the RSV response in bronchial epithelial cells from asthma patients and healthy donors, finding impaired antiviral responses in goblet and multiciliated cells in asthma.

The paper identifies three nasal DNA methylation CpG sites that predict childhood allergic disease with high accuracy, validated across Dutch and US Hispanic children.

The paper investigates how IL-33-induced gene expression in Th2 cells depends on IL-1RL1 haplotype and asthma status, finding stronger effects in risk haplotype carriers and a correlation with pauci-granulocytic asthma.

The paper identifies a corticosteroid-sensitive gene cluster in COPD patients using asthma-derived transcriptomic signatures and links it to mast cell numbers and lung function improvement.