Maarten van den Berge

A repair-associated bronchial epithelial differentiation trajectory through KRT14+ basal and hillock-like cells drives airway inflammation and remodelling in childhood-onset asthma

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.

Topology-Based Query Framework for Longitudinal Omics Trajectories

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

UnBlender: validating individual analyses in respiratory bulk RNA-seq cell type deconvolution

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

Genome-wide association study of extrapulmonary traits in the context of COPD

This study identifies genetic variants associated with extrapulmonary traits in COPD using genome-wide association analysis across two cohorts.

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.

FastCAR: Fast Correction for Ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets

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

Childhood-onset asthma is characterized by airway epithelial hillock-to-squamous differentiation in early life

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.

Genetic Regulators of Sputum Mucin Concentration and Their Associations with COPD Phenotypes

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

Airway epithelial response to RSV is impaired in multiciliated and goblet cells in asthma

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.

Nasal DNA methylation at three CpG sites predicts childhood allergic disease

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

IL-33 induced gene expression in activated Th2 effector cells is dependent on IL-1RL1 haplotype and disease status

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.

Genetic associations and architecture of asthma-chronic obstructive pulmonary disease overlap

This study identifies eight novel genetic signals associated with asthma-COPD overlap through a genome-wide association analysis involving multiple cohorts.

Multi-omics highlights ABO plasma protein as a causal risk factor for COVID-19

The paper uses multi-omics approaches to identify genes and plasma proteins associated with COVID-19, finding ABO plasma protein as a causal risk factor.

Gene Expression Network Analysis Provides Potential Targets Against SARS-CoV-2

The paper identifies co-expressed genes with ACE2 and TMPRSS2 in lung tissue and finds many have drug interactions, suggesting potential targets for COVID-19 therapeutics.

ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study

This study uses Mendelian randomization to examine if ACE inhibitors or cardiometabolic risk factors affect lung ACE2 and TMPRSS2 expression or plasma ACE2 levels, finding no overall association.

SNPs associated with HHIP expression have differential effects on lung function in males and females

The paper identifies SNPs with sex-specific effects on lung function traits using UK Biobank data, finding a significant interaction at rs7697189 near HHIP.

Novel Type 2-high gene clusters associated with corticosteroid sensitivity in COPD

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.

Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution

This study uses single-cell RNA sequencing to analyze smoking effects on bronchial epithelial cell types, identifying molecular changes and a novel subpopulation linked to premalignant lesions.

New genetic signals for lung function highlight pathways and pleiotropy, and chronic obstructive pulmonary disease associations across multiple ancestries

The paper identifies 279 new genetic signals for lung function across multiple ancestries, showing associations with COPD and pleiotropic effects.

Multiethnic Meta-analysis Identifies New Loci for Pulmonary Function

This study identifies over 50 new genetic loci associated with pulmonary function through a multiethnic meta-analysis of 90,715 individuals.

Leveraging lung tissue transcriptome to uncover candidate causal genes in COPD genetic associations

The paper identifies 12 novel COPD loci and candidate causal genes using GWAS and lung eQTL data from 129 risk loci.