Cisca Wijmenga

This paper develops an autologous co-culture system to study human intestinal IEL-epithelial interactions, showing both non-destructive and cytotoxic responses under different conditions.

This study compares hiPSC-derived intestinal epithelial cells cultured in organoids, Transwells, and intestine-on-chip systems, showing that the latter promotes stronger gene expression related to nutrient and drug metabolism and a more mature state.

This study shows that repeated cytokine exposure in endothelial cells induces memory-like responses, linking chronic inflammation to vascular disease risk through persistent transcriptional and epigenetic changes.

This study analyzes the gut microbiome of treated coeliac disease patients at strain level, revealing increased interindividual variation and specific microbial associations.

The paper develops interpretable neural networks for multi-omics data to predict smoking status, age, and LDL levels, showing improved performance and generalizability across cohorts.

This study develops multi-ancestry polygenic risk scores for venous thromboembolism using diverse GWAS data and shows improved predictive performance across European- and African-ancestry populations.

This paper introduces SBayesRC, a method that improves polygenic prediction of complex traits by integrating GWAS summary statistics with functional genomic annotations, showing significant accuracy gains across ancestries.

This study identifies two CpGs associated with the gut microbiome genus Eggerthella and shows microbiome mediates environmental effects on DNA methylation.

OTTERS is a TWAS framework that uses summary-level eQTL reference data to estimate eQTL weights and perform omnibus TWAS, showing improved power and applicability.

The paper identifies shorter QRS duration in asymptomatic PLN c.40_42delAGA carriers and links it to genetic sensitivity in symptomatic carriers.

This study identifies ancestry-specific eQTLs in TB-T2D patients using cis-eQTL mapping, revealing variants associated with gene expression that could guide therapeutic targets in African populations.

The paper introduces an omics-informed quality score to improve CNV detection and association analysis by reducing false positives and increasing statistical power.

The paper identifies host genetic loci associated with gut microbiome composition and function in a large cohort, finding significant associations near LCT and ABO genes.

The paper uses blood eQTL meta-analysis to explore the polygenic architecture of complex traits, finding that trans-eQTLs are more informative for identifying causal genes than cis-eQTLs.

The paper improves genetic mapping resolution in autoimmune diseases by identifying shared alleles across multiple conditions and reveals widespread shared mechanisms.

The paper identifies TRAFD1 as a master regulator of IFNγ signalling in celiac disease by systematically prioritizing candidate genes in disease loci using multiple computational methods.

The paper identifies 31 host genetic loci influencing gut microbiome composition through GWAS and suggests causal effects in inflammatory diseases.

This study identifies barriers and facilitators to implementing pharmacogenomic screening in Dutch outpatient care through stakeholder perspectives.

This paper introduces MR-link, a Mendelian randomization method that identifies causal relationships between gene expression and LDL-C levels, finding 19 causally linked genes including PVRL2.

The paper identifies 818 genes influencing DNA methylation in blood using genetic anchors and causal inference, revealing both transcription factors and non-DNA-binding proteins with regulatory roles.

The paper introduces Decon2, a method to deconvolute bulk blood eQTL effects into immune cell subpopulations, showing high concordance with experimental and single-cell studies.

This study investigates genetic variants in ACE2 and TMPRSS2 genes for associations with quantitative phenotypes and medication use in a population cohort, finding suggestive links with hypertension and inflammation-related drugs.

This paper introduces TWMR, a Mendelian Randomization method that identifies gene-trait associations by integrating GWAS and eQTL data, revealing 3,913 novel associations across 43 human phenotypes.

This study identifies novel HPE genes and oligogenic inheritance patterns in holoprosencephaly by integrating clinical data with exome sequencing and gene prioritization.

The paper identifies 49 gene drivers of downstream transcriptional changes using population genomics data and RNA-sequencing from 3,072 individuals.

This study shows environmental factors have a greater impact on human gut microbiota than host genetics, with microbiome data adding significant predictive value to phenotypes.

This study investigates the association between CpG methylation and educational attainment, finding limited significant associations that may be influenced by confounding factors.

GAVIN classifies variants with high sensitivity and specificity using gene-specific calibrations, outperforming 12 other tools in a clinical benchmark.

This paper introduces LifeLines DEEP, a sub-cohort with extensive biological samples and data layers, and describes its baseline characteristics and potential for studying genetic and metabolic variation in gastrointestinal health.

The paper identifies genetic variants affecting gene expression using genotypes derived from public RNA-seq data, finding cis-eQTLs for 8,034 genes and strong ASE effects for 34 rare pathogenic variants.