Marc Jan Bonder

The paper quantifies co-accessibility between cis-regulatory elements in Drosophila using single-molecule footprinting and long-read sequencing, revealing coordinated regulation across genomic distances.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

This study conducts an epigenome-wide association study (EWAS) meta-analysis of wellbeing using DNA methylation data, finding no significant methylation sites but suggesting the need for larger studies.

The paper identifies average polycomb CpG methylation as a hallmark of cellular aging using single-cell whole-genome methylation data, showing cell-to-cell variability and accelerated aging in faster proliferating cells.

The paper identifies dual-acting regulatory QTLs and gene regulatory networks in immune cells to better understand how genetic variation influences disease susceptibility.

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.

The paper maps cis- and trans-eQTLs in blood samples to infer gene regulatory networks and prioritize trait-relevant pathways.

The paper identifies host genetic effects on microbiome composition in rats and finds evidence of indirect genetic effects contributing to missing heritability.

The paper identifies highly cell-type-specific eQTLs using snRNA-seq data from brain and blood, showing that bulk analyses overestimate eQTL agreement.

The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

The paper identifies co-eQTLs that alter gene co-expression relationships in specific cell types, linking these variants to immune disease associations.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The paper shows that DNA methylation ageing is reflected in correlations between genomic loci, with a preference for 500 bp apart sites, and links this to PRC2-dependent H3K27me3 dilution.

The paper develops a Hi-C analysis pipeline to catalog TADs and loops in human genomes and quantifies the impact of SVs on chromatin structure and gene expression.

The paper presents a genome-scale CRISPRi perturbation map in human pluripotent stem cells using single-cell RNA sequencing to study trans gene regulation across diverse genetic backgrounds.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

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

The paper presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

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.

novoRNABreak detects novel splice junctions and fusion transcripts in cancer RNA-seq data with high sensitivity and efficiency.

pycoMeth provides a toolbox for differential methylation analysis of long-read ONT sequencing data, offering improved efficiency and performance over existing methods.

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.

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

This study evaluates normalization, aggregation, and statistical methods for sc-eQTL mapping to improve eQTL discovery in single-cell RNA-seq data.

The paper uses single-cell RNA sequencing to study genetic variant effects on dopaminergic neuron differentiation from iPSCs, identifying eQTL and cell fate markers.

The paper maps regulatory effects of human disease variants in pluripotent cells, identifying cis- and trans-QTL across 18,556 genes and linking them to GWAS traits.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

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

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.