Ole Madsen

This study examines how DNA methylation profiles change across three generations in quails exposed to genistein, finding that while methylation differences accumulate, genetic factors largely explain these changes.

SheepEpimap combines 516 histone CUT&Tag, ATAC-seq and RNA-seq datasets from 43 sheep tissues to annotate 2.93 million cis-regulatory elements and 145,407 allele-specific variants for trait interpretation.

This study profiles allele-specific expression across 42 tissues and 34 pig breeds using an open-source pipeline, revealing widespread and tissue-specific allelic imbalance.

The paper presents CattleGTEx, a resource characterizing regulatory effects in cattle, resolving GWAS signals and providing insights into adaptive evolution and selection.

The paper identifies sex-specific genetic regulatory effects in chickens using whole-genome sequencing and transcriptomes, revealing sex-dependent gene regulation and structural variants.

This study constructs a multi-tissue cell atlas of pigs, identifies cell-type-specific gene regulation, and links these to complex traits and human phenotypes.

The paper integrates tissue-specific epigenetic annotations into genomic predictions of gene expression in three pig breeds, improving eQTL mapping interpretability but facing challenges in cross-breed predictions.

The paper presents a multi-tissue sheep atlas identifying regulatory variants and their effects on molecular phenotypes, revealing allelic heterogeneity and evolutionary patterns.

The paper analyzes whole-genome data from wild boars to trace their demographic history and identify genetic signatures of local adaptation in Central Asia.

This paper models DNA methylation networks during pig fetal development using a joint fused ridge approach, revealing key roles for fetal-maternal immunity and the circulatory system.

The paper imputes diploid genotypes from low-coverage ancient cattle genomes using a modern reference panel, achieving high accuracy and SNP recovery across different downsample depths.

The paper presents PigGTEx, a resource linking genetic variants to transcriptomic phenotypes in pigs, showing pigs' similarity to humans in gene regulation and complex traits.

This study compares transcriptome profiles of pig intestinal organoids from different segments to assess their similarity to in vivo tissues and variability between adjacent sites.