Jesper Grud Skat Madsen

This study benchmarks ambient RNA decontamination methods using simulated and experimental datasets, finding that no single method is optimal across all scenarios, with CellBender, DecontX, and SoupX performing well.

DeepDive disentangles covariate effects on single-cell epigenomes, enabling counter-factual analyses and identifying diabetes-linked beta cell subtypes.

The paper identifies PAF15-PCNA assembly as a rate-limiting factor for lagging strand replication and replisome integrity, showing its regulation by the S-phase checkpoint.

This study examines transcriptional changes in human adipose tissue during weight loss from lifestyle and bariatric surgery, showing significant remodeling and reduced inflammation.

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

The paper conducts a large-scale rare variant GWAS meta-analysis of type 2 diabetes, identifying novel variants in monogenic diabetes genes and assessing their pathogenicity.

This study identifies PPAR-dependent mitochondrial programming as a limiting factor in the differentiation of human stem cell-derived β cells and shows that PPAR agonists can enhance β cell formation and function.

valiDrops improves sxRNA-seq data quality by identifying high-quality barcodes and flagging dead cells through data-adaptive filtering and clustering.