Ivo Kwee

WGCNA+ extends WGCNA to multi-omics data, enabling cross-omics module analysis and visualization with AI-powered interpretation.

The paper constructs a multi-omics biomolecular network in AML using proteins, metabolites, and histone PTMs to reveal functional entanglement between biomolecules.

PLAID provides an ultrafast and memory-efficient gene set enrichment method for single-sample analysis across transcriptomics and proteomics data, outperforming existing approaches.

NPmatch corrects latent batch effects in omics data using nearest-pair matching, outperforming existing methods across diverse datasets.

The paper compares gene and protein expression changes in MERS, SARS, and COVID-19 in vitro datasets to identify common patterns and differences across species and experimental conditions.

The paper applies a prize-collecting Steiner tree method to select a gene signature for classifying diffuse large B-cell lymphoma subtypes, outperforming existing methods.

OmicsNet integrates multi-omics data using multilayer networks to identify pathways linking genotypes to phenotypes, enabling functional analysis and drug response prediction.