Filip Van Nieuwerburgh

This study shows that disrupting the amino acid stress response pathway reduces tumor growth in multiple aggressive cancers by targeting chronic metabolic stress adaptation.

LCM-FFPEseq enables high-sensitivity transcriptomics from FFPE tissues with single-cell resolution, detecting over 14,000 genes per sample using as few as 30 cells.

This study characterizes multimeric artefacts in RPA and identifies temperature and T4 UvsX concentration as ways to reduce them.

This paper introduces equi-depth pooling to balance sequencing depth in bulk AIRRseq, reducing costs and eliminating sampling bias.

This study examines how osmotic stress affects gene expression and physiology in Caldimonas thermodepolymerans, showing increased PHA accumulation and changes in osmoprotection and metabolism.

The paper shows that many reported RNA-chromatin interactions are technical artifacts caused by DNA off-targeting, not true biological interactions.

The paper uses single-cell multi-omics to analyze DENV-1 infection, revealing interferon-driven immune responses and cell-type interactions in human blood.

This study evaluates Recombinase Polymerase Amplification (RPA) for amplifying forensic STR loci, showing successful singleplex amplification but challenges in multiplex formats.

The paper develops a multimodal model integrating chemical structure and transcriptomics to predict toxicity, achieving robust performance across multiple assays and providing mechanistic insights.

The paper uses machine learning to predict tobramycin susceptibility in Pseudomonas aeruginosa biofilms using multiple analytical methods, achieving high accuracy with MALDI-TOF MS and Raman spectroscopy.

This study examines genetic responses of Circaea lutetiana to forest edge dynamics, finding delayed genetic changes and highlighting the role of historical forest configuration in shaping current genetic diversity.

The paper generates a proteogenomic atlas of the human neural retina using long-read RNA-sequencing and mass spectrometry, identifying novel transcript isoforms and peptides.

The paper investigates methylome stability and parental effects in Lombardy poplar, finding stable CG methylation patterns and weak parental carry-over effects on phenotypic traits.

HIV-PULSE is a long-read sequencing assay that enables high-throughput, accurate characterization of HIV-1 proviral genomes without limiting dilution steps.

The paper develops a genotyping assay to accurately determine CYP2D6-CYP2D7 hybrid alleles using optimized nanopore sequencing and a new analysis pipeline.

The paper presents a high-quality draft genome assembly and annotation for the Taita White-eye, providing a genomic resource for evolutionary and comparative genomics studies.

The paper introduces ion-networks, a data format for DIA MS that captures full data integrity by representing reproducible fragment ions and their consistent co-elution across runs.

This study evaluates the use of Oxford Nanopore MinION sequencer for forensic STR profiling using standard primers and shows it can generate partial forensic profiles despite high error rates.