Nicolle J.M. Besselink

This study uses cfDNA sequencing in newborn foals to detect sepsis-causing bacteria and identifies host-related biomarkers associated with sepsis.

The paper develops a method to directly detect 8-oxo-dG using nanopore sequencing by creating synthetic DNA with context variability and training deep learning models.

This paper introduces NanoRCS, a method using nanopore sequencing and consensus calling to accurately estimate tumor fractions from cfDNA by analyzing SNVs, CNAs, and fragmentomics.

This study investigates the mutational consequences of global DNA hypomethylation by analyzing single-cell genetic variation in DNMT1-depleted cells, finding increased chromosomal instability without significant mutational burden or structural changes.

The paper compiles a comprehensive reference dataset of true somatic structural variations by analyzing melanoma and normal cell lines with multiple sequencing technologies and experimental validation.

GRIDSS2 identifies somatic structural variants by analyzing single breakends and phasing, achieving a 3.1% false negative rate in metastatic cancers and uncovering a novel duplication signature.

This study quantifies and characterizes mutation accumulation in human induced pluripotent stem cells and adult stem cells during in vitro culture, revealing distinct mutational signatures and higher mutation rates compared to in vivo.

This study prioritizes driver genes in patients with de novo genomic structural variants using integrative analysis of WGS data, phenotype information, and chromatin organization datasets.

A three-tool chain calls somatic structural variants, purity, ploidy and copy number from paired tumour/normal whole genomes, then clusters breakpoints into derivative chromosome structures and gene fusions.

The paper quantifies somatic mutation accumulation in fetal liver and intestinal stem cells, finding higher mutation rates and distinct mutation spectra in fetal liver compared to fetal intestine and adult tissues.

The paper shows that NER deficiency increases Signature 8 mutations in specific tissues and suggests this could be a biomarker for NER-deficiency in cancer.