Ruben van Boxtel

This study evaluates the impact of an individual-specific pangenome on somatic variant calling in a pediatric AML patient, finding reduced false positives and altered phylogenetic branching.

This study compares whole-genome sequences of adolescent and young adult solid cancers to older adult cancers, finding shared genetic drivers but age-related differences in mutational processes and germline variants.

The paper estimates the timing of genetic driver events and clonal expansion in rhabdoid tumors using whole-genome sequencing data from 97 tumors.

This study uses single-cell whole-genome sequencing to show that Burkitt lymphoma develops through convergent evolution, with early genetic diversity and accelerated mutation accumulation.

This study shows that localized hydrogen peroxide production induces p53-dependent resistance to DNA damage, with implications for chemotherapy protection.

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.

The paper introduces PTATO, a bioinformatic workflow for detecting somatic mutations in single-cell WGS data using PTA, achieving high sensitivity for base substitutions and indels.

This study compares mutational landscapes in somatic and germline cells across 29 anatomical structures, identifying key mutational signatures and their contributions to different cell types.

The paper introduces an updated R/Bioconductor package for analyzing mutational patterns, demonstrating its ability to detect mutational signatures and their biological implications using simulated and real data.

This study evaluates prime editing for modeling cancer mutations and repairing CFTR in intestinal organoids, showing its potential but also highlighting challenges in efficiency and off-target effects.

This paper demonstrates the use of prime editing to correct genetic mutations in patient-derived organoids, showing high efficiency and precision with minimal off-target effects.

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.

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.

MutationalPatterns analyzes mutational processes genome-wide to quantify mutational signatures and their relation to genomic features.