Jan Vijg

Direct probabilistic quantification of mosaic loss of chromosome Y from sequencing data

This paper introduces BaySeq-Y, a Bayesian method to directly quantify mosaic loss of chromosome Y from sequencing data, showing improved accuracy over existing methods.

The aging genome exhibits organized vulnerability to somatic mutations

This study identifies organized vulnerability in the aging genome, showing that certain genes and pathways are less mutated while others accumulate more mutations, suggesting a network-based mechanism for cellular decline.

Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity

This paper develops a mass spectrometry-based method to profile single-cell histone post-translational modifications, demonstrating its ability to detect treatment responses and chromatin heterogeneity.

SomaMutDB 2.0: A comprehensive database for exploring somatic mutations and their functional impact in normal human tissues

SomaMutDB 2.0 is a database that catalogs 8.9 million somatic mutations from 10,852 samples and provides functional annotations to assess their impact in normal human tissues.

Single-cell analysis of the somatic mutational landscape in human chondrocytes during aging and in osteoarthritis

This study analyzes somatic mutations in chondrocytes from aging and osteoarthritis patients using single-cell whole genome sequencing, finding age-related mutation accumulation with a lower rate in OA chondrocytes.

Uniquely high spontaneous mutational load in blood cells of XP-C patients

The paper identifies a high spontaneous mutational load in PBMCs of XP-C patients, linked to specific mutation signatures and replication-dependent mutagenesis.

Chromosomal Aneuploidy in Normal, Non-Neuronal Brain Nuclei of Glioblastoma Patients is Not a Cancer Driver

The paper examines aneuploidy in non-neuronal brain nuclei of GBM patients and finds it is common in normal tissue and not associated with GBM risk.

RNA sequence analysis of somatic mutations in aging and Parkinson's Disease

The paper analyzes RNA-seq data from Parkinson's Disease patients and controls to find increased somatic mutations in PD, with some clonal mutations being protective.

Polygenic prediction of human longevity on the supposition of pervasive pleiotropy

This study develops a polygenic score to predict exceptional longevity by modeling pleiotropic genetic variants linked to aging-related traits, showing improved lifespan prediction and identifying potential drug targets.

Chimera-suppressing error-corrected sequencing enables quantitative detection of rare somatic structural-variant breakpoints in human cells

This paper introduces SMM-SV-seq, a method to detect rare somatic structural-variant breakpoints in bulk DNA with high precision and recall, validated using human and Drosophila DNA mixtures and clinical treatments.

Negative Selection Allows DNA Mismatch Repair-Deficient Mouse Fibroblasts In Vitro to Tolerate High Levels of Somatic Mutations

This study shows that DNA mismatch repair-deficient mouse fibroblasts can tolerate high mutation burdens in vitro without significant growth effects, revealing mutation-driven population changes and negative selection.

Evidence for negative selection against somatic mutations in fibroblasts with high N-ethyl-N-nitrosourea-induced mutation load

The paper shows that human fibroblasts undergo negative selection against harmful mutations, maintaining growth despite high mutation loads.

Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell ageing

This study evaluates 14 metrics for measuring cell-to-cell expression variability in scRNA-seq data and applies the best-performing metric to analyze changes in variability during B cell ageing.

Analysis of somatic mutations in senescent cells using single-cell whole-genome sequencing

This study uses single-cell whole-genome sequencing to compare mutation burdens in early passage and deeply senescent human fibroblasts, finding increased single-nucleotide variations and aneuploidies in senescent cells.

Longevity-associated SMAD3 non-coding centenarian variant impairs a cell-type specific enhancer to reduce inflammation

The paper identifies a longevity-associated SMAD3 non-coding variant that impairs a cell-type specific enhancer, reducing inflammation and senescence in endothelial cells and improving healthspan in a mouse model.

Reduced frequency of clonal hematopoiesis in Parkinson's disease

The paper examines the association between clonal hematopoiesis and Parkinson's disease using whole exome sequencing data from controls and patients.

Expression of retrotransposons contributes to aging in Drosophila

This study investigates the role of retrotransposon expression and insertions in aging using Drosophila, finding that expression, not insertion, is linked to longevity.

A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A

The paper identifies a SIRT6 variant enriched in centenarians that improves genome stability through enhanced mADPr activity and interaction with Lamin A.

SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing

SCCNV identifies copy number variations from single-cell whole-genome sequencing data by adjusting for amplification bias.

The genome of North American beaver provides insights into the mechanisms of its longevity and cancer resistance

This study identifies genes contributing to beaver longevity and cancer resistance through genomic analysis of gene copy number, expression, and evolutionary changes.

Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver

The paper shows that somatic mutation frequencies increase with age in human liver hepatocytes but are lower in liver stem cells and organoids.

Single-cell whole-genome sequencing reveals mutational landscapes of DNA mismatch repair deficiency in mouse primary fibroblasts

This study uses single-cell whole-genome sequencing to analyze mutational landscapes in Msh2-deficient mouse fibroblasts, revealing elevated SNVs and INDELs with distinct mutational signatures.

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

This study uses single-cell whole-genome sequencing to analyze somatic mutations in B lymphocytes across the human lifespan, finding age-related mutation accumulation and potential cancer-related events.

Spontaneous retrotranspositions in normal tissues are rare and associated with cell-type-specific differentiation

The paper identifies rare spontaneous retrotranspositions in normal human tissues, showing cell-type-specific variation and association with differentiation processes.