Ruben Boers

Joint recording of past and present transcriptomes reconstructs single-cell trajectories

This paper introduces scReMeMber-Seq, a method to reconstruct single-cell trajectories by linking past and present transcriptomes using methylation-based memory recording.

Time-resolved single-cell state tracing exposes bidirectional state dynamics during differentiation

The paper uses single-cell state tracing to show bidirectional differentiation dynamics and rare transcriptome conversions across lineage boundaries in both in vivo and in vitro settings.

Sex-specific DNA methylation in adult skeletal muscle

The paper examines DNA methylation patterns in adult skeletal muscle, finding that sex, not spatial location, drives methylation variation and sex-specific transcriptional programs.

Improved circulating tumor DNA profiling by simultaneous extraction of DNA methylation and copy number information from Methylated DNA Sequencing data (MeD-seq)

The paper introduces MeD-seq, a method to profile circulating tumor DNA by analyzing DNA methylation and copy number changes, showing its effectiveness in detecting cancer-specific signals in plasma samples.

XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans

This study shows that XIST is required for XCI in human extraembryonic cells, which is essential for their survival and development.

Human DCM-time machine unravels cell state changes during primitive gut tube differentiation

The paper introduces DCM-time machine (DCM-TM) to track gene and enhancer activity during human iPSC differentiation, showing its ability to label active elements and correlate methylation changes with cell state transitions.

Genome-wide methylation profiling of cell-free DNA in maternal plasma using Methylated DNA Sequencing (MeD-seq)

This study uses MeD-seq to profile methylation in maternal cfDNA, identifying placental-specific methylation marks and 436 DMRs between pregnant and non-pregnant women.

DNA methylation database for gynecological cancer detection, classification and assay development

This study creates a DNA methylation database for gynecological cancers and develops qMSP assays for detection and classification.

XIST dampens X chromosome activity in a SPEN-dependent manner during early human development

The paper shows XIST reduces X chromosome activity through SPEN-dependent mechanisms before XCI in human embryos, while XACT does not significantly affect XIST function.

Retrospective analysis of enhancer activity and transcriptome history

The paper uses a novel method to track enhancer activity and transcriptome changes during intestinal stem cell differentiation, revealing insights into lineage decisions and chromatin dynamics.

Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells.

This study develops a mouse model to monitor Mecp2 reactivation in neural stem cells and identifies genetic and epigenetic factors influencing reactivation of the inactive X chromosome.

High throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by Methylated DNA sequencing (MeD-seq) of LpnPI digested fragments

This paper validates MeD-seq for cfDNA methylation profiling in cancer patients, showing distinct pre-surgical methylation patterns compared to healthy donors.