Joost H. Gribnau

scRIPT is a single-cell lineage-tracing method that improves coverage and reliability in differentiation protocols by integrating rapid barcoding, sorting, and sequencing with quality control.

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

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.

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

This study identifies Spp1⁺ macrophages as key hubs coordinating fibrotic remodeling in myeloproliferative neoplasms using NicheSphere, a novel computational method for cell communication analysis.

The paper shows that Wnt-dependent reprogramming of bone marrow niches drives fibrosis by activating osteolineage cells and altering hematopoietic support.

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.

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

The paper investigates the roles of Atf3, Zfp711, and Bcl6b in early hemato-endothelial lineage specification using scRNA-seq and KO mESCs, finding distinct effects on mesodermal and hematopoietic lineages.

The paper shows that X-chromosome upregulation occurs gene-by-gene at both RNA and protein levels in mouse pluripotent stem cells.

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.

This study identifies HCFC1 and YY1 as factors that recruit COMPASS and Integrator complexes to initiate X chromosome inactivation by regulating Xist and its cis-regulatory elements.

The paper identifies genome-lamina reorganization preceding long gene activation in mouse corticogenesis and links it to MeCP2 binding.

This study characterizes cytotrophoblast dynamics during pregnancy using single-cell RNA sequencing, identifying distinct subsets and their functional roles.

The paper identifies a novel XACT lncRNA transcript expressed in both active and inactive X chromosomes, with roles in erythroid differentiation and AML subtypes beyond its role in XCI.

This paper introduces two mouse embryoid models to study interactions between primitive endoderm and epiblast during early development, showing they replicate in vivo dynamics and cell fate decisions.

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.

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

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.

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.

This study uses multi-color dSTORM microscopy to analyze RAD51 and DMC1 organization at meiotic DSBs in Hormad1-/- mice, revealing altered recombinase configurations and synaptonemal complex structure.

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.

This study shows that SPEN is essential for Xist upregulation during X chromosome inactivation initiation in female mouse ESCs by silencing Tsix.

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

This study shows that RLIM deficiency in mice causes respiratory distress and neonatal death due to impaired BMP signaling in lung development.

This paper introduces an in vitro cross method using mitotic recombination in hybrid mouse embryonic stem cells to map species differences and generate mosaic mice.

This paper reviews the regulation of X-chromosome inactivation and its clinical implications for X-linked diseases in females.