Gert Jan C. Veenstra

Roles of Neuromedin-U and Endothelin-1 in human cardiac organoid differentiation

This study identifies Neuromedin-U (NMU) and Endothelin-1 (ET-1) as key signaling factors influencing cardiomyocyte differentiation and electrophysiology in human cardiac organoids.

DANSE: a pipeline for dynamic modelling of time-series multi-omics data

DANSE models time-series multi-omics data to identify key transcription factors driving biological processes, using iPSC differentiation datasets as examples.

Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment

The paper compares cardiac differentiation trajectories in different culture conditions and identifies ZNF711 as a regulator of cardiomyocyte commitment and lineage balance.

ONECUT2 restricts Microfold cell numbers in the small intestine; a multi-omics study

This study uses multi-omics to show ONECUT2 restricts M cell differentiation in mouse intestinal organoids by acting downstream of RANK/RANKL signaling.

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

The paper builds a genome-scale gene regulatory network for vertebrate mesendoderm development using multi-omic data integration and validates novel transcription factor interactions.

Loss of PRC2 subunits primes lineage choice during exit of pluripotency

The paper investigates the role of PRC2 subunits in lineage choice during pluripotency exit using single-cell transcriptomics in mouse embryoid bodies.

ANANSE: An enhancer network-based computational approach for predicting key transcription factors in cell fate determination

ANANSE predicts key transcription factors in cell fate determination by analyzing enhancer-based regulatory networks across 18 human tissues.

Combinatorial action of transcription factors in open chromatin contributes to early cellular heterogeneity and organizer mesendoderm specification.

The paper investigates how transcription factor combinations acting on open chromatin influence early cellular heterogeneity and organizer mesendoderm specification in Xenopus during gastrulation.

Two distinct functional axes of positive feedback-enforced PRC2 recruitment in mouse embryonic stem cells

The paper investigates how PRC2 sub-complexes recruit to target genes in mESCs, revealing mutual reinforcement and feedback mechanisms between PRC2.1, PRC2.2, and PRC1.

NCOR1 AND OCT4 FACILITATE EARLY REPROGRAMMING BY CO-SUPPRESSING FIBROBLAST GENE EXPRESSION

This study shows NCOR1 and OCT4 co-suppress fibroblast gene expression during early reprogramming, enabling successful iPSC generation by overcoming reprogramming bottlenecks.

Wdr5, Brca1 and Bard1 link the DNA damage response to the mesenchymal-to-epithelial transition during early reprogramming.

The paper identifies Brca1, Bard1, and Wdr5 as factors linking DNA damage response to MET during reprogramming, using siRNA screening and colony morphology analysis.