Berthold Göttgens

The paper uses scRNA-Seq and computational methods to predict and validate differentiation trajectories during early mammalian organogenesis, showing agreement between computational predictions and experimental outcomes.

The paper develops statistical tools to analyze gene knockouts in mouse embryos and applies them to study developmental disruptions and cancer therapy responses.

This study constructs a rabbit developmental atlas and compares it with mouse data to identify species-specific differences in gene regulation and extra-embryonic tissues.

The paper develops GASPACHO to identify dynamic eQTLs in antiviral responses using single-cell RNA-seq, uncovering thousands of eQTLs and linking them to disease risk loci.

The paper identifies NOTCH1-JAG1 cis interactions regulated by RADICAL FRINGE that maintain hematopoietic stem cell fate during development.

The paper identifies cell-type-specific regulatory roles of a heptad of transcription factors in human hematopoietic stem and progenitor cells.

The paper maps the multi-organ functions of the human yolk sac during early development, revealing its roles in hematopoiesis, nutrition, and oxygen regulation.

The paper shows that mesoderm-derived PDGFRA+ stromal cells in the AGM region support endothelial-to-hematopoietic transition and LT-HSC generation.

The paper identifies thousands of cell stage-specific enhancers that drive hematopoietic specification by responding to cytokine signals and transcription factors.

This study uses single-cell RNA-sequencing to analyze fetal bone marrow development and identifies disruptions in hematopoiesis in Down syndrome.

This study shows that endothelial-specific Gata3 expression is required for the maturation of haemogenic endothelial cells into haematopoietic stem cells during the endothelial-to-haematopoietic transition.

The paper shows p57Kip2 limits HSC numbers by restricting SNS progenitor size and catecholamine secretion in the AGM region via β2-adrenergic signaling.

This paper uses spatial transcriptomics to study mouse organogenesis, revealing spatial gene expression patterns and cell fate decisions not captured by single-cell RNA sequencing.

The paper identifies coordinated step-changes in gene expression kinetics during erythropoiesis in both mouse and human, challenging assumptions of RNA velocity analysis.

This study shows that Runx1 inhibits heart regeneration in zebrafish by promoting scar formation and reducing myocardial proliferation and survival.

The paper shows that Dll4 inhibits cell recruitment into aortic clusters, reducing hematopoietic stem cell formation.

The paper integrates epigenomic and transcriptomic data from mouse hematopoiesis to identify regulatory elements and their dynamics across cell types.

The paper integrates GATA transcription factors and epigenomes in mouse hematopoietic cells using IDEAS to map regulatory landscapes and identify candidate cis-regulatory elements.

This study identifies Nanog as a repressor of Pou3f1, which inhibits anterior neural fate during gastrulation in mouse embryos.

The paper uses single-cell transcriptomics to map hematopoiesis in human fetal liver, identifying cell differentiation trajectories and shifts in hematopoietic composition during development.

The paper identifies Lgr5+ hepatoblasts as bi-potent liver progenitors that contribute to liver development and reside at the apex of the embryonic hepatoblast hierarchy.

This paper introduces PAGA, a method that reconciles clustering with trajectory inference by creating a topology-preserving graph map of single-cell data, demonstrating its effectiveness across multiple datasets.

This study investigates how malaria infection alters the bone marrow microenvironment, leading to impaired haematopoietic stem cell function through changes in endothelium and osteoblasts.

This study evaluates spike-in normalization in single-cell RNA sequencing, finding it reliable despite technical noise and minor variance in spike-in RNA addition and behavior.

The paper proposes the Human Cell Atlas project to catalog all human cell types through molecular profiling and connects this data with classical cellular descriptions.

This paper establishes expanded potential stem cells (EPSCs) from mouse blastomeres and shows they can contribute to both embryo proper and trophoblasts in chimeras.