Dominic Grün

Notch-independent Her6 contributes to control of neural stem cell maintenance by shifting Notch signaling from lateral inhibition towards lateral induction mode

The paper shows Her6, a Notch-independent factor, shifts Notch signaling from lateral inhibition to lateral induction, aiding neural stem cell maintenance in zebrafish.

BARe-seq enables high-throughput dissection of cis-regulatory control of transcriptional bursting

BARe-seq measures transcriptional burst parameters in Drosophila cells using allele-resolved bulk sequencing, revealing distinct kinetic properties of promoters and enhancers.

HLiCA: An integrated cell atlas of the healthy human liver

The paper integrates multiple datasets to create a comprehensive human liver cell atlas, identifying new cell types and associations with demographic factors.

An immunobiliary single-cell atlas resolves crosstalk of type 2 cDCs and γδT cells in cholangitis

This study creates a single-cell atlas of the immunobiliary niche in cholangitis, revealing interactions between type 2 conventional dendritic cells and γδT cells that drive fibrosis.

NiCo Identifies Extrinsic Drivers of Cell State Modulation by Niche Covariation Analysis

NiCo identifies extrinsic drivers of cell state modulation by analyzing niche covariation in spatial transcriptomics data.

Spatio-temporal dynamics of the fibrotic niche in cardiac repair

This study uses single-cell RNA-sequencing and spatial transcriptomics to analyze the spatio-temporal dynamics of the fibrotic niche in cardiac repair after ventricular injury in adult mice, identifying key cell interactions and regulatory mechanisms.

Scalable identification of lineage-specific gene regulatory networks from metacells with NetID

NetID identifies lineage-specific gene regulatory networks from scRNA-seq data by improving GRN inference through metacell-based analysis and avoids spurious correlations.

Gene expression noise dynamics unveil functional heterogeneity of ageing hematopoietic stem cells

The paper develops VarID2 to quantify biological noise in single-cell RNA-seq data, revealing noise dynamics in hematopoietic stem cells during differentiation and ageing.

DOT1L activity affects cell lineage progression in the developing brain by controlling metabolic programs

This study shows that DOT1L activity regulates AP lineage progression in the developing mouse neocortex by controlling metabolic programs and gene expression.

Single-cell transcriptomic resolution of stem cells and their developmental trajectories in the hippocampus reveals epigenetic control of cell state perseverance

The paper uses single-cell RNA sequencing to study hippocampal development in DOT1L-mutant mice, identifying distinct neural stem cell populations and their developmental trajectories, revealing DOT1L's role in cell state preservation and hippocampal maturation.

Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation

The paper investigates the spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation using genetic fate labeling, imaging, and scRNA-seq.

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

A Human Liver Cell Atlas: Revealing Cell Type Heterogeneity and Adult Liver Progenitors by Single-Cell RNA-sequencing

This paper constructs a human liver cell atlas using single-cell RNA-sequencing to identify new cell subtypes and progenitors, and applies it to study liver disease and engraftment.

Deciphering the Regulatory Landscape of γδ T Cell Development by Single-Cell RNA-Sequencing

This study uses single-cell RNA-sequencing to uncover the developmental trajectory of γδ T cells, identifying c-MAF as a key regulator of IL-17-producing γδ T cell differentiation.

Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification

This study identifies Tdrd6a as a regulator of Buc protein aggregation, which is essential for forming subcellular compartments that drive germ cell specification in zebrafish.

The Polycomb-dependent epigenome controls β-cell dysfunction, dedifferentiation and diabetes

This study identifies chromatin-state signatures linked to β-cell dysfunction and diabetes by combining epigenome mapping with single-cell transcriptomics in mice and humans.

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

FateID quantifies cell fate bias in multipotent progenitors using single-cell RNA-seq data, revealing a common progenitor population for B cells and plasmacytoid dendritic cells.