Barbara Treutlein

This study identifies how SALL1 and neural microenvironmental context shape the identity of stem cell-derived human microglia-like cells in 2D and 3D cultures.

The paper introduces AIR-seq, a method that measures RNA dynamics without chemical conversion, improving RNA velocity inference and revealing hidden regulation.

The paper tracks mRNA mobility during human stem cell differentiation and finds that mRNA dynamics shift towards constrained patterns as cells acquire identity.

The paper benchmarks dopaminergic stem cell models and cell therapy candidates using a human brain atlas to identify off-target populations and lineage plasticity.

This study shows integrin-identity shapes fibroblast transcriptomes under mechanical confinement, with distinct gene clusters and states depending on integrin class and confinement duration.

The paper uses a multiplexed single-cell transcriptomic screen to study how morphogen cues affect regional specification in human neural organoids, finding that timing, concentration, and combination of morphogens strongly influence cell type and regional composition.

DISCO-seq enables 3D single-cell transcriptomics of whole tissues and organisms by combining tissue-clearing chemistry with imaging and transcriptomic profiling.

This paper introduces a scalable platform to generate regionally specified neural organoids from uniform single-lumen neuroepithelium, improving reproducibility and fidelity to natural brain development.

The paper integrates single-cell transcriptomes and spatial transcriptomics to identify therapeutic targets in pancreatic cancer by analyzing cell states and ligand-receptor interactions in tumoroids.

The paper programs human neuron subtypes using combinatorial patterning and scRNA-seq to identify diverse neuron types and their developmental signaling networks.

The paper uses live imaging and single-cell transcriptomics to study how extracellular matrix influences brain organoid development and regionalization.

The paper uses a microfluidic stem cell model to study early human neural patterning, identifying regional specification and fate determination during the epiblast stage.

This study maps the cell state transitions during human blood vessel organoid development using single-cell transcriptomics and identifies key regulators and disease associations.

CellFlow predicts single-cell phenotypes from complex perturbations using flow matching, demonstrating accuracy in cytokine stimulation, drug treatments, and developmental modeling.

The paper creates a multi-omic atlas of human neural organoids modeling the posterior brain and identifies morphogen conditions that expand organoid models.

Phospho-seq integrates phosphorylated protein profiling with scATAC-seq and scRNA-seq to study cell signaling and gene regulation in single cells.

This study identifies mesenchymal progenitors in mouse limb buds that regulate digit numbers and identities through BMP signaling and GREM1-mediated antagonism.

This paper integrates 36 single-cell transcriptomics datasets from human neural organoids into a unified atlas to assess cell type coverage and compare organoid protocols with primary brain tissue.

The paper reconstructs epigenomic trajectories in human neural organoids from pluripotency to terminal cell states using single-cell histone modification profiling.

The paper shows that vertebral segmentation during axolotl tail regeneration occurs via a buckling instability mechanism, distinct from the somite-based process in embryonic development.

This paper creates a human endoderm organoid cell atlas by integrating single-cell transcriptomes from multiple organoid types to compare cell states with primary tissues and disease models.

This study creates a prenatal human skin cell atlas, revealing immune cells' role in skin development and showing their impact on vascular and hair follicle formation.

The paper uses CRISPR and single-cell transcriptomics to screen ASD risk genes in brain organoids, identifying developmental defects and regulatory modules linked to autism.

The paper develops a scalable cortical organoid platform with quality control metrics and identifies early dysregulation of phosphatase and prefoldin genes in FTD-tau neurons.

The paper characterizes RNA content in individual phase-separated coacervate microdroplets using high-throughput sequencing and identifies sequence motifs associated with RNA accumulation.

This study uses single-cell genomics to analyze axolotl forebrain cell types, neurogenesis, and regeneration, identifying conserved neuron classes and injury responses.

This paper develops a multimodal approach to study human retinal organoid development, integrating spatial, transcriptomic, and chromatin accessibility data to create a virtual atlas of retinal development.

The paper uses single-cell genomic data from human cerebral organoids to infer gene regulatory networks and assess transcription factor roles in brain development.

This study uses single-cell transcriptomics to analyze liver regeneration after portal vein embolization, identifying changes in cell states and immune interactions.

This study uses scRNA-seq to analyze human intestinal development, identifying cell sources of niche factors and their functional roles in stem cell maintenance.