Barbara Treutlein

SALL1 and neural microenvironmental contextspecify identity of stem cell derived humanmicroglia-like cells

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.

Analog intrinsic recoding measures RNA dynamics without chemical conversion

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

Live single-molecule imaging reveals global shifts in mRNA mobility during human stem cell differentiation

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

A human developmental and adult brain atlas benchmarks dopaminergic stem cell models and cell therapy candidates

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

Integrin-identity shapes and mechanotemporally encodes the fibroblast transcriptome

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

Decoding morphogen patterning of human neural organoids with a multiplexed single-cell transcriptomic screen

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: 3D single-cell transcriptomics of intact biological systems

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

Unified Generation of Regionalized Neural Organoids from Single-Lumen Neuroepithelium

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.

Integrated cell atlas and tumoroids chart pancreatic cancer therapeutic targets

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.

Morphodynamics of human early brain organoid development

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

Mapping early patterning events in human neural development usingan in-vitro microfluidic stem cell model

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

Fate and state transitions during human blood vessel organoid development

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 enables generative single-cell phenotype modeling with flow matching

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

Multi-omic human neural organoid cell atlas of the posterior brain

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: Integrated, multi-modal profiling of intracellular protein dynamics in single cells

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

Single-cell profiling of penta- and tetradactyl mouse limb buds identifies mesenchymal progenitors controlling digit numbers and identities

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

An integrated transcriptomic cell atlas of human neural organoids

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.

Single-cell epigenomic reconstruction of developmental trajectories in human neural organoid systems from pluripotency

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

Buckling instability underlies vertebral segmentation during axolotl tail regeneration

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.

A human prenatal skin cell atlas reveals immune cell regulation of skin morphogenesis

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.

Single-cell brain organoid screening identifies developmental defects in autism

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.

Integrated Manufacturing Platform for Cortical Organoids Reveals Early Phosphatase and Prefoldin Dysregulation in MAPT V337M Neurons

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.

Characterization of RNA content in individual phase-separated coacervate microdroplets

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

Single-cell analyses of axolotl forebrain organization, neurogenesis, and regeneration

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

Multimodal spatiotemporal phenotyping of human organoid development

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.

Inferring and perturbing cell fate regulomes in human cerebral organoids

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

Cell atlas of the regenerating human liver after portal vein embolization

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

In vitro and in vivo development of the human intestine at single cell resolution

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

Ngn2 induces diverse neuronal lineages from human pluripotency

This study uses single-cell transcriptomics to show that Ngn2 overexpression in human iPSCs generates heterogeneous neurons, including peripheral nervous system-like populations, and that Ngn2 dosage affects neuron fate.

Cluster similarity spectrum integration of single-cell genomics data

This paper introduces a method to integrate single-cell genomics data across experiments and conditions while preserving biological information, showing it outperforms existing methods in certain scenarios.