F. J. Theis

Cell circuits underlying nanomaterial specific respiratory toxicology

This study uses single-cell RNA-sequencing to analyze how different nanomaterials affect lung inflammation in mice, identifying cell type-specific responses and mechanisms.

An integrated transcriptomic cell atlas of human endoderm-derived organoids

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.

HBV rewires liver cancer signaling by altering PP2A complexes

This study identifies how HBV alters PP2A complexes to drive liver cancer signaling, revealing potential therapeutic targets.

Ex vivo tissue perturbations coupled to single cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis

The paper uses ex vivo perturbations on human lung slices combined with single-cell RNA-seq to study fibrogenesis, showing similarities to in vivo cell circuits and drug effects.

Autocrine Sfrp1 inhibits lung fibroblast invasion during transition to injury induced myofibroblasts

The paper identifies Sfrp1 as an autocrine inhibitor of fibroblast invasion during lung fibrosis by analyzing fibroblast states and signaling pathways in mouse lung regeneration.

Proteomics of spatially identified tissues in whole organs

This paper introduces DISCO-MS, a method for spatial proteomics of whole organs, and shows it provides proteomics data comparable to fresh tissues in rodent and human samples.

T cells modulate the microglial response to brain ischemia

This study shows engineered T cells overexpressing IL-10 alter microglial gene expression to a pro-regenerative profile after stroke, highlighting T cell-microglia interactions in neuroinflammation.

Low numbers of cytokine transcripts drive inflammatory skin diseases by initiating amplification cascades in localized epidermal clusters

Identification and characterization of distinct murine brown adipocyte lineages

The paper identifies and characterizes distinct murine brown adipocyte lineages using single-cell RNA sequencing and functional analysis.

In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning

This paper introduces a method using fluorescent MFG-E8 and deep learning to identify apoptotic and EV-bound live cells in vivo, finding that most PS+ cells are live cells associated with EVs.

A Sparse Deep Learning Approach for Automatic Segmentation of Human Vasculature in Multispectral Optoacoustic Tomography

This paper introduces a sparse UNET model for automatic vascular segmentation in MSOT images, achieving high accuracy and reducing manual effort.

A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease

The paper uses single-cell transcriptomics to identify novel cell states in healthy and asthmatic lung tissues, revealing changes in cell communication and immune responses.