Christos Samakovlis

A repair-associated bronchial epithelial differentiation trajectory through KRT14+ basal and hillock-like cells drives airway inflammation and remodelling in childhood-onset asthma

The paper identifies a novel asthma-associated epithelial differentiation trajectory involving KRT14+ basal cells and hillock-like cells that contributes to airway inflammation and remodelling in childhood-onset asthma.

Cophenetic Spatial Topology Embedding reveals multiscale tissue architecture in spatial omics

COSTE embeds spatial relationships into a hierarchical metric space to reveal tissue architecture in spatial omics data, identifying spatially defined cell states and disease-associated patterns.

Branch extension and pruning share the same regulatory module in the developing Drosophila airways

The paper identifies a regulatory module that controls branch pruning in Drosophila airways by repurposing the branch extension program through Hox gene interference and extrinsic signaling.

Functional definition of the Drosophila airway progenitor field through overlapping compensatory regulators

The paper defines the Drosophila airway progenitor field through three cooperative regulatory programs and their roles in morphogenesis.

Mitochondrial COX4I2 drives pericyte-dependent inflammation and emphysema

This study shows that COX4I2 in pericytes drives inflammation and emphysema in COPD by increasing mtROS, and its deletion protects against these effects.

Probe set selection for targeted spatial transcriptomics

Spapros selects optimal probe sets for targeted spatial transcriptomics to improve cell type identification and spatial variation detection across multiple datasets.

High-parametric protein maps reveal the spatial organization in early-developing human lung

This study maps the spatial organization of the developing human lung using high-parametric protein imaging, revealing cell type composition and temporal changes across five developmental timepoints.

Single-cell transcriptomics identifies a p21-activated kinase important for survival of the zoonotic parasite Fasciola hepatica

The paper uses scRNA-seq to analyze Fasciola hepatica cells, identifies new cell types and gene expression patterns, and highlights PAK4's role in parasite survival.

Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways

This study identifies Emp as a key regulator of apical membrane morphogenesis in Drosophila airways by mediating endocytosis of luminal cargo proteins.

Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples

The paper introduces RRST, a spatial transcriptomics workflow that improves mRNA recovery from low-quality fresh frozen samples, demonstrating its effectiveness across multiple tissue types.

Fgfr2b signaling is essential for the maintenance of the alveolar epithelial type 2 lineage during lung homeostasis in mice

This study shows Fgfr2b signaling is essential for maintaining AT2 cells in adult mouse lungs, with IAAPs acting as potential progenitors.

An essential function for autocrine Hedgehog signaling in epithelial proliferation and differentiation in the trachea

This study identifies an autocrine role for Hedgehog signaling in regulating epithelial cell proliferation and differentiation in the trachea.

Developmental origins of cell heterogeneity in the human lung

The paper creates a comprehensive topographic atlas of early human lung development, identifying cell states, trajectories, and interactions to understand cell heterogeneity origins.

SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections

SCRINSHOT maps cell states in tissue sections at single-cell resolution, showing high correlation with scRNA-Seq data and enabling detailed spatial analysis of cell types.

Yorkie controls tube length and apical barrier integrity in the developing Drosophila airways

This paper identifies Yorkie's dual role in regulating tracheal tube length and apical barrier integrity in Drosophila airways through cytoplasmic and transcriptional mechanisms.