Spall: accurate and robust unveiling cellular landscapes from spatially resolved transcriptomics data using a decomposition network

BMC Bioinformatics, Год журнала: 2024, Номер 25(1)

Опубликована: Дек. 18, 2024

Recent developments in spatially resolved transcriptomics (SRT) enable the characterization of spatial structures for different tissues. Many decomposition methods have been proposed to depict cellular distribution within However, existing computational struggle balance continuity cell with preservation cell-specific characteristics. To address this, we propose Spall, a novel network that integrates scRNA-seq data SRT accurately infer type proportions. Spall introduced GATv2 module, featuring flexible dynamic attention mechanism capture relationships between spots. This improves identification patterns analysis. Additionally, incorporates skip connections loss information, thereby enhancing prediction capability rare types. Experimental results show outperforms state-of-the-art reconstructing on multiple datasets. Notably, reveals tumor heterogeneity human pancreatic ductal adenocarcinoma samples and delineates complex tissue structures, such as laminar organization mouse cerebral cortex cerebellum. These findings highlight ability provide reliable low-dimensional embeddings downstream analyses, offering new opportunities deciphering structures.

Язык: Английский

Distinct functional domains of Dystroglycan regulate inhibitory synapse formation and maintenance in cerebellar Purkinje cells

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 30, 2024

Dystroglycan is a cell adhesion molecule that localizes to synapses throughout the nervous system. While required maintain inhibitory from cerebellar molecular layer interneurons (MLIs) onto Purkinje cells (PCs) whether initial synaptogenesis during development dependent on has not been examined. We show conditional deletion of

Язык: Английский