António M. Palma

SC2Spa maps single-cell RNA-seq data to spatial coordinates using deep learning, improving resolution for low-resolution spatial transcriptomics data and identifying spatially variable genes.

CellNeighborEX identifies gene expression influenced by neighboring cells in spatial transcriptomics data, revealing new insights into cell-cell interactions in mouse embryos, brain, and liver cancer.

The paper introduces PIC-seq to study cell-cell contact-specific gene expression during mouse embryonic development and identifies novel gene expression signatures dependent on neighboring cell types.