Sami Saarenpää

ProbeST designs custom probe sets for spatial transcriptomics, validated on mouse enteroids infected with Salmonella, enabling detection of host and pathogen transcripts.

The paper optimizes MASC-seq for single-cell transcriptomics and imaging of microbial eukaryotic plankton, showing promise but limitations in resolving small cells.

This study uses spatial transcriptomics and snRNA-seq to analyze host-pathogen interactions in P. berghei-infected mouse liver tissues, revealing changes in lipid metabolism and inflammatory responses.

The paper demonstrates miniature spatial transcriptomics to study gene expression patterns in filarial worms and their Wolbachia endosymbionts, revealing spatial gene localization and interactions.

The paper introduces SmT, a spatial metatranscriptomics method to study host-microbe interactions in Arabidopsis thaliana, revealing microbial hotspots and spatial networks.

This study uses spatial transcriptomics to analyze liver tissue, revealing zonation patterns and previously uncharacterized structures in the spatial transcriptome.

Analysis of the ALS spinal cord using Spatial Transcriptomics reveals spatiotemporal dynamics of disease driven gene regulation.