Sokratia Georgaka

PISTACHIO improves spatial cell-type deconvolution in tumours using proteomics constraints and non-negative matrix factorization.

Mantpy is a framework for analyzing the extracellular matrix in spatial proteomics by representing it as spatial graphs and integrating it with cell data for joint analysis.

CellPie is a fast, unsupervised method for factor discovery in spatial transcriptomics using joint non-negative matrix factorization, showing improved performance on human cancer datasets.

The paper maps the spatial transcriptional changes in human liver cirrhosis, identifying gene signatures and cell state transitions linked to disease progression.

The paper introduces GPcounts, a non-parametric method for modeling temporal and spatial counts data in RNA-seq using a negative binomial likelihood, showing improved performance over Gaussian and Poisson models.