Blaž Zupan

This paper evaluates the transferability of single-cell foundation models across deep evolutionary distances using developmental atlases of Dictyostelium discoideum and Caenorhabditis elegans.

dictyExpress 3.0 integrates bulk and single-cell transcriptomics data for Dictyostelium, offering interactive visualizations and cross-modal analysis.

The paper introduces a visual analytics framework for survival analysis that enables non-programmers to perform biomarker discovery through interactive workflows and visualization tools.

openTSNE is a Python library for t-SNE dimensionality reduction that is faster than existing implementations and supports mapping new data to existing embeddings.

The paper proposes a method to reduce batch effects in single-cell data by embedding new data into a t-SNE visualization of a reference dataset, improving co-clustering of cells from different datasets.

The paper identifies milestone genes and regulons in Dictyostelium development through time-series RNA-sequencing, revealing new gene expression patterns and developmental transitions.