Domagoj Matijević

This paper benchmarks 26 spatial domain detection methods across real and semi-synthetic spatial transcriptomics data to identify performance drivers and introduce a modular benchmarking framework.

The paper proposes a method to identify a small set of marker genes that optimally separate cell types in single-cell RNA-seq data by considering expression variation within cell types.

The paper introduces a neural network method for metric multidimensional scaling that scales to large single-cell datasets and provides non-linear embeddings.

This paper introduces Trajan, a tool for comparing complex single-cell trajectories with branching points, demonstrating its ability to align biological processes and identify reprogramming barriers.