Julia Naas

The paper introduces scAtlasTb, a framework for building and optimizing single-cell reference atlases, demonstrating its application on three Human Cell Atlas projects.

CellREST reinterprets scRNA-seq trajectory reconstruction as a phylogenetic inference problem, uncovering circular processes and converging differentiation scenarios in simulated and experimental data.

The paper evaluates four organoid protocols to recreate human brain cell diversity, identifies factors affecting variability, and introduces a scoring system to assess differentiation propensities.

MultiMatch analyzes chain-like particle arrangements in multi-color microscopy using optimal transport, outperforming existing methods in recovering chain structures.

The paper identifies a stress signature in brain organoid scRNA-seq data and introduces Gruffi to remove stressed cells, improving developmental accuracy.