Joao MF Alves

Overall, this work provides a practical benchmark and a framework for integrating evolutionary and transcriptional analyses using single-cell RNA-seq data.

By mapping gene expression onto cell phylogenies, we also assessed the phylogenetic signal of transcriptional traits. Although most gene expression appears highly plastic, we found strong phylogenetic signal in cell-cycle and immune-related genes in one patient.

Our results show that:
- Variant calling from scRNA-seq remains challenging (low SNP recall, high allelic dropout).
- The choice of method strongly affects the inferred evolutionary history and not all tools consistently return phylogenetically informative genotypes.

In this study, we benchmarked six variant-calling strategies to evaluate their ability to recover somatic mutations and reconstruct single-cell phylogenies in 5 cancer patients.

Unraveling the Phylogenetic Signal of Gene Expression from Single-cell RNA-seq Data Abstract. Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of phenotypic heterogeneity. Although the predominant focus of scRNA-seq

Extremely happy to see this work finally published in GPB!
Together with @davidposada.bsky.social and Laura Tomas, we explored how far we can push scRNA-seq data beyond gene expression profiling.

doi.org/10.1093/gpbj...