Lareau, C. A., Chapman, M. S., Penter, L., Nawy, T. & Pe’er, D. Artefacts in single-cell mtDNA analyses misinform phylogenies. Nature https://doi.org/10.1038/s41586-026-10777-0 (2026).
Weng, C. et al. Deciphering cell states and genealogies of human hematopoiesis. Nature 627, 389–398 (2024).
Salk, J. J., Schmitt, M. W. & Loeb, L. A. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. Nat. Rev. Genet. 19, 269–285 (2018).
Bae, J. H. et al. Single duplex DNA sequencing with CODEC detects mutations with high sensitivity. Nat. Genet. 55, 871–879 (2023).
Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508–14513 (2012).
Weng, C., Weissman, J. S. & Sankaran, V. G. Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling. Preprint at bioRxiv https://doi.org/10.1101/2024.08.23.609473 (2024).
Rausser, S. et al. Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures. eLife 10, e70899 (2021).
Ju, Y. S. et al. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife 3, e02935 (2014).
Weng, C. et al. Deciphering cell states and genealogies of human haematopoiesis. Nature 627, 389–398 (2024).
Mitchell, E. et al. Clonal dynamics of haematopoiesis across the human lifespan. Nature 606, 343–350 (2022).
Wang, X. et al. Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells. Genome Biol. 26, 70 (2025).
An, J. et al. Mitochondrial DNA mosaicism in normal human somatic cells. Nat. Genet. 56, 1665–1677 (2024).
Árnadóttir, E. R. et al. The rate and nature of mitochondrial DNA mutations in human pedigrees. Cell 187, 3904–3918.e8 (2024).
Sashittal, P., Chen, V., Pasarkar, A. & Raphael, B. J. Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data. Bioinformatics 40, i218–i227 (2024).
Cossa, A. et al. MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics. Nat. Commun. https://doi.org/10.1038/s41467-026-71607-5 (2026).
Kozlov, A., Alves, J. M., Stamatakis, A. & Posada, D. CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data. Genome Biol. 23, 37 (2022).