Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.

ABSTRACT: Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational fram

SUBMITTER: Fu Y 

PROVIDER: S-EPMC12424799 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature