ArticleNature methods2018
FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 199 papers.
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199 citing papers in PubMed, 376 citations in OpenAlex.
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- Preterm birth skews the developmental trajectory of myeloid-derived suppressor cells in the first 48 hours of life: single-cell transcriptomics and inferred intercellular communication.Molecular medicine (Cambridge, Mass.) · 2026Article
- PalmaClust: A graph-fusion framework leveraging the Palma ratio for robust ultra-rare cell type detection in scRNA-seq data.bioRxiv : the preprint server for biology · 2026Article
- Inferring cell differentiation maps from lineage tracing data.Nature methods · 2026Article
- Simultaneous generation of transplantable RGC-like and corneal progenitor cells from hiPSCs using a dual-lineage platform.Stem cell research & therapy · 2025Article
- KANSL3 directs transcriptional programs essential for hepatic metabolism and differentiation.Life science alliance · 2025Article
139 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
To understand stem cell differentiation along multiple lineages, it is necessary to resolve heterogeneous cellular states and the ancestral relationships between them. We developed a robotic miniaturized CEL-Seq2 implementation to carry out deep single-cell RNA-seq of ∼2,000 mouse hematopoietic progenitors enriched for lymphoid lineages, and used an improved clustering algorithm, RaceID3, to identify cell types. To resolve subtle transcriptome differences indicative of lineage biases, we developed FateID, an iterative supervised learning algorithm for the probabilistic quantification of cell fate bias in progenitor populations. Here we used FateID to delineate domains of fate bias and enable the derivation of high-resolution differentiation trajectories, thereby revealing a common progenitor population of B cells and plasmacytoid dendritic cells, which we validated by in vitro differentiation assays. We expect that FateID will improve understanding of the process of cell fate choice in complex multi-lineage differentiation systems.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.