Quantification of cell identity from single-cell gene expression profiles

Idan Efroni, Pui Leng Ip, Tal Nawy, Alison Mello, Kenneth D. Birnbaum

Research output: Contribution to journalArticlepeer-review


The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify identities from single-cell RNA-seq profiles, accurately classifying cells from Arabidopsis root tips and human glioblastoma tumors. We apply our approach to single cells captured from regenerating roots following tip excision. Our technique exposes a previously uncharacterized transient collapse of identity distant from the injury site, demonstrating the biological relevance of a quantitative cell identity index.

Original languageEnglish (US)
Article number9
JournalGenome biology
Issue number1
StatePublished - Jan 22 2015

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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