De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

Dominic Grün, Mauro J. Muraro, Jean Charles Boisset, Kay Wiebrands, Anna Lyubimova, Gitanjali Dharmadhikari, Maaike van den Born, Johan van Es, Erik Jansen, Hans Clevers, Eelco J.P. de Koning, Alexander van Oudenaarden

Research output: Contribution to journalArticlepeer-review

375 Citations (Scopus)


Adult mitotic tissues like the intestine, skin, and blood undergo constant turnover throughout the life of an organism. Knowing the identity of the stem cell is crucial to understanding tissue homeostasis and its aberrations upon disease. Here we present a computational method for the derivation of a lineage tree from single-cell transcriptome data. By exploiting the tree topology and the transcriptome composition, we establish StemID, an algorithm for identifying stem cells among all detectable cell types within a population. We demonstrate that StemID recovers two known adult stem cell populations, Lgr5+ cells in the small intestine and hematopoietic stem cells in the bone marrow. We apply StemID to predict candidate multipotent cell populations in the human pancreas, a tissue with largely uncharacterized turnover dynamics. We hope that StemID will accelerate the search for novel stem cells by providing concrete markers for biological follow-up and validation.

Original languageEnglish
Pages (from-to)266-277
Number of pages12
JournalCell Stem Cell
Issue number2
Publication statusPublished - 4 Aug 2016


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