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Nat Methods. 2017 Oct;14(10):979-982. doi: 10.1038/nmeth.4402. Epub 2017 Aug 21.

Reversed graph embedding resolves complex single-cell trajectories.

Author information

1
Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA.
2
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
3
HERE Company, Chicago, Illinois, USA.
4
Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
5
Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, USA.

Abstract

Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However, learning the structure of complex trajectories with multiple branches remains a challenging computational problem. We present Monocle 2, an algorithm that uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner. We applied Monocle 2 to two studies of blood development and found that mutations in the genes encoding key lineage transcription factors divert cells to alternative fates.

PMID:
28825705
PMCID:
PMC5764547
DOI:
10.1038/nmeth.4402
[Indexed for MEDLINE]
Free PMC Article

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