反向图嵌入解析复杂的单细胞轨迹。

Qiu Xiaojie, Mao Qi, Tang Ying, Wang Li, Chawla Raghav, Pliner Hannah A, Trapnell Cole

Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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

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.

单细胞轨迹能够揭示基因调控如何决定细胞命运。然而，学习具有多个分支的复杂轨迹结构仍然是一个具有挑战性的计算问题。我们提出了Monocle 2，这是一种使用反向图嵌入以完全无监督的方式描述多个命运决定的算法。我们将Monocle 2应用于两项血液发育研究，发现编码关键谱系转录因子的基因突变会使细胞转向其他命运。