Reversed graph embedding resolves complex single-cell trajectories

X Qiu, Q Mao, Y Tang, L Wang, R Chawla, HA Pliner… - Nature …, 2017 - nature.com
Nature methods, 2017nature.com
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.
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.
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