Reversed graph embedding resolves complex single-cell trajectories

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

doi:10.1038/nmeth.4402

Reversed graph embedding resolves complex single-cell trajectories

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

2955 Citations (Scopus)

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.

Original language	English
Pages (from-to)	979-982
Number of pages	4
Journal	Nature Methods
Volume	14
Issue number	10
DOIs	https://doi.org/10.1038/nmeth.4402
Publication status	Published - 1 Oct 2017
Externally published	Yes

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10.1038/nmeth.4402

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title = "Reversed graph embedding resolves complex single-cell trajectories",

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.",

author = "Xiaojie Qiu and Qi Mao and Ying Tang and Li Wang and Raghav Chawla and Pliner, \{Hannah A.\} and Cole Trapnell",

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AU - Qiu, Xiaojie

AU - Mao, Qi

AU - Tang, Ying

AU - Wang, Li

AU - Chawla, Raghav

AU - Pliner, Hannah A.

AU - Trapnell, Cole

PY - 2017/10/1

Y1 - 2017/10/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85031017685

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DO - 10.1038/nmeth.4402

M3 - Article

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VL - 14

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JO - Nature Methods

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Reversed graph embedding resolves complex single-cell trajectories

Abstract

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