Reversed graph embedding resolves complex single-cell trajectories

Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However, learning the structure of complex trajectories with two or more branches remains a challenging computational problem. We present Monocle 2, which uses reversed graph embedding to describe multiple fate deci...

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Detalles Bibliográficos
Autores principales: Qiu, Xiaojie, Mao, Qi, Tang, Ying, Wang, Li, Chawla, Raghav, Pliner, Hannah A., Trapnell, Cole
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2017
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764547/
https://www.ncbi.nlm.nih.gov/pubmed/28825705
http://dx.doi.org/10.1038/nmeth.4402
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author Qiu, Xiaojie
Mao, Qi
Tang, Ying
Wang, Li
Chawla, Raghav
Pliner, Hannah A.
Trapnell, Cole
author_facet Qiu, Xiaojie
Mao, Qi
Tang, Ying
Wang, Li
Chawla, Raghav
Pliner, Hannah A.
Trapnell, Cole
author_sort Qiu, Xiaojie
collection PubMed
description Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However, learning the structure of complex trajectories with two or more branches remains a challenging computational problem. We present Monocle 2, which uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner. Applied to two studies of blood development, Monocle 2 revealed that mutations in key lineage transcription factors diverts cells to alternative fates.
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spelling pubmed-57645472018-02-21 Reversed graph embedding resolves complex single-cell trajectories Qiu, Xiaojie Mao, Qi Tang, Ying Wang, Li Chawla, Raghav Pliner, Hannah A. Trapnell, Cole Nat Methods Article Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However, learning the structure of complex trajectories with two or more branches remains a challenging computational problem. We present Monocle 2, which uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner. Applied to two studies of blood development, Monocle 2 revealed that mutations in key lineage transcription factors diverts cells to alternative fates. 2017-08-21 2017-10 /pmc/articles/PMC5764547/ /pubmed/28825705 http://dx.doi.org/10.1038/nmeth.4402 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Qiu, Xiaojie
Mao, Qi
Tang, Ying
Wang, Li
Chawla, Raghav
Pliner, Hannah A.
Trapnell, Cole
Reversed graph embedding resolves complex single-cell trajectories
title Reversed graph embedding resolves complex single-cell trajectories
title_full Reversed graph embedding resolves complex single-cell trajectories
title_fullStr Reversed graph embedding resolves complex single-cell trajectories
title_full_unstemmed Reversed graph embedding resolves complex single-cell trajectories
title_short Reversed graph embedding resolves complex single-cell trajectories
title_sort reversed graph embedding resolves complex single-cell trajectories
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764547/
https://www.ncbi.nlm.nih.gov/pubmed/28825705
http://dx.doi.org/10.1038/nmeth.4402
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