A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity

Farnaz Mohammadi; Shakthi Visagan; Sean M. Gross; Luka Karginov; J. C. Lagarde; Laura M. Heiser; Aaron S. Meyer

doi:10.1038/s42003-022-04208-9

Communications Biology (Nov 2022)

A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity

Farnaz Mohammadi,
Shakthi Visagan,
Sean M. Gross,
Luka Karginov,
J. C. Lagarde,
Laura M. Heiser,
Aaron S. Meyer

Affiliations

Farnaz Mohammadi: Department of Bioengineering, University of California
Shakthi Visagan: Department of Bioengineering, University of California
Sean M. Gross: Department of Biomedical Engineering, Oregon Health & Science University
Luka Karginov: Department of Bioengineering, University of Illinois
J. C. Lagarde: Department of Bioengineering, University of California
Laura M. Heiser: Department of Biomedical Engineering, Oregon Health & Science University
Aaron S. Meyer: Department of Bioengineering, University of California

DOI: https://doi.org/10.1038/s42003-022-04208-9
Journal volume & issue: Vol. 5, no. 1
pp. 1 – 14

Abstract

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A tree-based adaptation of a hidden Markov model captures heterogeneity and cell state transitions based on single-cell lineages, enabling the study of intrinsic or drug-induced plasticity in heterogeneous cell populations.

Published in Communications Biology

ISSN: 2399-3642 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General)
Website: https://www.nature.com/commsbio/

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