Universität zu Köln

Failmezger, Henrik, Dursun, Ezgi, Dümcke, Sebastian, Endele, Max, Poron, Don, Schroeder, Timm ORCID: 0000-0001-9320-0252, Krug, Anne ORCID: 0000-0002-9556-7207 and Tresch, Achim ORCID: 0000-0002-4146-6371 (2019). Clustering of samples with a tree-shaped dependence structure, with an application to microscopic time lapse imaging. Bioinformatics, 35 (13). S. 2291 - 2300. OXFORD: OXFORD UNIV PRESS. ISSN 1460-2059

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Abstract

Motivation Recent imaging technologies allow for high-throughput tracking of cells as they migrate, divide, express fluorescent markers and change their morphology. The interpretation of these data requires unbiased, efficient statistical methods that model the dynamics of cell phenotypes. Results We introduce treeHFM, a probabilistic model which generalizes the theory of hidden Markov models to tree structured data. While accounting for the entire genealogy of a cell, treeHFM categorizes cells according to their primary phenotypic features. It models all relevant events in a cell's life, including cell division, and thereby enables the analysis of event order and cell fate heterogeneity. Simulations show higher accuracy in predicting correct state labels when modeling the more complex, tree-shaped dependency of samples over standard HMM modeling. Applying treeHFM to time lapse images of hematopoietic progenitor cell differentiation, we demonstrate that progenitor cells undergo a well-ordered sequence of differentiation events. Availability and implementation The treeHFM is implemented in C++. We provide wrapper functions for the programming languages R (CRAN package, https://CRAN.R-project.org/package=treeHFM) and Matlab (available at Mathworks Central, http://se.mathworks.com/matlabcentral/fileexchange/57575-treehfml).

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Failmezger, Henrik UNSPECIFIED UNSPECIFIED UNSPECIFIED Dursun, Ezgi UNSPECIFIED UNSPECIFIED UNSPECIFIED Dümcke, Sebastian UNSPECIFIED UNSPECIFIED UNSPECIFIED Endele, Max UNSPECIFIED UNSPECIFIED UNSPECIFIED Poron, Don UNSPECIFIED UNSPECIFIED UNSPECIFIED Schroeder, Timm UNSPECIFIED orcid.org/0000-0001-9320-0252 UNSPECIFIED Krug, Anne UNSPECIFIED orcid.org/0000-0002-9556-7207 UNSPECIFIED Tresch, Achim UNSPECIFIED orcid.org/0000-0002-4146-6371 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-135906
DOI:	10.1093/bioinformatics/bty939
Journal or Publication Title:	Bioinformatics
Volume:	35
Number:	13
Page Range:	S. 2291 - 2300
Date:	2019
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1460-2059
Language:	English
Faculty:	Faculty of Medicine
Divisions:	Faculty of Medicine > Sonstiges > Zentrum für Versorgungsforschung Köln
Subjects:	Medical sciences Medicine
Uncontrolled Keywords:	Keywords Language CELL; QUANTIFICATION; CLASSIFICATION; SEGMENTATION; TRACKING; MODELS Multiple languages Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/13590