Centroid clustering of cellular lineage trees
Khakhutskyy V, Schwarzfischer M, Hubig N, Plant C, Marr C, Rieger MA, Schroeder T, Theis FJ (2014)
Publication Type: Conference contribution
Publication year: 2014
Journal
Publisher: Springer Verlag
Book Volume: 8649 LNCS
Pages Range: 15-29
Conference Proceedings Title: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Event location: DEU
ISBN: 9783319102641
DOI: 10.1007/978-3-319-10265-8_2
Abstract
Trees representing hierarchical knowledge are prevalent in biology and medicine. Some examples are phylogenetic trees, the hierarchical structure of biological tissues and cell lines. The increasing throughput of techniques generating such trees poses new challenges to the analysis of tree ensembles. Some typical tasks include the determination of common patterns of lineage decisions in cellular differentiation trees. Partitioning the dataset is crucial for further analysis of the cellular genealogies. In this work, we develop a method to cluster labeled binary tree structures. Furthermore, for every cluster our method selects a centroid tree that captures the characteristic mitosis patterns of the group. We evaluate this technique on synthetic data and apply it to experimental trees that embody the lineages of differentiating cells under specific conditions over time. The results of the cell lineage trees are thoroughly interpreted with expert domain knowledge. © 2014 Springer International Publishing.
Involved external institutions
Technische Universität München (TUM)
Germany (DE)
Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich
Germany (DE)
Universitätsklinikum Frankfurt am Main (KGU)
Germany (DE)
Eidgenössische Technische Hochschule Zürich (ETHZ) / Swiss Federal Institute of Technology in Zurich
Switzerland (CH)
Germany (DE)
Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich
Germany (DE)
Universitätsklinikum Frankfurt am Main (KGU)
Germany (DE)
Eidgenössische Technische Hochschule Zürich (ETHZ) / Swiss Federal Institute of Technology in Zurich
Switzerland (CH)
How to cite
APA:
Khakhutskyy, V., Schwarzfischer, M., Hubig, N., Plant, C., Marr, C., Rieger, M.A.,... Theis, F.J. (2014). Centroid clustering of cellular lineage trees. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pp. 15-29). DEU: Springer Verlag.
MLA:
Khakhutskyy, Valeriy, et al. "Centroid clustering of cellular lineage trees." Proceedings of the 5th International Conference on Information Technology in Bio- and Medical Informatics, ITBAM 2014, DEU Springer Verlag, 2014. 15-29.
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