Topological data analysis of single-cell Hi-C contact maps

DOI10.1007/978-3-030-43408-3_6MaRDI QIDQ5118363zbMATH OpenOpenAlexFDO

Authors Mathieu Carrière, R. Rabadán

Publication date 8 September 2020

Published in Topological Data Analysis (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1812.01360

zbMATH Keywords

DNA foldingtopological data analysis

Mathematics Subject Classification ID

Persistent homology and applications, topological data analysis (55N31) Applications of statistics to biology and medical sciences; meta analysis (62P10) Topological data analysis (62R40) Protein sequences, DNA sequences (92D20)

Abstract: In this article, we show how the recent statistical techniques developed in Topological Data Analysis for the Mapper algorithm can be extended and leveraged to formally define and statistically quantify the presence of topological structures coming from biological phenomena in datasets of CCC contact maps.

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Cites work

• Chi-Square Tests with One Degree of Freedom; Extensions of the Mantel- Haenszel Procedure
• Computational topology. An introduction
• Convergence between categorical representations of Reeb space and mapper
• Extending persistence using Poincaré and Lefschetz duality
• Hierarchical Clustering for Finding Symmetries and Other Patterns in Massive, High Dimensional Datasets
• scientific article; zbMATH DE number 48904 (Why is no real title available?)
• Multiscale mapper: topological summarization via codomain covers
• Persistence theory. From quiver representations to data analysis
• Stability of persistence diagrams
• Statistical analysis and parameter selection for Mapper
• Structure and stability of the 1-dimensional mapper
• Topology and data

Cited in

(8)

• Statistical analysis of Mapper for stochastic and multivariate filters
• Network modelling of topological domains using Hi-C data
• Topological Data Analysis for Genomics and Evolution
• Topological data analysis reveals principles of chromosome structure in cellular differentiation
• Efficient and accurate detection of topologically associating domains from contact maps
• A gradient sampling algorithm for stratified maps with applications to topological data analysis
• Statistical embedding: beyond principal components
• A topological approach for capturing high-order interactions in graph data with applications to anomaly detection in time-varying cryptocurrency transaction graphs

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