The shape of things to come: Topological data analysis and biology, from molecules to organisms. Issue 7 (13th April 2020)

• Record Type: Journal Article
• Authors: Amézquita, Erik J.; Quigley, Michelle Y.; Ophelders, Tim; Munch, Elizabeth; Chitwood, Daniel H.
• Is Part Of: Developmental dynamics. Volume 249:Issue 7(2020)
• Page Start: 816
• Page End: 833
• Publication Date: 2020-04-13
• Subjects: biology -- data science -- mathematical biology -- persistent homology -- shape -- topological data analysis; Morphogenesis -- Periodicals; Anatomy -- Periodicals; Anatomie -- Périodiques; Biologie du développement -- Périodiques; 571.833
• DOI: 10.1002/dvdy.175
• Languages: English
• ISSNs: 1058-8388

Abstract

Abstract: Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features—connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub‐disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data‐driven era where the meaningful interpretation of large data sets is a limiting factor.