ReviewDevelopmental dynamics : an official publication of the American Association of Anatomists2020
The shape of things to come: Topological data analysis and biology, from molecules to organisms.
Review in Developmental dynamics : an official publication of the American Association of Anatomists, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
36 citing papers in PubMed.
- Topological data analysis captures complex behavioral dynamics during naturalistic social interaction between domestic ferrets.bioRxiv : the preprint server for biology · 2026Article
- Topological data analysis for antibody-drug conjugate payload discovery: a computational framework for mechanistic classification and target validation.Journal of computer-aided molecular design · 2026Article
- Cross-modal integration of metabolomics and cardiac functionality captures dynamic metabotoxic effects of doxorubicin in engineered heart tissues.Stem cell reports · 2026Article
- Mapping life's disparity and evolutionary constraints in a geometric complexity space.Science advances · 2026Article
- Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population.PLoS computational biology · 2026Article
- Article
- Spatial ploidy inference using quantitative imaging.Cell reports methods · 2025Article
- Topological classification of tumour-immune interactions and dynamics.Journal of mathematical biology · 2025Article
- Spatial and Sequential Topological Analysis of Molecular Dynamics Simulations of IgG1 Fc Domains.Journal of chemical theory and computation · 2025Article
- Topological data analysis and machine learning for COVID-19 detection in CT scan lung images.BMC biomedical engineering · 2025Article
- A novel method for subgroup discovery in precision medicine based on topological data analysis.BMC medical informatics and decision making · 2025Article
- GenPath-PPH: Integrating gene expression and pathway networks via persistent path homology enhances detection of disease-relevant pathways.Computational and structural biotechnology journal · 2025Article
- Topological data analysis in single cell biology.Frontiers in immunology · 2025Review
- TopoLoop: A new tool for chromatin loop detection in live cells via single-particle tracking.The Journal of chemical physics · 2024Article
- Dissecting glial scar formation by spatial point pattern and topological data analysis.Scientific reports · 2024Article
- Article
- Morphological multiparameter filtration and persistent homology in mitochondrial image analysis.PloS one · 2024Article
- Simplicial complex entropy for time series analysis.Scientific reports · 2023Article
- Machine learning and topological data analysis identify unique features of human papillae in 3D scans.Scientific reports · 2023Article
- The Role of Geometry in Convolutional Neural Networks for Medical Imaging.Mayo Clinic proceedings. Digital health · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.