Using persistent homology and dynamical distances to analyze protein binding

DOI10.1515/sagmb-2015-0057zbMath1343.92380arXiv1412.1394OpenAlexW3100605491WikidataQ45952284 ScholiaQ45952284MaRDI QIDQ306659

Peter Bubenik, Violeta Kovacev-Nikolic, Dragan Nikolić, Giseon Heo

Publication date: 1 September 2016

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1412.1394

zbMATH Keywords

simplicial complexsupport vector machinepersistent homologydynamical distancepersistence landscape

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) General biostatistics (92B15) Protein sequences, DNA sequences (92D20)

Related Items (13)

Topological Data Analysis of Clostridioides difficile Infection and Fecal Microbiota Transplantation ⋮ Persistent Homology: A Topological Tool for Higher-Interaction Systems ⋮ Persistence landscapes of affine fractals ⋮ Atom-specific persistent homology and its application to protein flexibility analysis ⋮ Determining homology of an unknown space from a sample ⋮ Stabilizing the unstable output of persistent homology computations ⋮ The Persistence Landscape and Some of Its Properties ⋮ Persistent homology and the shape of evolutionary games ⋮ Topological features of multivariate distributions: dependency on the covariance matrix ⋮ Evolutionary de Rham-Hodge method ⋮ A persistence landscapes toolbox for topological statistics ⋮ Persistent homology detects curvature ⋮ Challenges in topological object data analysis

Uses Software

• Matlab
• R
• PLEX
• javaPlex
• AutoDock
• Inkscape
• Isomap

Cites Work

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• Confidence sets for persistence diagrams
• A note on two problems in connexion with graphs
• Fréchet means for distributions of persistence diagrams
• Nonparametric inference for extrinsic means on size-and-(reflection)-shape manifolds with applications in medical imaging
• Statistical analysis on manifolds: a nonparametric approach for inference on shape spaces
• Large sample theory of intrinsic and extrinsic sample means on manifolds. I
• Computing persistent homology
• Topological persistence and simplification
• Categorification of persistent homology
• A topological measurement of protein compressibility
• javaPlex: A Research Software Package for Persistent (Co)Homology
• Improving homology estimates with random walks
• Approximating cycles in a shortest basis of the first homology group from point data
• Probability measures on the space of persistence diagrams
• Statistical topology via Morse theory, persistence and nonparametric estimation
• Stochastic Convergence of Persistence Landscapes and Silhouettes
• Topological Analysis of Variance and the Maxillary Complex
• Statistical topological data analysis using persistence landscapes

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