🍩 Database of Original & Non-Theoretical Uses of Topology

1. HiDeF: Identifying Persistent Structures in Multiscale ‘Omics Data (2021)

   Fan Zheng, She Zhang, Christopher Churas, Dexter Pratt, Ivet Bahar, Trey Ideker

   Abstract

   In any ‘omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here, we use the concept of persistent homology, drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.

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   • Community detection
   • Protein
   • Protein-protein interaction network
   • Systems biology
   • Networks
   • Clustering
   • Persistent homology
   • Single-cell clustering