🍩 Database of Original & Non-Theoretical Uses of Topology

1. Acridine Derivatives as Inhibitors of the IRE1α–XBP1 Pathway Are Cytotoxic to Human Multiple Myeloma (2016)

   Dadi Jiang, Arvin B. Tam, Muthuraman Alagappan, Michael P. Hay, Aparna Gupta, Margaret M. Kozak, David E. Solow-Cordero, Pek Y. Lum, Nicholas C. Denko, Amato J. Giaccia, Quynh-Thu Le, Maho Niwa, Albert C. Koong

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   • acridine derivatives
   • drug discovery
   • multiple myeloma
   • unfolded protein
   • pathology
   • Innovate
   • mapper

2. A Multimodal Data Analysis Approach for Targeted Drug Discovery Involving Topological Data Analysis (TDA) (2016)

   Muthuraman Alagappan, Dadi Jiang, Nicholas Denko, Albert C. Koong

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   • Drug
   • medicine
   • clustering
   • mapper

3. Integrative Methods for Analyzing Big Data in Precision Medicine (2016)

   Vladimir Gligorijević, Noël Malod-Dognin, Nataša Pržulj

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   • Bioinformatics
   • Biomarkers discovery
   • Disease subtyping
   • Drug repurposing
   • Integration methods
   • Medicine
   • Personalized medicine
   • Mapper

4. ToDD: Topological Compound Fingerprinting in Computer-Aided Drug Discovery (2022)

   Andaç Demir, Baris Coskunuzer, Yulia Gel, Ignacio Segovia-Dominguez, Yuzhou Chen, Bulent Kiziltan

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   • Bioinformatics
   • medicine
   • medicine:drug
   • Graphs
   • Graphs:compound
   • Graphs:molecule
   • Persistent homology
   • Persistent homology:betti numbers

5. D-Gril: End-to-End Topological Learning With 2-Parameter Persistence (2026)

   Soham Mukherjee, Shreyas N. Samaga, Cheng Xin, Steve Oudot, Tamal K. Dey

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   • cheminformatics
   • cheminformatics:bioactivity prediction
   • drug discovery
   • machine learning
   • machine learning:graph learning
   • machine learning:graph learning:graph neural networks
   • ChEMBL bioactivity data
   • graphs
   • graphs:molecular graphs
   • generalized rank invariant landscape
   • persistent homology
   • persistent homology:differentiable persistence
   • persistent homology:multiparameter
   • persistent homology:multiparameter:bifiltration
   • topological machine learning