Biological Data Analysis

Papers

  • Coarse Graining of Data via Inhomogeneous Diffusion Condensation.
    With Nathan Brugnone, Alex Gonopolskiy, Mark W. Moyle, Manik Kuchroo, David van Dijk, Kevin R. Moon, Daniel Colon-Ramos, Guy Wolf and Smita Krishnaswamy.
    In Proceedings of the 2019 IEEE International Conference on Big Data, pages 2624–2633, 2019.
    pdf, arXiv, IEEE Xplore. Software.
  • Visualizing Structure and Transitions for Biological Data Exploration (PHATE).
    With Kevin R. Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel Burkhardt, William Chen, Kristina Yim, Antonia van den Elzen, Ronald R. Coifman, Natalia B. Ivanova, Guy Wolf and Smita Krishnaswamy.
    Nature Biotechnology, volume 37, pages 1482–1492, 2019.
    pdf (journal version), pdf (complete version, very large > 100 mb), bioRxiv, Nature Biotechnology. Software.
  • A Diffusion-based Condensation Process for Multiscale Analysis of Single Cell Data.
    With Tobias Welp, Guy Wolf and Smita Krishnaswamy.
    In ICML Workshop Computational Biology, New York, June 24, 2016.
    pdf, ICML WCB.