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Third-year Computational and Mathematical Engineering (ICME) PhD Candidate @ Stanford University passionate about research at the intersection of mathematics, computing, and biology.

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  • Academic
    University - Student Department: ICME Operations Position: Graduate

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All Publications

  • Topological Data Analysis Approaches to Uncovering the Timing of Ring Structure Onset in Filamentous Networks BULLETIN OF MATHEMATICAL BIOLOGY Ciocanel, M., Juenemann, R., Dawes, A. T., McKinley, S. A. 2021; 83 (3): 21

    Abstract

    In developmental biology as well as in other biological systems, emerging structure and organization can be captured using time-series data of protein locations. In analyzing this time-dependent data, it is a common challenge not only to determine whether topological features emerge, but also to identify the timing of their formation. For instance, in most cells, actin filaments interact with myosin motor proteins and organize into polymer networks and higher-order structures. Ring channels are examples of such structures that maintain constant diameters over time and play key roles in processes such as cell division, development, and wound healing. Given the limitations in studying interactions of actin with myosin in vivo, we generate time-series data of protein polymer interactions in cells using complex agent-based models. Since the data has a filamentous structure, we propose sampling along the actin filaments and analyzing the topological structure of the resulting point cloud at each time. Building on existing tools from persistent homology, we develop a topological data analysis (TDA) method that assesses effective ring generation in this dynamic data. This method connects topological features through time in a path that corresponds to emergence of organization in the data. In this work, we also propose methods for assessing whether the topological features of interest are significant and thus whether they contribute to the formation of an emerging hole (ring channel) in the simulated protein interactions. In particular, we use the MEDYAN simulation platform to show that this technique can distinguish between the actin cytoskeleton organization resulting from distinct motor protein binding parameters.

    View details for DOI 10.1007/s11538-020-00847-3

    View details for Web of Science ID 000609883600005

    View details for PubMedID 33452960

    View details for PubMedCentralID PMC7811524