Networks and Graphs in Biology: Topology, Geometry and Functions

Presentations

• Training Stress Patterns in 3D Reconfigurable Cellular Networks

  Invited-In-person · Invited

  March 16, 2026, 8:00 AM – March 16, 2026, 8:36 AM

  Presenters

  • Shabeeb Ameen

    • Syracuse University

  Authors

  • Shabeeb Ameen

    • Syracuse University

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• Random Runs on Random Networks: Trapping of Driven Cargo on Disordered Filament Arrays

  Oral-In-person

  March 16, 2026, 8:36 AM – March 16, 2026, 8:48 AM

  Presenters

  • Owen Santoso

    • University of California, San Diego

  Authors

  • Owen Santoso

    • University of California, San Diego

  • Elena Koslover

    • University of California, San Diego

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• Transport properties of 2D Octocorallia uncover niche specification

  Oral-In-person

  March 16, 2026, 8:48 AM – March 16, 2026, 9:00 AM

  Presenters

  • Asja Radja

    • Bryn Mawr College

  Authors

  • Asja Radja

    • Bryn Mawr College

  • Natalia Rodriguez

    • Harvard University

  • Seda Peacher

    • Bryn Mawr College

  • Brian Andrews

    • Drexel University

  • Maya Difrischia

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• A topological approach to describing multicellular network structures in bacterial biofilms

  Oral-In-person

  March 16, 2026, 9:00 AM – March 16, 2026, 9:12 AM

  Publication: Nam K.-M., Tai J.-S.B., Li C., Nijjer J., Zhang S., Yan J. Mechanisms of phenotypic sorting in developing bacterial biofilms. In preparation.

  Presenters

  • Kee Myoung (Chris) Nam

    • Yale University

  Authors

  • Kee Myoung (Chris) Nam

    • Yale University

  • Jung-Shen Benny Tai

    • Yale University

  • Jing Yan

    • Yale University

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• Cluster connectedness and spanning clusters in percolation models of aggregated and crystalline proteins

  Oral-In-person

  March 16, 2026, 9:12 AM – March 16, 2026, 9:24 AM

  Presenters

  • Miranda Lynch

    • State Univ of NY - Buffalo

  Authors

  • Miranda Lynch

    • State Univ of NY - Buffalo

  • Sarah Bowman

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• Beyond Message Passing: Learning Representations from Dynamics on Graphs

  Oral-In-person

  March 16, 2026, 9:24 AM – March 16, 2026, 9:36 AM

  Publication: Bhaskar D, Zhang Y, Moore J, Gao F, Rieck B, Wolf G, Khasawneh F, Munch E, Noah JA, Pushkarskaya H, Pittenger C, Greco V, Krishnaswamy S. Neurospectrum: A Geometric and Topological Deep Learning Framework for Uncovering Spatiotemporal Signatures in Neural Activity. bioRxiv [Preprint]. 2025 https://doi.org/10.1101/2023.03.22.533807.
  
  Bhaskar D, Sun X, Zhang Y, Xu C, Afrasiyabi A, Viswanath S, Fasina O, Nickel M, Wolf G, Perlmutter M, Krishnaswamy S. DYMAG: Rethinking Message Passing Using Dynamical-systems-based Waveforms. arXiv [Preprint]. 2025. https://doi.org/10.48550/arXiv.2309.09924
  
  
  

  Presenters

  • Dhananjay Bhaskar

    • University of Wisconsin-Madison

  Authors

  • Dhananjay Bhaskar

    • University of Wisconsin-Madison

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• Topology and Network Structure in Sparsely Sampled Neural Systems

  Oral-In-person

  March 16, 2026, 9:36 AM – March 16, 2026, 9:48 AM

  Presenters

  • Margaux Basart

    • Colorado School of Mines

  Authors

  • Margaux Basart

    • Colorado School of Mines

  • Om Biyani

    • Other

  • Bismah Rizwan

    • Colorado School of Mines

  • Ariun Bayasgalan

    • Colorado School of Mines

  • Lincoln Carr

    • Colorado School of Mines

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• A continuum limit for dense spatial networks

  Oral-In-person

  March 16, 2026, 9:48 AM – March 16, 2026, 10:00 AM

  Publication: https://doi.org/10.48550/arXiv.2301.07086

  Presenters

  • Sidney Holden

    • Flatiron Institute, Simons Foundation

  Authors

  • Sidney Holden

    • Flatiron Institute, Simons Foundation

  • Geoffrey Vasil

    • University of Edinburgh

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• Fixed and variable length generic string graphs for biological sequence defined polymers and human textual tokens, as a method for general dimensionality reduction and compression.

  Oral-In-person

  March 16, 2026, 10:00 AM – March 16, 2026, 10:12 AM

  Publication: C. J. Prybol, A. T. Hammack, E. A. Ashley, and M. P. Snyder, A Novel Approach for Accurate Sequence Assembly Using de Bruijn graphs, (2024). bioRxiv 2024.05.29.596541; doi: 10.1101/2024.05.29.596541
  
  

  Presenters

  • Aeron Hammack

    • Lawrence Berkeley National Labs

  Authors

  • Aeron Hammack

    • Lawrence Berkeley National Labs

  • Cameron Prybol

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• Topological Features of Random Networks in High Dimensions

  Oral-In-person

  March 16, 2026, 10:12 AM – March 16, 2026, 10:24 AM

  Presenters

  • Seongeun Chung

    • Georgia Institute of Technology

  Authors

  • Seongeun Chung

    • Georgia Institute of Technology

  • Anuk Dias

  • Audrey Sederberg

    • Georgia Institute of Technology

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• Tunable Regulatory Networks As Models of Chromosomal Copy Number Variations Across Cancers

  Oral-In-person

  March 16, 2026, 10:24 AM – March 16, 2026, 10:36 AM

  Presenters

  • Haina Wang

    • Princeton University

  Authors

  • Haina Wang

    • Princeton University

  • Dennis Discher

  • John Crocker

    • University of Pennsylvania

  • Andrea Liu

    • University of Pennsylvania

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• Convergent assembly of networks with designed building blocks

  Oral-In-person

  March 16, 2026, 10:36 AM – March 16, 2026, 10:48 AM

  Presenters

  • Jasper van der Kolk

    • Central European University

  Authors

  • Jasper van der Kolk

    • Central European University

  • Cory Glover

    • Northeastern University

  • Laszlo Barabasi

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• Viper Vision 2: Adaptive noisy vision systems reproduce pit viper ambush behavior

  Oral-In-person

  March 16, 2026, 10:48 AM – March 16, 2026, 11:00 AM

  Presenters

  • Zachary Miller

    • University of California, Riverside

  Authors

  • Zachary Miller

    • University of California, Riverside

  • SM Umayer

    • University of California, Riverside

  • Narendra Bam

  • Jacky Wan

    • University of California, Riverside

  • Nathaniel Gabor

    • University of California, Riverside

  View abstract →