Cell Fate Transitions II

Presentations

• Incorporating Waddington and fitness landscapes into a model of coordinated tissue development

  ORAL

  March 19, 2025, 6:00 PM – March 19, 2025, 6:12 PM

  Presenters

  • Casey Barkan

    University of California, Los Angeles

  Authors

  • Casey Barkan

    University of California, Los Angeles

  • Tom Chou

    University of California, Los Angeles

  View abstract →

• Leverage multi-scale dependencies of single cells through a physics-informed deep diffusion model

  ORAL

  March 19, 2025, 6:12 PM – March 19, 2025, 6:24 PM

  Publication: scDiffusion: ​​​​​​​Leverage multi-scale dependencies of single cells through a physics-informed deep diffusion model, in preparation.

  Presenters

  • Yu-Chen Liu

    Boston University

  Authors

  • Yu-Chen Liu

    Boston University

  • Lei Jiang

    University of Missouri

  • Simon L Lu

    Boston University

  • Dong Xu

    University of Missouri

  • Juexin Wang

    Indiana University

  • Chao Zhang

    Boston University

  View abstract →

• Evolving dynamical landscapes of cell fate transitions

  ORAL

  March 19, 2025, 6:24 PM – March 19, 2025, 6:36 PM

  Presenters

  • Victoria Mochulska

    McGill University

  Authors

  • Victoria Mochulska

    McGill University

  • Paul Francois

    Université de Montréal, Mila Québec, Universite de Montreal

  View abstract →

• AI-driven multiscale modeling for cell fate reconstruction using single-cell techniques

  ORAL

  March 19, 2025, 6:36 PM – March 19, 2025, 6:48 PM

  Presenters

  • Yuchi Qiu

    University of Illinois Chicago

  Authors

  • Yuchi Qiu

    University of Illinois Chicago

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• A quantitative framework for endothelial cell state transition in response to shear stress

  ORAL

  March 19, 2025, 6:48 PM – March 19, 2025, 7:00 PM

  Presenters

  • Matheus Viana

    Allen Institute for Cell Science

  Authors

  • Erin Angelini

    Allen Institute for Cell Science

  • Rebecca Zaunbrecher

    Allen Institute for Cell Science

  • Antoine Borensztejn

    Allen Institute for Cell Science

  • Jacqueline H Edmonds

    Allen Institute for Cell Science

  • Caroline Hookway

    Allen Institute for Cell Science

  • Benjamin Morris

    Allen Institute for Cell Science

  • Gouthamrajan Nadarajan

    Allen Institute for Cell Science

  • Serge Parent

    Allen Institute for Cell Science

  • Emmanuel E Sanchez

    Allen Institute for Cell Science

  • John Paul Thottam

    Allen Institute for Cell Science

  • Allen Institute for Cell Science

    Allen Institute for Cell Science

  • Gokhan Dalgin

    Allen Institute for Cell Science

  • Susanne M Rafelski

    Allen Institute for Cell Science

  • Julie A Theriot

    Department of Biology and Howard Hughes Medical Institute, University of Washington

  • Matheus Viana

    Allen Institute for Cell Science

  View abstract →

• Dynamics of emergent spatiotemporal patterning of synthetic Notch signal transduction in vivo.

  ORAL

  March 19, 2025, 7:00 PM – March 19, 2025, 7:12 PM

  Publication: https://www.biorxiv.org/content/10.1101/2023.07.12.548752v3.abstract

  Presenters

  • Jonathan E Dawson

    Whitworth University

  Authors

  • Jonathan E Dawson

    Whitworth University

  • Abdul N Malmi-Kakkada

    Augusta University

  • Paul Langridge

    Augusta University

  View abstract →

• Dissecting spatiotemporal single-cell transcriptomics data combining dynamical models and generative AI

  ORAL

  March 19, 2025, 7:12 PM – March 19, 2025, 7:24 PM

  Publication: Zhou, P., Bocci, F., Li, T. et al. Spatial transition tensor of single cells. Nat Methods 21, 1053–1062 (2024).
  Zhenyi Zhang, Tiejun Li, and Peijie Zhou. Learning Stochastic Dynamics from Snapshots through Regularized Unbalanced Optimal Transport. Arxiv Preprint 2024.
  Qiangwei Peng, Peijie Zhou and Tiejun Li. stVCR: Reconstructing spatio-temporal dynamics of cell development using optimal transport. Biorxiv Preprint 2024.
  Sha, Y., Qiu, Y., Zhou, P. and Nie, Q.. Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nat Mach Intell 6, 25–39 (2024).

  Presenters

  • Peijie Zhou

    Peking University

  Authors

  • Peijie Zhou

    Peking University

  • Tiejun Li

    Peking University

  • Zhenyi Zhang

    Peking University

  • Qiangwei Peng

    Peking University, Peking Univ

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• A stochastic model depicting the coordination of gene expression and organelle biogenesis

  ORAL

  March 19, 2025, 7:24 PM – March 19, 2025, 7:36 PM

  Presenters

  • Janna May Z Angeles

    Washington University in St. Louis

  Authors

  • Janna May Z Angeles

    Washington University in St. Louis

  • Ronan Hanley

    Washington University in St. Louis

  • Jacqueline Donaldson

    Washington University in St. Louis

  • Shankar Mukherji

    Washington University in St. Louis

  View abstract →

• Constructing and optimizing dynamical models of core transcription factor regulatory networks driving cell state transitions

  ORAL

  March 19, 2025, 7:36 PM – March 19, 2025, 7:48 PM

  Presenters

  • Mingyang Lu

    Northeastern University

  Authors

  • Mingyang Lu

    Northeastern University

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• Spatiotemporal constraints on concentrations improve cellular concentration sensing beyond classical limits

  ORAL

  March 19, 2025, 7:48 PM – March 19, 2025, 8:00 PM

  Presenters

  • ketevan danelia

    Emory University

  Authors

  • ketevan danelia

    Emory University

  • Sean A Ridout

    Emory University

  • Ilya M Nemenman

    Emory University

  View abstract →

• Inferring rates in biochemical networks using temporal fluctuations

  ORAL

  March 19, 2025, 8:00 PM – March 19, 2025, 8:12 PM

  Presenters

  • Bradley T Friesen

    University of Toronto Mississauga

  Authors

  • Bradley T Friesen

    University of Toronto Mississauga

  • Andreas Hilfinger

    University of Toronto

  View abstract →

• Reconstructing noisy intracellular expression dynamics using neural stochastic differential equations, Part I: Mathematical methods

  ORAL

  March 19, 2025, 8:12 PM – March 19, 2025, 8:24 PM

  Publication: https://arxiv.org/pdf/2401.11354

  Presenters

  • Mingtao Xia

    NYU

  Authors

  • Mingtao Xia

    NYU

  • Xiangting Li

    University of California, Los Angeles

  • Qijing Shen

    University of Oxford

  • Tom Chou

    University of California, Los Angeles

  View abstract →

• Reconstructing noisy intracellular expression dynamics using neural stochastic differential equations, Part II: Applications in cell biophysics

  ORAL

  March 19, 2025, 8:24 PM – March 19, 2025, 8:36 PM

  Presenters

  • Xiaolu Guo

    University of California, Los Angeles

  Authors

  • Xiaolu Guo

    University of California, Los Angeles

  • Jiancheng Zhang

    Department of Electrical and Computer Engineering, University of California, Riverside

  • Xiangting Li

    UCLA

  • Zhaoyi You

    CMU

  • Lucas Böttcher

    Frankfurt School of Finance and Management

  • Alex Mogilner

    Courant Institute of Mathematical Sciences, New York University

  • Alexander Hoffmann

    UCLA, University of California, Los Angeles

  • Tom Chou

    University of California, Los Angeles

  • Mingtao Xia

    NYU

  View abstract →

• Stress-induced Non-genetic memory loss in bacteria

  ORAL

  March 19, 2025, 8:36 PM – March 19, 2025, 8:48 PM

  Publication: Harsh Vashistha, Maryam Kohram, Hanna Salman "Non-genetic inheritance restraint of cell to-cell variation", eLife 10, e64779 (2021).

  Presenters

  • Joanna Jammal Touma

    University of Pittsburgh

  Authors

  • Hanna Salman

    University of Pittsburgh

  • Joanna Jammal Touma

    University of Pittsburgh

  View abstract →