Cell Fate Transitions II

Presentations

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

  ORAL

  March 19, 2025, 3:00 PM – March 19, 2025, 3:12 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, 3:12 PM – March 19, 2025, 3:24 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, 3:24 PM – March 19, 2025, 3:36 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, 3:36 PM – March 19, 2025, 3:48 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, 3:48 PM – March 19, 2025, 4:00 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, 4:00 PM – March 19, 2025, 4:12 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, 4:12 PM – March 19, 2025, 4:24 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

  View abstract →

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

  ORAL

  March 19, 2025, 4:24 PM – March 19, 2025, 4:36 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, 4:36 PM – March 19, 2025, 4:48 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, 4:48 PM – March 19, 2025, 5:00 PM

  Presenters

  • ketevan danelia

    • Emory University

  Authors

  • ketevan danelia

    • Emory University

  • Sean A Ridout

    • Emory University

  • Ilya M Nemenman

    • Emory University

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• Inferring rates in biochemical networks using temporal fluctuations

  ORAL

  March 19, 2025, 5:00 PM – March 19, 2025, 5:12 PM

  Presenters

  • Bradley T Friesen

    • University of Toronto Mississauga

  Authors

  • Bradley T Friesen

    • University of Toronto Mississauga

  • Andreas Hilfinger

    • University of Toronto

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

  ORAL

  March 19, 2025, 5:12 PM – March 19, 2025, 5:24 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, 5:24 PM – March 19, 2025, 5:36 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, 5:36 PM – March 19, 2025, 5:48 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 →