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).<br>Zhenyi Zhang, Tiejun Li, and Peijie Zhou. Learning Stochastic Dynamics from Snapshots through Regularized Unbalanced Optimal Transport. Arxiv Preprint 2024.<br>Qiangwei Peng, Peijie Zhou and Tiejun Li. stVCR: Reconstructing spatio-temporal dynamics of cell development using optimal transport. Biorxiv Preprint 2024.<br>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 →