Overview

Traditional bottom-up physical-mathematical models have longstanding popularity and success in studying cytoskeleton and mechanochemical machines driving cell movements and division.
These models brought and will continue to bring mechanistic insights into cell migration. However, such models are either too simple to embrace the complexity of the multiscale cell processes or are hopelessly cumbersome and unwieldy to be used to nimbly test multiple hypotheses. Machine learning and AI approaches have demonstrated immense strength in identifying statistical patterns in cytoskeletal machines and in predicting cytoskeletal dynamics
from microscopy data. However, these data-driven approaches largely neglect the laws of physics and chemistry needed to ground the discoveries in biological mechanisms. These complementary strengths and weaknesses between the traditional modeling and modern data-scientific approaches suggest a promising avenue forward: augmenting traditional models with data-scientific and AI methods for the sake of building more complex traditional models that can be directly connected with the enormous volumes of biological data of cytoskeletal machines.
This workshop will convene data scientists, experimental biologists, mathematical modelers and biophysicists using or interested in starting to use ML to study cytoskeletal dynamics, cell migration and mitosis. The goal is to foster an exchange of ideas between these research communities. The workshop is structured to help participants identify the most promising opportunities for developing and using ML tools to answer biological questions. The program includes both overview and research talks, poster sessions and lightning talks by poster presenters, and will have ample time for participants to get to know each other, exchange ideas and foster collaborations.
Schedule
November 03 2025 Monday
8:30 am - 8:50 am
Light Breakfast
8:50 am - 9:00 am
Welcome & Introduction of Institute
9:00 am - 9:45 am
"High resolution imaging of Spindle Structure in mitosis: From Plastic to Cryo" - Stefanie Redemann
9:45 am - 10:30 am
"Ongoing efforts to connect molecular and cellular scale behaviors in microtubule self-organization" - Daniel Needleman
10:30 am - 11:15 am
Coffee and Discussion
11:15 am - 12:00 pm
"A kinetochore tracking perspective - the complex mechanics of human cell division." - Nigel Burroughs
12:00 pm - 1:00 pm
Lunch
1:00 pm - 1:45 pm
"Data-centred approach and mechanics of the mitotic spindle" - Jacques Pécréaux
1:45 pm - 2:30 pm
"Extending Molecular Dynamics Timescales for Biological Macromolecules through Machine Learning Approaches" - Tamara Bidone
2:30 pm - 2:45 pm
Break
2:45 pm - 3:30 pm
"Modeling mechanisms of microtubule dynamics and polarity in living neurons" - Anna Nelson
3:30 pm - 4:15 pm
Lightning Talks
3:30-3:45: “Collective Nuclear Motion Driven by Mitotic Waves in the Drosophila Blastoderm” – Stanley Nicholson
3:45-4:00: “Engineering a Virtual Cell to Probe Spindle Assembly and Beyond” – Saptarshi Chatterjee
4:00-4:15: “Quantitative Characterization of Nonequilibrium Steady States for Dynamical Systems of Microtubules” – Sayandeepa Raha
4:15 pm - 6:00 pm
Welcome Reception
November 04 2025 Tuesday
8:30 am - 8:50 am
Light Breakfast
8:50 am - 9:00 am
Housekeeping
9:00 am - 9:45 am
"Learning the dynamics and interaction of migrating cells" - Chase Broedersz
9:45 am - 10:30 am
"Mechanical Information Processing in Adherent Cells" - Margaret Gardel
10:30 am - 11:15 am
Coffee and Discussion
11:15 am - 12:00 pm
"A dynamical systems framework applied to live cell imaging suggests a first-order phase transition between morphology-based cell states" - Susanne Rafelski
12:00 pm - 1:00 pm
Lunch
1:00 pm - 1:45 pm
"Studying Multicellular Living Systems with Graph Neural Networks" - Ming Guo
1:45 pm - 2:30 pm
"Unravelling Cellular Morphodynamic Heterogeneity with Live-Cell Imaging and Machine Learning" - Kwonmoo Lee
2:30 pm - 2:45 pm
Break
2:45 pm - 3:30 pm
"Beyond motility and migration: Cell shape and cytoskeleton as regulators of signals" - Gaudenz Danuser
3:30 pm - 4:00 pm
Lightning Talks
3:30-3:45: “Reconstructing Acting Dynamics of the Leading Edge from Observational Data” – Wenzheng Shi
3:45-4:00: “From Fading Stains to Foundation Models: Adapting Digital Pathology to Real World Complexity” – Binghao Chai
4:00 pm - 5:00 pm
Poster Session
November 05 2025 Wednesday
8:30 am - 8:50 am
Light Breakfast
8:50 am - 9:00 am
Housekeeping
9:00 am - 9:45 am
"Investigating models and mechanisms of cell migration to better understand and target cancer metastasis" - Madeline Oudin
9:45 am - 10:30 am
"Fantastic forces and where to find them" - Julian Berro
10:30 am - 11:15 am
Coffee and Discussion
11:15 am - 12:00 pm
"Opportunities and challenges in tracking mitotic subcellular structures" - Viji Draviam
12:00 pm - 1:00 pm
Lunch
1:00 pm - 1:45 pm
"Principles of Bipolar Spindle Formation Learned from an Energetic Framework" - Jing Chen
1:45 pm - 2:30 pm
"Biophysics of mitotic spindle-nuclear envelope coupling in closed mitosis" - Meredith Betterton
2:30 pm - 2:45 pm
Break
2:45 pm - 3:30 pm
"Organization of kinase signaling at the cell center for cytokinesis" - Radhika Subramanian
3:30 pm - 4:15 pm
"Decoding behavioral algorithms in single cells" - Ben Larson
4:15 pm - 5:00 pm
Group Discussion – Emergent Themes & Directions
Participants
Organizers
Scott Forth – Rensselaer Polytechnic Institute
Chris Miles – University of California, Irvine
Alex Mogilner – New York University
Invited Speakers
Shiladitya Banerjee – Georgia Tech (Speaker)
Julien Berro – Yale University (Speaker)
Meredith Betterton – University of Colorado Boulder (Speaker)
Tamara Bidone – University of Utah
Chase P. Broedersz – Vrije University Amsterdam (Speaker)
Nigel J. Burroughs – University of Warwick (Speaker)
Jing Chen – Virginia Tech (Speaker)
Gaudenz Danuser – Institute for Human Biology, Hoffmann-La Roche
Kinjal Dasbiswas – University of California Merced
Viji M. Draviam – Queen Mary University of London (Speaker)
Margaret Gardel – University of Chicago (Speaker)
Ming Guo – MIT (Speaker)
Benjamin Larson – Rensselaer Polytechnic Institute (Speaker)
Kwonmoo Lee – Harvard University (Speaker)
Daniel Needleman – Harvard University (Speaker)
Anna Nelson – University of New Mexico
Madeleine J. Oudin – Tufts University (Speaker)
Jacques Pécréaux – Université de Rennes (Speaker)
Susanne Rafelski – Allen Institute, Cell Science (Speaker)
Stefanie Redemann – University of Virginia (Speaker)
Radhika Subramanian – Harvard Medical School at Massachusetts General Hospital (Speaker)
Stefanie Zimyanin – University of Virginia
Invited Participants
Elie Alhajjar – RAND
Erin Angelini – Allen Institute, Cell Science
Ratul Biswas – NITMB
Kristina Braverman – Rensselaer Polytechnic Institute
Maryn Carlson – NITMB
Binghao Chai – University College London
Saptarshi Chatterjee – Virginia Tech
Giulia Garcia Lorenzana – NITMB
Doruk Efe Gokmen – NITMB
Sarthak Gupta – Center for Theoretical Biological Physics, Rice University
Alasdair Hastewell – NITMB
Christophe Heligon – CNRS
Charles Hoeffer – CU Boulder
Bram Hoogland – Vrije Universiteit Amsterdam
Jesselynn LaBelle – UC Merced
Milton Lin – NITMB
Aditya Mahadevan – NITMB
Ehssan Nazockdast – Allen Institute, Cell Science
Stanley Nicholson – Brown University
Sayandeepa Raha – University of Notre Dame
Gabriel Salmon – NITMB
Aashrith Saraswathibhatla – University of Minnesota Twin Cities
Mariya Savinov – NITMB
Hannah Scanlon – Duke University
Li Shen – NITMB
Wenzheng Shi – New York University
Tzu-Hsi Song – Boston Children’s Hospital
Daniel Sussman – Emory University
Yi Yang Tian – The University of British Columbia
Anushka Tiwari – State University of New York
Michael Vennettilli – University of California, Merced
Xueying Wang – NITMB
Yuehui Xu – Indiana University, Indianapolis
Kristina Wilson – University of Virginia
Guan’ao Yan – NITMB
Haiqian Yang – MIT
Lingxing Yao – University of Akron
Yuan-Nan Young – New Jersey Institute of Technology
Wenjun Zhao – Wake Forest University
Adrianne Zhong – NITMB
Jiali Zhu – University of North Carolina at Chapel Hill
Recordings
Stefanie Redemann
Recorded on 11/03/2025
Title: High resolution imaging of Spindle Structure in mitosis: From Plastic to Cryo
Daniel Needleman
Recorded on 11/03/2025
Title: Ongoing efforts to connect molecular and cellular scale behaviors in microtubule self-organization
Nigel Burroughs
Recorded on 11/03/2025
Title: A kinetochore tracking perspective – the complex mechanics of human cell division
Jacques Pécréaux
Recorded on 11/03/2025
Title: Data-centred approach and mechanics of the mitotic spindle
Tamara Bidone
Recorded on 11/03/2025
Title: Extending Molecular Dynamics Timescales for Biological Macromolecules through Machine Learning Approaches
Anna Nelson
Recorded on 11/03/2025
Title: Modeling mechanisms of microtubule dynamics and polarity in living neurons
Chase Broedersz
Recorded on 11/04/2025
Title: Learning the dynamics and interaction of migrating cells
Margaret Gardel
Recorded on 11/04/2025
Title: Mechanical Information Processing in Adherent Cells
Susanne Rafelski
Recorded on 11/04/2025
Title: A dynamical systems framework applied to live cell imaging suggests a first-order phase transition between morphology-based cell states
Ming Guo
Recorded on 11/04/2025
Title: Studying Multicellular Living Systems with Graph Neural Networks
Gaudenz Danuser
Recorded on 11/04/2025
Title: Beyond motility and migration: Cell shape and cytoskeleton as regulators of signals
Madeline Oudin
Recorded on 11/05/2025
Title: Investigating models and mechanisms of cell migration to better understand and target cancer metastasis
Julian Berro
Recorded on 11/05/2025
Title: Fantastic forces and where to find them
Viji Draviam
Recorded on 11/05/2025
Title: Opportunities and challenges in tracking mitotic subcellular structures
Jing Chen
Recorded on 11/05/2025
Title: Principles of Bipolar Spindle Formation Learned from an Energetic Framework
Meredith Betterton
Recorded on 11/05/2025
Title: Biophysics of mitotic spindle-nuclear envelope coupling in closed mitosis
Radhika Subramanian
Recorded on 11/05/2025
Title: Organization of kinase signaling at the cell center for cytokinesis
Ben Larson
Recorded on 11/05/2025
Title: Decoding behavioral algorithms in single cells