ArticleMolecular biology of the cell2015
Joint modeling of cell and nuclear shape variation.
Article in Molecular biology of the cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Vimentin promotes collective cell migration through collagen networks via increased matrix remodeling and spheroid fluidity.Communications biology · 2026Article
- Representing Mitochondrial Dynamics with Abstract Algebra.bioRxiv : the preprint server for biology · 2025Article
- Modelling cell shape in 3D structured environments: A quantitative comparison with experiments.PLoS computational biology · 2024Article
- Orientation-invariant autoencoders learn robust representations for shape profiling of cells and organelles.Nature communications · 2024Article
- Learning Morphological, Spatial, and Dynamic Models of Cellular Components.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Neutrophil nucleus: shaping the past and the future.Journal of leukocyte biology · 2023Article
- Basal body organization and cell geometry during the cell cycle inMolecular biology of the cell · 2023Article
- Article
- Image-derived models of cell organization changes during differentiation and drug treatments.Molecular biology of the cell · 2020Article
- Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations.Frontiers in physics · 2020Article
- Implementing VIPER for Imaging Cellular Proteins by Fluorescence Microscopy.Bio-protocol · 2019Article
- Evaluation of methods for generative modeling of cell and nuclear shape.Bioinformatics (Oxford, England) · 2019Article
- CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps.Journal of visualized experiments : JoVE · 2018Article
- Article
- QuimP: analyzing transmembrane signalling in highly deformable cells.Bioinformatics (Oxford, England) · 2018Article
- Computational Analysis of Cell Dynamics in Videos with Hierarchical-Pooled Deep-Convolutional Features.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance.PLoS computational biology · 2018Article
- Computational spatiotemporal analysis identifies WAVE2 and cofilin as joint regulators of costimulation-mediated T cell actin dynamics.Science signaling · 2016Article
- Building cell models and simulations from microscope images.Methods (San Diego, Calif.) · 2016Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Modeling cell shape variation is critical to our understanding of cell biology. Previous work has demonstrated the utility of nonrigid image registration methods for the construction of nonparametric nuclear shape models in which pairwise deformation distances are measured between all shapes and are embedded into a low-dimensional shape space. Using these methods, we explore the relationship between cell shape and nuclear shape. We find that these are frequently dependent on each other and use this as the motivation for the development of combined cell and nuclear shape space models, extending nonparametric cell representations to multiple-component three-dimensional cellular shapes and identifying modes of joint shape variation. We learn a first-order dynamics model to predict cell and nuclear shapes, given shapes at a previous time point. We use this to determine the effects of endogenous protein tags or drugs on the shape dynamics of cell lines and show that tagged C1QBP reduces the correlation between cell and nuclear shape. To reduce the computational cost of learning these models, we demonstrate the ability to reconstruct shape spaces using a fraction of computed pairwise distances. The open-source tools provide a powerful basis for future studies of the molecular basis of cell organization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.