Susanne M. Rafelski

Allen Institute for Cell Science — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

27h-index4.9kcitations74works12.42yr avg
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Research Topics

Cell Image Analysis Techniques(26), Mitochondrial Function and Pathology(13), Cellular Mechanics and Interactions(11), Pluripotent Stem Cells Research(11), Single-cell and spatial transcriptomics(11)

Publications74 total

BPS2026 – A dynamical systems framework applied to live cell imaging uncovers a first-order phase transition between morphology-based cell states
Biophysical Journal·2026
BPS2026 – Adherent hiPSC lumenoids: A robust 3D platform for bridging cellular dynamics, multicellular organization, and biophysical modeling
Biophysical Journal·2026
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds
Nature Methods·2025· 4 citedOpen Access
Cell shapes decode molecular phenotypes in image-based spatial proteomics
2025Open Access
Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories
Cell Systems·2025· 2 citedOpen Access
BPS2025 - Enhancing microscopy image analysis with streamlined deep-learning-based 3D segmentation
Biophysical Journal·2025
BPS2025 - Interpretable representation learning for 3D multi-piece intracellular structures in human induced pluripotent stem cells using point clouds
Biophysical Journal·2025
BPS2025 - Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories
Biophysical Journal·2025
BPS2025 - Interpretable representation learning for 3D multi-piece intracellular structures in human induced pluripotent stem cells using point clouds
Biophysical Journal·2025
BPS2025 - Enhancing microscopy image analysis with streamlined deep learning-based 3D segmentation
Biophysical Journal·2025
BPS2025 - Changes in collective behavior, organization, and state of human induced pluripotent stem cell-derived endothelial cells exposed to shear stress revealed by 3D microscopy and quantitative image analysis
Biophysical Journal·2025
A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)
2024· 2 citedOpen Access
4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics
2024Open Access
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds
2024Open Access
Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories
2024Open Access
Establishing a conceptual framework for holistic cell states and state transitions
Cell·2024· 76 citedOpen Access
Understanding metric-related pitfalls in image analysis validation
Nature Methods·2024· 152 citedOpen Access
Streamlining deep-learning-based segmentation methods for microscopy images
Biophysical Journal·2024
Quantifying biological variability using appropriate data representations of microscopy images
Biophysical Journal·2024Open Access
Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy
Nature Protocols·2023· 15 cited
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Frequent Co-authors

Matheus P. Viana(24), Julie A. Theriot(14), Ruwanthi N. Gunawardane(11), Melissa Hendershott(11), Angelique M. Nelson(10), Irina A. Mueller(10), Ruian Yang(9), Jianxu Chen(9), Derek Thirstrup(8), Joy Arakaki(8), Margaret A. Fuqua(8), Nathalie Gaudreault(8), Brock Roberts(7), Amanda Haupt(7), Tanya Grancharova(7), Caroline Hookway(7), Antoine Borensztejn(7), M. Sluzewski(7), Susan A. Ludmann(6), Ritvik Vasan(6)