The paper introduces Mask Interpreter, a method to improve interpretability of image-to-image translation models, validating biological relevance and identifying artifacts in in silico labeling.

bioRxiv · Aug 17, 2026 · PreprintCell Biology

Dynamics of ML-based Morphological Features Indicate a Shear Stress-Dependent Bifurcation of hiPSC-Derived Endothelial Cell States

Erin Angelini, Chantelle L. Leveille, Serge E. Parent, Rebecca J. Zaunbrecher, Tiffany Barszczewski, Julie C. Dixon, Fatwir S. Mohammed, Benjamin Morris, Jessica S. Yu, Joy Arakaki, Renske J. Dupar, Jacqueline H. Edmonds, Erik A. Ehlers, Clare Ruth Gamlin, Maxwell J. Hedayati, , Matheus Palhares Viana

The paper uses ML to analyze morphological dynamics of hiPSC-derived endothelial cells under shear stress, identifying a bifurcation between two stable cell states.

bioRxiv · Jul 11, 2026 · PreprintBiophysics

A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)

Caroline Hookway, Antoine Borensztejn, Leigh K. Harris, Tiffany Barszczewski, Sara G. Carlson, Gökhan Dalgin, Suraj Mishra, Ellen M. Adams, Julie C. Dixon, Renske J. Dupar, Jacqueline H. Edmonds, Erik A. Ehlers, Alexandra J. Ferrante, Margaret A. Fuqua, Clare Ruth Gamlin, , Susanne M. Rafelski

The paper presents a hiPS cell model to study EMTs by comparing 2D and 3D cultures, measuring changes in cell function, markers, organization, and environment.

Nature Methods · Jun 15, 2026Peer-reviewedCell Biology

Cell shapes decode molecular phenotypes in image-basedspatial proteomics

Trang H. Le, William D. Leineweber, Matheus Palhares Viana, Anthony J. Cesnik, Jan N. Hansen, Wei Ouyang, Susanne M. Rafelski, Emma K. Lundberg

The paper analyzes how cell shape correlates with proteomic features across multiple cell lines using image-based spatial proteomics data.

Cell Systems · Apr 20, 2026Peer-reviewedBioengineering

Multi-omic profiling of human antibody-secreting cells reveals diverse subsets sustain durable humoral immunity

David Richard Glass, Elisabeth M. Dornisch, Hang Yin, Susan A. Ludmann, Ashwin Samudre, Sydney Kuhl, Jocelin Malone, Aishwarya Chander, N Kaul, Cole G. Phalen, Vaishnavi Parthasarathy, Mebdh A. Dillon, Palak C. Genge, Tyanna J. Stuckey, Stephanie D. Anover-Sombke, , Marla C. Glass

The paper identifies diverse human antibody-secreting cell subsets using multi-omic methods and shows their distinct functional and spatial characteristics.

bioRxiv · Apr 17, 2026 · PreprintImmunology

Interpretable representation learning for 3D multi-piece intracellular structures using point clouds

Ritvik Vasan, Alexandra J. Ferrante, Antoine Borensztejn, Christopher L. Frick, Philip Garrison, Nathalie Gaudreault, Saurabh S. Mogre, Fatwir S. Mohammed, Benjamin Morris, Guilherme G. P. Freitas Pires, Daniel Saelid, Susanne M. Rafelski, Julie A. Theriot, Matheus Palhares Viana

This paper introduces a morphology-appropriate representation learning framework for 3D multi-piece intracellular structures, showing improved sub-cluster discovery and phenotypic profiling.

Nature Methods · Jul 1, 2025Peer-reviewedCell Biology

Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories

Julie A. Cass, Christopher L. Frick, Chantelle L. Leveille, Philip Garrison, P. A. Lee, Saurabh S. Mogre, Benjamin Morris, Nivedita Nivedita, Ritvik Vasan, Jianxu Chen, Cameron L. Fraser, Clare Ruth Gamlin, Leigh K. Harris, Melissa C. Hendershott, Graham T. Johnson, , Susanne M. Rafelski

The paper analyzes nuclear growth variations in hiPS cell colonies, finding context-dependent and inherited mechanisms shaping growth trajectories.

Cell Systems · May 1, 2025Peer-reviewedCell Biology