Fluctuation induced network patterns in active matter with spatially correlated noise

Sebastian Fehlinger, Kai Cui, Arooj Sajjad, Heinz Koeppl and Benno Liebchen

Soft Matter, 2025, 21, 5459
DOI: 10.1039/D5SM00245A

Learning Collective Cell Migratory Dynamics from a Static Snapshot with Graph Neural Networks

Haiqian Yang, Florian Meyer, Shaoxun Huang, Liu Yang, Cristiana Lungu, Monilola A. Olayioye, Markus J. Buehler and Ming Guo

PRX Life, 2024, 2
DOI: 10.1103/PRXLife.2.043010

Dissecting glial scar formation by spatial point pattern and topological data analysis

Daniel Manrique-Castano, Dhananjay Bhaskar and Ayman ElAli

Sci Rep, 2024, 14
DOI: 10.1038/s41598-024-69426-z

Quantifying Different Modeling Frameworks Using Topological Data Analysis: A Case Study with Zebrafish Patterns

Electa Cleveland, Angela Zhu, Björn Sandstede and Alexandria Volkening

SIAM J. Appl. Dyn. Syst., 2023, 22, 3233
DOI: 10.1137/22M1543082

Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion

Dhananjay Bhaskar, William Y. Zhang, Alexandria Volkening, Björn Sandstede and Ian Y. Wong

npj Syst Biol Appl, 2023, 9
DOI: 10.1038/s41540-023-00302-8

Integration of topological data analysis and entropy features for the prediction of lithium-ion battery state-of-health

Manoj K. Singh, Anuj Kumar, Sangeeta Pant, Shshank Chaube, Kriti Misra, Jitendra Pal Singh and Ketan Kotecha

Future Batteries, 2025, 6, 100059
DOI: 10.1016/j.fub.2025.100059

Three-dimensional granular deposits characterized by persistent homology

Sergio Ardanza-Trevijano, Roberto Arévalo, Sahily Estradé, Diego Maza and Iker Zuriguel

Phys. Rev. E, 2025, 111
DOI: 10.1103/PhysRevE.111.045413

Neural network approaches, including use of topological data analysis, enhance classification of human induced pluripotent stem cell colonies by treatment condition

Alexander Ruys de Perez, Paul E. Anderson, Elena S. Dimitrova, Melissa L. Kemp and Serdar Bozdag

PLoS Comput Biol, 2025, 21, e1012801
DOI: 10.1371/journal.pcbi.1012801

Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment

Bernadette J. Stolz, Jagdeep Dhesi, Joshua A. Bull, Heather A. Harrington, Helen M. Byrne and Iris H. R. Yoon

Bull Math Biol, 2024, 86
DOI: 10.1007/s11538-024-01353-6

Topological Data Analysis of Ninjin'yoeito Effects Unraveling Complex Interconnections in Patients With Frailty: A Pilot Study

Nobuo Okui, Tadashi Ikegami and Machiko Okui

Cureus, 2024
DOI: 10.7759/cureus.74855

Topological data analysis of pattern formation of human induced pluripotent stem cell colonies

Iryna Hartsock, Eunbi Park, Jack Toppen, Peter Bubenik, Elena S. Dimitrova, Melissa L. Kemp and Daniel A. Cruz

Sci Rep, 2025, 15
DOI: 10.1038/s41598-025-90592-1

Topological classification of tumour-immune interactions and dynamics

Jingjie Yang, Heidi Fang, Jagdeep Dhesi, Iris H. R. Yoon, Joshua A. Bull, Helen M. Byrne, Heather A. Harrington and Gillian Grindstaff

J. Math. Biol., 2025, 91
DOI: 10.1007/s00285-025-02253-6

Computational topology of Drosophila melanogaster embryos: Emergent anatomy from the spatiotemporal distributions of hemocytes

Xinrui Hu, Nickolay Korabel, Tom H. Millard and Thomas Andrew Waigh

Phys. Rev. E, 2025, 112
DOI: 10.1103/mc9z-kw1q

Topological data analysis in single cell biology

Enrique Hernández-Lemus

Front. Immunol., 2025, 16
DOI: 10.3389/fimmu.2025.1615278

Stable Topological Summaries for Analyzing the Organization of Cells in a Packed Tissue

Nieves Atienza, Maria-Jose Jimenez and Manuel Soriano-Trigueros

Mathematics, 2021, 9, 1723
DOI: 10.3390/math9151723

Tracking the time evolution of soft matter systems via topological structural heterogeneity

Ingrid Membrillo Solis, Tetiana Orlova, Karolina Bednarska, Piotr Lesiak, Tomasz R. Woliński, Giampaolo D’Alessandro, Jacek Brodzki and Malgosia Kaczmarek

Commun Mater, 2022, 3
DOI: 10.1038/s43246-021-00223-1

Contact temporal network during motility-induced phase separation

Italo Salas, Francisca Guzmán-Lastra, Denisse Pastén and Ariel Norambuena

Phys. Rev. E, 2025, 112
DOI: 10.1103/t3k6-hcmr

Deep learning-based high-information-content graph representation of early stage bacterial biofilms

Lev E. Nersesyan, Daniil A. Boiko, Saniyat Kurbanalieva, Lilya U. Dzhemileva, Konstantin S. Kozlov and Valentine P. Ananikov

npj Biofilms Microbiomes, 2026
DOI: 10.1038/s41522-026-00971-3

Ultrafast-relaxing and photopolymerizable PEG hydrogels enable viscoelasticity-mediated cell remodeling in synthetic matrices

Bruce E. Kirkpatrick, Abhishek P. Dhand, Lea Pearl Hibbard, Matthew W. Jaeschke, Tvishi Yendamuri, Benjamin R. Nelson, Joshua S. Lee, Kaustav Bera, Hannah M. Zlotnick, Carly A. Fox, Bianca Meurer-Zeman, Connor E. Miksch, Nathaniel P. Skillin, Michael R. Blatchley, Timothy J. White, Christopher N. Bowman, Jason A. Burdick and Kristi S. Anseth

Matter, 2026, 9, 102524
DOI: 10.1016/j.matt.2025.102524

Two-Stage Structural and Slowing-Down Percolation Transitions in the Densifying Cancer Cell Monolayer

Chun-Yu Liu, Yun-Xuan Zhang and Lin I

Phys. Rev. Lett., 2022, 129
DOI: 10.1103/PhysRevLett.129.148102