Preprints

4

2025

• Bavisetty VSN, Wheeler M, Kadelka C. Attractors are less stable than their basins: Canalization creates a coherence gap in gene regulatory networks. bioRxiv [Preprint]. 2025 Nov 8:2025.11.06.687062. doi: 10.1101/2025.11.06.687062. PMID: 41279382; PMCID: PMC12637702.
• Min B, Choi J, Laubenbacher R. Attractor Stability of Boolean networks under noise. ArXiv [Preprint]. 2025 Jun 18:arXiv:2506.15581v1. PMID: 40980768; PMCID: PMC12447722.
• Minsuk SB, Sego TJ, Umulis DM, Mullins MC, Glazier JA. Modeling Epithelial Morphogenesis and Cell Rearrangement during Zebrafish Epiboly: Tissue Deformation, Cell-Cell Coupling, and the Mechanical Response to Stress. bioRxiv [Preprint]. 2025 Jun 21:2025.02.12.637977. doi: 10.1101/2025.02.12.637977. PMID: 39990311; PMCID: PMC11844516.

2024

• Adam C. Knapp, Daniel A. Cruz, Borna Mehrad, Reinhard C. Laubenbacher. Personalizing computational models to construct medical digital twins. bioRxiv 2024.05.31.596692; doi: 10.1101/2024.05.31.596692.
• Nord D, Brunson JC, Langerude L, Moussa H, Gill B, Machuca T, Rackauskas M, Sharma A, Lin C, Emtiazjoo A, Atkinson C. Predicting Primary Graft Dysfunction in Lung Transplantation: Machine Learning-Guided Biomarker Discovery. bioRxiv [Preprint]. 2024 Sep 23:2024.05.24.595368. doi: 10.1101/2024.05.24.595368. PMID: 39386627; PMCID: PMC11463600.
• Murrugarra D, Veliz-Cuba A, Dimitrova E, Kadelka C, Wheeler M, Laubenbacher R. Modular control of Boolean network models. ArXiv [Preprint]. 2024 Nov 4:arXiv:2401.12477v3. PMID: 38344220; PMCID: PMC10854280.
• T.J. Sego, Matthias König, Luis L. Fonseca, Baylor Fain, Adam C. Knapp, Krishna Tiwari, Henning Hermjakob, Herbert M. Sauro, James A. Glazier, Reinhard C. Laubenbacher, Rahuman S. Malik-Sheriff. EFECT – A Method and Metric to Assess the Reproducibility of Stochastic Simulation Studies. arXiv. 2024, June 24.  doi: 10.48550/arXiv.2406.16820.
• Fonseca LL, Böttcher L, Mehrad B, Laubenbacher RC. Surrogate modeling and control of medical digital twins. ArXiv [Preprint]. 2024 May 20:arXiv:2402.05750v2. PMID: 38827450; PMCID: PMC11142319. doi: 10.48550/arXiv.2402.05750
• Böttcher L, Fonseca LL, Laubenbacher RC. Control of Medical Digital Twins with Artificial Neural Networks. bioRxiv [Preprint]. 2024 Mar 20:2024.03.18.585589. doi: 10.1101/2024.03.18.585589. PMID: 38562787; PMCID: PMC10983973.

2023

• Kadelka C, Wheeler M, Veliz-Cuba A, Murrugarra D, Laubenbacher R. Modularity of biological systems: a link between structure and function. bioRxiv [Preprint]. 2023 Sep 12:2023.09.11.557227. doi: 10.1101/2023.09.11.557227. Update in: J R Soc Interface. 2023 Oct;20(207):20230505. doi: 10.1098/rsif.2023.0505. PMID: 37745485; PMCID: PMC10515856.

2022

• Chesnais F, Sego TJ, Engstler E, Battilocchi M, Danovi D, Glazier JA, Veschini L. A spatialised agent-based model of NOTCH signalling pathway in Endothelial Cells predicts emergent heterogeneity due to continual dynamic phenotypic adjustments. bioRxiv. 2022 Aug 6. doi: 10.1101/2022.08.06.503043.
• Harshman N, Knapp A. Topological Exchange Statistics in One Dimension. 2021 Aug 25. arXiv: 2108.05653
• Gianlupi JF, Sego TJ, Sluka JP, Glazier JA. PhenoCellPy: A Python package for biological cell behavior modeling. bioRxiv. 2023 Apr 14. doi: 10.1101/2023.04.12.535625.
• Brunson JC, Skaf Y. Fixed and adaptive landmark sets for finite pseudometric spaces. 2022 Dec 21. arXiv: 2212.09826
• Kadelka C, Keilty B, Laubenbacher R. Collectively canalizing Boolean functions. 2020 Oct 5. arXiv: 2008.13741