L. Sordo Vieira*, D.A. Cruz*, I. Ramirez-Zuniga, C. Atkinson, B. Mehrad, and R.C. Laubenbacher. Mathematical Modeling of the Complement System: a Scoping Review. Bulletin of Mathematical Biology 88: 193, (2026). DOI: 10.1007/s11538-026-01723-2
A.C. Knapp*, D.A. Cruz*, B. Mehrad, R.C. Laubenbacher. Personalizing computational models to construct medical digital twins. Journal of the Royal Society Interface 22, 20250055 (2025). DOI: 10.1098/rsif.2025.0055
I. Hartsock*, E. Park*, J. Toppen, E.S. Dimitrova, M.L. Kemp, P. Bubenik, D.A. Cruz. Topological data analysis of pattern formation of human induced pluripotent stem cell colonies. Scientific Reports 15, 11544 (2025). DOI: 10.1038/s41598-025-90592-1
D.A. Cruz*, M.L Kemp*. Hybrid computational modeling methods for systems biology. Progress in Biomedical Engineering 4 (2021) 012002. DOI: 10.1088/2516-1091/ac2cdf
D.A. Cruz*, M.M. Ferrari*, N. Jonoska*, L. Nabergall*, M. Saito*. Insertions yielding equivalent double occurrence words. Fundamenta Informaticae 171: 1–4, (2020) 113–132. DOI: 10.3233/FI-2020-1875
J. Braun*, D. Cruz*, N. Jonoska*. Platform color designs for interactive molecular arrangements. Unconventional Computation and Natural Computation LNCS (M.J. Patitz, M. Stannett, eds) 10240, (2017) 69-81. DOI: 10.1007/978-3-319-58187-3_6
R.C. Laubenbacher, J.L. Hellerstein, S. Wiley, H.M. Sauro, S.S. Andrews, V.S.N. Bavisetty, D.A. Cruz, E. Dimitrova, S. Feng, L.L. Fonseca, C. Kadelka, D. Murrugarra, D.R. Plaugher, T.J. Sego, S.A. Tsiorintsoa, A. Veliz-Cuba, and M. Wheeler. Modularity in Biological Systems: Toward a Formal Conceptual Foundation. Accepted at npj Systems Biology and Applications (2026). Manuscript available upon request.
D.A. Cruz, J. Toppen, E. Park, M.L. Kemp, E.S. Dimitrova. Estimating the long-term behavior of biologically inspired agent-based models. In preparation (2026); partial preprint: https://arxiv.org/abs/2211.00630.
E. Park*, D.A. Cruz*, J. Toppen, E.S. Dimitrova, M.L. Kemp. Extraction of transcriptional network within human induced pluripotent colonies via Boolean logic. In preparation (2026).