Research
We study how principles from control theory, machine learning, and systems engineering can be used to understand and design living systems.
Neural-network–like computation can be implemented directly within living cells using genetic, enzymatic, and CRISPR-based circuits. Recent work demonstrates that biomolecular networks can operate as linear and nonlinear classifiers, enabling pattern recognition. These results establish a foundation for neuromorphic computing using biological substrates.
- Leon, C. M., Wang, Y., Bisso, F. B., Mehta, A., & Samaniego, C. C. (2025). CRISPR-based neuromorphic computing for solving regression and classification. https://doi.org/10.64898/2025.12.03.692209
- Bisso, F. B., Shree, D., Zhu, Y., & Samaniego, C. C. (2025). Design principles of neuromorphic computing using genetic circuits. https://doi.org/10.64898/2025.12.01.691482
- Britto Bisso, F., Aguilar, R., Shree, D., Zhu, Y., Espinoza, M., Diaz, B., & Cuba Samaniego, C. (2025). Pattern recognition in living cells through the lens of machine learning. https://doi.org/10.1098/rsob.240377
Biomolecular circuits operate in environments where transcriptional and translational resources are inherently shared. This line of research examines how resource competition alters the behavior of protein and genetic neural networks. Sequestration-based designs reveal strategies that allow reliable computation even under strong cellular constraints.
- He, E., Britto Bisso, F., & Cuba Samaniego, C. (2025). Sequestration-based protein neural networks tolerate the effects of shared translational resources. https://doi.org/10.64898/2025.12.01.691641
- Moghimianavval, H., Gispert, I., Castillo, S. R., Corning, O. B. W. H., Liu, A. P., & Cuba Samaniego, C. (2024). Engineering sequestration-based biomolecular classifiers with shared resources. https://doi.org/10.1021/acssynbio.4c00270
We apply principles of feedback and adaptive control to regulate gene expression and cellular behavior. Our work focuses on biomolecular controllers that restore and stabilize dynamic behaviors, including sustained oscillations and cell-fate regulation, in the presence of uncertainty and disturbances.
- Britto Bisso, F., Giordano, G., & Cuba Samaniego, C. (2025). Engineering cell fate with adaptive feedback control. https://doi.org/10.1021/acssynbio.5c00299
- Bisso, F. B., Dey, S., Stan, G.-B., & Cuba Samaniego, C. (2024). Design of a biomolecular adaptive controller to restore sustained periodic behavior. https://doi.org/10.1101/2024.10.11.617962
Predictable biological behavior requires circuits with well-defined and tunable dynamics. Work in this area focuses on sequestration-based architectures that generate pulsing, oscillatory, and computational responses. These design principles support the construction of modular and scalable circuits for complex biological functions.
- Nakamura, E., Samaniego, C. C., Blanchini, F., Giordano, G., & Franco, E. (2024). Design of a sequestration-based network with tunable pulsing dynamics. https://doi.org/10.1109/CDC56724.2024.10886733
- Samaniego, C. C., Wallace, E., Blanchini, F., Franco, E., & Giordano, G. (2024). Neural networks built from enzymatic reactions can operate as linear and nonlinear classifiers. https://doi.org/10.1101/2024.03.23.586372