Namboothiri, H. R. & Hu, C. Y*. Gain-Scheduled Optogenetic Feedback for Disturbance Rejection in Bacterial Batch Cultures. bioRxiv 2026.04.04.716495 (2026). doi:10.64898/2026.04.04.716495

Hu, C. Y*. and Namboothiri, H. R. Gene Expression Across Growth Stages (GEAGS): Modeling Circuit Dynamics in Batch Cultures. Synthetic Gene Circuits: Methods and Protocols. New York, NY: Springer US. in press

Hu, C. Y*. Antithetic integral feedback control redesigned for improved dynamics and lower noise. Cell Syst. 17, 101565 (2026).

Namboothiri, H. R., Pochana, K., Jaiswal, B., Emami, A. & Hu, C. Y.* Closed-Loop Optogenetic Control in a Microplate Reader. ACS Synth. Biol. (2026). doi:10.1021/acssynbio.6c00003

Namboothiri, H. R.; Pandey, A.; Hu, C. Y*. Resolving emergent transient oscillations in gene circuits with a growth-coupled model. Sci Adv 2026, 12 (6), eadz2310. DOI: 10.1126/sciadv.adz2310.

Hu, C. Y.*; McManus, J.; Aghlmand, F.; Mei, T.; Larsson, E.; Emami, A.; Murray, R. M. A Portable Arsenic Sensor Integrating Bacillus megaterium with CMOS Technology. ACS Synthetic Biology2025, 14 (5), 1615-1624. DOI: 10.1021/acssynbio.4c00895.

Aghlmand, F., Hu, C. Y., Sharma, S., Pochana K., Murray, R. M. & Emami, A. A 65mm CMOS Fluorescence Sensor for Dynamic Monitoring of Living Cells”. The Journal of Solid State Circuits. Aug. 2023, doi: 10.1109/JSSC.2023.3308853 

Aghlmand, F., Hu, C.Y., Sharma, S., Pochana, K., Murray, R., and Emami, A., “A 65nm CMOS Living-Cell Dynamic Fluorescence Sensor with 1.05fA Sensitivity at 600/700nm Wavelengths,” in IEEE Int. Solid-State Circuits Conf., Feb. 2023, doi:10.1109/ISSCC42615.2023.10067325

Hu, C. Y.*, & Murray, R. M. Layered Feedback Control Overcomes Performance Trade-off in Synthetic Biomolecular Networks. Nat Commun 13, 5393 (2022). https://doi.org/10.1038/s41467-022-33058-6

Green, L. N., Hu, C. Y., Ren, X. Y., & Murray, R. M. (2019). Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design. bioRxiv,19(7), 3217–15. http://doi.org/10.1101/659714

Hu, C. Y., Takahashi, M. K., Zhang, Y., & Lucks, J. B. (2018). Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design. ACS Synthetic Biology, 7(6), 1507–1518. http://doi.org/10.1021/acssynbio.7b00440

Hu, C. Y., Varner, J. D., & Lucks, J. B. (2015). Generating Effective Models and Parameters for RNA Genetic Circuits. ACS Synthetic Biology, 4(8), 914–926. http://doi.org/10.1021/acssynbio.5b00077