The Zhang Lab develops programmable gene and cell therapies by bringing together synthetic biology, machine learning, and human disease models. We engineer molecular regulatory systems, synthetic gene circuits, and mammalian cells that sense, compute, and respond to disease-relevant signals. By integrating AI-guided molecular and circuit design, high-throughput functional screening, and 3D engineered tissue models, we seek to uncover fundamental principles of gene regulation and cellular control, and to harness these principles to create new therapeutic strategies for cardiovascular disease, genetic disorders, cancer, and other diseases where precise control of cell behavior could transform treatment.

Education

• Postdoctoral Research Associate, Massachusetts Institute of Technology & Wyss Institute at Harvard, 2021 - 2025
• Ph.D., Biomedical Engineering, Boston University, 2020
• M.S., Bioengineering, University of Pennsylvania, 2014
• B.S., Biomedical Engineering, University of Michigan Ann Arbor, 2012
• B.S., Electrical Engineering and Computer Science, 2012
   

Selected Publications

Zhang, K.*, Kim, N.*, Jin, W.*, Zhou, K.*, Nori, D., Du, J., Liu, J., Hoff, J. T., Lalwani, M. A., Chen, J. C., Tan, X., Ha, S. K., Chen, J. X., Ovchinnikov, S.,  & Collins, J. J. Deep generative design of RNA elements for translational control. in revision. 

Kim, N.*, De Carluccio, G.*, Zhang, K.*, & Collins, J. J. (2026) Generative AI for synthetic biology: designing biological parts, circuits, and genomes. Cell Systems, 17(2):101533.

Gayet, R. V., Ilia, K., Razavi, S., Tippens, N. D., Lalwani, M. A., Zhang, K., Chen, J. X., Chen, J. C., Vargas-Asencio, J., & Collins, J. J. (2023). Autocatalytic base editing for RNA-responsive translational control. Nature Communications, 14(1), 1339. 

Zhao, E. M., Mao, A. S., de Puig, H., Zhang, K., Tippens, N. D., Tan, X., Ran, F. A., Han, I., Nguyen, P. Q., Chory, E. J., Hua, T. Y., Ramesh, P., Thompson, D. B., Oh, C. Y., Zigon, E. S., English, M. A., & Collins, J. J. (2022). RNA-responsive elements for eukaryotic translational control. Nature Biotechnology, 40(4), 539–545. 

Zhang, K., Cloonan, P. E., Sundaram, S., Liu, F., Das, S. L., Ewoldt, J. K., Bays, J. L., Tomp, S., Toepfer, C. N., Marsiglia, J. D. C., Gorham, J., Reichart, D., Eyckmans, J., Seidman, J. G., Seidman, C. E., & Chen, C. S. (2021). Plakophilin-2 truncating variants impair cardiac contractility by disrupting sarcomere stability and organization. Science Advances, 7(42), eabh3995.

Jayne, R. K.*, Karakan, M. Ç.*, Zhang, K.*, Pierce, N., Michas, C., Bishop, D. J., Chen, C. S., Ekinci, K. L., & White, A. E. (2021). Direct laser writing for cardiac tissue engineering: a microfluidic heart on a chip with integrated transducers. Lab on a Chip, 21(9), 1724–1737. 

Zhao, B., Zhang, K., Chen, C. S., & Lejeune, E. (2021). Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes. PLoS Computational Biology, 17(10), e1009443. 

Chopra, A.*, Kutys, M. L.*, Zhang, K.*, Polacheck, W. J., Sheng, C. C., Luu, R. J., Eyckmans, J., Hinson, J. T., Seidman, J. G., Seidman, C. E., & Chen, C. S. (2018). Force Generation via β-Cardiac Myosin, Titin, and Actinin Drives Cardiac Sarcomere Assembly from Cell-Matrix Adhesions. Developmental Cell, 44(1), 87–96.e5.

Alferiev, I. S., Iyer, R., Croucher, J. L., Adamo, R. F., Zhang, K., Mangino, J. L., Kolla, V., Fishbein, I., Brodeur, G. M., Levy, R. J., & Chorny, M. (2015). Nanoparticle-mediated delivery of a rapidly activatable prodrug of SN-38 for neuroblastoma therapy. Biomaterials, 51, 22–29.

Tengood, J. E., Alferiev, I. S., Zhang, K., Fishbein, I., Levy, R. J., & Chorny, M. (2014). Real-time analysis of composite magnetic nanoparticle disassembly in vascular cells and biomimetic media. Proceedings of the National Academy of Sciences of the United States of America, 111(11), 4245–4250.