Publication

GoogleScholar

  1. Zhang, R., Yang, W., Zhang, R., Godar, A., Rijal, S., Youssef, A., Nielsen, D.R., Zheng, W., Tian, X.-J.*, Phase Separation to Buffer Growth-Mediated Dilution in Synthetic Circuits. Cell. 2025.
  2. Zhang, R., Zhang, R.r, Tian, X.-J.*, Integrating Recombinase-Based Feedback and Feedforward Control for Optimal Resource Decoupling. Nucleic Acids Research. 2025, 53(17), gkaf913.
  3. Rijal, S., Standage-Beier K., Zhang, R.r, Stone, A.+, Youssef, A., Wang, X., and Tian, X.-J.*, CRISPR-Linked Multi-Module Negative Feedback Loops to Address Winner-Take-All Resource Competition. 2025. 14, 9, 3646-3654. ACS Synthetic Biology.
  4. Goetz, H.+, Zhang, R.r, Wang, X., Tian, X.-J.*, Resource Competition-Driven Bistability and Stochastic Switching Amplify Gene Expression Noise. PLOS Computational Biology. 2025, 21(4): e1012931.
  5. Kong L-W, Shi W, Tian X.-J., and Ying-Cheng Lai Y-C.*, Effects of growth feedback on gene circuits: A dynamical understanding. eLife, 12:RP89170, 2025.
  6. Tian, X.-J.*, Zhang, R., “Economics Paradox” with Cells in Synthetic Gene Circuits. Synthetic Biology Journal. 2025, 6 (3), 532.
  7. Tian, X.-J.*, Zhang, R., Ferro, M. V., and Goetz, H. Modeling ncRNA-Mediated Circuits in Cell Fate Decision: From Systems Biology to Synthetic Biology. Computational Biology of Non-Coding RNA: Methods and Protocols, 139-154, 2025.
  8. Stone, A.+, Youssef, A., Rijal, S., Zhang, R.r, and Tian, X.-J.*, Context-Dependent Redesign of Robust Synthetic Gene Circuits. Trends in Biotechnology. Trends in Biotechnology. 42, 895-909, 2024. 
  9. Stone, A.+, Zhang, R.r, Rijal, S., and Tian, X.-J.*, Enhancing Circuit Stability Under Growth Feedback with Supplementary Repressive Regulation. Nucleic Acids Research, gkad1233, 2024.
  10. Chakravarty S., Guttal, R.#, Zhang, R.r, Tian, X.-J.*, Mitigating Winner-Take-All Resource Competition Through Antithetic Control Mechanism. ACS Synthetic Biology, 13(12):4050-4060, 2024.
  11. Gui, Y., Yu, Y., Wang, W., Wang, Y., Lu, H., Mozdzierz, S., Kirollos E., Lin Y-H., Li H., Tian, X.-J., Liu S., Zhou D., Proteomes characterization of liver-kidney comorbidity after microbial sepsis. The FASEB Journal, 38:e23597, 2024.
  12. Chakravarty S.r, Zhang, R.r, Tian, X.-J.*, Noise Reduction in Resource-Coupled Multimodule Gene Circuits through Antithetic Feedback Control. IEEE 63rd Conference on Decision and Control (CDC), 2024, 5566-5571.
  13. Melendez-Alvarez, , Zhang, R.r,*, and Tian X.-J.*, Growth Feedback Confers Cooperativity in Resource-Competing Synthetic Gene Circuits. Chaos, Solitons and Fractals, 173, 113713, 2023.
  14. Bowes, D.A., Driver, E.M., Kraberger, S., Fontenele, R.S., Holland, L.A., Wright, J., Johnston, B., Savic S., Newell, M.E., Adhikari, S., Kumar, R., Goetz, H., Binsfeld, A., Nessi, K., Watkins, P., Mahant, A., Zevitz J., Deitrick, S., Brown, P., Dalton, R., Garcia, C., Inchausti, R., Holmes, W., Tian, X.-J., Varsani, A., Lim, E.S., Scotch, M., Halden, R.U. Cycling through epidemics: Lessons learned from a population-based study leveraging an established neighborhood-level, open access wastewater monitoring network to rapidly address public health priorities. The Lancet Microbe, 4(1):e29-e37, 2023.
  15. Zhang, R.r, Goetz, H., Melendez-Alvarez, , Li, J.∞, Ding, T., Wang, X., and Tian, X.-J.*, Winner-Takes-All Resource Competition Redirects Cascading Cell Fate Transitions. Nature Communications, 12, 853, 2021.
  16. Zhang, R.r,+, Li, J.∞,+, Melendez-Alvarez, J., Chen, X., Sochor, P., Zhang, Q., Goetz, H., Ding, T., Wang, X.*, and Tian, X.-J.*, Topology-Dependent Interference of Synthetic Gene Circuit Function by Growth Feedback, Nature Chemical Biology, 16, 695-701, 2020.
  17. Melendez-Alvarez, , and Tian, X.-J.*, Emergence of Qualitative States in Synthetic Circuit Driven by Ultrasensitive Growth Feedback. PLOS Computational Biology, 18(9): e1010518. 2022.
  18. Goetz, H.+, Stone, A.+, Zhang, R.r, Lai, Y.-C., and Tian, X.-J.*, Double-edged role of resource competition in gene expression noise and control. Advanced Genetics, 3, 2100050, 2022.
  19. Stone, A., Ryan, R. J., Tang, X., and Tian, X.-J.*, Negatively Competitive Regulatory Feedforward Loops Mitigate Winner-Take-All Resource Competition. ACS Synthetic Biology, 11, 12, 3986–3995, 2022.
  20. Zhang, J., Ren, H., Jayasuriya, H., Tian, X.-J., Chae, J., The memory effect in microbial fuel cell biosensors. IEEE Sensors Journal, 22, 18, 17698-17705, 2022.
  21. Melendez-Alvarez, , He, C., Zhang, R.r,*, Kuang, Y., and Tian X.-J.*, Emergent Damped Oscillation Induced by Nutrient-Modulating Growth Feedback. ACS Synthetic Biology, 10, 5, 1227-1236, 2021.
  22. Stone, A., Zhang, R.r, and Tian, X.-J.*, Coupling Shared and Tunable Negative Competition Against Winner-Take-All Resource Competition Via CRISPRi Moieties. 2021 American Control Conference (ACC),
  23. Fu H., Gui Y., Liu, S., Wang, Y., Bastacky, S., Qiao, Y., Zhang, R.r, Bonin, C., Hargis, G., Yu, Y., Donald, K., Biswas, P., Zhou, Y., Wang, Y., Tian, X.-J.*, Liu, Y.*, and Zhou, D*., The Hepatocyte Growth Factor Pathway is a Key Determinant of the Fibrotic Kidney Local Microenvironment. iScience, 24(10), 103112, 2021.
  24. Liu, S., Gui, Y., Wang, M., Zhang, L., Xu, T., Pan, Y., Zhang, K., Yu, Y., Xiao, L., Qiao, Y., Bonin, C., Hargis, G., Huan, T., Yu, Y., Tao, J., Zhang, R.r, Kreutzer, D., Zhou, Y., Tian, X.-J., Wang, Y., Fu, H., An, X., Liu, S., Zhou, D., Serum integrative omics reveals the landscape of human diabetic kidney disease. Molecular Metabolism, 54, 101367, 2021.
  25. Barra, D., Melendez-Alvarez, J., and Tian, X.-J.*, Control of tissue homeostasis, regeneration, and degeneration by coupled bi-directional bistable switches. PLOS Computational Biology, 17(11): e1009606. 2021.
  26. Goetz, H.+, Melendez-Alvarez, +, Chen, L., and Tian, X.-J.*, A Plausible Accelerating Function of Partial EMT States in Cancer Metastasis, PLOS Computational Biology, 16(3):e1007682. 2020.
  27. Tian, X.-J.*,+, Zhou, D.+, Fu, H.+, Zhang, R.r, Wang, X., Huang, S., Liu, Y.*, and Xing, J.*, Sequential Wnt Agonist then Antagonist Treatment Accelerates Tissue Repair and Minimizes Fibrosis, iScience, 23(5): 101047.
  28. Menn, D.J., Sochor, P., Goetz, H., Tian, X.-J.*, and Wang X.*, Intracellular noise level determines ratio control strategy confined by speed-accuracy tradeoff, ACS Synthetic Biology, 8(6):1352-60, 2019.
  29. Chen, Y.-J., Cheng, Y.-Y., Wang, W., Tian, X.-J., Lefever, D.E., Taft, D.A., Zhang, J., and Xing, J., Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in, Biology Methods and Protocols, 5(1): bpaa006.
  30. Xing, J.*, and Tian, X.-J.*, Investigating Epithelial-To-Mesenchymal Transition with Integrated Computational and Experimental Approaches. Physical Biology, 16(3):031001,
  31. Singh, M.+, Tian, X.-J.+, Donnenberg, V.S., Watson, A.M., Zhang, J., Stabile, L.P., Watkins, S.C., Xing, J., and Sant, S., Targeting the Temporal Dynamics of Hypoxia-Induced Tumor-Secreted Factors Halts Tumor Migration. Cancer Research, 79(11):2962-77, 2019.
  32. Fu, H., Liu, S., Bastacky, S., Wang, X., Tian, X.-J., and Zhou, D. Diabetic Kidney Diseases Revisited: A New Perspective for A New Era. Molecular Metabolism, 30, 250-263,
  33. Tian, X.-J.*, Manuela Vanegas, V., and Goetz, H., Modeling ncRNA-mediated circuits in cell fate decision. Computational Biology of non-coding RNA in Biomedicine, 411-426, 2019.
  34. Li, J.∞, Liu, D., Tian, X.-J., Koseki, S., Chen, S., Ye, X., and Ding, T. Novel Antibacterial Modalities Against Methicillin Resistant Staphylococcus Aureus Derived from Plants. Critical Reviews in Food Science and Nutrition, 59(sup1):S153-S161, 2018.
  35. Zhang, J.+, Tian, X.-J.+, Chen, Y.-J., Wang, W., Watkins, S., and Xing, J., Pathway crosstalk enables cells to interpret TGF-β duration. npj Systems Biology and Applications, 4:18, 2018.
  36. Zhou, D., Fu, H., Xiao, L., Mo, H., Zhuo, H., Tian, X.-J, Lin, L., Xing, J., and Liu, Y.*, Fibroblast-Specific β-catenin Signaling Dictates the Outcome of AKI. Journal of the American Society of Nephrology 29 (4), 1257-1271, 2018.
  37. Tian, X.-J.+, Zhang, H.+, Sannerud, J., and Xing, J., Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design. PNAS, 113: E2889-98, 2016.
  38. Tian, X.-J.*, Zhang, H., Zhang, J., and Xing, J., mRNA-miRNA Reciprocal Regulation Enabled Bistable Switch Directs Cell Fate Decision. FEBS Lett, 590: 3443-55, 2016.
  39. Zhang, J., Tian, X.-J., and Xing, J.*, Signal Transduction Pathways of EMT Induced by TGFβ, SHH, and WNT and Their Crosstalks. J Clin Med, 5: 41, 2016. (Citation=411).
  40. Xing, J., Yu, J., Zhang, H., and Tian, X.-J., Computational modeling to elucidate mechanisms of epigenetic memory, in Epigenetic Technological Applications, 245-264. Academic Press, 2015.
  41. Zhang, J.+, Tian, X.-J.+, Zhang, H., Teng, Y., Li, R., Bai, F., Elankumaran, S., and Xing, J., TGFβ-induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops. Sci Signal, 7: ra91, 2014. (Citation=551)
  42. Zhang, H., Tian, X.-J., Mukhopadhyay, A., Kim, K. S., and Xing, J., Statistical mechanics model for the dynamics of collective epigenetic histone modification. Phys Rev Lett, 112: 068101, 2014.
  43. Wang, P., Song, C., Zhang, H., Wu, Z., Tian, X.-J., and Xing, J., Epigenetic state network approach for describing cell phenotypic transitions. Interface Focus, 4: 20130068, 2014.
  44. Zhang, Q.-H., Tian, X.-J., Liu, F., and Wang, W., A switch-like dynamic mechanism for the initiation of replicative senescence. FEBS Lett, 588: 4369-74, 2014.
  45. Tian, X.-J., Zhang, H., and Xing, J., Coupled reversible and irreversible bistable switches underlying TGFβ-induced epithelial to mesenchymal transition. Biophys J, 105: 1079-89, 2013. (Citation 326).
  46. Hu, Y., Ru, N., Xiao, H., Chaturbedi, A., Hoa, N. T., Tian, X.-J., Zhang, H., Ke, C., Yan, F., Nelson, J., Li, Z., Gramer, R., Yu, L., Siegel, E., Zhang, X., Jia, Z., Jadus, M. R., Limoli, C. L., Linskey, M. E., Xing, J., and Zhou, Y. H., Tumor-specific chromosome mis-segregation controls cancer plasticity by maintaining tumor heterogeneity. PLoS One, 8: e80898, 2013.
  47. Tian, X.-J., Liu, F., Zhang, X. P., Li, J., and Wang, W., A two-step mechanism for cell fate decision by coordination of nuclear and mitochondrial p53 activities. PLoS One, 7: e38164, 2012.
  48. Tian, X.-J., Zhang, X. P., Liu, F., and Wang, W., Interlinking positive and negative feedback loops creates a tunable motif in gene regulatory networks. Phys Rev E, 80: 011926, 2009. (Citation 139).