Publication

GoogleScholar

  1. Goetz H.+, Stone A.+, Zhang 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.
  2. Zhang, R.r,+, Goetz, H+, Melendez-Alvarez, J.+, 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.
  3. 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.
  4. Melendez-Alvarez, J.+, 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.
  5. 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), 1882-1882, 2021.
  6. 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, 103112,  2021.
  7. 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.
  8. Goetz, H. +, Melendez-Alvarez, J. +, Chen, L., and Tian, X.-J.* A Plausible Accelerating Function of Partial EMT States in Cancer Metastasis, PLOS Computational Biology, 16(3):e1007682. 2020.
  9. 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. 2020.
  10. 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. 2020.
  11. 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.
  12. 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.
  13. Xing, J.*, and Tian, X.-J.*, Investigating Epithelial-To-Mesenchymal Transition with Integrated Computational and Experimental Approaches. Physical Biology, 16(3):031001, 2019.
  14. 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.
  15. 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, 2019.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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= 240)
  22. 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= 314)
  23. 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.
  24. 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.
  25. 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.
  26. 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= 183)
  27. 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.
  28. Xing, J., Yu, J., Zhang, H., and Tian, X.-J., Computational modeling to elucidate mechanisms of epigenetic memory, in Epigenetic Technological Applications, Elsevier (2015).
  29. 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.
  30. 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.