{"id":45,"date":"2015-02-06T18:07:20","date_gmt":"2015-02-06T18:07:20","guid":{"rendered":"http:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/?page_id=45"},"modified":"2026-09-18T11:24:47","modified_gmt":"2026-09-18T15:24:47","slug":"publications","status":"publish","type":"page","link":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/?page_id=45","title":{"rendered":"Publications"},"content":{"rendered":"

82. Ma, A., Nussinov, R., Chen, J., Xing, J.<\/strong>, Xiao, J., Xu, D., Lin, M., Delafrouz, P., Royston, T., Tang, K., Ye, B., & Zhang, J. (2026). Jie Liang (1964\u20132024): Introduction to modeling biology at multiple scales: From macromolecules to cells, dedicated to Jie Liang. Biophysical Journal, 125<\/em>(18), E1\u2013E6. https:\/\/doi.org\/10.1016\/j.bpj.2026.08.015<\/a> Author note: Ma and Xing are co-corresponding authors.<\/p>\n

81. Zeng, Z., Yu, S., Ni, K., Zhang, Y., Shin, U., Huang, C., Cao, N., Weissman, J., Xing, J.<\/strong>, & Qiu, X. (in press). Predictive modeling of single-cell transcriptomic dynamics with Dynamo. Nature Protocols<\/em>. Author note: Zeng, Yu, Ni, and Zhang are co-first authors; Xing and Qiu are co-corresponding authors.<\/p>\n

80. Das, B., Xing, J.<\/strong>, Sharma, A. K., & Ge, H. (2026). Hook stiffness as a mechanical switch for torque regulation in the bacterial flagellar motor. Biophysical Journal, 125<\/em>(18), 5243\u20135253. https:\/\/doi.org\/10.1016\/j.bpj.2026.02.018<\/a><\/p>\n

79. Hu, S., Lu, Y., Yu, G., Zheng, Z., Ni, K., Giri, A., Zhang, J., Zhang, Y., Yao, G., & Xing, J.<\/strong> (2026). Single cell snapshot analyses under proper representation reveal that epithelial-mesenchymal transition couples at G1 and G2\/M. Communications Biology, 9<\/em>(1), 212. https:\/\/doi.org\/10.1038\/s42003-025-09487-6<\/a><\/p>\n

78. Nguyen, H.-T., Nguyen, T.-H., Lam, B.-T., Vu, V., Nguyen, B. X., Xing, J.<\/strong>, Wang, T., Li, X., & Xu, M. (2026). Adaptive knowledge transferring with switching dual-student framework for semi-supervised medical image segmentation. Pattern Recognition, 175<\/em>, 113115. https:\/\/doi.org\/10.1016\/j.patcog.2026.113115<\/a><\/p>\n

77. Wiley, H. S., Lopez, C. F., Rodin, A. S., Rockne, R. C., Yankeelov, T. E., Sauro, H. M., Hassan, G., Prabhakaran, S., Demir, E., Hu, M., Fuxman Bass, J., Luddy, K. A., Newman, H., Mochel, J. P., Costello, J. C., Xing, J.<\/strong>, Afify, S. M., Acar, A., Haden Gephart, M., et al. (2025). A roadmap for the future of systems biology in cancer research. Cancer Research, 85<\/em>(24), 4880\u20134889. https:\/\/doi.org\/10.1158\/0008-5472.can-25-0700<\/a><\/p>\n

76. Wang, H., Ardila, C., Jindal, A., Aggarwal, V., Wang, W., Vande Geest, J., Jiang, Y., Xing, J.<\/strong>, & Sant, S. (2025). Protrusion force and cell-cell adhesion-induced polarity alignment govern collective migration modes. Biophysical Journal, 124<\/em>(10), 1674\u20131692. https:\/\/doi.org\/10.1016\/j.bpj.2025.04.010<\/a> Author note: Xing and Sant are co-corresponding authors.<\/p>\n

75. Ni, K., Yu, G., Zheng, Z., Lu, Y., Hu, S., Poe, D., Zhang, S., Sanborn, M., Uddin, M., Wang, Z., Zhou, S., Chen, Y., Zhan, X., Wang, W., & Xing, J.<\/strong> (2025). LivecellX: Corrective deep learning for object-oriented single-cell analysis in live-cell imaging [Preprint]. bioRxiv<\/em>. https:\/\/doi.org\/10.1101\/2025.02.23.639532<\/a><\/p>\n

74. Zhang, J., Wang, S., Watkins, S. C., & Xing, J.<\/strong> (in press). Long-range genomic loci stochastically assemble into hierarchical chromosome structures. Genome Biology<\/em>. Preprint available at https:\/\/doi.org\/10.1101\/2025.02.10.637328<\/a><\/p>\n

73. Chen, Y., Zhang, Y., Gan, J., Ni, K., Chen, M., Bahar, I., & Xing, J.<\/strong> (2025). GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells. Nature Communications, 16<\/em>(1), 7831. https:\/\/doi.org\/10.1038\/s41467-025-62784-w<\/a><\/p>\n

72. Hong, T., & Xing, J.<\/strong> (2024). Data\u2010 and theory\u2010driven approaches for understanding paths of epithelial\u2013mesenchymal transition. Genesis, 62<\/em>(2), e23591. https:\/\/doi.org\/10.1002\/dvg.23591<\/a><\/p>\n

71. Wang, W., Ni, K., Poe, D., & Xing, J.<\/strong> (2024). Transiently increased coordination in gene regulation during cell phenotypic transitions. PRX Life, 2<\/em>(4), 043009. https:\/\/doi.org\/10.1103\/prxlife.2.043009<\/a><\/p>\n

70. Cang, H., Liu, Y., & Xing, J.<\/strong> (2024). Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging. Bioinformatics, 40<\/em>(1), btad784. https:\/\/doi.org\/10.1093\/bioinformatics\/btad784<\/a><\/p>\n

69. Zhang, Y., Qiu, X., Ni, K., Weissman, J., Bahar, I., & Xing, J.<\/strong> (2023). Graph-Dynamo: Learning stochastic cellular state transition dynamics from single cell data [Preprint]. bioRxiv<\/em>. https:\/\/doi.org\/10.1101\/2023.09.24.559170<\/a><\/p>\n

68. Hettinger, Z. R., Hu, S., Mamiya, H., Sahu, A., Iijima, H., Wang, K., Gilmer, G., Miller, A., Nasello, G., D\u2019Amore, A., Vorp, D. A., Rando, T. A., Xing, J.<\/strong>, & Ambrosio, F. (2023). Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate [Preprint]. bioRxiv<\/em>. https:\/\/doi.org\/10.1101\/2023.02.24.529950<\/a> Author note: Hettinger and Hu are co-first authors; Rando, Xing, and Ambrosio are co-corresponding authors.<\/p>\n

67. Xing, J.<\/strong> (2022). Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology. Physical Biology, 19<\/em>(6), 061001. https:\/\/doi.org\/10.1088\/1478-3975\/ac8c16<\/a><\/p>\n

66. Wang, W., Poe, D., Yang, Y., Hyatt, T., & Xing, J.<\/strong> (2022). Epithelial-to-mesenchymal transition proceeds through directional destabilization of multidimensional attractor. eLife, 11<\/em>, e74866. https:\/\/doi.org\/10.7554\/elife.74866<\/a><\/p>\n

65. Qiu, X., Zhang, Y., Martin-Rufino, J. D., Weng, C., Hosseinzadeh, S., Yang, D., Pogson, A. N., Hein, M. Y., Hoi (Joseph) Min, K., Wang, L., Grody, E. I., Shurtleff, M. J., Yuan, R., Xu, S., Ma, Y., Replogle, J. M., Lander, E. S., Darmanis, S., Bahar, I., et al. (2022). Mapping transcriptomic vector fields of single cells. Cell, 185<\/em>(4), 690\u2013711. https:\/\/doi.org\/10.1016\/j.cell.2021.12.045<\/a> Author note: Qiu and Zhang are co-first authors; Qiu, Xing, and Weissman are co-corresponding authors.<\/p>\n

64. Zhang, Y., Krieger, J., Mikulska-Ruminska, K., Kaynak, B., Sorzano, C. O. S., Carazo, J.-M., Xing, J.<\/strong>, & Bahar, I. (2021). State-dependent sequential allostery exhibited by chaperonin TRiC\/CCT revealed by network analysis of Cryo-EM maps. Progress in Biophysics and Molecular Biology, 160<\/em>, 104\u2013120. https:\/\/doi.org\/10.1016\/j.pbiomolbio.2020.08.006<\/a><\/p>\n

63. Xing, J.<\/strong> (2020). Bidirectional interplay between physical and biological approaches on studying the epithelial-to-mesenchymal transition. Physical Biology, 17<\/em>(2), 020201. https:\/\/doi.org\/10.1088\/1478-3975\/ab73d0<\/a><\/p>\n

62. Wang, W., Douglas, D., Zhang, J., Kumari, S., Enuameh, M. S., Dai, Y., Wallace, C. T., Watkins, S. C., Shu, W., & Xing, J.<\/strong> (2020). Live-cell imaging and analysis reveal cell phenotypic transition dynamics inherently missing in snapshot data. Science Advances, 6<\/em>(36), eaba9319. https:\/\/doi.org\/10.1126\/sciadv.aba9319<\/a><\/p>\n

61. Yang, J., Antin, P., Berx, G., Blanpain, C., Brabletz, T., Bronner, M., Campbell, K., Cano, A., Casanova, J., Christofori, G., Dedhar, S., Derynck, R., Ford, H. L., Fuxe, J., Garc\u00eda\u00a0de\u00a0Herreros, A., Goodall, G. J., Hadjantonakis, A.-K., Huang, R. Y. J., Kalcheim, C., et al. (2020). Guidelines and definitions for research on epithelial\u2013mesenchymal transition. Nature Reviews Molecular Cell Biology, 21<\/em>(6), 341\u2013352. https:\/\/doi.org\/10.1038\/s41580-020-0237-9<\/a><\/p>\n

60. Tripathi, S., Xing, J.<\/strong>, Levine, H., & Jolly, M. K. (2020). Mathematical modeling of plasticity and heterogeneity in EMT. In K. Campbell & E. Theveneau (Eds.), The epithelial-to-mesenchymal transition: Methods and protocols<\/em> (pp. 385\u2013413). Humana Press. https:\/\/doi.org\/10.1007\/978-1-0716-0779-4_28<\/a><\/p>\n

59. Tian, X.-J., Zhou, D., Fu, H., Zhang, R., Wang, X., Huang, S., Liu, Y., & Xing, J.<\/strong> (2020). Sequential Wnt agonist then antagonist treatment accelerates tissue repair and minimizes fibrosis. iScience, 23<\/em>(5), 101047. https:\/\/doi.org\/10.1016\/j.isci.2020.101047<\/a><\/p>\n

58. Chen, Y.-J., Cheng, Y.-Y., Wang, W., Tian, X.-J., Lefever, D. E., Taft, D. A., Zhang, J., & Xing, J.<\/strong> (2020). Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in. Biology Methods and Protocols, 5<\/em>(1), bpaa006. https:\/\/doi.org\/10.1093\/biomethods\/bpaa006<\/a><\/p>\n

57. Igoshin, O. A., Chen, J., Xing, J.<\/strong>, Liu, J., Elston, T. C., Grabe, M., Kim, K. S., Nirody, J. A., Rangamani, P., Sun, S. X., Wang, H., & Wolgemuth, C. (2019). Biophysics at the coffee shop: lessons learned working with George Oster. Molecular Biology of the Cell, 30<\/em>(16), 1882\u20131889. https:\/\/doi.org\/10.1091\/mbc.e19-02-0107<\/a><\/p>\n

56. Xing, J.<\/strong>, & Tian, X.-J. (2019). Investigating epithelial-to-mesenchymal transition with integrated computational and experimental approaches. Physical Biology, 16<\/em>(3), 031001. https:\/\/doi.org\/10.1088\/1478-3975\/ab0032<\/a><\/p>\n

55. Fujimaki, K., Li, R., Chen, H., Della Croce, K., Zhang, H. H., Xing, J.<\/strong>, Bai, F., & Yao, G. (2019). Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch. Proceedings of the National Academy of Sciences, 116<\/em>(45), 22624\u201322634. https:\/\/doi.org\/10.1073\/pnas.1915905116<\/a><\/p>\n

54. Zhang, J., Chen, H., Li, R., Taft, D. A., Yao, G., Bai, F., & Xing, J.<\/strong> (2019). Spatial clustering and common regulatory elements correlate with coordinated gene expression. PLOS Computational Biology, 15<\/em>(3), e1006786. https:\/\/doi.org\/10.1371\/journal.pcbi.1006786<\/a><\/p>\n

53. Xing, J.<\/strong> (n.d.). CRISPR techniques can accelerate research on the epithelial-to-mesenchymal transition [Expert opinion]. ResearchGate. https:\/\/www.researchgate.net\/publication\/325934143_CRISPR_techniques_can_accelerate_research_on_the_epithelial-to-mesenchymal_transition<\/a><\/p>\n

52. Singh, M., Tian, X.-J., Donnenberg, V. S., Watson, A. M., Zhang, J., Stabile, L. P., Watkins, S. C., Xing, J.<\/strong>, & Sant, S. (2019). Targeting the temporal dynamics of hypoxia-induced tumor-secreted factors halts tumor migration. Cancer Research, 79<\/em>(11), 2962\u20132977. https:\/\/doi.org\/10.1158\/0008-5472.can-18-3151<\/a><\/p>\n

51. Wang, W., Taft, D. A., Chen, Y.-J., Zhang, J., Wallace, C. T., Xu, M., Watkins, S. C., & Xing, J.<\/strong> (2019). Learn to segment single cells with deep distance estimator and deep cell detector. Computers in Biology and Medicine, 108<\/em>, 133\u2013141. https:\/\/doi.org\/10.1016\/j.compbiomed.2019.04.006<\/a><\/p>\n

50. Zhang, J., Tian, X.-J., Chen, Y.-J., Wang, W., Watkins, S., & Xing, J.<\/strong> (2018). Pathway crosstalk enables cells to interpret TGF-\u03b2 duration. npj Systems Biology and Applications, 4<\/em>(1), 18. https:\/\/doi.org\/10.1038\/s41540-018-0060-5<\/a><\/p>\n

49. Zhou, D., Fu, H., Xiao, L., Mo, H., Zhuo, H., Tian, X., Lin, L., Xing, J.<\/strong>, & Liu, Y. (2018). Fibroblast-specific \u03b2-catenin signaling dictates the outcome of AKI. Journal of the American Society of Nephrology, 29<\/em>(4), 1257\u20131271. https:\/\/doi.org\/10.1681\/asn.2017080903<\/a><\/p>\n

48. Kwon, J. S., Everetts, N. J., Wang, X., Wang, W., Della Croce, K., Xing, J.<\/strong>, & Yao, G. (2017). Controlling depth of cellular quiescence by an Rb-E2F network switch. Cell Reports, 20<\/em>(13), 3223\u20133235. https:\/\/doi.org\/10.1016\/j.celrep.2017.09.007<\/a><\/p>\n

47. Tian, X.-J., Zhang, H., Zhang, J., & Xing, J.<\/strong> (2016). Reciprocal regulation between mRNA and microRNA enables a bistable switch that directs cell fate decisions. FEBS Letters, 590<\/em>(19), 3443\u20133455. https:\/\/doi.org\/10.1002\/1873-3468.12379<\/a><\/p>\n

46. Xing, J.<\/strong> (2016). Neurons use physics for receptor selection. Cell Systems, 2<\/em>, 290. https:\/\/www.cell.com\/cell-systems\/fulltext\/S2405-4712%2816%2930152-1<\/a><\/p>\n

45. Tian, X.-J., Zhang, H., Sannerud, J., & Xing, J.<\/strong> (2016). Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design. Proceedings of the National Academy of Sciences, 113<\/em>(21), E2889\u2013E2898. https:\/\/doi.org\/10.1073\/pnas.1601722113<\/a><\/p>\n

44. Zhang, J., Tian, X.-J., & Xing, J.<\/strong> (2016). Signal transduction pathways of EMT induced by TGF-\u03b2, SHH, and WNT and their crosstalks. Journal of Clinical Medicine, 5<\/em>(4), 41. https:\/\/doi.org\/10.3390\/jcm5040041<\/a><\/p>\n

43. Xing, J.<\/strong>, & Lee, R. E. C. (2015). Putting it all on pigmentation: Heuristics of a bold and stochastic cell fate decision. Science Signaling, 8<\/em>(397), fs17. https:\/\/doi.org\/10.1126\/scisignal.aad2816<\/a><\/p>\n

42. Teng, Y., Yue, W., Wang, J., Zhang, H., Du, J., Li, J., Zheng, L., Zhou, J., Tian, X.-J., He, L., Nan, X., Xing, J.<\/strong>, Jiang, Y., He, F., & Pei, X. (n.d.). Integrative microRNA and proteomic approaches from a hESC-based in vitro model of definitive endoderm differentiation reveal novel post-regulation interactions [Manuscript submitted for publication]. Author note: Zhang is a co-first author; Xing is a co-corresponding author.<\/p>\n

41. Zhang, J., Tian, X.-J., Zhang, H., Teng, Y., Li, R., Bai, F., Elankumaran, S., & Xing, J.<\/strong> (2014). TGF-\u03b2\u2013induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops. Science Signaling, 7<\/em>(345), ra91. https:\/\/doi.org\/10.1126\/scisignal.2005304<\/a> Author note: J. Zhang and Tian are co-first authors.<\/p>\n

40. Mondal, D., Dougherty, E., Mukhopadhyay, A., Carbo, A., Yao, G., & Xing, J.<\/strong> (2014). Systematic reverse engineering of network topologies: A case study of resettable bistable cellular responses. PLoS ONE, 9<\/em>(8), e105833. https:\/\/doi.org\/10.1371\/journal.pone.0105833<\/a><\/p>\n

39. Xing, J.<\/strong>, Mather, W., & Hong, C. (2014). Computational cell biology: past, present and future. Interface Focus, 4<\/em>(3), 20140027. https:\/\/doi.org\/10.1098\/rsfs.2014.0027<\/a><\/p>\n

38. Wang, P., Song, C., Zhang, H., Wu, Z., Tian, X.-J., & Xing, J.<\/strong> (2014). Epigenetic state network approach for describing cell phenotypic transitions. Interface Focus, 4<\/em>(3), 20130068. https:\/\/doi.org\/10.1098\/rsfs.2013.0068<\/a><\/p>\n

37. Chen, C., Baumann, W. T., Xing, J.<\/strong>, Xu, L., Clarke, R., & Tyson, J. J. (2014). Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer. Journal of the Royal Society Interface, 11<\/em>(96), 20140206. https:\/\/doi.org\/10.1098\/rsif.2014.0206<\/a><\/p>\n

36. Zhang, H., Tian, X.-J., Mukhopadhyay, A., Kim, K. \u2009S., & Xing, J.<\/strong> (2014). Statistical mechanics model for the dynamics of collective epigenetic histone modification. Physical Review Letters, 112<\/em>(6), 068101. https:\/\/doi.org\/10.1103\/physrevlett.112.068101<\/a><\/p>\n

35. Tian, X.-J., Zhang, H., & Xing, J.<\/strong> (2013). Coupled reversible and irreversible bistable switches underlying TGF\u03b2-induced epithelial to mesenchymal transition. Biophysical Journal, 105<\/em>(4), 1079\u20131089. https:\/\/doi.org\/10.1016\/j.bpj.2013.07.011<\/a><\/p>\n

34. 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., et al. (2013). Tumor-specific chromosome mis-segregation controls cancer plasticity by maintaining tumor heterogeneity. PLoS ONE, 8<\/em>(11), e80898. https:\/\/doi.org\/10.1371\/journal.pone.0080898<\/a> Author note: Xing is a co-corresponding author.<\/p>\n

33. Zhan, Y., Sun, C., Cao, Z., Bao, N., Xing, J.<\/strong>, & Lu, C. (2012). Release of intracellular proteins by electroporation with preserved cell viability. Analytical Chemistry, 84<\/em>(19), 8102\u20138105. https:\/\/doi.org\/10.1021\/ac302462s<\/a><\/p>\n

32. Glaros, T., Fu, Y., Xing, J.<\/strong>, & Li, L. (2012). Molecular mechanism underlying persistent induction of LCN2 by lipopolysaccharide in kidney fibroblasts. PLoS ONE, 7<\/em>(4), e34633. https:\/\/doi.org\/10.1371\/journal.pone.0034633<\/a><\/p>\n

31. Fu, Y., Jiang, X., Zhang, H., & Xing, J.<\/strong> (2012). A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli. BMC Systems Biology, 6<\/em>(Suppl. 3), S6. https:\/\/doi.org\/10.1186\/1752-0509-6-s3-s6<\/a><\/p>\n

30. Hong, T., Xing, J.<\/strong>, Li, L., & Tyson, J. J. (2012). A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. BMC Systems Biology, 6<\/em>, 66. https:\/\/doi.org\/10.1186\/1752-0509-6-66<\/a><\/p>\n

29. Fu, Y., Glaros, T., Zhu, M., Wang, P., Wu, Z., Tyson, J. J., Li, L., & Xing, J.<\/strong> (2012). Network topologies and dynamics leading to endotoxin tolerance and priming in innate immune cells. PLoS Computational Biology, 8<\/em>(5), e1002526. https:\/\/doi.org\/10.1371\/journal.pcbi.1002526<\/a><\/p>\n

28. Bai, F., Minamino, T., Wu, Z., Namba, K., & Xing, J.<\/strong> (2012). Coupling between switching regulation and torque generation in bacterial flagellar motor. Physical Review Letters, 108<\/em>(17), 178105. https:\/\/doi.org\/10.1103\/physrevlett.108.178105<\/a><\/p>\n

27. Wu, Z., & Xing, J.<\/strong> (2012). Functional roles of slow enzyme conformational changes in network dynamics. Biophysical Journal, 103<\/em>(5), 1052\u20131059. https:\/\/doi.org\/10.1016\/j.bpj.2012.08.008<\/a><\/p>\n

26. Bai, F., Wu, Z., Jin, J., Hochendoner, P., & Xing, J.<\/strong> (2012). Slow protein conformational change, allostery and network dynamics. Protein-Protein Interactions – Computational and Experimental Tools. https:\/\/doi.org\/10.5772\/38519<\/a><\/p>\n

25. Wu, Z., Nogales, E., & Xing, J.<\/strong> (2012). Comparative studies of microtubule mechanics with two competing models suggest functional roles of alternative tubulin lateral interactions. Biophysical Journal, 102<\/em>(12), 2687\u20132696. https:\/\/doi.org\/10.1016\/j.bpj.2012.05.003<\/a><\/p>\n

24. Hong, T., Xing, J.<\/strong>, Li, L., & Tyson, J. J. (2011). A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Computational Biology, 7<\/em>(7), e1002122. https:\/\/doi.org\/10.1371\/journal.pcbi.1002122<\/a><\/p>\n

23. Xing, J.<\/strong>, & Kim, K. S. (2011). Application of the projection operator formalism to non-Hamiltonian dynamics. The Journal of Chemical Physics, 134<\/em>(4), 044132. https:\/\/doi.org\/10.1063\/1.3530071<\/a><\/p>\n

22. Fu, Y., Zhu, M., & Xing, J.<\/strong> (2010). Resonant activation: a strategy against bacterial persistence. Physical Biology, 7<\/em>(1), 016013. https:\/\/doi.org\/10.1088\/1478-3975\/7\/1\/016013<\/a><\/p>\n

21. Xing, J.<\/strong>, Mu, W., & Ou-Yang, Z. (2012). Fluctuation-dissipation relations for steady-state systems. EPL (Europhysics Letters), 100<\/em>(2), 20001. https:\/\/doi.org\/10.1209\/0295-5075\/100\/20001<\/a><\/p>\n

20. Xing, J.<\/strong> (2010). Mapping between dissipative and Hamiltonian systems. Journal of Physics A: Mathematical and Theoretical, 43<\/em>(37), 375003. https:\/\/doi.org\/10.1088\/1751-8113\/43\/37\/375003<\/a><\/p>\n

19. Wu, Z., Wang, H.-W., Mu, W., Ouyang, Z., Nogales, E., & Xing, J.<\/strong> (2009). Simulations of tubulin sheet polymers as possible structural intermediates in microtubule assembly. PLoS ONE, 4<\/em>(10), e7291. https:\/\/doi.org\/10.1371\/journal.pone.0007291<\/a><\/p>\n

18. Xing, J.<\/strong> (2009). Mori\u2013Zwanzig projection formalism: From linear to nonlinear [Preprint]. arXiv<\/em>. https:\/\/arxiv.org\/abs\/0904.2691<\/a><\/p>\n

17. Qian, H., Shi, P.-Z., & Xing, J.<\/strong> (2009). Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity. Physical Chemistry Chemical Physics, 11<\/em>(24), 4861. https:\/\/doi.org\/10.1039\/b900335p<\/a><\/p>\n

16. Wu, Z., Elgart, V., Qian, H., & Xing, J.<\/strong> (2009). Amplification and detection of single-molecule conformational fluctuation through a protein interaction network with bimodal distributions. The Journal of Physical Chemistry B, 113<\/em>(36), 12375\u201312381. https:\/\/doi.org\/10.1021\/jp903548d<\/a><\/p>\n

15. Bai, F., Lo, C.-J., Berry, R. M., & Xing, J.<\/strong> (2009). Model studies of the dynamics of bacterial flagellar motors. Biophysical Journal, 96<\/em>(8), 3154\u20133167. https:\/\/doi.org\/10.1016\/j.bpj.2009.01.023<\/a><\/p>\n

14. Xing, J.<\/strong>, & Chen, J. (2008). The Goldbeter-Koshland Switch in the First-Order Region and Its Response to Dynamic Disorder. PLoS ONE, 3<\/em>(5), e2140. https:\/\/doi.org\/10.1371\/journal.pone.0002140<\/a><\/p>\n

13. Xing, J.<\/strong> (2007). Nonequilibrium dynamic mechanism for allosteric effect. Physical Review Letters, 99<\/em>(16), 168103. https:\/\/doi.org\/10.1103\/physrevlett.99.168103<\/a><\/p>\n

12. Xing, J.<\/strong>, & Kim, K. S. (2006). Protein fluctuations and breakdown of time-scale separation in rate theories. Physical Review E, 74<\/em>(6), 061911. https:\/\/doi.org\/10.1103\/physreve.74.061911<\/a><\/p>\n

11. Xing, J.<\/strong>, Bai, F., Berry, R., & Oster, G. (2006). Torque\u2013speed relationship of the bacterial flagellar motor. Proceedings of the National Academy of Sciences, 103<\/em>(5), 1260\u20131265. https:\/\/doi.org\/10.1073\/pnas.0507959103<\/a><\/p>\n

10. Xing, J.<\/strong>, Liao, J.-C., & Oster, G. (2005). Making ATP. Proceedings of the National Academy of Sciences, 102<\/em>(46), 16539\u201316546. https:\/\/doi.org\/10.1073\/pnas.0507207102<\/a><\/p>\n

9. Xing, J.<\/strong>, Wang, H., & Oster, G. (2005). From continuum Fokker\u2013Planck models to discrete kinetic models. Biophysical Journal, 89<\/em>(3), 1551\u20131563. https:\/\/doi.org\/10.1529\/biophysj.104.055178<\/a><\/p>\n

8. Xing, J.<\/strong>, Wang, H., von Ballmoos, C., Dimroth, P., & Oster, G. (2004). Torque generation by the Fo motor of the sodium ATPase. Biophysical Journal, 87<\/em>(4), 2148\u20132163. https:\/\/doi.org\/10.1529\/biophysj.104.042093<\/a><\/p>\n

7. Xing, J.<\/strong>, Coronado, E. A., & Miller, W. H. (2001). Some new classical and semiclassical models for describing tunneling processes with real-valued classical trajectories. The Journal of Physical Chemistry B, 105<\/em>(28), 6574\u20136578. https:\/\/doi.org\/10.1021\/jp0046086<\/a><\/p>\n

6. Xing, J.<\/strong> (2001). Statistical thermodynamics of lattice models. The Journal of Chemical Physics, 115<\/em>(17), 8038\u20138043. https:\/\/doi.org\/10.1063\/1.1410115<\/a><\/p>\n

5. Coronado, E. A., Xing, J.<\/strong>, & Miller, W. H. (2001). Ultrafast non-adiabatic dynamics of systems with multiple surface crossings: a test of the Meyer\u2013Miller Hamiltonian with semiclassical initial value representation methods. Chemical Physics Letters, 349<\/em>(5-6), 521\u2013529. https:\/\/doi.org\/10.1016\/s0009-2614(01)01242-8<\/a><\/p>\n

4. Chen, B., Xing, J.<\/strong>, & Siepmann, J. I. (2000). Development of polarizable water force fields for phase equilibrium calculations. The Journal of Physical Chemistry B, 104<\/em>(10), 2391\u20132401. https:\/\/doi.org\/10.1021\/jp993687m<\/a><\/p>\n

3. Kim, Y., Corchado, J. C., Vill\u00e0, J., Xing, J.<\/strong>, & Truhlar, D. G. (2000). Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions. The Journal of Chemical Physics, 112<\/em>(6), 2718\u20132735. https:\/\/doi.org\/10.1063\/1.480846<\/a><\/p>\n

2. Li, J., Xing, J.<\/strong>, Cramer, C. J., & Truhlar, D. G. (1999). Accurate dipole moments from Hartree\u2013Fock calculations by means of class IV charges. The Journal of Chemical Physics, 111<\/em>(3), 885\u2013892. https:\/\/doi.org\/10.1063\/1.479199<\/a><\/p>\n

1. Zhao, X., Xing, J.<\/strong>, Li, P., Xie, X., Xia, X., Li, H., Huang, C., Li, T., & Xu, L. (1995). Effects of adsorption and reaction on the second harmonic generation of Langmuir\u2013Blodgett films. Langmuir, 11<\/em>(10), 3620\u20133622. https:\/\/doi.org\/10.1021\/la00010a004<\/a><\/p>\n\n\n

<\/p>\n\n\n\n

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<\/p>\n","protected":false},"excerpt":{"rendered":"

82. Ma, A., Nussinov, R., Chen, J., Xing, J., Xiao, J., Xu, D., Lin, M., Delafrouz, P., Royston, T., Tang, K., Ye, B., & Zhang, J. (2026). Jie Liang (1964\u20132024): Introduction to modeling biology at multiple scales: From macromolecules to cells, dedicated to Jie Liang. Biophysical Journal, 125(18), E1\u2013E6. https:\/\/doi.org\/10.1016\/j.bpj.2026.08.015 Author note: Ma and Xing […]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"templates\/template-onecolumn.php","meta":{"footnotes":""},"class_list":["post-45","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=\/wp\/v2\/pages\/45","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=45"}],"version-history":[{"count":116,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=\/wp\/v2\/pages\/45\/revisions"}],"predecessor-version":[{"id":844,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=\/wp\/v2\/pages\/45\/revisions\/844"}],"wp:attachment":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/xing\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=45"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}