Publications – Xing Lab

2013-Present

78. Das, B., Xing, J., Sharma, A. K., Ge, H., The asymmetric torque-speed relationships reveal that the hook behaves as a clutch in bacterial transmission system, to be submitted (Xing and Ge are co-corresponding authors).

77. Wang, H., Ardila, C., Jindal, A., Aggarwal, V., Wang, W., Geest, J. V., Jiang, Y., Xing, J., Sant, S., Protrusion force and cell-cell adhesion play a critical role in collective tumor cluster migration, BioRxiv, 2024 (Xing and Sant co-corresponding authors)

76., Ni, K., Yu, G., Zheng, Z., Lu, Y., Poe, D., Zhou, S., Wang, W., Xing, J., LivecellX: A Deep-learning-based, Single-Cell Object-Oriented Framework for Quantitative Analysis in Live-Cell Imaging, BioRxiv, 2025

75. Hu, S., Lu, Y., Yu, G., Zheng, Z., Wang, W., Ni, K., Giri, A., Zhang, J., Zhang, Y., Watanabe, K., Yao, G., Xing, J., Epithelial-mesenchymal transition couples with cell cycle arrest at various stages, BioRxiv, 2025

74. Zhang, J., Wang, S., Watkins, S. C., Xing, J., Long-range genomic loci stochastically assemble into combinatorial forms of chromosome skeleton, BioRxiv, 2025

73. Chen, Y., Zhang, Y., Gan, J., Ni, K, Chen, Y., Bahar, I, Xing, J., GraphVelo allows inference of multi-modal single cell velocities and molecular mechanisms, BioRxiv, 2024

72. Zachary R. Hettinger, Sophia Hu, Hikaru Mamiya, Amrita Sahu, Hirotaka Iijima, Kai Wang, Gabrielle Gilmer, Amanda Miller, Gabriele Nasello, Antonio D’Amore, David Vorp, Thomas A. Rando, Jianhua Xing, Fabrisia Ambrosio, Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate, BioRxiv, 2023.02.24.529950 (Hettinger and Hu are co-first authors, Rando, Xing, and Ambrosio are co-corresponding authors).

71. Zhang, Y., Qiu, X., Ni, K., Weissman, J., Bahar, I., Xing, J., Graph-Dynamo: Learning stochastic cellular state transition dynamics from single cell data, BioRxiv, 2023.09.24.559170.

70. Hong, T., Xing, J., Data- and theory-driven approaches for understanding paths of epithelial–mesenchymal transition, Genesis, 62:e23591 (2024).

69. Wang, W., Ni, K., Poe, D. & Xing, J. Transiently Increased Coordination in Gene Regulation During Cell Phenotypic Transitions, PRX Life, 2:043009 (2024).

68. Cang, H., Liu, Y., Xing, J., Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging, Bioinformatics, btad784 (2024).

67. Xing, J. Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology. Physical Biology, 19:061001 (2022).

66. Wang, W., Poe, D., Yang, Y., Hyatt, T. & Xing, J. Epithelial-to-mesenchymal transition proceeds through directional destabilization of multidimensional attractor. eLife, e74866 (2022).

65. Qiu, X., Zhang, Y., Martin-Rufino, J. D., Weng, C., Hosseinzadeh, S., Yang, D., Wang, L., Yuan, R., Xu, S., Ma, Y., Replogle, J., Lander, E., Darmanis, S., Bahar., I., Sankaran, V., Xing, J. H., Weissman, J. S., Mapping transcriptomic vector field of single cells, Cell, 185:690 (2022) (Qiu and Zhang as co-first authors, Qiu, Xing and Weissman as co-corresponding authors).

64. Yan Zhang, James Krieger, Karolina Mikulska-Ruminska, Burak Kaynak, Carlos Oscar S. Sorzano, José-María Carazo, Jianhua Xing^,Ivet Bahar, State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps, Progress in Biophysics and Molecular Biology, 160:104-120 (2021).

63. Jianhua Xing, Bidirectional interplay between physical and biological approaches on studying the epithelial-to-mesenchymal transition, Physical Biology, 17:020201 (2020).

62. Weikang Wang, Diana L. Douglas, Jingyu Zhang, Sangeeta Kumari, Metewo Selase Enuameh, Yan Dai, Callen T. Wallace, Simon C. Watkins, Weiguo Shu, Jianhua Xing, Live cell imaging and analysis reveal cell phenotypic transition dynamics inherently missing in snapshot data, Science Advances, 6 (36): eaba9319 (2020).

61. Jing Yang et al., Guidelines and Definitions for Research on Epithelial-Mesenchymal Transition, Nat Rev Mol Cell Biol, 21, 341-352 (2020).

60. Shubham Tripathi, Jianhua Xing, Herbert Levine and Mohit Kumar Jolly, Mathematical Modeling of Plasticity and Heterogeneity in EMT, (arXiv copy), Book chapter in the Epithelial-to Mesenchymal Transition: Methods and Protocols (Editors: Kyra Campbell, PhD and Eric Theveneau, PhD), Springer (2020).

59. X. -J. Tian, D. Zhou, H. Fu, R. Zhang, X. Wang, S. Huang, Y. Liu, and J. H. Xing, Sequential Wnt Agonist then Antagonist Treatment Accelerates Tissue Repair and Minimizes Fibrosis, iScience, 23(5): 101047 (2020).

58 Y. J. Chen, W. Wang, X.-J. Tian, D. E. Lefever, D. A. Taft, and J. H. Xing, Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in, Biology Methods & Protocols, accepted.

57. Oleg Igoshin, Jing Chen, Jianhua Xing, Jian Liu, et al., Biophysics at the coffee shop: lessions learned working with George Oster, Mol Biol Cell, 30 (16): 1882-1889(2019).

56. Jianhua Xing, Xiao-Jun Tian, Investigating Epithelial-to-Mesenchymal Transitin with Integrated Computational and Experimental Approaches, Physical Biology, 16:031001 (2019).

55. Kotaro Fujimaki, Ruoyan Li, Hengyu Chen, Kimiko Della Croce, Hao Helen Zhang, Jianhua Xing, Fan Bai, Guang Yao, A lysosomal dimmer switch regulates cellular quiescence depth, PNAS, 116 (45) 22624-22634 (2019).

54. Jingyu Zhang, Hengyu Chen, Ruoyan Li, Guang Yao, Fan Bai, and Jianhua Xing, Spatial clustering and common regulatory elements correlated with TGF-beta induced concerted gene expression, PLoS Comp Biol, 15(3): e1006786 (2019).

53. Jianhua Xing, CRISPR techniques can accelerate research on the epithelial-to-mesenchymal transition, Researchgate expert’s opinion.

52. M. Singh, X.-J. Tian, V. S. Donnenberg, A. Watson, J. Zhang, L. Stabile, S. C. Watkins, J. H. Xing, and S. Sant, Targeting the temporal dynamics of hypoxia-induced tumor-secreted factors halts tumor migration, Cancer Research, 79:2962-2977 (2019).

51 W. Wang, D. A. Taft, Y.-J. Chen, J. Zhang, C. Wallace, M. Xu, S. C. Watkins, J. H. Xing, Learn to segment single cells with deep distance estimator and deep cell detector. Computers in Biology and Medicine, 108: 133-141 (2019).

50 J. Zhang, X.-J. Tian, Y.-J. Chen, W. Wang, S. C. Watkins, and J. H. Xing, Pathway crosstalk enables cells to interpret TGF-beta duration, NPJ Sys Biol App, 4: 18 (2018).

49 Zhou, H. Fu, L. Xiao, H. Mo, H Zhuo, X.-J. Tian, J. H. Xing, Y. Liu, Fibroblast-specific β-catenin signaling dictates the outcome of AKI, J. Am. Soc. Nephrol., 29 (4): 1257-1271 (2018)

48 S. Kwon, N. J. Everetts, X. Wang, W. Wang, K. D. Croce, J. H. Xing, and G. Yao, Controlling depth of cellular quiescence by an Rb-E2F network switch, Cell Reports, 20:3223-3235 (2017).

47. Xiao-Jun Tian, Hang Zhang, Jingyu Zhang and Jianhua Xing , mRNA-miRNA reciprocal regulation enabled bistable switch directs cell fate decision, FEBS Letters, 590, 3443-3455 (2016).

46. Jianhua Xing, Neurons use physics for receptor selection, Cell Systems, 2:290 (2016).

45. Xiao-Jun Tian, Hang Zhang, Jens Sannerud and Jianhua Xing , Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design, PNAS, 113:2889 (2016). list of news coverage.

44. Jingyu Zhang, Xiao-Jun Tian and Jianhua Xing, Signal transduction pathways of EMT induced by TGF-beta, SHH, and WNT and their crosstalks, J. Clinic Med., 5:41 (2016).

43. Jianhua Xing and Robin Lee, Putting it all on pigmentation: Heuristics of a bold and stochastic cell fate decision, Science Signaling, 8:fs17 (2015).

42. Yue Teng, Wen Yue, Jingxue Wang, Hang Zhang, Jichao Du, Jingli Li, Liangtao Zheng, Jun Zhou, Xiao-Jun Tian, Lijuan He, Xue Nan, Jianhua Xing, Ying Jiang, Fuchu He, Xuetao Pei, Integrative MicroRNA and Proteomic Approaches from a hESCs-based in vitro model of Definitive Endoderm Differentiation Reveal Novel Post-regulation Interactions, submitted. Hang Zhang is co-first author, Xing is co-corresponding author.

41. Jingyu Zhang*, Xiao-Jun Tian*, Hang Zhang, Elankumaran Subbiah, Jianhua Xing, TGF-β-induced epithelial-to-mesenchymal transition proceeds through step-wise activation of multiple feedback loops, Science Signaling, 7: ra91 (2014). * co-first author.

40. D. Mondal, A. Mukhopadhyay, E. Dougherty, A. Carbo, G. Yao, and J. H. Xing, Systematic Reverse Engineering of Network Topologies: A Case Study of Resettable Bistable Cellular Responses, Plos One, 9(8):e105833 (2014).

39. J. H. Xing, W. Mather, C. Hong, Computational cell biology: past, present and future, Interface Focus 4(3):20140027 (2014).

38. P. Wang, C. Song, H. Zhang, Z. Wu, X-J Tian, J. H. Xing, Epigenetic State Network Approach For Describing Cell Phenotypic Transitions, J. Roy. Soc. Interface Focus 4(3):20130068 (2014).

37. Chun Chen, William T Baumann, Jianhua XIng, Lingling Xu, Robert Clarke, John Tyson, Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer, J. Roy. Soc. Interface 11:20140206 (2014).

36. H. Zhang, X-J Tian, K. Kim, J. H. Xing, Statistical mechanics model for the dynamics of collective epigenetic histone modification, Phys. Rev. Lett., 112: 068101 (2014).

35. X-J Tian, H. Zhang, J. H. Xing, Coupled Reversible and Irreversible Bistable Switches Underlying TGF-beta-induced Epithelial to Mesenchymal Transition, Biophys, J., 105:1079 (2013).

34. Yuanjie Hu, Ning Ru, Huasheng Xiao, Abhishek Chaturbedi, Neil T. Hoa, Xiao-Jun Tian, Hang Zhang, Chao Ke, Fengrong Yan, Jodi Nelson, Zhenzhi Li, Robert Gramer, Liping Yu, Eric Siegel, Xiaona Zhang, Zhenyu Jia, Martin R. Jadus, Charles L. Limoli, Mark E. Linskey, Jianhua Xing, Y-H Zhou, Tumor-Specific Chromosome Mis-Segregation Controls Cancer Plasticity by Maintaining Tumor Heterogeneity, Plos One, 8(11):e80898 (2013). Xing is co-corresponding author.

2007-2012

33. Y. Zhan, C. Chen, Z. Cao, N. Bao, J. H. Xing, C. Lu, Release of intracellular proteins by electroporation with preserved cell viability, Analytical chemistry, 84:8102-8105 (2012).

32. T Glaros, Y Fu, J Xing, and L Li. Molecular mechanism underlying persistent induction of LCN2 by lipopolysaccharide in kidney fibroblasts. Plos One 7(4):e34633 (2012)

31. Y. Fu, X. Jiang, H. Zhang, J. H. Xing, A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli, BMC Sys Biol 6:S6 (2012)

30. T. Hong, J. H. Xing, L. Li, J. J. Tyson, A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells, BMC Sys Biol, 6:66 (2012).

29. Y. Fu, T. Glaros, M. Zhu, P. Wang, Z. Wu, J. J. Tyson, L. Li, J. H. Xing, Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells, PLOS Comp Biol 8(5): e1002526 (2012).

28. F. Bai, T. Minamino, Z. Wu, K. Namba, J. H. Xing, Coupling between switching regulation and torque generation in bacterial flagellar motor, Phys. Rev. Lett. 108:178105 (2012).

27. Z. Wu, J. Xing, Functional Roles of Slow Enzyme Conformational Changes in Network Dynamics, Biophys. J. 103:1052-1059 (2012).

26. F. Bai, Z. Wu, J. Jin, P. Hochendoner, and J. H. Xing, Slow protein conformational change, allostery, and network dynamics, in Protein Interactions (II), Intech Open Access Publisher.

25. Z. Wu, E. Nogales, and J. H. Xing, Comparative Studies of Microtubule Mechanics with Two Competing Models Suggest Functional Roles of Alternative Tubulin Lateral Interactions, Biophys J. 102:2687-2696 (2012).

24. T Hong, JH Xing, L Li, and J Tyson, A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells, PlosCompBiol, 7:e1002122 (2011).

23. J.H. Xing and K. Kim, “Application of the projection operator formalism to non-Hamiltonian dynamics” J. Chem. Phys. 134, 044132 (2011); Statistical Mechanics arXiv:0908.4340v3; also in Virtual Journal of Biological Physics Search, Vol 21, Issue 3 (2011)

22. Y. Fu, M. Zhu, J.H.Xing, “Resonant activation: a strategy against bacterial persistence” Phys. Biol. 7, 016013 (2010) ( IOPselect article and Phys. Biol. 2010 featured article), Selected News Coverage.

21. J.H. Xing, W. Mu, Z.C. Ouyang, “Fluctuation-dissipation relations for steady-state systems” , Eur. Phys. Lett. 100:20001 (2012), (2010)

20. J.H. Xing,“Mapping between dissipative and Hamiltonian systems”J. Phys. A: Math. Theor. 43, 37500 (2010);Statistical Mechanics rXiv:0908.4526

19. Z. Wu, H.W. Wang, W.H. Mu, Z.C. Ouyang, Eva Nogales, J.H. Xing, “Simulations of Tubulin Sheet Polymers as Possible Structural Intermediates in Microtubule Assembly” PLoS ONE (2009)

18. J.H. Xing, “Mori-Zwanzig projection formalism: from linear to nonlinear” Statistical Mechanics arXiv:0904.2691 (2009)

17. H. Qian, P. Shi, J.H. Xing, “Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity” Phys. Chem. Chem. Phys., 11, 4861-4870 (2009) [PDF]

16. Z. Wu, V. Elgart, H. Qian, J.H. Xing, “Amplification and Detection of Single-Molecule Conformational Fluctuation through a Protein Interaction Network with Bimodal Distributions” J. Phys. Chem. B, 113, 36 (2009) [PDF]

15. F. Bai, CJ Lo, R. Berry, J.H. Xing, “Model studies of the Dynamics of Bacterial Flagellar Motors” Biophys. J. 96, 3154-3167 (2009) [PDF]

14. J.H. Xing, J. Chen, “The Goldbeter-Koshland Switch in the First-Order Region and Its Response to Dynamic Disorder” PLoS ONE, 3(5), e2140 (2008)

13. J.H. Xing, “Nonequilibrium mechanism for allosteric effect” Phys. Rev. Lett. 99, 168103 (2007) [PDF]

Before 2007

12. J.H. Xing, K. Kim, “Protein fluctuations and breakdown of time-scale separation in rate theories” Phys. Rev. E,74,061911 (2006)

11. J.H. Xing, F. Bai, R. Berry, G.Oster, “The torque-speed relationship of the bacterial flagellar motor” PNAS, 103, 1260-1265 (2006)

10. J.H. Xing, JC Liao, G.Oster, “Making ATP” PNAS 102, 16539-16546 (2005)

9. J.H. Xing, H. Wang, G. Oster, “From continuum Fokker-Planck models to discrete kinetic models” Biophysical Journal 89, 1551-1563 (2005)

8. J.H. Xing, H. Wang, C. von Ballmoos, P. Dimroth, G. Oster, “Torque generation by the Fo motor of the sodium ATPase” Biophysical Journal 87, 2148-2163 (2004)

7. J.H. Xing, E.A. Coronado, William H. Miller, “Some new classical and semiclassical models for describing tunneling processes with real-valued classical trajectories” Journal of Physical Chemistry B 105, 28, 6574-6578 (2001)

6. J.H. Xing, “Statistical thermodynamics of lattice models”Journal of Chemical Physics 115, 17, 8038 (2001)

5. E.A. Coronado, J.H. Xing, William H. Miller, “Ultrafast non-adiabatic dynamics of systems with multiple surface crossings: a test of the Meyer-Miller Hamiltonian with semiclassical initial value representation methods”Chemical Physics Letters 349 (5-6) 521 (2001)

4. B. Chen, J.H. Xing, JI Siepmann, “Development of Polarizable Water Force Fields for Phase Equilibrium Calculations” J. Phys. Chem. B 104, 10, 2391-2401 (2000)

3. Y. Kim, J.C. Corchado, J. Villa, J.H. Xing, Donald G. Truhlar, “Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions” Journal of Chemical Physics 112, 6, 2718 (2000)

2. J.B. Li, J.H. Xing, C.J. Cramer, Donald G. Truhlar,“Accurate dipole moments from Hartree-Fock calculations by means of class IV charges” Journal of Chemical Physics 111, 3, 885 (1999)

1. X.S. Zhao, J.H. Xing, et. al., “Effects of adsorption and reaction on the 2nd-harmonic generation of Langmuir-Blodgett Films”, Langmuir 11, 10, 3620 (1995)