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Chen Jia
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Publications

      Submitted papers

    1. Bingjie Wu, Chen Jia*. Parameter inference and nonequilibrium identification for Markovian systems based on coarse-grained observations. [arxiv].
    2. Shan Liu, Bingjie Wu, Chen Jia*. Exact switching time distributions for autoregulated gene expression models with mRNA and protein descriptions. [bioRxiv].
    3. 吴秉杰, 贾晨*. 马氏过程的环流理论及其应用 [arxiv].
    4. 贾晨*. 单细胞随机基因表达动力学的数学模型与解析理论 [arxiv].

      5. Published papers

      2024

    5. Chen Jia, Ramon Grima*. Holimap: an accurate and efficient method for solving stochastic gene network dynamics. Nature Communications 15(1):6557, 2024.
    6. Feng Jiao, Jing Li, Ting Liu, Yifeng Zhu, Wenhao Che, Leonidas Bleris, Chen Jia*. What can we learn when fitting a simple telegraph model to a complex gene expression model? PLOS Computational Biology 20(5):e1012118, 2024.
    7. Chen Jia*, Hong Qian, Michael Q. Zhang. Exact power spectrum in a minimal hybrid model of stochastic gene expression oscillations. SIAM Journal on Applied Mathematics 84(3):1204-1226, 2024.
    8. Ying Sheng, Genghong Lin*, Feng Jiao*, Chen Jia*. Geometric theory of distribution shapes for autoregulatory gene circuits. To appear in SIAM Journal on Applied Mathematics 2024.
    9. Bingjie Wu, James Holehouse, Ramon Grima*, Chen Jia*. Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition. The Journal of Chemical Physics 160(7):074105, 2024.

      10. In this work, we give the complete spectral characterization for a non-symmetric Markovian model of stochastic gene regulation. The eigenfunctions are Heun functions with four singularities and the eigenvalues satisfy a nontrivial continued fraction equation.

    10. Chen Jia*, Da-Quan Jiang*, Bingjie Wu*. Large deviations for the empirical measure and empirical flow of Markov renewal processes with a countable state space. Electronic Journal of Probability 29(46):1-49, 2024.
    11. Xian Chen, Yong Chen, Yumin Cheng, Chen Jia*. Moderate and Lp maximal inequalities for diffusion processes and conformal martingales. Journal of Theoretical Probability 37(4):2990-3014, 2024.

      12. 2023

    12. Chen Jia, Ramon Grima*. Coupling gene expression dynamics to cell size dynamics and cell cycle events: exact and approximate solutions of the extended telegraph model. iScience 26(1):105746, 2023.
    13. Chen Jia*, Youming Li. Analytical time-dependent distributions for gene expression models with complex promoter switching mechanisms. SIAM Journal on Applied Mathematics 83(4):1341-1653, 2023.
    14. Xinyu Wang, Youming Li, Chen Jia*. Poisson representation: a bridge between discrete and continuous models of stochastic gene regulatory networks. Journal of the Royal Society Interface 20(208):20230467, 2023.
    15. Yuhao Jiang, Bingjie Wu, Chen Jia*. Large deviations and fluctuation theorems for cycle currents defined in the loop-erased and spanning tree manners: a comparative study. Physical Review Research 5(1):013207, 2023.

      16. 2022

    16. Chen Jia, Abhyudai Singh, Ramon Grima*. Concentration fluctuations in growing and dividing cells: insights into the emergence of concentration homeostasis. PLOS Computational Biology 18(10):e1010574, 2022.
    17. Chen Jia, Abhyudai Singh, Ramon Grima*. Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: an analytical approach. PLOS Computational Biology 18(1):e1009793, 2022.
    18. Chen Jia, Ziqi Liu, Zhimin Zhang*. Some mathematical aspects of Anderson localization: boundary effect, multimodality, and bifurcation. Communications in Theoretical Physics 74(11):115005, 2022.

      19. 2021

    19. Chen Jia, Ramon Grima*. Frequency domain analysis of fluctuations of mRNA and protein copy numbers within a cell lineage: theory and experimental validation. Physical Review X 11(2):021032, 2021.

      20. In this work, we provide the first frequency domain analysis of gene expression fluctuations in growing and dividing cells. We make a number of theoretical predictions, some of which are in excellent agreement with experiments.

    20. Chen Jia, Abhyudai Singh, Ramon Grima*. Cell size distribution of lineage data: analytic results and parameter inference. iScience 24(3):102220, 2021.
    21. Hao Ge*, Chen Jia*, Xiao Jin. Martingale structure for general thermodynamic functionals of diffusion processes under second-order averaging. Journal of Statistical Physics 184(2):17, 2021.
    22. Youming Li, Da-Quan Jiang*, Chen Jia*. Steady-state joint distribution for first-order stochastic reaction kinetics. Physical Review E 104(2):024408, 2021.
    23. Chen Jia, Zhimin Zhang*, Lewei Zhao*. Two-parameter localization and related phase transition for a Schrodinger operator in balls and spherical shells. Journal of Mathematical Physics 62(9):091505, 2021.
    24. Chen Jia, Da-Quan Jiang*, Youming Li. Detailed balance, local detailed balance, and global potential for stochastic chemical reaction networks. Advances in Applied Probability, 53(3):886-922, 2021.

      25. 2020

    25. Chen Jia*. Kinetic foundation of zero-inflated negative binomial models for single-cell RNA sequencing data. SIAM Journal on Applied Mathematics 80(3):1336-1355, 2020.
    26. Chen Jia, Ramon Grima*. Small protein number effects in autoregulated bursty gene expression. The Journal of Chemical Physics 152(8):084115, 2020.
    27. Chen Jia, Ramon Grima*. Dynamic phase diagram of an auto-regulated gene in fast switching conditions. The Journal of Chemical Physics 152(17):174110, 2020.
    28. Xian Chen, Chen Jia*. Mathematical foundation of nonequilibrium fluctuation-dissipation theorems for inhomogeneous diffusion processes with unbounded coefficients. Stochastic Processes and Their Applications 130(1):171-202, 2020.
    29. Xian Chen, Chen Jia*. Limit theorems for generalized density-dependent Markov chains and bursty gene regulatory networks. Journal of Mathematical Biology 80(4):959-994, 2020.
    30. Chen Jia*, Guohuan Zhao*. Moderate maximal inequalities for the Ornstein-Uhlenbeck process. Proceedings of the American Mathematical Society 148(8):3607-3615, 2020.

      31. 2019

    31. Chen Jia*, Le Y. Wang, George G. Yin, Michael Q. Zhang. Single-cell stochastic gene expression kinetics with positive-plus-negative feedback. Physical Review E 100(5):052406, 2019.

      32. This work was selected by the editors of Physical Review E as part of a PRE Spotlight on Noise in Genetic Networks. Only four papers from 2005-2021 were selected.

    32. Chen Jia*. Sharp moderate maximal inequalities for upward skip-free Markov chains. Journal of Theoretical Probability 32(3):1382-1398, 2019.

      33. 2018

    33. Chen Jia, Hong Qian, Min Chen*, Michael Q. Zhang*. Relaxation rates of gene expression kinetics reveal the feedback signs of autoregulatory gene networks. The Journal of Chemical Physics 148(9):095102, 2018.

      34. 2017

    34. Chen Jia*, Michael Q. Zhang*, Hong Qian*. Emergent Lévy behavior in single-cell gene expression. Physical Review E 96(4):040402(R), 2017.
    35. Hao Ge, Chen Jia*, Daquan Jiang*. Cycle symmetry, limit theorems, and fluctuation theorems for diffusion processes on the circle. Stochastic Processes and Their Applications 127(6):1897-1925, 2017.
    36. Chen Jia, Peng Xie, Min Chen*, Michael Q. Zhang*. Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level. Scientific Reports 7(1):16037, 2017.
    37. Chen Jia*. Simplification of Markov chains with infinite state space and the mathematical theory of random gene expression bursts. Physical Review E 96(3):032402, 2017.
    38. Chen Jia*. Nonequilibrium nature of adaptation in bacterial chemotaxis: A fluctuation-dissipation theorem approach. Physical Review E 95(4):042116, 2017.
    39. Xian Chen, Chen Jia*. Identification of unstable fixed points for randomly perturbed dynamical systems with multistability. Journal of Mathematical Analysis and Applications 446(1):521-545, 2017.
    40. Yong Chen, Chen Jia*, Daquan Jiang*. Fluctuation-dissipation theorems for inhomogeneous Markov jump processes and a biochemical application. Journal of Mathematical Physics 58(2):023302, 2017.

      41. 2016

    41. Chen Jia*, Daquan Jiang*, Minping Qian. Cycle symmetries and circulation fluctuations for discrete-time and continuous-time Markov chains. The Annals of Applied Probability 26(4):2454-2493, 2016.
    42. Chen Jia*. A solution to the reversible embedding problem for finite Markov chains. Statistics & Probability Letters 116:122-130, 2016.

      43. In this work, we have solved the embedding problem for finite Markov chains, which is a long-lasting open problem in probability theory, in the reversible special case.

    43. Chen Jia*. Model simplification and loss of irreversibility. Physical Review E 93(5): 052149, 2016.
    44. Chen Jia*, Minping Qian. Nonequilibrium enhances adaptation efficiency in stochastic biochemical systems. PLOS ONE 11(5): e0155838, 2016.
    45. Chen Jia*. Reduction of Markov chains with two-time-scale state transitions. Stochastics: An International Journal of Probability and Stochastic Processes 88(1):73-105, 2016.
    46. Chen Jia*. Simplification of irreversible Markov chains by removal of states with fast leaving rates. Journal of Theoretical Biology 400:129-137, 2016.
    47. Liu Hong, Chen Jia, Yi Zhu, Wen-An Yong*. Novel dissipation properties for the master equation. Journal of Mathematical Physics 57(10):103303, 2016.

      48. 2015

    48. Chen Jia, Yong Chen*. A second perspective on the Amann-Schmiedl-Seifert criterion for non-equilibrium in a three-state system. Journal of Physics A: Mathematical and Theoretical 48(20):205001, 2015.

      49. 2014

    49. Chen Jia, Minping Qian, Yu Kang, Da-Quan Jiang*. Modeling stochastic phenotype switching and bet-hedging in bacteria: stochastic nonlinear dynamics and critical state identification. Quantitative Biology 2(3):110-125, 2014.
    50. Chen Jia, Da-Quan Jiang*, Minping Qian. An allosteric model of the inositol trisphosphate receptor with nonequilibrium binding. Physical Biology 11(5):056001, 2014.
    51. Chen Jia, Minping Qian, Da-Quan Jiang*. Overshoot in biological systems modelled by Markov chains: a non-equilibrium dynamic phenomenon. IET Systems Biology 8(4):138-145, 2014.

      52. 2012

    52. Chen Jia, Xufeng Liu, Minping Qian, Da-Quan Jiang*, Yuping Zhang. Kinetic behavior of the general modifier mechanism of Botts and Morales with non-equilibrium binding. Journal of Theoretical Biology 296:13-20, 2012.

      53. 2009

    53. Chen Jia*, Zhongjie Xie*. The acting factor analysis and the prediction based on the principal component analysis of the residual of Chinese welfare lottery sales. Journal of Applied Statistics and Management 28(2):191-203, 2009.
    54. Chen Jia*, Yihan Li, Minping Qian. A general analysis of single IP3 receptors modulated by cytosolic Ca2+ and IP3 The Third International Symposium on Optimization and Systems Biology 89-101, 2009.