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Chen Jia
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Publications

      Submitted papers

    1. Youming Li, Chen Jia*. Effective Markovian dynamics method for solving non-Markovian dynamics of stochastic gene expression. [Biorxiv].
    2. Chen Jia*. Single-cell stochastic gene expression dynamics: mathematical models and analytical theory (in Chinese). [Biorxiv].
    3. Shan Liu, Bingjie Wu, Chen Jia*. Exact switching time distributions for autoregulated gene expression models with mRNA and protein descriptions. [Biorxiv].

      4. Published papers

      2025

    4. Bingjie Wu, Chen Jia*. Parameter inference and nonequilibrium identification for Markov networks based on coarse-grained observations. Physical Review Letters 134(8):087103, 2025.
    5. 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 2025.
    6. Bingjie Wu, Chen Jia*. Circulation theory for Markov processes and its applications (in Chinese). To appear in SCIENTIA SINICA Mathematica 2025.

      7. 2024

    7. Chen Jia, Ramon Grima*. Holimap: an accurate and efficient method for solving stochastic gene network dynamics. Nature Communications 15(1):6557, 2024.

      8. In this work, we develop an accurate and highly efficient method for solving stochastic gene network dynamics. The gene network can be very general, including transcriptional networks, post-transcriptional networks, and post-translational networks. Comparing with the classical Gillespie algorithm, our method can reduce computational time by over 60 fold. Within the same computational time, our method can enhance the accuracy by over 3 fold.

    8. 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.
    9. 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.
    10. 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.

      11. 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.

    11. 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.
    12. 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.

      13. 2023

    13. 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.
    14. 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.
    15. 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.
    16. 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.

      17. 2022

    17. 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.
    18. 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.
    19. 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.

      20. 2021

    20. 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.

      21. 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.

    21. Chen Jia, Abhyudai Singh, Ramon Grima*. Cell size distribution of lineage data: analytic results and parameter inference. iScience 24(3):102220, 2021.
    22. 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.
    23. Youming Li, Da-Quan Jiang*, Chen Jia*. Steady-state joint distribution for first-order stochastic reaction kinetics. Physical Review E 104(2):024408, 2021.
    24. 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.
    25. 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.

      26. 2020

    26. 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.
    27. Chen Jia, Ramon Grima*. Small protein number effects in autoregulated bursty gene expression. The Journal of Chemical Physics 152(8):084115, 2020.
    28. 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.
    29. 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.
    30. 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.
    31. Chen Jia*, Guohuan Zhao*. Moderate maximal inequalities for the Ornstein-Uhlenbeck process. Proceedings of the American Mathematical Society 148(8):3607-3615, 2020.

      32. 2019

    32. 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.

      33. 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.

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

      34. 2018

    34. 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.

      35. 2017

    35. Chen Jia*, Michael Q. Zhang*, Hong Qian*. Emergent Lévy behavior in single-cell gene expression. Physical Review E 96(4):040402(R), 2017.
    36. 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.
    37. 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.
    38. 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.
    39. Chen Jia*. Nonequilibrium nature of adaptation in bacterial chemotaxis: A fluctuation-dissipation theorem approach. Physical Review E 95(4):042116, 2017.
    40. 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.
    41. 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.

      42. 2016

    42. 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.
    43. Chen Jia*. A solution to the reversible embedding problem for finite Markov chains. Statistics & Probability Letters 116:122-130, 2016.

      44. 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.

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

      49. 2015

    49. 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.

      50. 2014

    50. 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.
    51. Chen Jia, Da-Quan Jiang*, Minping Qian. An allosteric model of the inositol trisphosphate receptor with nonequilibrium binding. Physical Biology 11(5):056001, 2014.
    52. 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.

      53. 2012

    53. 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.

      54. 2009

    54. 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.
    55. 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.