HAO GE GROUP

Monograph/textbook:

1. Qian, H. and Ge, H.: Stochastic Chemical Reaction Systems in Biology. in Lecture Notes on Mathematical Modeling in the Life Sciences (LMML) series. Springer (2021)

Public science:

1. Ge, Y.B.: From Geocentric to Heliocentric: How Discoveries Are Made. translated by Liu, Z.C., Xu, Q. and Ge, H. Springer (2021)

Preprint:

1. Das, B. and Ge, H.: A mechanistic model for the asymmetric torque-speed relationships of a bacterial flagellar motor. arXiv:2109.01813 (2023+)

2024

1. Chen, C.Y. and Ge, H.: Sample-path large deviation principle for a 2-D stochastic interacting vortex dynamics with singular kernel. Annals of Applied Probability (2024)
2. Han, X., Zhang, Y. and Ge, H.: Cover-time Gumbel Fluctuations in Finite-Range, Symmetric, Irreducible Random Walks on Torus. Journal of Physics A 57, 285203 (2024)
3. Wan, R.S., Zhang, Y.H., Peng, Y.L., Tian, F., Gao, G., Tang, F.C., Jia, J.Z.* and Ge, H.*: Unveiling gene regulatory networks during cellular state transitions without linkage across time points. Scientific Reports 14, 12355 (2024) (*co-corresponding authors)

2023

1. 葛颢: 随机数学理论与单分子和单细胞生物物理化学的交叉. 中国科学:数学, 53(9): 1163–1180 (2023)
2. Yang, H.R. and Ge, H.: Fluctuation Theorems and Thermodynamic Inequalities for Nonequilibrium Processes Stopped at Stochastic Times. Physical Review E 108, L052104 (2023)

2022

1. Guo, X.L., Tang, T., Duan, M.X., Zhang, L.* and Ge, H.*: The Nonequilibrium Mechanism of Noise-Enhanced Drug Synergy in HIV Latency Reactivation. iScience 25，104358 (2022) (*co-corresponding authors)
2. Wang, R., Li, J.Y., Zhou, X., Mao, Y.N., ..., Ge, H., Fu, W.* and Tang, F.C.*: Single-cell genomic and transcriptomic landscapes of primary and metasatic colorectal cancer tumors. Genome Medicine 14:93 (2022)

2021

1. Ge, H., Jia, C. and Jin, X.: Martingale structure for general thermodynamic functionals of diffusion processes under second-order averaging. Journal of Statistical Physics 184:17 (2021)

2020

1. Peng, Y.L., Qian, H., Beard, D. and Ge, H.*: Universal Relation Between Thermodynamic Driving Force and One-Way Fluxes in a Nonequilibrium Chemical Reaction with Complex Mechanism. Physical Review Research 2, 033089 (2020)
2. Li, J.W., Ge, H.*, and Zhang, Y.X.: Fluctuating-rate model with multiple gene states. Journal of Mathematical Biology 81:1099–1141 (2020)

1. Deng, M.X., Wang, Y., Zhang, L., Yang, Y., Huang, S.S., Wang, J.G., Ge, H., Ishibashi. T. and Yan, Y.: Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs. Development 146: dev179754 (2019)
2. Zhang, Y.L., Liang, K.X., Liu, M.L., Li, Y. Ge, H. * and Zhao, H.Y.*: SCRIBE: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data. MLCB2019 (2019) (co-corresponding authors)

2018

1. Ge, H. *, Wu, P.P., Qian, H. and Xie, X.S.: Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stablizing the uninduced phenotypic state. Plos Comput. Biol. 14(3): e1006051 (2018)
2. Jin, X. and Ge, H. *: Nonequilibrium steady state of biochemical cycle kinetics under non-isothermal conditions. New J. Phys. 20: 043030 (2018)
3. Liu, Y.W., Fan, X.Y., Wang, R., Lu, X.Y., Dang, Y.L., Wang, H.Y., Lin, H.Y., Zhu, C., Ge, H., Cross, J.C. and Wang, H.M.: Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta. Cell Research 28:819–832 (2018)
4. Gao, S., …, Ge, H. *, Qiao, J. * and Tang, F.C. *: Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nat. Cell Biol. 20, 721–734 (2018) (co-corresponding authors)
5. Yang, S.X., and Ge, H. *: Decomposition of the entropy production rate and nonequilibrium thermodynamics of switching diffusion processes. Phys. Rev. E 98, 012418 (2018)
6. You, Z.Y., Li, L.Y., Lu, J.F. * and Ge, H. *: Integrated tempering enhanced sampling method as the infinite switching limit of simulated tempering. J. Chem. Phys. 149, 084114 (2018) (*co-corresponding authors)
7. Bai, S.N., Ge, H. and Qian, H.: Structure for energy cycle: a unique status of the second law of thermodynamics for living systems. Sci China Life Sci 61(10), 1266-1273 (2018)

2017

1. Ge, H. and Qian, H.: Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law. J. Stat. Phys. 166:190–209 (2017)
2. Ge, H., Jiang, D.Q. and Jia, C.: Cycle symmetry, limit theorems, and fluctuation theorems for diffusion processes on the circle. Stoc. Proc. Appl. 127: 1897–1925 (2017)
3. Ai, G.K., Liu, P.F., and Ge, H. *: Torque-coupled thermodynamic model for FoF1-ATPase. Phys. Rev. E 95, 052413 (2017)
4. Yang, L., Ma, Z.C., Cao, C., Zhang, Y.H., Wu, X.L., Lee, R., Hu, B.Q., Wen, L., Ge, H., Huang, Y.Y., Lao, K.Q., Tang, F.C: MR-seq: measuring a single cell’s transcriptome repeatedly by RNA-seq. Science Bulletin 62: 391-398 (2017)
5. Xu, B.X., Ge, H. and Zhang, Z.H.: An efficient and assumption-free method to approximate protein level distribution in the two-states gene expression model. J. Theor. Biol. 433, 1-7 (2017)
6. Guo, Y.Y., You, Z.Y., Ge, H. *: Robustness and relative stability of multiple attractors in a stochastic Boolean network (in Chinese). Sci Sin Math 47, 1831-1852 (2017)

2016

1. Ge, H. and Qian, H.: Nonequilibrium thermodynamic formalism of nonlinear chemical reaction systems with Waage–Guldberg’s law of mass action. Chemical Physics 472, 241–248 (2016)
2. Zhao, Z.Q., Xie, X.S. and Ge, H.: Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J. Phys. Chem. B 120, 2869−2877 (2016)
3. Pu, Y.Y., Zhao, Z.L., Li, Y.X., Zou, J., Ma, Q., Zhao, Y.N., Ke, Y.H., Zhu, Y., Chen, H.Y., Baker, M., Ge, H., Sun. Y.J., Xie, X.S. and Bai, F.: Enhanced efflux activity facilitates drug tolerance in dormant bacterial cells. Mol. Cell 62, 284–294 (2016)
4. Chen, Y., Ge, H., Xiong, J. and Xu, L.H.: The large deviation principle and steady-state fluctuation theorem for the entropy production rate of a stochastic process in magnetic fields. J. Math. Phys. 57, 073302 (2016)
5. Dai, H.Q., Wang, B.A., Yang, L., Chen, J.J., Zhu, G.C, Sun, M.L., Ge, H., Wang, R., Chapman, D.L., Tang, F.C., Sun, X. and Xu, G.L.: TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signaling. Nature 538, 528-532 (2016)
6. Ge, H. and Qian, H.: Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory. Phys. Rev. E 94, 052150 (2016)

2015

1. Chen, H.Y., Shiroguchi, K., Ge, H. * and Xie, X.S. *: Genome-wide study of mRNA degradation and transcript elongation in E.coli.  Mol Syst Biol.  11: 781 (2015) (co-corresponding author)
2. Ge, H.: Macroscopic fluxes and local reciprocal relation in second-order stochastic processes far from equilibrium. J. Stat. Mech. P01005 (2015)
3. Ge, H., Qian, H. and Xie, X.S.: Stochastic phenotype transition of a single cell in an intermediate region of gene state switching. Phys. Rev. Lett. 114, 078101 (2015)
4. Wen, L., Li, J., Guo, H., Liu, X., Zheng, S., Zhang, D., Zhu, W., Qu, J., Guo, L., Du, D., Jin, X., Zhang, Y., Gao, Y., Shen, J., Ge, H., Tang, F., Huang, Y., Peng, J.: Genome-scale detection of hypermethylated CpG islands in circulating cell free DNA of hepatocellular carcinoma patients. Cell Res.  25 (11):1250-64 (2015)
5. Gu, C., Zhang, J., Yang, Y.I., Chen, X., Ge, H., Sun, Y., Su, X., Yang, L., Xie, X.S. and Gao, Y.Q.: DNA Structural Correlation in Short and Long Ranges. J. Phys. Chem. B. 119(44):13980-90 (2015)
6. Ge, H.: Mathematical laws of randomness. In Voices: Expanding the Biology Toolkit. Cell 163, 1306 (2015)

2014

1. Ge, H.: Time reversibility and nonequilibrium thermodynamics of second-order stochastic processes. Phys. Rev. E 89, 022127 (2014)
2. Ge, H.: Stochastic Theory of Nonequilibrium Statistical Physics (review). Advances in Mathematics(China) 43, 161-174 (2014)
3. Chong, S.S., Chen, C.Y., Ge, H. and Xie, X.S.: Mechanism of transcriptional bursting in bacteria. Cell 158, 314–326 (2014)
4. Ouyang, X.H., Huang, X., Jin, X., Chen, Z., Yang, P.Y., Ge, H., Li, S.G. and Deng, X.W.: Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling. Proc. Nat. Acad. Sci. 111,  11539–11544 (2014)
5. 赵新生, 高毅勤, 黄岩谊, 孙育杰, 葛颢, 王任小, 徐平勇, 尉志武: 生物物理化学研究进展。化学通报 77, 699 (2014)

2013

1. Kim, S., Broströmer, E., Xing, D., Jin, J.S., Chong, S.S., Ge, H., Wang, S.Y., Gu, C., Yang, L., Gao, Y.Q., Su, X.D., Sun, Y.J. and Xie, X.S.: Probing allostery through DNA. Science 339 816 (2013)
2.  Ge, H. and Qian, H.: Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open systems. Phys. Rev. E 87 062125 (2013)
3. Xu, X.L.#, Ge, H. #, Gu, C., Gao, Y. Q., Wang, S.Y., Thio, B., Hynes, J., Xie, X.S. and Cao, J.S.: Modeling spatial correlation of DNA deformation: DNA allostery in protein binding. J. Phys. Chem. B 117, 13378−13387 (2013) (co-first-author)
4. Ge, H. and Qian, H.: Book chapters in Encyclopedia of Systems Biology, Springer 2013

    Chemical master equation

    Stochastic processes, Fokker-Planck equation

5. Qian, H. and Ge, H.: Book review "Featured Review: Random Perturbations of Dynamical Systems. Third Edition. " SIAM review 55, 569-574 (2013)

2012

1. Ge, H., Qian, M. and Qian,H.: Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics. Phys. Rep. 510, 87-118 (2012)
2. Ge, H., Pressé, S., Ghosh, K. and Dill, K.: Markov processes follow from the principle of maximum caliber. J. Chem. Phys. 136, 064108 (2012) (Research highlighted)
3. Ge, H.: Multivariable fluctuation theorems in the steady-state cycle kinetics of single enzyme with competing substrates. J. Phys. A: Math. Theor. 45 215002 (2012) (Research highlighted)
4. Ge, H. and Qian, H.: Landscapes of nongradient dynamics without detailed balance: stable limit cycles and multiple attractors. Chaos: An interdisciplinary journal of nonlinear science 22, 023140 (2012)
5. Ge, H. and Qian, H.: Analytical mechanics in stochastic dynamics: most probable path, large-deviation rate function and Hamilton–Jacobi equation. International Journal of Modern Physics B 26, 1230012 (2012)
6. Qian, H. and Ge, H.: Mesoscopic Biochemical Basis of Isogenetic Inheritance and Canalization: Stochasticity, Nonlinearity, and Emergent Landscape.  Molecular & cellular biomechanics, 9, 1-16 (2012)
7. Zhang, Y.X., Ge, H. and Qian, H.: One-Dimensional Birth-Death Process and Delbruck-Gillespie Theory of Mesoscopic Nonlinear Chemical Reactions.Studies in applied mathematics 129, 328–345 (2012)

2011

1. Ge, H. and Qian, H.: Nonequilibrium phase transition in a mesoscoipic biochemical system: From stochastic to nonlinear dynamics and beyond. J. Roy. Soc. Interface 8 107-116 (2011)

2010

1. Ge, H. and Qian, H.: The physical origins of entropy production, free energy dissipation and their mathematical representations. Phys. Rev. E 81 051133 (2010)
2. Zhou, D., Wu, B. and Ge, H.: Evolutionary stability and quasi-stationary strategy in stochastic evolutionary game dynamics. J. Theor. Biol. 264 874-881 (2010)

2009

1. Ge, H. and Qian, M.: Boolean network approach to negative feedback loops of the p53 pathways: Synchronized dynamics and stochastic limit cycles.  J. Comput. Biol. 16, 119-132  (2009)
2. Ge, H. and Qian, M.: Theoretical analysis of the relationship between positive/negative cooperativity and enzyme activation/inhibition. Interdiscip. Sci. Comput. Life Sci. 1: 204–213 (2009)
3. Ge, H.: Extended forms of the second law for general time-dependent stochastic processes. Phys. Rev. E 80 021137 (2009)
4. Ge, H. and Qian, H.: Thermodynamic limit of a nonequilibrium steady state: Maxwell-type construction for a bistable biochemical system. Phys. Rev. Lett. 103, 148103 (2009)
5. Ge, H.: Stochastic-process approach to nonequilibrium thermodynamics and biological signal transduction. In Frontiers in Computational and Systems Biology (J.-F. Feng, W.-J. Fu & F.-Z. Sun, eds.) Springer-Verlag (2009)

2008

1. Ge, H., Qian, H. and Qian, M.: Synchronized dynamics and nonequilibrium steady states in a yeast cell-cycle network. Math. Biosci. 211 132-152 (2008)
2. Ge, H.: Waiting cycle times and generalized Haldane equality in the steady-state cycle kinetics of single enzymes. J. Phys. Chem. B 112 61-70 (2008)
3. Ge, H. and Jiang, D.Q.: Generalized Jarzynski’s equality of multidimensional inhomogeneous diffusion processes. J. Stat. Phys. 131 675–689 (2008)
4. Ge, H. and Qian, M.: Steady-state cycle kinetics of single enzymes: competing substrates and multi-conformations. J. Theor. Comput. Chem. 7(5), 1001-1027 (2008)
5. Ge, H. and Qian, M.: Sensitivity amplification in the phosphorylation-dephosphorylation cycle: nonequilibrium steady states, chemical master equation and temporal cooperativity.  J. Chem. Phys. 129, 015104 (2008)

2007

1. Ge, H. and Qian, M.: Reversibility and potentiality of exclusion processes on countable discrete groups. Appl. Math. Lett. 20 1110-1114 (2007)
2. Ge, H. and Qian, M.: Generalized Jarzynski’s equality in inhomogeneous Markov chains. J. Math. Phys. 48 053302 (2007)
3. Ge, H. and Jiang, D.Q.: Transient fluctuation theorem of sample entropy production for general stochastic processes. J. Phys. A 40 F713-F723 (2007)

2006

1. Ge, H., Jiang, D.Q. and Qian, M.: A simple discrete model of Brownian motors: time-periodic Markov chains. J. Stat. Phys. 123(4), 831–859 (2006)
2. Ge, H., Jiang, D.Q. and Qian, M.: Reversibility and entropy production of inhomogeneous Markov chains. J. Appl. Prob. 43(4) 1028–1043 (2006)