Stochastic process and statistical learning in statistical physics, chemistry, and biology.

1. Stochastic theory of nonequilibrium thermodynamics and statistical mechanics;

2. High-dimensional statistical learning in single-cell biology;

3. Stochastic modeling in systems biology and biophysical chemistry.

1. Outstanding Youth Foundation, National Natural Science Foundation of China. 2017–2019 Project: Interfaces between stochastic processes and biophysical chemistry. Principle Investigator (Grant no. 11622101, 1,300,000 RMB)                                         

2. National High-Tech Research and Development Program of China.                        2015–2017 Project: Technology and device for real-time 3D imaging of single-cell dynamics. Co-Principle Investigator (Grant no. 2015AA020406, 600,000 RMB)                                                                                                                                       

3. General Program, National Natural Science Foundation of China.                            2014–2017 Project: Theory and models for DNA allostery. Principle Investigator (Grant no. 21373021, 600,000 RMB)                                                                                                

4. Foundation for National Excellent Doctoral Dissertations, China.                               2011–2015 Project: Stochastic models in biochemistry and statistical physics. Principle Investigator (Grant no. 201119, 560,000 RMB)                                                                                         

5. Youth Program, National Natural Science Foundation of China                                                                                 2010–2012 Project: Applications of stochastic processes in modern nonequilibrum statistical physics and biochemical models.        Principle Investigator (Grant no. 10901040, 160,000 RMB)

1. 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)

2. 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)

3. 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)

4. 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)

5. 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) (*co-corresponding authors)

6. 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)

7. Chong, S.S., Chen, C.Y., Ge, H. and Xie, X.S.: Mechanism of transcriptional bursting in bacteria. Cell 158, 314–326 (2014)

8. 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)

9. Ge, H. and Qian, H.: The physical origins of entropy production, free energy dissipation and their mathematical representations. Phys. Rev. E 81 051133 (2010)

10. 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)