International Workshop on Applications of Probability and Statistics to Biology, July 11--13, 2019 ––In Honor of Professor Minping Qian’s 80th Birthday

References

[1] Qian, M. P., and Gong, G. L. (1997) Theory of Stochastic Processes. Peking University Press, (In Chinese)

[2] Gong, G. L. and Qian, M. P. (2004) Applied Stochastic Processes. Tsinghua University Press, (In Chinese)

[3] Jiang, D. Q., Qian, M. and Qian, M. P. (2004) Mathematical Theory of Nonequilibrium Steady States. Springer

[4] Feng, J. F., Jost, J. and Qian, M. P. (2007) Networks: from Biology to Theory. Springer

[5] Feng, J. F., Fu, W. J. and Sun, F. Z. (2010) Frontiers in Computational and Systems Biology. Springer

[6] Qian, M. P. and Qian, M. (1982) Circulation for recurrent Markov chains. Probab. Theory Relat. Fields, 59, 203–210

[7] Gong, G. L. and Qian, M. P. (1998) The symmetry of diffusions and the circulations of their projection processes. Sci. China Ser. A Math., 41, 1017–1022

[8] Qian, M. P., Qian, M. and Gong, G. L. (1991) The reversibility and the entropy production of Markov processes. Contemp. Math., 118, 255–261

[9] Gong, G. L. and Qian, M. P. (1997) Entropy production of stationary diffusions on non-compact Riemannian manifolds. Sci. China Ser. A Math., 40, 926–931

[10] Chen, Y., Chen, X. and Qian, M. P. (2006) The Green-Kubo Formula, autocorrelation function and fluctuation spectrum for finite Markov chains with continuous time. J. Phys. Math. Gen., 39, 2539–2550

[11] Qian, M. P. and Jiang, D. Q. (2017) Non-equilibrium stochastic dynamics. Scientia Sinica Mathematica, 47, 1703–1716

[12] Chen, D. Y., Feng, J. F. and Qian, M. P. (1996) Metastability of exponentially perturbed Markov chains. Sci. China Ser. A Math., 39, 7–28

[13] Chen, D. Y., Feng, J. F. and Qian, M. P. (1997) The metastable behavior of the three-dimensional stochastic Ising model I. Sci. China Ser. A Math., 40, 832–842

[14] Li, Y. L. and Qian, M. P. (1998) Hierarchical structure of attractors of dynamical systems. Sci. China Ser. A Math., 41, 1128–1134

[15] Deng, Y. C., Peng, S. L., Qian, M. P. and Feng, J. F. (2003) Identification transition rates of ionic channels via observations at a single state. J. of Physiscs A: Math & General, 36, 1195–1212

[16] Qian, M., Qian, M. P. and Zhang, X. J. (2003) Fundamental facts concerning reversible master equation. Phys. Lett . A 309, 371–376

[17] Zhang, Y. P., Qian, M. P., Ouyang, Q., Deng, M. H., Li, F. T. and Tang, C. (2006) Stochastic model of yeast cell cycle network. Physica. D, 219, 35–39

[18] Jia, C., Liu, X. F., Qian, M. P., Jiang, D. Q. and Zhang, Y. P. (2012) Kinetic behavior of the general modifier mechanism of Botts and Morales with non-equilibrium binding. J. Theor. Biol., 296, 13–20

[19] Zhou, D., Wu, D. M., Li, Z., Qian, M. P. and Zhang, M. Q. (2013) Population dynamics of cancer cells with cell-state conversions. Quant. Biol., 1, 201–208

[20] Jia, C., Jiang, D. Q. and Qian, M. P. (2014) An allosteric model of the inositol trisphosphate receptor with nonequilibrium binding. Phys. Biol., 11, 056001

[21] Jia, C., Qian, M. P. and Jiang, D. Q. (2014) Overshoot in biological systems modelled by Markov chains: a non-equilibrium dynamic phenomenon. IET Syst. Biol., 8, 1–8

[22] Jia, C., Qian, M. P., Kang, Y. and Jiang, D. Q. (2014) Modeling stochastic phenotype switching and bet-hedging in bacteria: stochastic nonlinear dynamics and critical state identification. Quant. Biol., 2, 110–125

[23] Liang, Z. Y., Li, G., Wang, Z., Djekidel, M. N., Li, Y., Qian, M.-P., Zhang, M. Q. and Chen, Y. (2017) BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions. Nat. Commun., 8, 1622

[24] Qian, M. P., Gong, G. L. and Clark, J. W. (1991) Relative entropy and learning rules. Phys. Rev. A, 43, 1061–1070

[25] Albeverio, S., Feng, J. F. and Qian, M. P. (1995) Role of noises in neural networks. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics, 52, 6593–6606

[26] Fang, H. T., Gong, G. L. and Qian, M. P. (1997) Annealing of iterative stochastic schemes. SIAM J. Contr. Optim., 35, 1886–1907

[27] Fang, H. T., Qian, M. P. and Gong, G. L. (1997) An improved annealing method and its large Time Behavior. Stochastic Processes and Their Appl., 71, 55–74

[28] Gong, G. L., Liu, Y. and Qian, M. P. (2001) An adaptive simulated annealing algorithm. Stochastic Process. Appl., 94, 95–103

[29] Gong, G. L., Qian, M. P. and Xie, J. (2001) Reversible algorithm of simulating multivariate densities with multi-hump. Sci. China Ser. A Math., 44, 357–364

[30] Xu, M. X., Han, W., Qian, M., Ma, X., Ding, P., Wang, Y., Xia, D., Rui, M., Wang, L., Zhang, Y., (2004) Last intron of the chemokine like factor gene contains a putative promoter for the downstream CKLF super family member 1 gene. Biochem. Biophys. Res. Commun., 313, 135–141

[31] Yan, X., Deng, M., Fung, W. K. and Qian, M. (2005) Detecting differentially expressed genes by relative entropy. J. Theor. Biol., 234, 395–402

[32] Duan, S. J., Wan, L., Fu, W. J., Pan, H., Ding, Q., Chen, C., Han, P., Zhu, X., Du, L., Liu, H., (2009) Nonlinear cooperation of p53-ING1-induced bax expression and protein S-nitrosylation in GSNO-induced thymocyte apoptosis: a quantitative approach with cross-platform validation. Apoptosis, 14, 236–245

[33] Wan, L., Li, D., Zhang, D., Liu, X., Fu, W. J., Zhu, L., Deng, M., Sun, F. and Qian, M. (2008) Conservation and implications of eukaryote transcriptional regulatory regions across multiple species. BMC Genomics, 9, 623

[34] Wan, L., Sun, K., Ding, Q., Cui, Y., Li, M., Wen, Y., Elston, R. C., Qian, M. and Fu, W. J. (2009) Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation. Nucleic Acids Res., 37, e117

[35] Wang, Q., Peng, P. C., Qian, M. P., Wan, L. and Deng, M. H. (2012) Hybridization and amplification rate correction for affymetrix SNP arrays. BMC Med. Genomics, 5, 24

[36] Wang, F. G., Chen, R., Ji, D., Bai, S. N., Qian, M. P. and Deng, M. H. (2013) Adjustment method for microarray data generated using two-cycle RNA labeling protocol. BMC Genomics, 14, 31

ACKNOWLEDGEMENTS

We would like to thank Michael Waterman at USC for proofreading the report and all the speakers for their presentations and contributions to the report.

RIGHTS & PERMISSIONS

2019 Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature