Publication in Refereed Academic Journals/Books

[1] Shihao Yang, Mauricio Santillana and Samuel Kou (2015). Accurate estimation of influenza epidemics using Google search data via ARGO. Proceedings of the National Academy of Sciences, 112, 14473-14478.

       R package for computation; package instruction.

       Media coverage:
           @ PNAS' News and Newsworthy column
           @ Harvard Gazette
           @ Ars Technica
           @ Forschung aktuell (the daily science magazine of Deutschlandfunk) (in German)
           @ SINC (in Spanish)
           @ Rue89 (in French)

[2] Shihao Yang, Samuel Kou, Fred Lu, John Brownstein, Nicholas Brooke and Mauricio Santillana (2017). Advances in using Internet searches to track dengue. PLOS Computational Biology, 13(7): e1005607.

       Media coverage:
           @ CNN
           @ Press release by PLOS at Science Daily, at Eurekalert!
           @ PLOS Research News
           @ Healio
           @ Deutsches Arzteblatt (the official journal of the German Medical Association and the National Association of Statutory Health Insurance Physicians) (in German)

[3] Shihao Yang, Mauricio Santillana, John Brownstein, Josh Gray, Stewart Richardson and Samuel Kou (2017). Using electronic health records and Internet search information for accurate influenza forecasting. BMC Infectious Diseases, 17:332.
       Supporting material: Model details.
       Animation showing the real-time estimation and forecast of our model.

[4] Samuel Kou, Sunney Xie and Jun Liu (2005). Bayesian analysis of single-molecule experimental data (with discussion). J. Roy. Statist. Soc., C, 54, 469-506.
      Download the experimental data sets: DNAhairpinData.zip

[5] Samuel Kou and Sunney Xie (2004). Generalized Langevin equation with fractional Gaussian noise: subdiffusion within a single protein molecule. Physical Review Letters, 93, 180603(1)-180603(4).

[6] Wei Min, Guobin Luo, Binny Cherayil, Samuel Kou and Sunney Xie (2005). Observation of a power law memory kernel for fluctuations within a single protein molecule . Physical Review Letters, 94, 198302(1)-198302(4).

[7] Samuel Kou, Binny Cherayil, Wei Min, Brian English and Sunney Xie (2005). Single-molecule Michaelis-Menten equations (feature article). Journal of Physical Chemistry, B, 109, 19068-19081.
       The article is featured on the journal cover page.

[8] Wei Min, Brian English, Guobin Luo, Binny Cherayil, Samuel Kou and Sunney Xie (2005). Fluctuating enzymes: lessons from single-molecule studies. Accounts of Chemical Research, 38, 923-931.

[9] Wei Min, Liang Jiang, Ji Yu, Samuel Kou, Hong Qian and Sunney Xie (2005). Nonequilibrium steady state of a nanometric biochemical system: determining the thermodynamic driving force from single enzyme turnover time traces. Nano Letters, 5, 2373-2378.

[10] B. English, W. Min, A. M. van Oijen, K. T. Lee, G. Luo, H. Sun, B. J. Cherayil, S. C. Kou, X. S. Xie (2006). Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nature Chemical Biology, 2, 87-94.
       The article is featured on the journal cover page.
       Read comments by N. Walter featuring the article.

[11] W. Min, I. V. Gopich, B. English, S. C. Kou, X. S. Xie and A. Szabo (2006). When does the Michaelis-Menten equation hold for fluctuating enzymes? Journal of Physical Chemistry, B, 110, 20093-20097.

[12] Srabanti Chaudhury, Samuel Kou and Binny Cherayil (2007). Model of fluorescence intermittency in single enzymes. Journal of Physical Chemistry, B, 111, 2377-2384.

[13] Samuel Kou (2008). Stochastic modeling in nanoscale biophysics: subdiffusion within proteins. Annals of Applied Statistics, 2, 501-535.

[14] Samuel Kou (2008). Stochastic networks in nanoscale biophysics: modeling enzymatic reaction of a single protein. J. Amer. Statist. Assoc., 103, 961-975.

[15] Samuel Kou (2009). A selective view of stochastic inference and modeling problems in nanoscale biophysics. Science in China, A, 52, 1181-1211.

[16] P. C. Blainey, G. Luo, S. C. Kou, W. F. Mangel, G. L. Verdine, B. Bagchi and X. S. Xie (2009). Nonspecifically bound proteins spin while diffusing along DNA. Nature Structural & Molecular Biology, 16, 1224-1229.

[17] Chao Du and Samuel Kou (2012). Correlation analysis of enzymatic reaction of a single protein molecule. Annals of Applied Statistics, 6, 950-976.

[18] Hong Qian and Samuel Kou (2014). Statistics and related topics in single-molecule biophysics. Annual Review of Statistics and Its Application, 1, 465-492.

[19] Yang Chen, Kuang Shen, Shu-Ou Shan and Samuel Kou (2016). Analyzing single-molecule protein transportation experiments via hierarchical hidden Markov models. J. Amer. Statist. Assoc., 111, 951-966.

[20] Samuel Kou, Qing Zhou and Wing Wong (2006). Equi-energy sampler with applications in statistical inference and statistical mechanics (with discussion). Ann. Statist., 34, 1581-1652.

[21] Xia Hua and Samuel Kou (2011). Convergence of the equi-energy sampler and its application to the Ising model. Statistica Sinica, 21, 1687-1711.

[22] Samuel Kou, Jason Oh and Wing Wong (2006). A study of density of states and ground states in HP protein folding models by equi-energy sampling. Journal of Chemical Physics, 124, 244903(1)-244903(11).

[23] Jinfeng Zhang, Samuel Kou and Jun Liu (2007). Biopolymer structure simulation and optimization via fragment re-growth Monte Carlo. Journal of Chemical Physics, 126, 225101(1)-225101(7).

[24] Samuel Kou and Peter McCullagh (2009). Approximating the alpha-permanent. Biometrika, 96, 635-644.
       Supplementary material: matrices used in the paper.

[25] Samuel Kou, Benjamin Olding, Martin Lysy and Jun Liu (2012). A multiresolution method for parameter estimation of diffusion processes. J. Amer. Statist. Assoc., 107, 1558-1574.

[26] Samuel Wong, Jun Liu and Samuel Kou (2017). Fast de novo discovery of low-energy protein loop conformations. Proteins: Structure, Function, and Bioinformatics, 85, 1402-1412.
       Supporting information.
       Code for Linux systems.

[27] Samuel Kou and Bradley Efron (2002). Smoothers and the Cp, GML and EE criteria: a geometric approach. J. Amer. Statist. Assoc., 97, 766-782.

[28] Samuel Kou (2003). On the efficiency of selection criteria in spline regression. Probab. Theory Relat. Fields, 127, 153-176.

[29] Samuel Kou (2003). Is Cp an empirical Bayes method for smoothing parameter choice? Statist. Probab. Lett., 65, 139-146.

[30] Samuel Kou (2004). From finite sample to asymptotics: a geometric bridge for selection criteria in spline regression. Ann. Statist., 32, 2444-2468.

[31] Tingting Zhang and Samuel Kou (2010). Nonparametric inference of doubly stochastic Poisson process data via the kernel method. Annals of Applied Statistics, 4, 1913-1941.
       Supplementary material: proofs of theoretical results.

[32] Xianchao Xie, Samuel Kou and Lawrence D. Brown (2012). SURE estimates for a heteroscedastic hierarchical model. J. Amer. Statist. Assoc., 107, 1465-1479.

[33] Xianchao Xie, Samuel Kou and Lawrence D. Brown (2016). Optimal shrinkage estimation of mean parameters in family of distributions with quadratic variance. Ann. Statist., 44, 564-597.

[34] Chao Du, Chu-Lan Kao and Samuel Kou (2016). Stepwise signal extraction via marginal likelihood. J. Amer. Statist. Assoc., 111, 314-330.
       Supplementary material: proofs of theoretical results.
       R packages: For all platforms; Windows binaries.
       Matlab package: For all platforms.

[35] Samuel Kou and Justin J. Yang (2017). Optimal shrinkage estimation in heteroscedastic hierarchical linear models. In Big and Complex Data Analysis: Methodologies and Applications, (edited by S. Ejaz Ahmed), 249-284. Springer, New York.

[36] Robert J. Adler, Kevin Bartz, Samuel Kou, Anthea Monod (2017). Estimating thresholding levels for random fields via Euler characteristics. arXiv preprint: arXiv:1704.08562.

[37] Samuel Kou and Steve Kou (2003). Modeling growth stocks via birth-death processes. Advances in Applied Probability, 35, 641-664.

[38] Samuel Kou and Steve Kou (2004). A diffusion model for growth stocks. Mathematics of Operations Research, 29, 191-212.

[39] Samuel Kou and Steve Kou (2007). A tale of two growths: stochastic endogenous growth and growth stocks. Preprint.

Publication in Refereed Conference Proceedings and Industrial Journals

[1] Samuel Kou, Sunney Xie and Jun Liu (2003). Markov chain Monte Carlo in the analysis of single-molecule experimental data. The Monte Carlo Method in the Physical Sciences, (edited by J. E. Gubernatis), 123-133, AIP Press, Melville, New York.

[2] Samuel Kou and Steve Kou (2001). Modeling growth stocks. RISK, S34-S37, December 2001.

[3] Samuel Kou and Steve Kou (2002). Modeling growth stocks (II). Proceedings of the 2002 Winter Simulation Conference, 1524-1529, IEEE Press, New York.