Publication in Refereed Academic Journals/Books
- Analysis and Mining of Big Data
[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:
@ Ars Technica
@ Harvard Gazette
@ PNAS’ News and Newsworthy column
@ 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] K.-H. Yu, T.-L. Lee, C.-S. Wang, Y.-J. Chen, C. Re, S. C. Kou, J.-H. Chiang, I. S. Kohane and M. Snyder (2018). Systematic protein prioritization for targeted proteomics studies through literature mining. Journal of Proteome Research, 17, 1383-1396.
Online supporting information.
[5] K.-H. Yu, T.-L. Lee, Y.-J. Chen, C. Re, S. C. Kou, J.-H. Chiang, M. Snyder and I. S. Kohane (2018). A cloud-based metabolite and chemical prioritization system for the biology/disease-driven human proteome project. Journal of Proteome Research, 17, 4345-4357.
Online supporting information.
[6] K.-H. Yu , O. Miron, N. Palmer, D. Lemos, K. Fox, S. C. Kou, M. Sahin, and I. S. Kohane (2018). Data-driven analyses revealed the comorbidity landscape of tuberous sclerosis complex. Neurology, 91, 974-976.
[7] Shaoyang Ning, Shihao Yang and Samuel Kou (2019). Accurate regional influenza epidemics tracking using Internet search data. Scientific Reports, 9, 5238.
Supporting information.
Download the R package at CRAN.
[8] S. Yang, K.-H. Yu, N. Palmer, K. Fox, S. C. Kou, and I. S. Kohane (2020). Autoimmune effects of lung cancer immunotherapy revealed by data-driven analysis on a nationwide cohort. Clinical Pharmacology & Therapeutics, 107, 388-396.
Supporting information.
[9] K.-H. Yu, T.-L. Lee, M.-H. Yen, S. C. Kou, B. Rosen, J.-H. Chiang, and I. S. Kohane (2020). Reproducible machine learning methods for lung cancer detection using computed tomography images: algorithm development and validation. Journal of Medical Internet Research, 22(8), e16709.
[10] Samuel Kou, Shihao Yang, Chia-Jung Chang, Teck-Hua Ho, and Lisa Graver (2020). Unmasking the actual COVID-19 case count. Clinical Infectious Diseases, 71, 2949-2951.
[11] Dingdong Yi, Shaoyang Ning, Chia-Jung Chang, and Samuel Kou (2021). Forecasting unemployment using Internet search data via PRISM. J. Amer. Statist. Assoc., 116, 1662-1673.
Download the R package at CRAN.
[12] Shihao Yang, Shaoyang Ning, and Samuel Kou (2021). Use Internet search data to accurately track state level influenza epidemics. Scientific Reports, 11, 4023.
Supporting information.
Download the R package at CRAN.
[13] F. Wang, S. Yang, N. Palmer, K. Fox, I. S. Kohane, K. P. Liao, K.-H. Yu, and S. C. Kou (2021). Real-world data analyses unveiled the immune-related adverse effects of immune checkpoint inhibitors across cancer types. npj Precision Oncology, 5, 82.
Supporting information.
[14] F. Wang, N. Palmer, K. Fox, K. P. Liao, K.-H. Yu, and S. C. Kou (2023). Large-scale real-world data analyses of cancer risks among patients with rheumatoid arthritis. International Journal of Cancer, 153(6), 1139‐1150.
Supporting information.
- Stochastic Inference and Modeling in Biophysics
[15] 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
[16] 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).
[17] 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).
[18] 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.
[19] 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.
[20] 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.
[21] 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.
[22] 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.
[23] Srabanti Chaudhury, Samuel Kou and Binny Cherayil (2007). Model of fluorescence intermittency in single enzymes. Journal of Physical Chemistry, B, 111, 2377-2384.
[24] Samuel Kou (2008). Stochastic modeling in nanoscale biophysics: subdiffusion within proteins. Annals of Applied Statistics, 2, 501-535.
[25] Samuel Kou (2008). Stochastic networks in nanoscale biophysics: modeling enzymatic reaction of a single protein. J. Amer. Statist. Assoc., 103, 961-975.
[26] Samuel Kou (2009). A selective view of stochastic inference and modeling problems in nanoscale biophysics. Science in China, A, 52, 1181-1211.
[27] 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.
[28] Chao Du and Samuel Kou (2012). Correlation analysis of enzymatic reaction of a single protein molecule. Annals of Applied Statistics, 6, 950-976.
[29] Hong Qian and Samuel Kou (2014). Statistics and related topics in single-molecule biophysics. Annual Review of Statistics and Its Application, 1, 465-492.
[30] 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.
[31] Chao Du and Samuel Kou (2020). Statistical methodology in single-molecule experiments. Statistical Science, 35, 75-91.
Supplementary information.
- Bayesian and Monte Carlo Inference
[32] 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.
[33] Xia Hua and Samuel Kou (2011). Convergence of the equi-energy sampler and its application to the Ising model. Statistica Sinica, 21, 1687-1711.
[34] 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).
[35] 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).
[36] Samuel Kou and Peter McCullagh (2009). Approximating the alpha-permanent. Biometrika, 96, 635-644.
Supplementary material: matrices used in the paper.
[37] 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.
[38] 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.
[39] Samuel Wong, Jun Liu and Samuel Kou (2018). Exploring the conformational space for protein folding with sequential Monte Carlo. Annals of Applied Statistics, 12, 1628-1654.
[40] Dongming Huang, Nathan Stein, Donald Rubin and Samuel Kou (2020). Catalytic prior distributions with application to generalized linear models. Proceedings of the National Academy of Sciences, 117, 12004-12010.
[41] Shihao Yang, Samuel Wong and Samuel Kou (2021). Inference of dynamic systems from noisy and sparse data via manifold-constrained Gaussian processes. Proceedings of the National Academy of Sciences, 118, e2020397118.
Download the R package at CRAN. Download the Matlab, R and Python packages at GitHub.
[42] Samuel Wong, Shihao Yang and Samuel Kou (2023). Estimating and assessing differential equation models with time-course data. Journal of Physical Chemistry, B, 127, 11, 2362–2374.
- Nonparametric Methods, Empirical Bayes and Model Selection
[43] Samuel Kou and Bradley Efron (2002). Smoothers and the Cp, GML and EE criteria: a geometric approach. J. Amer. Statist. Assoc., 97, 766-782.
[44] Samuel Kou (2003). On the efficiency of selection criteria in spline regression. Probab. Theory Relat. Fields, 127, 153-176.
[45] Samuel Kou (2003). Is Cp an empirical Bayes method for smoothing parameter choice? Statist. Probab. Lett., 65, 139-146.
[46] Samuel Kou (2004). From finite sample to asymptotics: a geometric bridge for selection criteria in spline regression. Ann. Statist., 32, 2444-2468.
[47] 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.
[48] Xianchao Xie, Samuel Kou and Lawrence D. Brown (2012). SURE estimates for a heteroscedastic hierarchical model. J. Amer. Statist. Assoc., 107, 1465-1479.
[49] 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.
[50] 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.
[51] 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.
[52] Robert J. Adler, Kevin Bartz, Samuel Kou, Anthea Monod (2017). Estimating thresholding levels for random fields via Euler characteristics. arXiv preprint: arXiv:1704.08562.
- Economic and Financial Modeling
[53] Samuel Kou and Steve Kou (2003). Modeling growth stocks via birth-death processes. Advances in Applied Probability, 35, 641-664.
[54] Samuel Kou and Steve Kou (2004). A diffusion model for growth stocks. Mathematics of Operations Research, 29, 191-212.
[55] Samuel Kou and Steve Kou (2007). A tale of two growths: stochastic endogenous growth and growth stocks. Preprint.
Publication in Refereed Conference Proceedings, Industrial Journals and Society Magazines
[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.
[4] Samuel Kou (2018). Digital disease detection with big data. Bernoulli News, 25(1), 6-10.