Articles in refereed journals and peer-reviewed edited volumes

1. Wang, X., Stokes, L., Lim, J., Chen, M., (2006). Concomitants of multivariate order statistics with application to judgment poststratification. Journal of the American Statistical Association 101(476), 1693–1704.

2. Stokes, L., Wang, X., Chen, M., (2007). Judgment post-stratification with multiple rankers. Journal of Statistical Theory and Applications 6, 344–356.

3. Chen, M., Dyer, J., (2009). Inevitable disappointment in projects selected on the basis of forecasts. SPE Journal 14(2), 216–221.

4. Chen, M., Xia, Y., Wang, X., (2010). Managing supply uncertainties through Bayesian information update. IEEE Transactions on Automation Science and Engineering 7(1), 24–36.

5. Liu, Z., Li, A., Schulz, V., Chen, M., Tuck, D., (2010). MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells. PloS One 5 (6), e10909. PMID: 20532221. PMCID: PMC2879364.

6. Chen, M., Cho, J., Zhao, H., (2011). Detecting epistatic SNPs associated with complex diseases via a Bayesian classification tree search method. Annals of Human Genetics 75 (1), 112–121. PMID: 21121902. PMCID: PMC3178841.

7. Chen, M., Cho, J., Zhao, H., (2011). Incorporating biological pathways via a Markov random field model in genome-wide association studies. PLoS Genetics 7 (4), e1001353. PMID: 21490723. PMCID: PMC3072362.

8. Chen, M., Lim, J., (2011). Estimating variances of strata in ranked set sampling. Journal of Statistical Planning and Inference 141(8), 2513–2518.

9. Chen, M., Wang, X., (2011). Approximate Predictive Densities and Their Applications in Generalized Linear Models. Computational Statistics & Data Analysis 55 (4), 1570–1580. PMID: 21516223. PMCID: PMC3079213.

10. Chen, M., Xie, Y., Story, M., (2011). An Exponential-Gamma Convolution Model for Background Correction of Illumina BeadArray Data. Communications in Statistics: Theory and Methods 40 (17), 3055–3069. PMID: 21769162. PMCID: PMC3137271.

11. Allen, J. D., Wang, S., Chen, M., Girard, L., Minna, J. D., Xie, Y., Xiao, G., (2012). Probe mapping across multiple microarray platforms. Briefings in Bioinformatics 13 (5), 547–554. PMID: 22199380. PMCID: PMC3431719.

12. Allen, J. D., Xie, Y., Chen, M., Girard, L., Xiao, G., (2012). Comparing statistical methods for constructing large scale gene networks. PloS One 7 (1), e29348. PMID: 22272232. PMCID: PMC3260142.

13. Han, T. W., Kato, M., Xie, S., Wu, L. C., Mirzaei, H., Pei, J., Chen, M., Xie, Y., Allen, J., Xiao, G., McKnight, S. L., (2012). Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell 149 (4), 768–779. PMID: 22579282.

14. Wang, X., Chen, M., Khodursky, A. B., Xiao, G., (2012). Bayesian Joint Analysis of Gene Expression Data and Gene Functional Annotations. Statistics in Biosciences 4, 300–318.

15. Bu, D., Lewis, C. M., Sarode, V., Chen, M., Ma, X., Lazorwitz, A. M., Rao, R., Leitch, M., Moldrem, A., Andrews, V., Gazdar, A., Euhus, D., (2013). Identification of breast cancer DNA methylation markers optimized for fine-needle aspiration samples. Cancer Epidemiology, Biomarkers & Prevention 22 (12), 2212–2221. PMID: 24089458.

16. Chen, M., Zang, M., Wang, X., Xiao, G., (2013). A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies. Bioinformatics 29 (7), 862–869. PMID: 23418184. PMCID: PMC3605602.

17. Chun, H., Chen, M., Li, B., Zhao, H., (2013). Joint conditional Gaussian graphical models with multiple sources of genomic data. Frontiers in Genetics 4, 294. PMID: 24381584. PMCID: PMC3865369.

18. Horikoshi, N., Kumar, P., Sharma, G. G., Chen, M., Hunt, C. R., Westover, K., Chowdhury, S., Pandita, T. K., (2013). Genome-wide distribution of histone H4 Lysine 16 acetylation sites and their relationship to gene expression. Genome Integrity 4 (1), 3. PMID: 23587301. PMCID: PMC3667149.

19. Tam, K. W., Zhang, W., Soh, J., Stastny, V., Chen, M., Sun, H., Thu, K., Rios, J. J., Yang, C., Marconett, C. N., Selamat, S. A., Laird-Offringa, I. A., Taguchi, A., Hanash, S., Shames, D., Ma, X., Zhang, M. Q., Lam, W. L., Gazdar, A., (2013). CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer. Journal of Thoracic Oncology 8 (11), 1378–1388. PMID: 24077454. PMCID: PMC3951422.

20. Zhou, H., Chen, M., Zhao, D., (2013). Longitudinal MRI evaluation of intracranial development and vascular characteristics of breast cancer brain metastases in a mouse model. PloS One 8 (4), e62238. PMID: 23638013. PMCID: PMC3639286.

21. Chen, M., Ahn, S., Wang, X., Lim, J., (2014). Generalized isotonized mean estimators for judgment post-stratification with multiple rankers. Journal of Agricultural, Biological, and Environmental Statistics 19(4), 405–418.

22. Chen, M., Cho, J., Zhao, H., (2014). “Graphical modeling of biological pathways in genome-wide association studies.” In: Probabilistic Graphical Models for Genetics, Genomics and Postgenomics. Ed. by C. Sinoquet and R. Mourad. Oxford University Press. Chap. 6.

23. Hou, L., Chen, M., Zhang, C. K., Cho, J., Zhao, H., (2014). Guilt by rewiring: gene prioritization through network rewiring in genome wide association studies. Human molecular genetics 23 (10), 2780–2790. PMID: 24381306. PMCID: PMC3990172.

24. Lim, J., Chen, M., Park, S., Wang, X., Stokes, L., (2014). Kernel density estimator from ranked set samples. Communications in Statistics - Theory and Methods 43(10-12), 2156–2168.

25. Yu, Q., Peng, Y., Mishra, V., Ouyang, A., Li, H., Zhang, H., Chen, M., Liu, S., Huang, H., (2014). Microstructure, length, and connection of limbic tracts in normal human brain development. Frontiers in aging neuroscience 6, 228. PMID: 25221509. PMCID: PMC4147394.

26. Jeon, T., Mishra, V., Ouyang, M., Chen, M., Huang, H., (2015). Synchronous Changes of Cortical Thickness and Corresponding White Matter Microstructure During Brain Development Accessed by Diffusion MRI Tractography from Parcellated Cortex. Frontiers in Neuroanatomy 9, 158. PMID: 26696839. PMCID: PMC4667005.

27. Zang, X., Chen, M., Zhou, Y., Xiao, G., Xie, Y., Wang, X., (2015). Identifying CDKN3 Gene Expression as a Prognostic Biomarker in Lung Adenocarcinoma via Meta-analysis. Cancer Informatics 14 (Suppl 2), 183–191. PMID: 26052221. PMCID: PMC4444140.

28. Bai, O., Chen, M., Wang, X., (2016). Bayesian Estimation and Testing in Random Effects Meta-analysis of Rare Binary Adverse Events. Statistics in Biopharmaceutical Research 8 (1), 49–59. PMID: 27127551. PMCID: PMC4845966.

29. Chen, Y., Wang, Y., Xuan, Z., Chen, M., Zhang, M. Q., (2016). De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. Nucleic Acids Research 44 (11), e106. PMID: 27060148. PMCID: PMC4914103.

30. Park, S., Kim, S. J., Yu, D., Pena-Llopis, S., Gao, J., Park, J. S., Chen, B., Norris, J., Wang, X., Chen, M., Kim, M., Yong, J., Wardak, Z., Choe, K., Story, M., Starr, T., Cheong, J.-H., Hwang, T. H., (2016). An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types. Bioinformatics 32 (11), 1643–1651. PMID: 26635139. PMCID: PMC4892411.

31. Goodwin, J., Neugent, M. L., Lee, S. Y., Choe, J. H., Choi, H., Jenkins, D. M. R., Ruthenborg, R. J., Robinson, M. W., Jeong, J. Y., Wake, M., Abe, H., Takeda, N., Endo, H., Inoue, M., Xuan, Z., Yoo, H., Chen, M., Ahn, J.-M., Minna, J. D., Helke, K. L., Singh, P. K., Shackelford, D. B., Kim, J.-W., (2017). The distinct metabolic phenotype of lung squamous cell carcinoma defines selective vulnerability to glycolytic inhibition. Nature Communications 8, 15503. PMID: 28548087. PMCID: PMC5458561.

32. Jia, C., Xie, P., Chen, M., Zhang, M. Q., (2017). Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level. Scientific Reports 7 (1), 16037. PMID: 29167445. PMCID: PMC5700158.

33. Pavlovic, M., Ray, P., Pavlovic, K., Kotamarti, A., Chen, M., Zhang, M. Q., (2017). DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. Bioinformatics 33 (19), 2986–2994. PMID: 28505334. PMCID: PMC5870843.

34. Dai, Q., Bao, C., Hai, Y., Ma, S., Zhou, T., Wang, C., Wang, Y., Huo, W., Liu, X., Yao, Y., Xuan, Z., Chen, M., Zhang, M. Q., (2018). MTGIpick allows robust identification of genomic islands from a single genome. Briefings in Bioinformatics 19 (3), 361–373. PMID: 28025178. PMCID: PMC6454522.

35. Jia, C., Qian, H., Chen, M., Zhang, M. Q., (2018). Relaxation rates of gene expression kinetics reveal the feedback signs of autoregulatory gene networks. The Journal of Chemical Physics 148(9), 095102. PMCID: PMC5832468.

36. Ouyang, M., Jeon, T., Sotiras, A., Peng, Q., Mishra, V., Halovanic, C., Chen, M., Chalak, L., Rollins, N., Roberts, T. P. L., Davatzikos, C., Huang, H., (2019). Differential cortical microstructural maturation in the preterm human brain with diffusion kurtosis and tensor imaging. Proceedings of the National Academy of Sciences of the United States of America 116 (10), 4681–4688. PMID: 30782802. PMCID: PMC6410816.

37. Zhang, C., Chen, M., Wang, X., (2020). Statistical Methods for Quantifying Between-study Heterogeneity in Meta-analysis with Focus on Rare Binary Events. Statistics and Its Interface 13 (4), 449–464. PMID: 33628357. PMCID: PMC7901832.

38. Cao, Y., Zhang, Y., Wang, X., Chen, M., (2021). “Graphical Modeling of Multiple Biological Pathways in Genomic Studies.” In: Modern Statistical Methods for Health Research. Ed. by Y. Zhao and D.-G. Chen, pp.431–459.

39. Wang, G., Cheng, Y., Chen, M., Wang, X., (2021). Jackknife empirical likelihood confidence intervals for assessing heterogeneity in meta-analysis of rare binary event data. Contemporary Clinical Trials 107, 106440. PMID: 34015509. PMCID: PMC8429181.

40. Zhang, C., Wang, X., Chen, M., Wang, T., (2021). A comparison of hypothesis tests for homogeneity in meta-analysis with focus on rare binary events. Research Synthesis Methods 12 (4), 408–428. PMID: 34231330.