Refereed Journal Articles:

  1. Shen, S., Park, J.W., Huang, J., Dittmar, K.A., Lu, Z., Zhou, Q., Carstens, R.P., and Xing, Y. (2012). MATS: A Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Research, 40: e61.
  2. Zhou, Q. (2011). Multi-domain sampling with applications to structural inference of Bayesian networks. Journal of the American Statistical Association, 106: 1317-1330. [Reprint]
  3. Chen, G. and Zhou, Q. (2011). Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells. BMC Genomics, 12: 515.
  4. Zhou, Q. (2011). Random walk over basins of attraction to construct Ising energy landscapes. Physical Review Letters, 106: 180602. [Preprint].
  5. Zhou, Q. (2010). On weight matrix and free energy models for sequence motif detection. Journal of Computational Biology, 17: 1621-1638. [Preprint].
  6. Mason, M.J., Plath, K., and Zhou, Q. (2010). Identification of context-dependent motifs by contrasting ChIP binding data. Bioinformatics, 26: 2826-2832. [Software].
  7. Chen, G. and Zhou, Q. (2010). Heterogeneity in DNA multiple alignments: Modeling, inference, and applications in motif finding. Biometrics, 66: 694-704. [Preprint] [Software].
  8. Ouyang, Z., Zhou, Q., and Wong, W.H. (2009). ChIP-seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proceedings of the National Academy of Sciences USA, 106: 21521-21526.
  9. Mason, M.J., Fan, G., Plath, K., Zhou, Q.*, and Horvath, S.* (2009). Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics, 10: 327. (*Corresponding authors.)
  10. Gao, K., Zhou, H., Zhang, L., Lee, J.W., Zhou, Q., Hu, S., Wolinsky, L.E., Farrell, J., Eibl, G., and Wong, D.T. (2009). Systemic disease-induced salivary biomarker profiles in mouse models of melanoma and non-small cell lung cancer. PLoS One, 4: e5875.
  11. Zhou, Q. and Wong, W.H. (2009). Energy landscape of a spin-glass model: Exploration and characterization. Physical Review E, 79: 051117.
  12. Sridharan, R.*, Tchieu, J.*, Mason, M.J.*, Yachechko, R., Kuoy, E., Horvath, S., Zhou, Q., and Plath, K. (2009). Role of the murine reprogramming factors in the induction of pluripotency. Cell, 136: 364-377. (*Equally contributed authors.)
  13. Zhou, Q. and Wong, W.H. (2008). Reconstructing the energy landscape of a distribution from Monte Carlo samples. Annals of Applied Statistics, 2: 1307-1331. [Reprint].
  14. Zhou, Q. and Liu, J.S. (2008). Extracting sequence features to predict protein-DNA interactions: A comparative study. Nucleic Acids Research, 36: 4137-4148. [Preprint] [Supplemental materials].
  15. Zhou, Q., Chipperfield, H., Melton, D.A., and Wong, W.H. (2007). A gene regulatory network in mouse embryonic stem cells.  Proceedings of the National Academy of Sciences USA, 104: 16438-16443.
  16. Zhou, Q. and Wong, W.H. (2007). Coupling hidden Markov models for the discovery of cis-regulatory modules in multiple species. Annals of Applied Statistics, 1: 36-65. [Reprint] [Webpage].
  17. Kou, S.C.*, Zhou, Q.*, and Wong, W.H. (2006). Equi-energy sampler with applications in statistical inference and statistical mechanics (with discussion). Annals of Statistics, 34: 1581-1652. (*Equally contributed authors.) [Reprint] [Discussion and Rejoinder].
  18. Johnson, D.S., Zhou, Q., Yagi, K., Satoh, N., Wong, W.H., and Sidow, A. (2005). De novo discovery of a tissue-specific gene regulatory module in a chordate. Genome Research, 15: 1315-1324.
  19. Hong, P., Liu, X.S., Zhou, Q., Lu, X., Liu, J.S., and Wong, W.H. (2005). A boosting approach for motif modeling using ChIP-chip data. Bioinformatics, 21: 2636-2643.
  20. Zhou, Q. and Wong, W.H. (2004). CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proceedings of the National Academy of Sciences USA, 101: 12114-12119. [Webpage].
  21. Zhou, Q. and Liu, J.S. (2004). Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics, 20: 909-916. [Webpage] [Supplementary Notes].
  22. Jensen, S.T., Liu, X.S., Zhou, Q. and Liu, J.S. (2004). Computational discovery of gene regulatory binding motifs: A Bayesian perspective. Statistical Science, 19: 188-204. [Reprint].
  23. Zhou, Q. and Li, Y.D. (2003). Directed variation in evolution strategies. IEEE Transactions on Evolutionary Computation, 7: 356-366.
  24. Ji, H.K.*, Zhou, Q.*, Wen, F., Xia, H.Y., Lu, X., and Li, Y.D. (2001). AsMamDB: An alternative splice database of mammals. Nucleic Acids Research, 29: 260-263. (*Equally contributed authors.)

Other Publications:

  1. Liu J.S. and Zhou, Q. (2011). Predictive modeling approaches for studying protein-DNA binding. Proceedings of the 4th International Congress of Chinese Mathematicians, Vol. 4: 151-167, Higher Education Press and International Press.
  2. Zhou, Q. (2010). Review of "A Guide to QTL Mapping with R/qtl" by Broman and Sen. Journal of Statistical Software, 32: Book Review 5.
  3. Zhou, Q. and Gupta, M. (2009). Regulatory motif discovery: From decoding to meta-analysis. New Developments in Biostatistics and Bioinformatics, chp 8: 179-208, World Scientific. [Preprint].
  4. Zhou, Q. (2006). Detecting cis-regulatory modules by modeling correlated structures in genomic sequences. Ph.D. Dissertation, Statistics, Harvard University.

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