2008

• Leung, Y. F. *, Ma, P.*, Link, B. A. and Dowling, J.(2008) Factorial microarray analysis of zebrafish retinal development , Proceedings of the National Academy of Sciences, accepted. [Microarray Data](* joint first authors)

• Ma, P. and Zhong, W.(2008) Penalized clustering of large scale functional data with multiple covariates, Journal of the American Statistical Association, 103 (482), 625-636.

• Ma, P., Zhong, W., Feng, Y., and Liu, J. S. (2008) Bayesian functional data clustering for temporal microarray data, International Journal of Plant Genomics, 2008 (2008) Article ID 231897. [Software]

2007

• Leung, Y.F. *, Ma, P.*, and Dowling, J. (2007) Gene expression profiling of zebrafish embryonic retinal pigment epithelium in vivo, Investigative Ophthalmology & Visual Science, 48(2), 881-890. [Microarray Data](* joint first authors)

• Jiang, L., Smith, J. N., Anderson, S. L., Ma, P., Mizzen, C. A., and Kelleher, N. L. (2007) Global assessment of combinatorial post-translational modification of core histones in yeast using contemporary mass spectrometry: Lys4 trimethylation correlates with degree of acetylation on the same H3 tail, Journal of Biological Chemistry, 282(38): 27923-34.

• van der Hilst, R.D., de Hoop. M.V., Wang, P., Shim,S.-H., Ma, P., Tenorio, L. (2007) Seismo-stratigraphy and thermal structure of Earth's core-mantle boundary region, Science, 315(5820), 1813-1817. [Supplementary material]

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• Ma, P., Wang, P., Tenorio, L., de Hoop, M. V., and van der Hilst, R. D. (2007) Imaging of structure at and near the core mantle boundary using a generalized Radon transform: 2. Statistical inference of singularities, Journal of Geophysical Research , 112, B08303, doi:10.1029/2006JB004513.

2006

• Wang, P., de Hoop, M. V., van der Hilst, R. D., Ma, P., and Tenorio, L. (2006) Imaging of structure at and near the core mantle boundary using a generalized Radon transform: 1. Construction of image gathers, Journal of Geophysical Research, 111, B12304, doi:10.1029/2005JB004241.

• The article is featued in SIAM: Society for Industrial and Applied Mathematics

• Yuan, G.C. *, Ma, P.*, Zhong, W., and Liu, J. S. (2006) Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae, Genome Biology, 7(8):R70. [Supplementary material] (* joint first authors)

• Ma, P.*, Castillo-Davis, C.*, Zhong, W., and Liu, J. S. (2006) A data-driven clustering method for time course gene expression data, Nucleic Acids Research, 34(4), 1261-1269. [Software](* joint first authors)

2005

• Zhong, W., Zeng, P., Ma , P., Liu, J. S., and Zhu, Y. (2005) RSIR: regularized sliced inverse regression for motif discovery, Bioinformatics, 21(22), 4169-4175. [Software]

• Gu, C. and Ma, P. (2005) Optimal smoothing in nonparametric mixed-effect models, Annals of Statistics, 33(3), 1357-1379. [Software]

• Gu, C. and Ma, P. (2005) Generalized nonparametric mixed-effect models, Journal of Computational and Graphical Statistics, 14(2), 485-504. [Software]

2004

• Vio, R., Ma, P., Zhong, W., Nagy, J., Tenorio, L., and Wamsteker, W. (2004) Estimation of regularization parameters in multiple-image deblurring, Astronomy & Astrophysics, 423, 1179--1186.