PUBLICATIONS

Kuan, P., Chun, H., and Keles, S. (2008). CMARRT: A tool for the analysis of
ChIP-Chip data from tiling arrays by incorporating the correlation structure.
Pac Symposium of Biocomputing, 515-526. [pdf] Supplementary materials [pdf]
Software: Rpackage CMARRT

Wei, H.*, Kuan, P.*, Tian, S., Yang, C., Nie, J., Sengupta, S., Ruotti, V.,
Jonsdottir, G.A., Keles, S., Thomson, J.A., and Stewart, R. (2008). A study
of the relationships between oligonucleotide properties and hybridization signal
intensities from NimbleGen microarray datasets. Nucleic Acids Research, 36
(9): 2926-2938. * Joint first authors [pdf]

Zhang, X.D., Kuan, P., Ferrer, M., Shu, X., Liu, Y.C., Gates, A.T., Kunapuli,
P., Stec, E.M., Xu, M., Marine S.D., Holder, D.J., Strulovici, B., Heyse, J.F.,
and Espeseth, A.S. (2008). Hit selection with false discovery rate control in
genome-scale RNAi screens. Nucleic Acids Research, 36 (14): 4667-4679. [pdf]

Chung, N., Zhang, X.D., Kreamer, A., Locco, L., Kuan, P., Bartz, S., Lins-
ley, P.S., Ferrer, M., and Strulovici, B. (2008). Median absolute deviation to
improve hit selection for genome-scale RNAi screens. Journal of Biomolecular
Screening, 13 (2): 149-158. [pdf]

Kuan, P., Huebert, D., Gasch, A., and Keles, S. (2008). A non-homogeneous
hidden Markov model on first order differences for automatic detection of nu-
cleosome positions. Technical Report No.1150, University of Wisconsin, Madison.
(submitted). [pdf]

Peters, J., Mooney, R. A., Kuan, P., Rowland, J., Keles, S. and Landick, R.
(2008). Transcription Termination Factor Rho Targets Stable RNAs. (submit-
ted).

Meyer, M., Zella, L., Nerenz, R., Kuan, P., Keles, S. and Pike, J. (2008). The
vitamin D analog gs1790 fails to induce hypercalcemia in vivo as a result of
both gene-selective and receptor-specific actions in calcium-regulating tissues.
(submitted).

Kuan, P., Pan, G., Stewart, R., and Keles, S. (2009). A hierarchical semi-Markov
model for detecting enrichment with application to ChIP-Seq experiments.
Technical Report No.1151, University of Wisconsin, Madison.
(submitted). [pdf]

MANUSCRIPTS IN PREPARATION

A robust permutation test for the analysis of tiling array data.