Publications

PAPERS IN PRESS

    2015

  1. Sun, W., Liu, Y., Crowley, J., Chen, T., Zhou, H., Chu, H., Huang, S., Kuan, P.,
    Li, Y., Miller, D., Shaw, G., Wu, Y., Zhabotynsky, V., McMillan, L., Zou, F.,
    Sullivan, P., de Villena, F. (2015). IsoDOT Detects Differential RNA-isoform Usage
    with respect to a Categorical or Continuous Covariate with High Sensitivity and
    Specificity. To appear in the Journal of the American Statistical Association.

  2. Stuhlmiller, T., Miller, S., Zawistowski, J., Nakamura, K., Beltran, A., Duncan, J.,
    Angus, S., Collins, K., Granger, D., Reuther, R., Graves, L., Gomez, S., Kuan, P.,
    Parker, J., Chen, X., Sciaky, N., Carey, L., Earp, H., Jin, J., Johnson, G. (2015).
    Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast
    Cancer by Targeting BET Family Bromodomains. To appear in Cell Reports.

  3. Xiong, L., Kuan, P., Tian, J., Keles, S., Wang, S. (2015). Multivariate boosting
    for integrative analysis of high dimensional cancer genomic data.
    To appear in Cancer Informatics.

  4. Conway, K., Edmiston, S., Tse, C., Bryant, C., Kuan, P., Hair, B., Parrish, E.,
    May, R., Swift-Scanlan, T. (2015). Racial variation in breast tumor promoter
    methylation in the Carolina Breast Cancer Study. To appear in Cancer Epidemiology,
    Biomarkers and Prevention
    .

  5. Carson, C., Moschos, S., Edmiston, S., Darr, D., Nikolaishvili-Feinberg, N.,
    Groben, P.,Zhou, X., Kuan, P., Pandey, S., Chan, K., Jordan, J., Hao, H.,
    Frank, J., Hopkinson, D., Gibbs, C., Alldredge, V., Parrish, E., Hanna, S.,
    Berkowitz, P., Rubenstein, D., Miller, R., Bear, J., Ollila, D., Sharpless, N.,
    Conway, K., Thomas, N. (2015). IL-2 Inducible T-cell Kinase, a Novel Therapeutic
    Target in Melanoma. To appear in Clinical Cancer Research.

  6. 2014

  7. Kuan, P. (2014). Covariate adjusted differential variability analysis of DNA
    methylation with propensity score method. Statistical Applications
    in Genetics and Molecular Biology
    , 13 (6): 645-658.

  8. Kuan, P. (2014). Propensity score method for partially matched omics studies.
    Cancer Informatics, 13 (Suppl 7): 1-10.

  9. Huang, B., and Kuan, P. (2014). Time-to-event continual reassessment
    method incorporating treatment cycle information with application to an
    oncology phase I trial. Biometrical Journal, 56 (6): 933-946. .

  10. Conway, K., Edmiston, S., May, R., Kuan, P., H, Chu., Bryant, C., Tse, C.,
    Swift-Scanlan, T., Troester, M., Geradts, J., Millikan, R. (2014). DNA
    methylation profiling in the Carolina Breast Cancer Study defines cancer
    subclasses differing in clinicopathologic characteristics.
    Breast Cancer Research, 16 (450): doi:10.1186/s13058-014-0450-6. .

  11. Speck, O., Tang, W., Morgan, D., Kuan, P., Meyes, M., Dominguez, R.,
    Martinez, E., Gulley, M. (2014). Three molecular subtypes of gastric
    adenocarcinoma have distinct histochemical features reflecting Epstein-Barr
    virus infection status and neuroendocrine differentiation. To appear in
    Applied Immunohistochemistry and Molecular Morphology.

  12. Thomas, N., Slater, N., Edmiston, S., Zhou, X., Kuan, P., Groben, P., Carson, C.,
    Hao, H., Parrish, E., Moschos, S., Berwick, M., Ollila, D., Conway, K. (2014)
    DNA-methylation Profiles in Primary Cutaneous Melanomas are Associated with
    Clinically Significant Pathologic Features. Pigment Cell and Melanoma Research,
    27 (6): 1097-1105.

  13. Taylor, J., Zhang, T., Herenu, C., Messi, M., Wang, Z., Kuan, P., Delbono, O.
    (2014). The Cavβ1a subunit is a transcription factor that suppresses myogenin
    in muscle progenitor cells. Journal of Cell Biology, 205 (6) 829-846.

  14. Makowski, L., Zhou, C., Zhong, Y., Kuan, P., Cheng, F., Difurio, M., Bae-Jump, V.
    (2014). Obesity increases tumor aggressiveness in a genetically engineered
    mouse model of serous ovarian cancer. Gynecologic Oncology, 133 (1): 90-97.

  15. Wu, M., Joubert, B. Kuan, P., Haberg, S., Nystad, W., Peddada, S., London, S.
    (2014). A Systematic Assessment of Normalization Approaches for the Infinium
    450k Methylation Platform. Epigenetics, 9 (2): 318-329.

  16. Simon, J., Hacker, K., Singh, D., Brannon, A., Parker, J., Weiser, M., Ho, T.,
    Kuan, P., Jonasch, E., Furey, T., Prins, J., Lieb, J., Rathmell, K., Davis. I.
    (2014). Variation in chromatin accessibility in human kidney cancer links H3K36
    methyltransferase loss with widespread RNA processing defects.
    Genome Research, 24 (2): 241-250.

  17. 2013

  18. Kuan, P., and Huang, B. (2013). A Simple and Robust Method for Partially
    Matched Samples Using the P-Values Pooling Approach.
    Statistics in Medicine, 32 (19): 3247-3259.

  19. Huff, L., DeCristo, M., Trembath, D., Kuan, P., Yim, M., Liu, J., Cook, D.,
    Miller, C., Der, C., Cox, A. (2013). The role of Ect2 nuclear RhoGEF activity in
    ovarian cancer cell transformation. Genes & Cancer, 4 (11-12): 460-475.

  20. Cooper, M., Cox, N., Zimmerman, E., Dewar, B., Duncan, J., Whittle, M.,
    Nguyen, T., Jones, L., Ghoseroy, S., Smalley, D., Kuan, P., Richards, K.,
    Christopherson, R., Jin, J., Frye, S., Johnson, G., Baldwin, A., Graves, L.
    (2013). Application of Multiplexed Kinase Inhibitor Beads to Study Kinome
    Adaptations in Drug Resistant Leukemia. PLoS One, 8 (6): e66755.

  21. Hanna, S., Krishnan, B., Bailey, S., Moschos, S., Kuan, P., Shimamura, T.,
    Osborne, L., Siegel, M., Duncan, L., O'Brien, T., Superfine, R., Miller, R.,
    Simon, C., Wong, K., Kim, W. (2013). HIF1-alpha and HIF2-alpha independently
    activate SRC to promote melanoma invasion and metastases.
    Journal of Clinical Investigation, 123 (5): 2078-2093.

  22. Schlegel, J., Sambade, M., Sather, S., Moschos, S., Tan, A., Wingers, A.,
    DeRykere, D., Carson, C., Trembath, D., Tentler, J., Eckhardt, G., Kuan, P.,
    Hamilton, R., Duncan, L., Miller, R., Nikolaishvili-Feinberg, N., Midkiff, B.,
    Wang, X., Liu, J., Zhang, W., Yang, C., Frye, S., Earp, S., Shields, J.,
    Graham, D. (2013). Mer receptor tyrosine kinase is a novel therapeutic target
    in melanoma. Journal of Clinical Investigation, 123 (5): 2257-2267.

  23. 2012

  24. Kuan, P., and Chiang, D. (2012). Integrating Prior Knowledge in Multiple Testing
    under Dependence with Applications to Detecting Differential DNA Methylation.
    Biometrics, 68 (3): 774-783.
    Software: Rpackage NHMMfdr

  25. Huebert, D.J., Kuan, P., Keles, S., and Gasch, A.P. (2012). Dynamic changes
    in nucleosome occupancy are not predictive of gene expression dynamics
    but linked to transcription and chromatin regulators.
    Molecular and Cellular Biology, 32 (9): 1645-1653.

  26. Duncan, J., Whittle, M., Nakamura, K., Abell, A., Midland, A., Zawistowski, J.,
    Johnson, N., Granger, D., Jordan, N., Darr, D., Usary, J., Kuan, P., Smalley, D.,
    Major, B., He, X., Hoadley, K., Sharpless, N., Perou, C., Gomez, S., Chen, X.,
    Jin, J., Frye, S., Earp, S., Graves, L., and Johnson, G. (2012). Dynamic
    Reprogramming of the Kinome in Response to Targeted MEK Inhibition in
    Triple Negative Breast Cancer. Cell, 142 (2): 307-321.

  27. Hu, Y., Huang, Y., Du, Y., Orellana, C., Singh, D., Johnson, A., Monroy, A.,
    Kuan, P. , Hammond, S., Makowski, L., Randell, S., Chiang, D., Hayes,
    D., Jones, C., Liu, Y., Prins, J., Liu, J. (2012). DiffSplice: the Genome-Wide
    Detection of Differential Splicing Events with RNA-seq.
    Nucleic Acids Research, 41 (2): e39. doi: 10.1093/nar/gks1026.

  28. Tang, W., Morgan, D., O Meyers, M., Dominguez, R., Martinez, E., Kakudo, K.,
    Kuan, P., Banet, N., Muallem, H., Woodward, K., Speck, O., Gulley, M. (2012).
    Epstein-Barr Virus Infected Gastric Adenocarcinoma Expresses Latent and Lytic
    Viral Transcripts and has a Distinct Human Gene Expression Profile.
    Infectious Agents and Cancer, 7 (21), doi:10.1186/1750-9378-7-21.

  29. Wang, P., Dong, Q., Chong, Z., Kuan, P., Liu, Y., Jeck, W., Jiang, W., Savich, G.,
    Tan, T., Andersen, J., Auman, T., Hoskins, J., Misher, A., Moser, C., Yourstone, S.,
    Kim, J., Cibulskis, K., Getz, G., Hunt, H.,Thorgeirsson, S., Roberts, L., Ye, D.,
    Guan, K., Xiong, Y., Qin, L., Chiang, D.Y. (2012). Mutations in Isocitrate
    Dehydrogenase 1 and 2 are Associated with DNA Hypermethylation in Intrahepatic
    Cholangiocarcinomas. Oncogene, 32 (25): 3091-3100.

  30. Sampey, B., Freemerman, A., Zhang, J., Kuan, P., Galanko, J., O'Connell, T.,
    Ilkayeva, O., Muehlbauer, M., Stevens, R., Newgard, C., Brauer, H.,
    Troester, M., and Makowski, L. (2012). Mitochondrial-Derived Lipid Biomarkers
    that Drive Obesity-Associated Inflammation. PLoS One, 7 (6): e38812.
    doi:10.1371/journal.pone.0038812.

  31. 2011

  32. Kuan, P., Chung, D., Pan, G., Thomson, J., Stewart, R., and Keles, S. (2011).
    A Statistical Framework for the Analysis of ChIP-Seq Data. Journal of the
    American
    Statistical Association, doi:10.1198/jasa.2011.ap09706.
    Software: Rpackage mosaics

  33. Chung, D., Kuan, P., Li, B., Sanalkumar. R., Liang, K., Bresnick, E.,
    Dewey, C., and Keles, S. (2011). Discovering transcription factor binding
    sites in highly repetitive regions of genomes with multi-read analysis of
    ChIP-seq data. PLoS Computational Biology, 7 (7): e1002111.
    doi:10.1371/journal.pcbi.1002111.

  34. Stevens, E., Banet, N., Onesto, C., Plachco, A., Alan, J., Nikolaishvili-Feinberg, N.,
    Midkiff, B., Kuan, P., Liu, J., Miller, R., Vigil, D., Graves, L., and Channing-Der J.
    (2011). RhoGDI2 antagonizes ovarian carcinoma growth, invasion and metastasis.
    Small GTPases, 2 (4): 202-210.

  35. Chu, H., Lofgren, E., Halloran, M.E., Kuan, P., Hudgens, M., and Cole, S.R.
    (2011). Performance of rapid influenza H1N1 diagnostic tests: a meta-analysis.
    Influenza and Other Respiratory Viruses, doi: 10.1111/j.1750-2659.2011.00284.x.

  36. Conway, K., Edmiston, S., Khondker, Z., Groben, P., Zhou, X., Chu, H.,
    Kuan, P., Hao, H., Carson, C., Berwick, M., Olilla, D., and Thomas, N.
    (2011). DNA-methylation profiling distinguishes malignant melanomas from
    benign nevi. Pigment Cell & Melanoma Research:
    doi: 10.1111/j.1755-148X.2011.00828.x.

  37. 2010

  38. Kuan, P., Wang, S., Zhou, X., and Chu, H. (2010). A statistical framework for
    Illumina DNA methylation arrays. Bioinformatics, 26 (22): 2849-2855.
    Software: Rpackage LumiWCluster

  39. Zacher, B., Kuan, P., and Tresch, A. (2010). Starr: Simple Tiling ARRay
    analysis of Affymetirx ChIP-chip data. BMC Bioinformatics, 11 (194):
    doi:10.1186/1471- 2105-11-194.

  40. 2009

  41. Kuan, P., Huebert, D., Gasch, A., and Keles, S. (2009). A non-homogeneous
    hidden state model on first order differences for automatic detection of nu-
    cleosome positions. Statistical Applications in Genetics and Molecular Biology,
    8, Article 29.

  42. Peters, J., Mooney, R. A., Kuan, P., Rowland, J., Keles, S. and Landick, R.
    (2009). Transcription Termination Factor Rho Targets Stable RNAs.
    PNAS
    , 106 (36): 15406-15411.

  43. 2008

  44. 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.
    Software: Rpackage CMARRT

  45. 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

  46. 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.

  47. 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.

  48. Technical Reports

  49. Kuan, P., Pan, G., Thomson, J., Stewart, R., and Keles, S. (2010).
    A hierarchical semi-Markov model for detecting enrichment with application
    to ChIP-Seq experiments.

  50. Kuan, P. (2009). Statistical methods for the analysis of genomic data from
    tiling arrays and next generation sequencing technologies.
    Ph.D. Dissertation, University of Wisconsin-Madison.