PUBLICATIONS

PAPERS IN PRESS

This page has not been updated regularly since 2023

Please see PI's Google Scholar profile for complete publication list

Link to Google Scholar Profile

*Underlined denoted group member

    Preprints

  1. Li, K., Li, J., Wang, X., Kuan, P. (2022). Mixture Network Regularization of Generalized Linear Model With Application in Genomics Data. bioRxiv, 678029.
    Software: Rpackage glmaag
    [Article Link]

    2. 2023

  2. Natale, G., Kritikos, M., Kuan, P., Carr, M., Yang, X., Yang, Y., Kotov, R., Bromet, E., Clouston, S., Luft, B (2023). Glial suppression and post-traumatic stress disorder: A cross-sectional study of 1,520 world trade center responders. Brain, Behavior, & Immunity-Health , 30, 100631
    [PubMed] [Article Link]

  3. Kritikos, M., Diminich, E., Meliker, J., Mielke, M., Bennett, D., Finch, C., Gandy, S., Carr, M., Yang, X., Kotov, R., Kuan, P., Bromet, E., Clouston, S., Luft, B. (2023). Plasma amyloid beta 40/42, phosphorylated tau 181, and neurofilament light are associated with cognitive impairment and neuropathological changes among World Trade Center responders: A prospective cohort study of exposures and cognitive aging at midlife. Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring , 15 (1): e12409
    [PubMed] [Article Link]

  4. Gorlov, I., Conway, K., Edmiston, S., Parrish, E., Hao, H., Amos, C., Tsavachidis, S., Gorlova, O., Begg, C., Hernando, E., Cheng, C., Shen, R., Orlow, I., Luo, L., Ernstoff, M., Kuan, P., Ollila, D., Tsai, S., Berwick, M., Thomas N. (2023). Methylation of nonessential genes in cutaneous melanoma-Rule Out hypothesis. Melanoma Research , 33 (3): 163-172
    [PubMed] [Article Link]

  5. Orlow, I., Sadeghi, K., Edmiston, S., Kenney, J., Lezcano, C., Wilmott, J., Cust, A., Scolyer, R., Mann, G., Lee, T., Burke, H., Jakrot, V., Shang, P., Ferguson, P., Boyce. T., Funchain, P., Ko, J., Ngo, P., Rees, J., O'Connell, K., Hao, H., Parrish, E., Conway, K., Googe, P., Ollila, D., Moschos, S., Hernando, E., Hanniford, D., Argibay, D., Amos, C., Lee, J., Osman, I., Luo, L., Kuan, P., Aurora, A., Rothberg, B., Bosenberg, M., Gerstenblith, M., Thompson, C., Bogner, P., Gorlov, I., Holmen, S., Brunsgaard, E., Saenger, Y., Shen, R., Seshan, V., Nagore, E., Ernstoff, M., Busam, K., Begg, C., Thomas, N., Berwick, M. (2023). InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. Plos one , 18 (4): e0269324
    [PubMed] [Article Link]

  6. Mann, F., Clouston, S., Cuevas, A., Waszczuk, M., Kuan, P., Carr, M., Docherty, A., Shabalin, A., Gandy, S., Luft, B. (2023). Genetic Liability, Exposure Severity, and Post-Traumatic Stress Disorder (PTSD) Predict Cognitive Impairment in World Trade Center Responders. Journal of Alzheimer's Disease 1-12
    [PubMed] [Article Link]

  7. Waszczuk, M., Kuan, P., Yang, X., Miao, J., Kotov, R., Luft, B. (2023). Discovery and replication of blood-based proteomic signature of PTSD in 9/11 responders. Translational Psychiatry 13 (1): 8
    [PubMed] [Article Link]

  8. Feng, Q., Liu, P., Kuan, P., Zou, F., Chen, J., Li, J. (2023). A network approach to compute hypervolume under receiver operating characteristic manifold for multi-class biomarkers. Statistics in Medicine. 42 (6): 834-859
    [Article Link]

  9. Cui, Y., Dong, G., Kuan, P., Huang, B. (2023). Evidence synthesis analysis with prioritized benefit outcomes in oncology clinical trials. Journal of Biopharmaceutical Statistics. 1-17
    [Article Link]

    10. 2022

  10. Song, J., Kuan, P. (2022). A systematic assessment of cell type deconvolution algorithms for DNA methylation data. Briefings in Bioinformatics. bbac449
    Software: Rpackage methylDeConv
    [PubMed] [Article Link]

  11. Koraishy, F., Mann, F., Waszczuk, M., Kuan, P., Jonas, K., Yang, X., Docherty, A., Shabalin, A., Clouston, S., Kotov, R., Luft, B. (2022). Polygenic association of glomerular filtration rate decline in world trade center responders. BMC Nephrology. 23 (1): 1-10
    [PubMed] [Article Link]

  12. Kuan, P., Yang, X., Kotov, R., Clouston, S., Bromet, E., Luft, B. (2022). Metabolomics analysis of post-traumatic stress disorder symptoms in World Trade Center responders. Translational psychiatry. 12 (1): 1-7
    [PubMed] [Article Link]

  13. Li, K. , Yao, S., Zhang, Z., Cao, B., Wilson, C., Kalos, D., Kuan, P., Zhu, R., Wang, X. (2022). Efficient gradient boosting for prognostic biomarker discovery. Bioinformatics. 38 (6): 1631-1638
    [PubMed] [Article Link]

  14. Luo, L., Shen, R., Arora, A., Orlow, I., Busam, K., Lezcano, C., Lee, T., Hernando, E., Gorlov. I., Amos, C., Ernstoff, M., Seshan, V., Cust, A., Wilmott, J., Scolyer, R., Mann, R., Nagore, E., Funchain, P., Ko, J., Ngo, P., Edmiston, S., Conway, K., Googe, P., Ollila, D., Lee, J., Fang, F., Rees, J., Thompson. C., Gerstenblith, M., Bosenberg, M., Rothberg, B., Osman, I., Saenger, Y., Reynolds, A., Schwartz, M., Boyce, T., Holmen, S., Brunsgaard, E., Bogner, P., Kuan, P., Wiggins, C., Thomas, N., Begg, C., Berwick, M., InterMEL. (2022). Landscape of mutations in early stage primary cutaneous melanoma: An InterMEL study. Pigment Cell and Melanoma Research. 35 (6): 605-612
    [PubMed] [Article Link]

  15. Clouston, S., Kritikos, M., Huang, C., Kuan, P., Vaska, P., Pellecchia, A., Santiago-Michels, S., Carr, M., Gandy, S., Sano, M., Bromet, E., Lucchini, R., Luft, B. (2022). Reduced cerebellar cortical thickness in World Trade Center responders with cognitive impairment. Translational psychiatry. 12 (1): 1-9
    [PubMed] [Article Link]

  16. Podgorniak, T., Dhanasiri, A., Chen, X., Ren, X., Kuan, P., Fernandes, J. (2022). Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics. 1-18
    [PubMed] [Article Link]

  17. Waszczuk, M, Docherty, A, Shabalin, A, Miao, M, Kuan, P., Bromet, E., Kotov, R., Luft. B.J. (2022). Polygenic Prediction of PTSD Trajectories in 9/11 Responders. Psychological Medicine. 52 (10): 1981-198.
    [PubMed] [Article Link]

  18. Conway, K., Tsai, Y., Edmiston, S., Parker, J., Parrish, E., Hao, H., Kuan, P., Scott, G., Frank, J., Googe, P., Ollila, D., Thomas, N. (2022). Characterization of the CpG island hypermethylated phenotype (CIMP) subclass in primary melanomas. Journal of Investigative Dermatology. 142 (7): 1869-1881.e10.
    [PubMed] [Article Link]

    19. 2021

  19. Kuan, P., Yang, X., Ren, X. , Che, C. , Waszczuk, M., Kotov, R., Clouston, S., Singh, P., Glenn, S., Cortes Gomez, E., Wang, J., Bromet, E. and Luft, B. (2021). Mapping the transcriptomics landscape of post-traumatic stress disorder symptoms and dimensions in World Trade Center responders. Translational Psychiatry. 11 (1): 1-9
    [PubMed] [Article Link]

  20. Kuan, P., Ren, X. , Clouston, S., Yang, X., Jonas, K., Kotov, R., Bromet, E. and Luft, B. (2021). PTSD is associated with accelerated transcriptional aging in World Trade Center responders. Translational Psychiatry. 11 (1): 1-8
    [PubMed] [Article Link]

  21. Kuan, P., Clouston, S., Yang, X., Che, C. , Gandy, S., Kotov, R., Bromet, E., Luft, B. (2021). Single-cell transcriptomics analysis of mild cognitive impairment in World Trade Center disaster responders. Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring. 13 (1): e12154
    [PubMed] [Article Link]

  22. Koraishy, F., Coca, S., Cohen, B., Scherrer, J., Mann, F., Kuan, P., Luft, B., Clouston, S. (2021). The Association of Post-Traumatic Stress Disorder with longitudinal change in Glomerular Filtration Rate in World Trade Center responders. Psychosomatic Medicine. In Press
    [PubMed] [Article Link]

  23. Chen, A., Clouston, S., Kritikos, M., Richmond, L., Meliker, J., Mann, F., Santiago-Michels, S., Pellecchia, A., Carr, M., Kuan, P., Bromet, E., Luft, B. (2021). A deep learning approach for monitoring parietal-dominant Alzheimer's disease at midlife. Brain Communications. 3 (3): fcab145
    [PubMed] [Article Link]

  24. Wilson, C., Li, K. , Sun, Q., Kuan, P. , Wang, X. (2021). Fenchel duality of Cox partial likelihood with an application in survival kernel learning. Artificial Intelligence In Medicine. 116: 102077
    [PubMed] [Article Link]

  25. Diminich, E., Clouston, S., Kranidis, A., Kritikos, M., Kotov, R., Kuan, P., Carr, M., Bromet, E., Luft, B. (2021). Chronic posttraumatic stress disorder and comorbid cognitive and physical impairments in World Trade Center responders. Journal of Traumatic Stress. 34 (3): 616-627.
    [PubMed] [Article Link]

    26. 2020

  26. Kuan, P., Clouston, S., Yang, X., Kotov, R., Bromet, E. and Luft, B.J. (2020). Molecular linkage between post-traumatic stress disorder and cognitive impairment: a targeted proteomics study of World Trade Center responders. Translational Psychiatry. 10 (1): 1-15
    [PubMed] [Article Link]

  27. Ren, X., Kuan, P. (2020). RNAAgeCalc: A multi-tissue transcriptional age calculator. PLOS One. 15 (8): e0237006
    Software: Rpackage RNAAgeCalc
    [PubMed] [Article Link]

  28. Ren, X., Kuan, P. (2019). Negative Binomial Additive Model for RNA-Seq Data Analysis. BMC Bioinformatics. (21): 1-15
    Software: Rpackage NBAMSeq
    [PubMed] [Article Link]

  29. Smith, A.K., Ratanatharathorn, A., Maihofer, A.X., Naviaux, R.K., ..., Kuan, P., ..., Uddin, M., Nievergelt, C. M. (2020). Epigenome-wide meta-analysis of PTSD across 10 military and civilian cohorts identifies methylation changes in AHRR. Nature Communications. 11 (1): 1-9
    [PubMed] [Article Link]

  30. Yang, J., Kuan, P., Li, J. (2020). Non-monotone transformation of biomarkers to improve diagnostic and screening accuracy in a DNA methylation study with trichotomous phenotypes. Statistical Methods in Medical Research. 29 (8): 2360-2389.
    [PubMed] [Article Link]

    31. 2019

  31. Clouston, S., Kuan, P., Kotov, R., Mukherjee, S., Thompson-Carino, P., Bromet, E., Luft, B. (2019). Risk factors for incident prostate cancer in a cohort of world trade center responders. BMC Psyhiatry. 19 (1): 1-8
    [PubMed] [Article Link]

  32. Wilson, C., Li, K., Yu, X., Kuan, P., Wang, X. (2019). Multiple-kernel learning for genomic data mining and prediction. BMC Bioinformatics. 20 (1): 426
    [PubMed] [Article Link]

  33. Kuan, P., Yang, X., Ren, X., Kotov, R., Clouston, S., Waszczuk, M., Singh, P., Glenn, S., Cortes Gomez, E., Wang, J., Bromet, E., Luft, B. (2019). Cell type specific gene expression patterns associated with posttraumatic stress disorder in World Trade Center responders. Translational Psychiatry. 9 (1): 1-11
    [PubMed] [Article Link]

  34. Thomas, N., Edmiston, S., Tsai, Y., Parker, J., Googe, P., Busam, K., Scott,, G., Zedek, D., Parrish, E., Hao, H., Slater, N., Pearlstein, M., Frank, J., Kuan, P., Ollila, D., Conway, K. (2019). Utility of TERT Promoter Mutations for Cutaneous Primary Melanoma Diagnosis. The American Journal of Dermatopathology. 41 (4): 264-272
    [PubMed] [Article Link]

  35. Li, K., He, K., Nie, L., Zhu, W., Kuan, P. (2019) Nonparametric Tests for Jump Detection via False Discovery Rate Control: A Monte Carlo Study. Journal of Risk Model Validation. 13 (3): 23-44
    Software: Rpackage JumpTest
    [Article Link]

  36. Conway, K., Edmiston, S., Parker, J., Kuan, P., Tsai, Y., Groben, P., Zedek, D., Scott, G., Frank, J., Parrish, E., Carson, C., Hao, H., Pearlstein, M., Wilkerson, M., Zhao, X., Moschos, S., Ollila, D., Thomas, N. (2019). Identification of a robust methylation predictor for melanoma diagnosis. Journal of Investigative Dermatology. 139 (6): 1349-1361
    [PubMed] [Article Link]

  37. Ren, X., Kuan, P. (2019). methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics. 35 (11): 1958-1959
    Software: Rpackage methylGSA
    [PubMed] [Article Link]

  38. Kuan, P., Mi, Z., Georgopoulos, P., Luft, B., Boffetta, P. (2019). Enhanced exposure assessment and genome-wide DNA methylation in World Trade Center disaster responders. European Journal of Cancer Prevention. 28 (3): 225-233
    [PubMed] [Article Link]

  39. Huang, B., Talukder, E., Han, L., Kuan, P. (2019). Quantitative Decision Criteria in Phase 2 Oncology Clinical Trials. Journal of Biopharmaceutical Statistics. 29 (1): 189-202.
    [PubMed] [Article Link]

  40. Thomas, N.,Edmiston, S., Tsai, Y., Parker, J., Googe, P., Busam, K., Groben, P., Scott, G., Zedek, D., Parrish, E., Hao, H., Slater, N., Pearlstein, M., Frank, J., Kuan, P., Ollila, D., Conway, K. (2019). Utility of TERT promoter mutations for cutaneous primary melanoma diagnosis. The American Journal of Dermatopathology. 41 (1): 264-272.
    [PubMed] [Article Link]

    41. 2018

  41. Uddin, M., Ratanatharathorn, A., Armstrong, D., Kuan, P., Aiello, A., Bromet, E., Galea, S., Koenen, K., Luft, B., Ressler, K., Wildman, D., Nievergelt, C., Smith, A. (2018). Epigenetic meta-analysis across three civilian cohorts identifies NRG1 and HGS as blood-based biomarkers for post-traumatic stress disorder. Epigenomics. 10 (12): 1585-1601.
    [PubMed] [Article Link]

  42. Wu, M., Kuan, P. (2018). A Guide to Illumina BeadChip Data Analysis. Methods Mol Biol., 1708: 303-330.
    [PubMed] [Article Link]

  43. Huang, B., Kuan, P. (2018). Comparison of the restricted mean survival time with the hazard ratio superiority trials with a time-to-event endpoint. Pharmaceutical Statistics, 17: 202-213.
    [PubMed] [Article Link]

    44. 2017

  44. Kuan, P., Waszczuk, M., Kotov, R., Marsit, C., Guffanti, G., Yang, X., Koenen, K., Bromet, E., Luft, B. (2017). An epigenome-wide DNA methylation study of PTSD and depression in World Trade Center responders. Translational Psychiatry, 7(6): e1158.
    [PubMed] [Article Link]

  45. Kuan, P., Powers, S., He, S., Li, K., Zhao, X., Huang, B. (2017). A systematic evaluation of nucleotide properties for CRISPR sgRNA design. BMC Bioinformatics, 18: 297.
    Software: Rpackage predictSGRNA
    [PubMed] [Article Link]

  46. Kuan, P., Waszczuk, M., Kotov, R., Yang, X., Singh, P., Glenn, S., Cortes Gomez, E., Wang, J., Bromet, E., Luft, B. (2017). Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study. Translational Psychiatry, 7:1297.
    [PubMed] [Article Link]

  47. Kuan, P., Song, J., He, S. (2017). methyldmv: Simultaneous detection of differential DNA methylation and variability with confounder adjustment. Pacific Symposium of Biocomputing, 22: 461-472.
    Software: Rpackage methylDMV
    [PubMed] [Article Link]

  48. Poe, J., Jia, W., Su, H., Anand, S., Rose, J., Tata, P., Suthers, A., Jones, C., Kuan, P., Vincent, B., Serody, J., Horwitz, Pavletic, S., Hakim, F., Owzar, K., Zhang, D., Blazar, B., Siebel, C., Chao, N., Maillard, I., Sarantopoulos, S. (2017) An Aberrant NOTCH2-BCR Signaling Axis in B Cells from Patients with Chronic GVHD. Blood, 130 (19): 2131-2145.
    [PubMed] [Article Link]

  49. Ratanatharathorn, A., Boks, M., Maihofer, A., Aiello, A., Amstadter, ., Ashley-Koch, A., Baker, D., Beckham, J., Bromet, E., Dennis, M., Garrett, M., Geuze, E., Guffanti, G., Hauser, M., Kilaru, V., Kimbrel, N., Koenen, K., Kuan, P., Logue, M., Luft, B., Miller, M., Mitchell, C., Nugent, N., Ressler, K., Rutten, B., Stein, M., Vermetten, E., Vinkers, C., Youssef, N., Uddin, M., Nievergelt, C., Smith, A. (2017) Epigenome-wide Association of PTSD from Heterogeneous Cohorts with a Common Multi-Site Analysis Pipeline. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 174(6): 619-630.
    [PubMed] [Article Link]

  50. Conway, K., Edmiston, S., Parrish, E., Bryant, C., Tse, C., Swift-Scanlan, T., McCullough, L., Kuan, P. (2017) Breast tumor DNA methylation patterns associated with smoking in the Carolina Breast Cancer Study. Breast Cancer Research and Treatment, 163(2): 349-361.
    [PubMed] [Article Link]

    51. 2016

  51. Kuan, P., Huang, B. (2016). Opportunities of enrichment designs in the era of precision medicine. In JSM Proceedings, Biopharmaceutical Section, Marriott Wardman Park, Washington D.C.: American Statistical Association., 3990-4001.
    [Article Link]

  52. Huang, B., Kuan, P. (2016). Improved Designs and Analyses of Safety and Efficacy in Immuno-Oncology. In JSM Proceedings, Biopharmaceutical Section, Chicago, Illinois: American Statistical Association, 1001-1013.
    [Article Link]

    53. 2015

  53. 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. Journal of the American Statistical Association, 110 (511): 975-986.
    [PubMed] [Article Link]

  54. 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. Cell Reports, 11 (3): 390-404.
    [PubMed] [Article Link]

  55. Xiong, L., Kuan, P., Tian, J., Keles, S., Wang, S. (2015). Multivariate boosting for integrative analysis of high dimensional cancer genomic data. Cancer Informatics, 13 (Suppl 7): 123-31.
    [PubMed] [Article Link]

  56. 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. Cancer Epidemiology, Biomarkers and Prevention, 24 (6): 921- 930.
    [PubMed] [Article Link]

  57. 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. Clinical Cancer Research, 21 (9): 2167- 2176.
    [PubMed] [Article Link]

    58. 2014

  58. 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.
    [PubMed] [Article Link]

  59. Kuan, P. (2014). Propensity score method for partially matched omics studies. Cancer Informatics, 13 (Suppl 7): 1-10.
    [PubMed] [Article Link]

  60. 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.
    [PubMed] [Article Link]

  61. 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 (5): 450.
    [PubMed] [Article Link]

  62. 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. Applied Immunohistochemistry and Molecular Morphology, 23 (9): 633-645.
    [PubMed] [Article Link]

  63. 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.
    [PubMed] [Article Link]

  64. 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.
    [PubMed] [Article Link]

  65. 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.
    [PubMed] [Article Link]

  66. 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.
    [PubMed] [Article Link]

  67. 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.
    [PubMed] [Article Link]

    68. 2013

  68. 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.
    [PubMed] [Article Link]

  69. 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. (2013). DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq. Nucleic Acids Research, 41 (2): e39. doi: 10.1093/nar/gks1026.
    [PubMed] [Article Link]

  70. 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.
    [PubMed] [Article Link]

  71. 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.
    [PubMed] [Article Link]

  72. 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.
    [PubMed] [Article Link]

  73. 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). MERTK receptor tyrosine kinase is a therapeutic target in melanoma. Journal of Clinical Investigation, 123 (5): 2257-2267.
    [PubMed] [Article Link]

    74. 2012

  74. 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
    [PubMed] [Article Link]

  75. 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.
    [PubMed] [Article Link]

  76. 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.
    [PubMed] [Article Link]

  77. 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.
    [PubMed] [Article Link]

  78. 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.
    [PubMed] [Article Link]

  79. 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.
    [PubMed] [Article Link]

    80. 2011

  80. 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
    [PubMed] [Article Link]

  81. 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.
    [PubMed] [Article Link]

  82. 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.
    [PubMed] [Article Link]

  83. 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, 6 (2): 80-86.
    [PubMed] [Article Link]

  84. 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, 24 (2): 352-360.
    [PubMed] [Article Link]

    85. 2010

  85. 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
    [PubMed] [Article Link]

  86. 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.
    [PubMed] [Article Link]

    87. 2009

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

  88. Peters, J., Mooney, R. A., Kuan, P., Rowland, J., Keles, S. and Landick, R. (2009). Rho directs widespread termination of intragenic and stable RNA transcription. PNAS, 106 (36): 15406-15411.
    [PubMed] [Article Link]

    89. 2008

  89. 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
    [PubMed] [Article Link]

  90. 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
    [PubMed] [Article Link]

  91. 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.
    [PubMed] [Article Link]

  92. Chung, N., Zhang, X.D., Kreamer, A., Locco, L., Kuan, P., Bartz, S., Linsley, 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.
    [PubMed] [Article Link]

    93. Technical Reports

  93. 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.
    [Article Link]

  94. 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.
    [Article Link]