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Items: 1 to 50 of 58

1.

Non-monotone transformation of biomarkers to improve diagnostic and screening accuracy in a DNA methylation study with trichotomous phenotypes.

Yang J, Kuan PF, Li J.

Stat Methods Med Res. 2019 Oct 23:962280219882047. doi: 10.1177/0962280219882047. [Epub ahead of print]

PMID:
31640479
2.

Multiple-kernel learning for genomic data mining and prediction.

Wilson CM, Li K, Yu X, Kuan PF, Wang X.

BMC Bioinformatics. 2019 Aug 15;20(1):426. doi: 10.1186/s12859-019-2992-1.

3.

Cell type-specific gene expression patterns associated with posttraumatic stress disorder in World Trade Center responders.

Kuan PF, Yang X, Clouston S, Ren X, Kotov R, Waszczuk M, Singh PK, Glenn ST, Gomez EC, Wang J, Bromet E, Luft BJ.

Transl Psychiatry. 2019 Jan 15;9(1):1. doi: 10.1038/s41398-018-0355-8.

4.

Identification of a Robust Methylation Classifier for Cutaneous Melanoma Diagnosis.

Conway K, Edmiston SN, Parker JS, Kuan PF, Tsai YH, Groben PA, Zedek DC, Scott GA, Parrish EA, Hao H, Pearlstein MV, Frank JS, Carson CC, Wilkerson MD, Zhao X, Slater NA, Moschos SJ, Ollila DW, Thomas NE.

J Invest Dermatol. 2019 Jun;139(6):1349-1361. doi: 10.1016/j.jid.2018.11.024. Epub 2018 Dec 6.

PMID:
30529013
5.

Epigenetic meta-analysis across three civilian cohorts identifies NRG1 and HGS as blood-based biomarkers for post-traumatic stress disorder.

Uddin M, Ratanatharathorn A, Armstrong D, Kuan PF, Aiello AE, Bromet EJ, Galea S, Koenen KC, Luft B, Ressler KJ, Wildman DE, Nievergelt CM, Smith A.

Epigenomics. 2018 Dec;10(12):1585-1601. doi: 10.2217/epi-2018-0049. Epub 2018 Nov 20.

6.

methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.

Ren X, Kuan PF.

Bioinformatics. 2019 Jun 1;35(11):1958-1959. doi: 10.1093/bioinformatics/bty892.

PMID:
30346483
7.

Utility of TERT Promoter Mutations for Cutaneous Primary Melanoma Diagnosis.

Thomas NE, Edmiston SN, Tsai YS, Parker JS, Googe PB, Busam KJ, Scott GA, Zedek DC, Parrish EA, Hao H, Slater NA, Pearlstein MV, Frank JS, Kuan PF, Ollila DW, Conway K.

Am J Dermatopathol. 2019 Apr;41(4):264-272. doi: 10.1097/DAD.0000000000001259.

PMID:
30211730
8.

Enhanced exposure assessment and genome-wide DNA methylation in World Trade Center disaster responders.

Kuan PF, Mi Z, Georgopoulos P, Hashim D, Luft BJ, Boffetta P.

Eur J Cancer Prev. 2019 May;28(3):225-233. doi: 10.1097/CEJ.0000000000000460.

PMID:
30001286
9.

Quantitative decision-making in randomized Phase II studies with a time-to-event endpoint.

Huang B, Talukder E, Han L, Kuan PF.

J Biopharm Stat. 2019;29(1):189-202. doi: 10.1080/10543406.2018.1489400. Epub 2018 Jul 3.

PMID:
29969380
10.

Comparison of the restricted mean survival time with the hazard ratio in superiority trials with a time-to-event end point.

Huang B, Kuan PF.

Pharm Stat. 2018 May;17(3):202-213. doi: 10.1002/pst.1846. Epub 2017 Dec 28.

PMID:
29282880
11.

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study.

Kuan PF, Waszczuk MA, Kotov R, Clouston S, Yang X, Singh PK, Glenn ST, Cortes Gomez E, Wang J, Bromet E, Luft BJ.

Transl Psychiatry. 2017 Dec 18;7(12):1297. doi: 10.1038/s41398-017-0050-1.

12.

A Guide to Illumina BeadChip Data Analysis.

Wu MC, Kuan PF.

Methods Mol Biol. 2018;1708:303-330. doi: 10.1007/978-1-4939-7481-8_16.

PMID:
29224151
13.

An aberrant NOTCH2-BCR signaling axis in B cells from patients with chronic GVHD.

Poe JC, Jia W, Su H, Anand S, Rose JJ, Tata PV, Suthers AN, Jones CD, Kuan PF, Vincent BG, Serody JS, Horwitz ME, Ho VT, Pavletic SZ, Hakim FT, Owzar K, Zhang D, Blazar BR, Siebel CW, Chao NJ, Maillard I, Sarantopoulos S.

Blood. 2017 Nov 9;130(19):2131-2145. doi: 10.1182/blood-2017-05-782466. Epub 2017 Aug 29.

14.

Epigenome-wide association of PTSD from heterogeneous cohorts with a common multi-site analysis pipeline.

Ratanatharathorn A, Boks MP, Maihofer AX, Aiello AE, Amstadter AB, Ashley-Koch AE, Baker DG, Beckham JC, Bromet E, Dennis M, Garrett ME, Geuze E, Guffanti G, Hauser MA, Kilaru V, Kimbrel NA, Koenen KC, Kuan PF, Logue MW, Luft BJ, Miller MW, Mitchell C, Nugent NR, Ressler KJ, Rutten BPF, Stein MB, Vermetten E, Vinkers CH, Youssef NA; VA Mid-Atlantic MIRECC Workgroup; PGC PTSD Epigenetics Workgroup, Uddin M, Nievergelt CM, Smith AK.

Am J Med Genet B Neuropsychiatr Genet. 2017 Sep;174(6):619-630. doi: 10.1002/ajmg.b.32568. Epub 2017 Jul 10.

15.

An epigenome-wide DNA methylation study of PTSD and depression in World Trade Center responders.

Kuan PF, Waszczuk MA, Kotov R, Marsit CJ, Guffanti G, Gonzalez A, Yang X, Koenen K, Bromet E, Luft BJ.

Transl Psychiatry. 2017 Jun 27;7(6):e1158. doi: 10.1038/tp.2017.130.

16.

A systematic evaluation of nucleotide properties for CRISPR sgRNA design.

Kuan PF, Powers S, He S, Li K, Zhao X, Huang B.

BMC Bioinformatics. 2017 Jun 6;18(1):297. doi: 10.1186/s12859-017-1697-6.

17.

Breast tumor DNA methylation patterns associated with smoking in the Carolina Breast Cancer Study.

Conway K, Edmiston SN, Parrish E, Bryant C, Tse CK, Swift-Scanlan T, McCullough LE, Kuan PF.

Breast Cancer Res Treat. 2017 Jun;163(2):349-361. doi: 10.1007/s10549-017-4178-8. Epub 2017 Mar 8.

18.

methylDMV: SIMULTANEOUS DETECTION OF DIFFERENTIAL DNA METHYLATION AND VARIABILITY WITH CONFOUNDER ADJUSTMENT.

Kuan PF, Song J, He S.

Pac Symp Biocomput. 2017;22:461-472. doi: 10.1142/9789813207813_0043.

19.

IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity.

Sun W, Liu Y, Crowley JJ, Chen TH, Zhou H, Chu H, Huang S, Kuan PF, Li Y, Miller DR, Shaw GD, Wu Y, Zhabotynsky V, McMillan L, Zou F, Sullivan PF, de Villena FP.

J Am Stat Assoc. 2015;110(511):975-986. Epub 2015 Nov 7.

20.

Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data.

Xiong L, Kuan PF, Tian J, Keles S, Wang S.

Cancer Inform. 2015 Nov 15;13(Suppl 7):123-31. doi: 10.4137/CIN.S16353. eCollection 2015.

21.

IL2 Inducible T-cell Kinase, a Novel Therapeutic Target in Melanoma.

Carson CC, Moschos SJ, Edmiston SN, Darr DB, Nikolaishvili-Feinberg N, Groben PA, Zhou X, Kuan PF, Pandey S, Chan KT, Jordan JL, Hao H, Frank JS, Hopkinson DA, Gibbs DC, Alldredge VD, Parrish E, Hanna SC, Berkowitz P, Rubenstein DS, Miller CR, Bear JE, Ollila DW, Sharpless NE, Conway K, Thomas NE.

Clin Cancer Res. 2015 May 1;21(9):2167-76. doi: 10.1158/1078-0432.CCR-14-1826.

22.

Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains.

Stuhlmiller TJ, Miller SM, Zawistowski JS, Nakamura K, Beltran AS, Duncan JS, Angus SP, Collins KA, Granger DA, Reuther RA, Graves LM, Gomez SM, Kuan PF, Parker JS, Chen X, Sciaky N, Carey LA, Earp HS, Jin J, Johnson GL.

Cell Rep. 2015 Apr 21;11(3):390-404. doi: 10.1016/j.celrep.2015.03.037. Epub 2015 Apr 9.

23.

Racial variation in breast tumor promoter methylation in the Carolina Breast Cancer Study.

Conway K, Edmiston SN, Tse CK, Bryant C, Kuan PF, Hair BY, Parrish EA, May R, Swift-Scanlan T.

Cancer Epidemiol Biomarkers Prev. 2015 Jun;24(6):921-30. doi: 10.1158/1055-9965.EPI-14-1228. Epub 2015 Mar 25.

24.

Propensity score method for partially matched omics studies.

Kuan PF.

Cancer Inform. 2014 Oct 29;13(Suppl 7):1-10. doi: 10.4137/CIN.S16352. eCollection 2014. Review.

25.

Three Molecular Subtypes of Gastric Adenocarcinoma Have Distinct Histochemical Features Reflecting Epstein-Barr Virus Infection Status and Neuroendocrine Differentiation.

Speck O, Tang W, Morgan DR, Kuan PF, Meyers MO, Dominguez RL, Martinez E, Gulley ML.

Appl Immunohistochem Mol Morphol. 2015 Oct;23(9):633-45. doi: 10.1097/PAI.0000000000000122.

26.

Covariate adjusted differential variability analysis of DNA methylation with propensity score method.

Kuan PF.

Stat Appl Genet Mol Biol. 2014 Dec;13(6):645-58. doi: 10.1515/sagmb-2013-0072.

PMID:
25332296
27.

DNA methylation profiling in the Carolina Breast Cancer Study defines cancer subclasses differing in clinicopathologic characteristics and survival.

Conway K, Edmiston SN, May R, Kuan PF, Chu H, Bryant C, Tse CK, Swift-Scanlan T, Geradts J, Troester MA, Millikan RC.

Breast Cancer Res. 2014 Oct 7;16(5):450. doi: 10.1186/s13058-014-0450-6.

28.

DNA methylation profiles in primary cutaneous melanomas are associated with clinically significant pathologic features.

Thomas NE, Slater NA, Edmiston SN, Zhou X, Kuan PF, Groben PA, Carson CC, Hao H, Parrish E, Moschos SJ, Berwick M, Ollila DW, Conway K.

Pigment Cell Melanoma Res. 2014 Nov;27(6):1097-105. doi: 10.1111/pcmr.12289. Epub 2014 Jul 14.

29.

The Cavβ1a subunit regulates gene expression and suppresses myogenin in muscle progenitor cells.

Taylor J, Pereyra A, Zhang T, Messi ML, Wang ZM, Hereñú C, Kuan PF, Delbono O.

J Cell Biol. 2014 Jun 23;205(6):829-46. doi: 10.1083/jcb.201403021. Epub 2014 Jun 16.

30.

Time-to-event continual reassessment method incorporating treatment cycle information with application to an oncology phase I trial.

Huang B, Kuan PF.

Biom J. 2014 Nov;56(6):933-46. doi: 10.1002/bimj.201300261. Epub 2014 Jun 3.

PMID:
24895140
31.

Obesity increases tumor aggressiveness in a genetically engineered mouse model of serous ovarian cancer.

Makowski L, Zhou C, Zhong Y, Kuan PF, Fan C, Sampey BP, Difurio M, Bae-Jump VL.

Gynecol Oncol. 2014 Apr;133(1):90-7. doi: 10.1016/j.ygyno.2013.12.026.

32.

The Role of Ect2 Nuclear RhoGEF Activity in Ovarian Cancer Cell Transformation.

Huff LP, Decristo MJ, Trembath D, Kuan PF, Yim M, Liu J, Cook DR, Miller CR, Der CJ, Cox AD.

Genes Cancer. 2013 Nov;4(11-12):460-75. doi: 10.1177/1947601913514851.

33.

A systematic assessment of normalization approaches for the Infinium 450K methylation platform.

Wu MC, Joubert BR, Kuan PF, Håberg SE, Nystad W, Peddada SD, London SJ.

Epigenetics. 2014 Feb;9(2):318-29. doi: 10.4161/epi.27119. Epub 2013 Nov 15.

34.

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects.

Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ.

Genome Res. 2014 Feb;24(2):241-50. doi: 10.1101/gr.158253.113. Epub 2013 Oct 24.

35.

Application of multiplexed kinase inhibitor beads to study kinome adaptations in drug-resistant leukemia.

Cooper MJ, Cox NJ, Zimmerman EI, Dewar BJ, Duncan JS, Whittle MC, Nguyen TA, Jones LS, Ghose Roy S, Smalley DM, Kuan PF, Richards KL, Christopherson RI, Jin J, Frye SV, Johnson GL, Baldwin AS, Graves LM.

PLoS One. 2013 Jun 24;8(6):e66755. doi: 10.1371/journal.pone.0066755. Print 2013.

36.

MERTK receptor tyrosine kinase is a therapeutic target in melanoma.

Schlegel J, Sambade MJ, Sather S, Moschos SJ, Tan AC, Winges A, DeRyckere D, Carson CC, Trembath DG, Tentler JJ, Eckhardt SG, Kuan PF, Hamilton RL, Duncan LM, Miller CR, Nikolaishvili-Feinberg N, Midkiff BR, Liu J, Zhang W, Yang C, Wang X, Frye SV, Earp HS, Shields JM, Graham DK.

J Clin Invest. 2013 May;123(5):2257-67. doi: 10.1172/JCI67816. Epub 2013 Apr 15.

37.

HIF1α and HIF2α independently activate SRC to promote melanoma metastases.

Hanna SC, Krishnan B, Bailey ST, Moschos SJ, Kuan PF, Shimamura T, Osborne LD, Siegel MB, Duncan LM, O'Brien ET 3rd, Superfine R, Miller CR, Simon MC, Wong KK, Kim WY.

J Clin Invest. 2013 May;123(5):2078-93. doi: 10.1172/JCI66715. Epub 2013 Apr 8.

38.

A simple and robust method for partially matched samples using the p-values pooling approach.

Kuan PF, Huang B.

Stat Med. 2013 Aug 30;32(19):3247-59. doi: 10.1002/sim.5758. Epub 2013 Feb 17.

39.

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J.

Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15.

40.

Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile.

Tang W, Morgan DR, Meyers MO, Dominguez RL, Martinez E, Kakudo K, Kuan PF, Banet N, Muallem H, Woodward K, Speck O, Gulley ML.

Infect Agent Cancer. 2012 Aug 28;7(1):21. doi: 10.1186/1750-9378-7-21.

41.

Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas.

Wang P, Dong Q, Zhang C, Kuan PF, Liu Y, Jeck WR, Andersen JB, Jiang W, Savich GL, Tan TX, Auman JT, Hoskins JM, Misher AD, Moser CD, Yourstone SM, Kim JW, Cibulskis K, Getz G, Hunt HV, Thorgeirsson SS, Roberts LR, Ye D, Guan KL, Xiong Y, Qin LX, Chiang DY.

Oncogene. 2013 Jun 20;32(25):3091-100. doi: 10.1038/onc.2012.315. Epub 2012 Jul 23.

42.

Metabolomic profiling reveals mitochondrial-derived lipid biomarkers that drive obesity-associated inflammation.

Sampey BP, Freemerman AJ, Zhang J, Kuan PF, Galanko JA, O'Connell TM, Ilkayeva OR, Muehlbauer MJ, Stevens RD, Newgard CB, Brauer HA, Troester MA, Makowski L.

PLoS One. 2012;7(6):e38812. doi: 10.1371/journal.pone.0038812. Epub 2012 Jun 12.

43.

Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.

Duncan JS, Whittle MC, Nakamura K, Abell AN, Midland AA, Zawistowski JS, Johnson NL, Granger DA, Jordan NV, Darr DB, Usary J, Kuan PF, Smalley DM, Major B, He X, Hoadley KA, Zhou B, Sharpless NE, Perou CM, Kim WY, Gomez SM, Chen X, Jin J, Frye SV, Earp HS, Graves LM, Johnson GL.

Cell. 2012 Apr 13;149(2):307-21. doi: 10.1016/j.cell.2012.02.053.

44.

Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators.

Huebert DJ, Kuan PF, Keleş S, Gasch AP.

Mol Cell Biol. 2012 May;32(9):1645-53. doi: 10.1128/MCB.06170-11. Epub 2012 Feb 21.

45.

Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation.

Kuan PF, Chiang DY.

Biometrics. 2012 Sep;68(3):774-83. doi: 10.1111/j.1541-0420.2011.01730.x. Epub 2012 Jan 19.

46.

RhoGDI2 antagonizes ovarian carcinoma growth, invasion and metastasis.

Stevens EV, Banet N, Onesto C, Plachco A, Alan JK, Nikolaishvili-Feinberg N, Midkiff BR, Kuan PF, Liu J, Miller CR, Vigil D, Graves LM, Der CJ.

Small GTPases. 2011 Jul;2(4):202-210. Epub 2011 Jul 1.

47.

Performance of rapid influenza H1N1 diagnostic tests: a meta-analysis.

Chu H, Lofgren ET, Halloran ME, Kuan PF, Hudgens M, Cole SR.

Influenza Other Respir Viruses. 2012 Mar;6(2):80-6. doi: 10.1111/j.1750-2659.2011.00284.x. Epub 2011 Aug 31.

48.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keleş S.

PLoS Comput Biol. 2011 Jul;7(7):e1002111. doi: 10.1371/journal.pcbi.1002111. Epub 2011 Jul 14.

49.

DNA-methylation profiling distinguishes malignant melanomas from benign nevi.

Conway K, Edmiston SN, Khondker ZS, Groben PA, Zhou X, Chu H, Kuan PF, Hao H, Carson C, Berwick M, Olilla DW, Thomas NE.

Pigment Cell Melanoma Res. 2011 Apr;24(2):352-60. doi: 10.1111/j.1755-148X.2011.00828.x. Epub 2011 Feb 18.

50.

A Statistical Framework for the Analysis of ChIP-Seq Data.

Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, Keleş S.

J Am Stat Assoc. 2011;106(495):891-903. Epub 2012 Jan 24.

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