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David M Rocke

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InstitutionUniversity of California Davis
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Halloran JT, Rocke D. A Matter of Time: Faster Percolator Analysis via Efficient SVM Learning for Large-Scale Proteomics. J Proteome Res. 2018 May 04; 17(5):1978-1982. PMID: 29607643.
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    2. Albrecht H, Yang HY, Kiuru M, Maksaereekul S, Durbin-Johnson B, Wong MS, Stevenson TR, Rocke D, Isseroff RR. The Beta 2 Adrenergic Receptor Antagonist Timolol Improves Healing of Combined Burn and Radiation Wounds. Radiat Res. 2018 Apr; 189(4):441-445. PMID: 29373090.
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    3. Almario RU, Buchan WM, Rocke D, Karakas SE. Glucose-lowering effect of whey protein depends upon clinical characteristics of patients with type 2 diabetes. BMJ Open Diabetes Res Care. 2017; 5(1):e000420. PMID: 28761664.
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    4. Rice RH, Durbin-Johnson BP, Salemi M, Schwartz ME, Rocke D, Phinney BS. Proteomic profiling of Pachyonychia congenita plantar callus. J Proteomics. 2017 Aug 08; 165:132-137. PMID: 28648685.
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    5. Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke D, Parker GJ, Rice RH. Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides. Proteomics. 2017 Jul; 17(13-14). PMID: 28544375.
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    6. Pignolo RJ, Durbin-Johnson BP, Rocke D, Kaplan FS. Joint-specific risk of impaired function in fibrodysplasia ossificans progressiva (FOP). Bone. 2018 Apr; 109:124-133. PMID: 28627475.
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    7. Dimachkie MM, Abuzinadah AR, Barohn RJ, Oskarsson B, Rocke D, Dengel K, Richman DP. Myasthenia gravis exacerbation after discontinuing mycophenolate: A single-center cohort study. Neurology. 2016 Nov 08; 87(19):2067-2068. PMID: 27821567.
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    8. Parker GJ, Leppert T, Anex DS, Hilmer JK, Matsunami N, Baird L, Stevens J, Parsawar K, Durbin-Johnson BP, Rocke D, Nelson C, Fairbanks DJ, Wilson AS, Rice RH, Woodward SR, Bothner B, Hart BR, Leppert M. Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome. PLoS One. 2016; 11(9):e0160653. PMID: 27603779; PMCID: PMC5014411.
    9. Rice RH, Durbin-Johnson BP, Ishitsuka Y, Salemi M, Phinney BS, Rocke D, Roop DR. Proteomic Analysis of Loricrin Knockout Mouse Epidermis. J Proteome Res. 2016 08 05; 15(8):2560-6. PMID: 27418529.
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    10. Perkins SM, Bacchetti P, Davey CS, Lindsell CJ, Mazumdar M, Oster RA, Peduzzi PN, Rocke D, Rudser KD, Kim M. Best Practices for Biostatistical Consultation and Collaboration in Academic Health Centers. Am Stat. 2016; 70(2):187-194. PMID: 27777443.
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    11. Oskarsson B, Rocke D, Dengel K, Richman DP. Myasthenia gravis exacerbation after discontinuing mycophenolate: A single-center cohort study. Neurology. 2016 Mar 22; 86(12):1159-63. PMID: 26850977; PMCID: PMC4820129 [Available on 03/22/17].
    12. Pignolo RJ, Bedford-Gay C, Liljesthröm M, Durbin-Johnson BP, Shore EM, Rocke D, Kaplan FS. The Natural History of Flare-Ups in Fibrodysplasia Ossificans Progressiva (FOP): A Comprehensive Global Assessment. J Bone Miner Res. 2016 Mar; 31(3):650-6. PMID: 27025942; PMCID: PMC4829946 [Available on 03/01/17].
    13. Ruhaak LR, Barkauskas DA, Torres J, Cooke CL, Wu LD, Stroble C, Ozcan S, Williams CC, Camorlinga M, Rocke D, Lebrilla CB, Solnick JV. The Serum Immunoglobulin G Glycosylation Signature of Gastric Cancer. EuPA Open Proteom. 2015 Mar 01; 6:1-9. PMID: 25685702.
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    14. Satake N, Duong C, Chen C, Barisone GA, Diaz E, Tuscano J, Rocke D, Nolta J, Nitin N. Targeted therapy with MXD3 siRNA, anti-CD22 antibody and nanoparticles for precursor B-cell acute lymphoblastic leukaemia. Br J Haematol. 2014 Nov; 167(4):487-99. PMID: 25196579.
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    15. Laatsch CN, Durbin-Johnson BP, Rocke D, Mukwana S, Newland AB, Flagler MJ, Davis MG, Eigenheer RA, Phinney BS, Rice RH. Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis. PeerJ. 2014; 2:e506. PMID: 25165623; PMCID: PMC4137660.
    16. Xia J, Rocke D, Perry G, Ray M. Differential network analyses of Alzheimer's disease identify early events in Alzheimer's disease pathology. Int J Alzheimers Dis. 2014; 2014:721453. PMID: 25147748.
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    17. Ibáñez AM, Martinelli F, Reagan RL, Uratsu SL, Vo A, Tinoco MA, Phu ML, Chen Y, Rocke D, Dandekar AM. Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder. Plant Sci. 2014 Mar; 217-218:87-98. PMID: 24467900.
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    18. Ozcan S, Barkauskas DA, Renee Ruhaak L, Torres J, Cooke CL, An HJ, Hua S, Williams CC, Dimapasoc LM, Han Kim J, Camorlinga-Ponce M, Rocke D, Lebrilla CB, Solnick JV. Serum glycan signatures of gastric cancer. Cancer Prev Res (Phila). 2014 Feb; 7(2):226-35. PMID: 24327722.
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    19. Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke D, Eigenheer RA, Phinney BS, Schmuth M, Gruber R. Distinguishing ichthyoses by protein profiling. PLoS One. 2013; 8(10):e75355. PMID: 24130705; PMCID: PMC3793978.
    20. Mall C, Rocke D, Durbin-Johnson B, Weiss RH. Stability of miRNA in human urine supports its biomarker potential. Biomark Med. 2013 Aug; 7(4):623-31. PMID: 23905899; PMCID: PMC3885156.
    21. Stewart DN, Lango J, Nambiar KP, Falso MJ, FitzGerald PG, Rocke D, Hammock BD, Buchholz BA. Carbon turnover in the water-soluble protein of the adult human lens. Mol Vis. 2013; 19:463-75. PMID: 23441119; PMCID: PMC3580966.
    22. Rice RH, Winters BR, Durbin-Johnson BP, Rocke D. Chicken corneocyte cross-linked proteome. J Proteome Res. 2013 Feb 01; 12(2):771-6. PMID: 23256538; PMCID: PMC3569041.
    23. Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke D, Eigenheer RA, Phinney BS, Sundberg JP. Differentiating inbred mouse strains from each other and those with single gene mutations using hair proteomics. PLoS One. 2012; 7(12):e51956. PMID: 23251662; PMCID: PMC3522583.
    24. Yunis R, Albrecht H, Kalanetra KM, Wu S, Rocke D. Genomic characterization of a three-dimensional skin model following exposure to ionizing radiation. J Radiat Res. 2012 Nov 01; 53(6):860-75. PMID: 22915785; PMCID: PMC3483859.
    25. Kitterman JA, Strober JB, Kan L, Rocke D, Cali A, Peeper J, Snow J, Delai PL, Morhart R, Pignolo RJ, Shore EM, Kaplan FS. Neurological symptoms in individuals with fibrodysplasia ossificans progressiva. J Neurol. 2012 Dec; 259(12):2636-43. PMID: 22752062; PMCID: PMC3523705.
    26. Ray M, Yunis R, Chen X, Rocke D. Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks. BMC Genomics. 2012 May 17; 13:190. PMID: 22594378; PMCID: PMC3443446.
    27. Fritz HM, Buchholz KR, Chen X, Durbin-Johnson B, Rocke D, Conrad PA, Boothroyd JC. Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts. PLoS One. 2012; 7(2):e29998. PMID: 22347997; PMCID: PMC3278417.
    28. Romano PS, Marcin JP, Dai JJ, Yang XD, Kravitz RL, Rocke D, Dharmar M, Li Z. Impact of public reporting of coronary artery bypass graft surgery performance data on market share, mortality, and patient selection. Med Care. 2011 Dec; 49(12):1118-25. PMID: 22002641.
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    29. Albrecht H, Durbin-Johnson B, Yunis R, Kalanetra KM, Wu S, Chen R, Stevenson TR, Rocke D. Transcriptional response of ex vivo human skin to ionizing radiation: comparison between low- and high-dose effects. Radiat Res. 2012 Jan; 177(1):69-83. PMID: 22029842; PMCID: PMC3549263.
    30. Buchholz KR, Fritz HM, Chen X, Durbin-Johnson B, Rocke D, Ferguson DJ, Conrad PA, Boothroyd JC. Identification of tissue cyst wall components by transcriptome analysis of in vivo and in vitro Toxoplasma gondii bradyzoites. Eukaryot Cell. 2011 Dec; 10(12):1637-47. PMID: 22021236; PMCID: PMC3232729.
    31. Afify AM, Tate S, Durbin-Johnson B, Rocke D, Konia T. Expression of CD44s and CD44v6 in lung cancer and their correlation with prognostic factors. Int J Biol Markers. 2011 Jan-Mar; 26(1):50-7. PMID: 21279958.
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    32. Chen Y, Wu R, Felton J, Rocke D, Chakicherla A. A Method to Detect Differential Gene expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Biomed Inform Insights. 2010 Mar 05; 2010(3):1-10. PMID: 20798791.
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    33. Chen Y, Wu R, Felton J, Rocke D, Chakicherla A. A Method to Detect Differential Gene Expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Biomed Inform Insights. 2010; 3:1-10. PMID: 28190956.
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    34. Barkauskas DA, Rocke D. A general-purpose baseline estimation algorithm for spectroscopic data. Anal Chim Acta. 2010 Jan 11; 657(2):191-7. PMID: 20005331; PMCID: PMC2806822.
    35. Li B, Li D, Lau DH, Farwell DG, Luu Q, Rocke D, Newman K, Courquin J, Purdy JA, Chen AM. Clinical-dosimetric analysis of measures of dysphagia including gastrostomy-tube dependence among head and neck cancer patients treated definitively by intensity-modulated radiotherapy with concurrent chemotherapy. Radiat Oncol. 2009 Nov 12; 4:52. PMID: 19909531; PMCID: PMC2785826.
    36. Martinelli F, Uratsu SL, Reagan RL, Chen Y, Tricoli D, Fiehn O, Rocke D, Gasser CS, Dandekar AM. Gene regulation in parthenocarpic tomato fruit. J Exp Bot. 2009; 60(13):3873-90. PMID: 19700496; PMCID: PMC2736898.
    37. Barkauskas DA, Kronewitter SR, Lebrilla CB, Rocke D. Analysis of MALDI FT-ICR mass spectrometry data: a time series approach. Anal Chim Acta. 2009 Aug 26; 648(2):207-14. PMID: 19646586; PMCID: PMC2772212.
    38. Berglund SR, Santana AR, Li D, Rice RH, Rocke D, Goldberg Z. Proteomic analysis of low dose arsenic and ionizing radiation exposure on keratinocytes. Proteomics. 2009 Apr; 9(7):1925-38. PMID: 19294697; PMCID: PMC2666104.
    39. Rice RH, Rocke D, Tsai HS, Silva KA, Lee YJ, Sundberg JP. Distinguishing mouse strains by proteomic analysis of pelage hair. J Invest Dermatol. 2009 Sep; 129(9):2120-5. PMID: 19295613; PMCID: PMC2853740.
    40. Corbett BA, Constantine LJ, Hendren R, Rocke D, Ozonoff S. Examining executive functioning in children with autism spectrum disorder, attention deficit hyperactivity disorder and typical development. Psychiatry Res. 2009 Apr 30; 166(2-3):210-22. PMID: 19285351; PMCID: PMC2683039.
    41. Sivamani RK, Pullar CE, Manabat-Hidalgo CG, Rocke D, Carlsen RC, Greenhalgh DG, Isseroff RR. Stress-mediated increases in systemic and local epinephrine impair skin wound healing: potential new indication for beta blockers. PLoS Med. 2009 Jan 13; 6(1):e12. PMID: 19143471; PMCID: PMC2621262.
    42. Li Z, Kravitz RL, Marcin JP, Romano PS, Rocke D, Denton TA, Brindis RG, Dai J, Amsterdam EA. Survival enhancing indications for coronary artery bypass graft surgery in California. BMC Health Serv Res. 2008 Dec 16; 8:257. PMID: 19087305; PMCID: PMC2621199.
    43. Barkauskas DA, An HJ, Kronewitter SR, de Leoz ML, Chew HK, de Vere White RW, Leiserowitz GS, Miyamoto S, Lebrilla CB, Rocke D. Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. Bioinformatics. 2009 Jan 15; 25(2):251-7. PMID: 19073586; PMCID: PMC2639011.
    44. Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia AP, An K, Chou HH, Rocke D, Lee GC, Schnable PS, An G, Buell CR, Ronald PC. Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One. 2008 Oct 06; 3(10):e3337. PMID: 18836531; PMCID: PMC2556097.
    45. Xi Y, Rocke D. Baseline correction for NMR spectroscopic metabolomics data analysis. BMC Bioinformatics. 2008 Jul 29; 9:324. PMID: 18664284; PMCID: PMC2516527.
    46. Lu R, Lee GC, Shultz M, Dardick C, Jung K, Phetsom J, Jia Y, Rice RH, Goldberg Z, Schnable PS, Ronald P, Rocke D. Assessing probe-specific dye and slide biases in two-color microarray data. BMC Bioinformatics. 2008 Jul 19; 9:314. PMID: 18638416; PMCID: PMC2496918.
    47. Zwienenberg-Lee M, Hartman J, Rudisill N, Madden LK, Smith K, Eskridge J, Newell D, Verweij B, Bullock MR, Baker A, Coplin W, Mericle R, Dai J, Rocke D, Muizelaar JP. Effect of prophylactic transluminal balloon angioplasty on cerebral vasospasm and outcome in patients with Fisher grade III subarachnoid hemorrhage: results of a phase II multicenter, randomized, clinical trial. Stroke. 2008 Jun; 39(6):1759-65. PMID: 18420953.
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    48. Marcin JP, Li Z, Kravitz RL, Dai JJ, Rocke D, Romano PS. The CABG surgery volume-outcome relationship: temporal trends and selection effects in California, 1998-2004. Health Serv Res. 2008 Feb; 43(1 Pt 1):174-92. PMID: 18211524; PMCID: PMC2323152.
    49. Ye J, Liu H, Kirmiz C, Lebrilla CB, Rocke D. On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve. BMC Bioinformatics. 2007 Dec 12; 8:477. PMID: 18076765; PMCID: PMC2211327.
    50. Berglund SR, Rocke D, Dai J, Schwietert CW, Santana A, Stern RL, Lehmann J, Hartmann Siantar CL, Goldberg Z. Transient genome-wide transcriptional response to low-dose ionizing radiation in vivo in humans. Int J Radiat Oncol Biol Phys. 2008 Jan 01; 70(1):229-34. PMID: 17996396; PMCID: PMC2754180.
    51. An HJ, Tillinghast JS, Woodruff DL, Rocke D, Lebrilla CB. A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins. J Proteome Res. 2006 Oct; 5(10):2800-8. PMID: 17022651.
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    52. Rea MA, Zhou L, Qin Q, Barrandon Y, Easley KW, Gungner SF, Phillips MA, Holland WS, Gumerlock PH, Rocke D, Rice RH. Spontaneous immortalization of human epidermal cells with naturally elevated telomerase. J Invest Dermatol. 2006 Nov; 126(11):2507-15. PMID: 16778798.
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    53. Goldberg Z, Rocke D, Schwietert C, Berglund SR, Santana A, Jones A, Lehmann J, Stern R, Lu R, Hartmann Siantar C. Human in vivo dose-response to controlled, low-dose low linear energy transfer ionizing radiation exposure. Clin Cancer Res. 2006 Jun 15; 12(12):3723-9. PMID: 16778099.
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    54. Dai JJ, Lieu L, Rocke D. Dimension reduction for classification with gene expression microarray data. Stat Appl Genet Mol Biol. 2006; 5:Article6. PMID: 16646870.
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    55. Lehmann J, Stern RL, Daly TP, Rocke D, Schwietert CW, Jones GE, Arnold ML, Siantar CL, Goldberg Z. Dosimetry for quantitative analysis of the effects of low-dose ionizing radiation in radiation therapy patients. Radiat Res. 2006 Feb; 165(2):240-7. PMID: 16435922.
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    56. Abel K, Rocke D, Chohan B, Fritts L, Miller CJ. Temporal and anatomic relationship between virus replication and cytokine gene expression after vaginal simian immunodeficiency virus infection. J Virol. 2005 Oct; 79(19):12164-72. PMID: 16160143; PMCID: PMC1211549.
    57. Rocke D, Goldberg Z, Schweitert C, Santana A. A method for detection of differential gene expression in the presence of inter-individual variability in response. Bioinformatics. 2005 Nov 01; 21(21):3990-2. PMID: 16159922.
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    58. Zhou L, Rocke D. An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics. 2005 Nov 01; 21(21):3983-9. PMID: 16159924.
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    59. Rocke D. Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol. 2004 Dec; 15(6):703-13. PMID: 15561590.
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    60. Scarlett RF, Rocke D, Kantanie S, Patel JB, Shore EM, Kaplan FS. Influenza-like viral illnesses and flare-ups of fibrodysplasia ossificans progressiva. Clin Orthop Relat Res. 2004 Jun; (423):275-9. PMID: 15232462.
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    61. Durbin BP, Rocke D. Variance-stabilizing transformations for two-color microarrays. Bioinformatics. 2004 Mar 22; 20(5):660-7. PMID: 15033873.
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    62. Purohit PV, Rocke D, Viant MR, Woodruff DL. Discrimination models using variance-stabilizing transformation of metabolomic NMR data. OMICS. 2004; 8(2):118-30. PMID: 15268771.
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    63. Geller SC, Gregg JP, Hagerman P, Rocke D. Transformation and normalization of oligonucleotide microarray data. Bioinformatics. 2003 Sep 22; 19(14):1817-23. PMID: 14512353.
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    64. Rocke D, Durbin B, Wilson M, Kahn HD. Modeling uncertainty in the measurement of low-level analytes in environmental analysis. Ecotoxicol Environ Saf. 2003 Sep; 56(1):78-92. PMID: 12915142.
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    65. Purohit PV, Rocke D. Discriminant models for high-throughput proteomics mass spectrometer data. Proteomics. 2003 Sep; 3(9):1699-703. PMID: 12973728.
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    66. Durbin B, Rocke D. Estimation of transformation parameters for microarray data. Bioinformatics. 2003 Jul 22; 19(11):1360-7. PMID: 12874047.
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    67. Rocke D, Durbin B. Approximate variance-stabilizing transformations for gene-expression microarray data. Bioinformatics. 2003 May 22; 19(8):966-72. PMID: 12761059.
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    68. Zhao Y, Chen BP, Miao H, Yuan S, Li YS, Hu Y, Rocke D, Chien S. Improved significance test for DNA microarray data: temporal effects of shear stress on endothelial genes. Physiol Genomics. 2002 Dec 26; 12(1):1-11. PMID: 12399447.
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    69. Nguyen DV, Rocke D. Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics. 2002 Dec; 18(12):1625-32. PMID: 12490447.
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    70. Nguyen DV, Rocke D. Multi-class cancer classification via partial least squares with gene expression profiles. Bioinformatics. 2002 Sep; 18(9):1216-26. PMID: 12217913.
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    71. Nguyen DV, Rocke D. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics. 2002 Jan; 18(1):39-50. PMID: 11836210.
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