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David Rocke

TitleDistinguished Professor
InstitutionUniversity of California Davis
DepartmentPublic Health Sciences
AddressMed Sci 1C Bldg.
CA 95616
Phone530-752-6999
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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 DM. 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.
      View in: PubMed
    2. Almario RU, Buchan WM, Rocke DM, 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.
      View in: PubMed
    3. Wu PW, Mason KE, Durbin-Johnson BP, Salemi M, Phinney BS, Rocke DM, 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.
      View in: PubMed
    4. Ruhaak LR, Barkauskas DA, Torres J, Cooke CL, Wu LD, Stroble C, Ozcan S, Williams CC, Camorlinga M, Rocke DM, Lebrilla CB, Solnick JV. The Serum Immunoglobulin G Glycosylation Signature of Gastric Cancer. EuPA Open Proteom. 2015 Mar 01; 6:1-9. PMID: 25685702.
      View in: PubMed
    5. Satake N, Duong C, Chen C, Barisone GA, Diaz E, Tuscano J, Rocke DM, 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.
      View in: PubMed
    6. Laatsch CN, Durbin-Johnson BP, Rocke DM, 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.
    7. Xia J, Rocke DM, 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.
      View in: PubMed
    8. Ibáñez AM, Martinelli F, Reagan RL, Uratsu SL, Vo A, Tinoco MA, Phu ML, Chen Y, Rocke DM, Dandekar AM. Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder. Plant Sci. 2014 Mar; 217-218:87-98. PMID: 24467900.
      View in: PubMed
    9. 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.
      View in: PubMed
    10. Mall C, Rocke DM, 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.
    11. Stewart DN, Lango J, Nambiar KP, Falso MJ, FitzGerald PG, Rocke DM, 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.
    12. Rice RH, Winters BR, Durbin-Johnson BP, Rocke DM. Chicken corneocyte cross-linked proteome. J Proteome Res. 2013 Feb 01; 12(2):771-6. PMID: 23256538; PMCID: PMC3569041.
    13. Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, 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.
    14. Yunis R, Albrecht H, Kalanetra KM, Wu S, Rocke DM. 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.
    15. Ray M, Yunis R, Chen X, Rocke DM. 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.
    16. Albrecht H, Durbin-Johnson B, Yunis R, Kalanetra KM, Wu S, Chen R, Stevenson TR, Rocke DM. 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.
    17. Afify AM, Tate S, Durbin-Johnson B, Rocke DM, 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.
      View in: PubMed
    18. Chen Y, Wu R, Felton J, Rocke DM, 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.
      View in: PubMed
    19. Chen Y, Wu R, Felton J, Rocke DM, 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.
      View in: PubMed
    20. Martinelli F, Uratsu SL, Reagan RL, Chen Y, Tricoli D, Fiehn O, Rocke DM, Gasser CS, Dandekar AM. Gene regulation in parthenocarpic tomato fruit. J Exp Bot. 2009; 60(13):3873-90. PMID: 19700496; PMCID: PMC2736898.
    21. Berglund SR, Santana AR, Li D, Rice RH, Rocke DM, 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.
    22. Li Z, Kravitz RL, Marcin JP, Romano PS, Rocke DM, 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.
    23. Barkauskas DA, An HJ, Kronewitter SR, de Leoz ML, Chew HK, de Vere White RW, Leiserowitz GS, Miyamoto S, Lebrilla CB, Rocke DM. 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.
    24. Xi Y, Rocke DM. Baseline correction for NMR spectroscopic metabolomics data analysis. BMC Bioinformatics. 2008 Jul 29; 9:324. PMID: 18664284; PMCID: PMC2516527.
    25. Lu R, Lee GC, Shultz M, Dardick C, Jung K, Phetsom J, Jia Y, Rice RH, Goldberg Z, Schnable PS, Ronald P, Rocke DM. Assessing probe-specific dye and slide biases in two-color microarray data. BMC Bioinformatics. 2008 Jul 19; 9:314. PMID: 18638416; PMCID: PMC2496918.
    26. Ye J, Liu H, Kirmiz C, Lebrilla CB, Rocke DM. 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.
    27. Berglund SR, Rocke DM, 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.
    28. An HJ, Tillinghast JS, Woodruff DL, Rocke DM, 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.
      View in: PubMed
    29. Goldberg Z, Rocke DM, 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.
      View in: PubMed
    30. 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.
      View in: PubMed
    31. Lehmann J, Stern RL, Daly TP, Rocke DM, 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.
      View in: PubMed
    32. Abel K, Rocke DM, 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.
    33. Rocke DM, 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.
      View in: PubMed
    34. Zhou L, Rocke DM. An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics. 2005 Nov 01; 21(21):3983-9. PMID: 16159924.
      View in: PubMed
    35. Rocke DM. Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol. 2004 Dec; 15(6):703-13. PMID: 15561590.
      View in: PubMed
    36. Durbin BP, Rocke DM. Variance-stabilizing transformations for two-color microarrays. Bioinformatics. 2004 Mar 22; 20(5):660-7. PMID: 15033873.
      View in: PubMed
    37. Purohit PV, Rocke DM, Viant MR, Woodruff DL. Discrimination models using variance-stabilizing transformation of metabolomic NMR data. OMICS. 2004; 8(2):118-30. PMID: 15268771.
      View in: PubMed
    38. Geller SC, Gregg JP, Hagerman P, Rocke DM. Transformation and normalization of oligonucleotide microarray data. Bioinformatics. 2003 Sep 22; 19(14):1817-23. PMID: 14512353.
      View in: PubMed
    39. Rocke DM, 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.
      View in: PubMed
    40. Purohit PV, Rocke DM. Discriminant models for high-throughput proteomics mass spectrometer data. Proteomics. 2003 Sep; 3(9):1699-703. PMID: 12973728.
      View in: PubMed
    41. Durbin B, Rocke DM. Estimation of transformation parameters for microarray data. Bioinformatics. 2003 Jul 22; 19(11):1360-7. PMID: 12874047.
      View in: PubMed
    42. Rocke DM, Durbin B. Approximate variance-stabilizing transformations for gene-expression microarray data. Bioinformatics. 2003 May 22; 19(8):966-72. PMID: 12761059.
      View in: PubMed
    43. Zhao Y, Chen BP, Miao H, Yuan S, Li YS, Hu Y, Rocke DM, 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.
      View in: PubMed
    44. Nguyen DV, Rocke DM. Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics. 2002 Dec; 18(12):1625-32. PMID: 12490447.
      View in: PubMed
    45. Nguyen DV, Rocke DM. Multi-class cancer classification via partial least squares with gene expression profiles. Bioinformatics. 2002 Sep; 18(9):1216-26. PMID: 12217913.
      View in: PubMed
    46. Nguyen DV, Rocke DM. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics. 2002 Jan; 18(1):39-50. PMID: 11836210.
      View in: PubMed