Superfund Research Program

David M. Rocke

University of California-Davis
Center for Image Processing and Integrated Computing
2343 Academic Surge Building
One Shields Avenue
Davis, California 95616
Phone: 530-752-0510
Fax: 530-752-2924
Email: dmrocke@ucdavis.edu

Projects

• University of California-Davis: Statistical Analysis of Toxics Measurement Data (1995-2010)

Publications

2016

• Parker GJ, Leppert T, Anex DS, Hilmer JK, Matsunami N, Baird L, Stevens J, Parsawar K, Durbin-Johnson BP, Rocke DM, Nelson C, Fairbanks DJ, Wilson A, Rice RH, Woodward SR, Bothner B, Hart B, Leppert M. 2016. Demonstration of protein-based human identification using the hair shaft proteome. PLoS One 11(9):e0160653. doi:10.1371/journal.pone.0160653 PMID:27603779 PMCID:PMC5014411
• Rice RH, Durbin-Johnson BP, Ishitsuka Y, Salemi MR, Phinney BS, Rocke DM, Roop DR. 2016. Proteomic analysis of loricrin knockout mouse epidermis. J Proteome Res 15(8):2560-2566. doi:10.1021/acs.jproteome.6b00108 PMID:27418529

2014

• Laatsch CN, Durbin-Johnson BP, Rocke DM, Mukwana S, Newland AB, Flagler MJ, Davis MG, Eigenheer RA, Phinney BS, Rice RH. 2014. Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis. PeerJ 2:e506. doi:10.7717/peerj.506 PMID:25165623 PMCID:PMC4137660

2013

• Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Schmuth M, Gruber R. 2013. Distinguishing ichthyoses by protein profiling. PLoS One 8(10):e75355. doi:10.1371/journal.pone.0075355 PMID:24130705 PMCID:PMC3793978
• Rice RH, Winters BR, Durbin-Johnson BP, Rocke DM. 2013. Chicken corneocyte cross-linked proteome. J Proteome Res 12(2):771-776. doi:10.1021/pr301036k PMID:23256538 PMCID:PMC3569041
• Stewart DN, Lango J, Nambiar KP, Falso MS, Fitzgerald PG, Rocke DM, Hammock BD, Buchholz BA. 2013. Carbon turnover in the water-soluble protein of the adult human lens. Mol Vis 19:463-475. PMID:23441119 PMCID:PMC3580966

2012

• Rice RH, Bradshaw KM, Durbin-Johnson BP, Rocke DM, Eigenheer RA, Phinney BS, Sundberg JP. 2012. Differentiating inbred mouse strains from each other and those with single gene mutations using hair proteomics. PLoS One 7(12):e51956. doi:10.1371/journal.pone.0051956 PMID:23251662 PMCID:PMC3522583

2009

• Barkauskas DA, An HJ, Kronewitter SR, de Leoz M, Chew HK, de Vere White RW, Leiserowitz GS, Miyamoto S, Lebrilla CB, Rocke DM. 2009. Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. Bioinformatics 25(2):251-257. doi:10.1093/bioinformatics/btn610 PMID:19073586 PMCID:PMC2639011
• Barkauskas DA, Kronewitter SR, Lebrilla CB, Rocke DM. 2009. Analysis of MALDI FT-ICR mass spectrometry data: a time series approach. Anal Chim Acta 648(2):207-214. doi:10.1016/j.aca.2009.06.064 PMID:19646586 PMCID:PMC2772212
• Berglund SR, Santana A, Rice RH, Rocke DM, Goldberg Z, Li D. 2009. Proteomic analysis of low dose arsenic and ionizing radiation exposure on keratinocytes. Proteomics 9(7):1925-1938. doi:10.1002/pmic.200800118 PMID:19294697 PMCID:PMC2666104
• Sivamani R, Pullar CE, Manabat-Hidalgo C, Rocke DM, Carlsen RC, Greenhalgh DG, Isseroff RR. 2009. Stress-mediated increases in systemic and local epinephrine impair skin wound healing: potential new indication for beta blockers. PLoS Med 6(1):e12. doi:10.1371/journal.pmed.1000012 PMID:19143471 PMCID:PMC2621262

2008

• Berglund SR, Rocke DM, Dai JJ, Schwietert C, Santana A, Stern RL, Lehmann J, Hartmann Siantar CL, Goldberg Z. 2008. Transient genome-wide transcriptional response to low-dose ionizing radiation in vivo in humans. Int J Radiat Oncol Biol Phys 70(1):229-34. PMID:17996396
• Lu R, Lee G, Shultz MA, Dardick C, Jung K, Rice RH, Phetsom J, Jia Y, Goldberg Z, Schnable PS, Ronald P, Rocke DM. 2008. Assessing probe-specific dye and slide biases in two-color microarray data. BMC Bioinformatics 9:314. doi:10.1186/1471-2105-9-314 PMID:18638416 PMCID:PMC2496918
• Xi Y, Rocke DM. 2008. Baseline correction for NMR spectroscopic metabolomics data analysis. BMC Bioinformatics 9:324. doi:10.1186/1471-2105-9-324 PMID:18664284 PMCID:PMC2516527

2007

• Corbett BA, Kantor AB, Shulman H, Walker WL, Lit L, Ashwood P, Rocke DM, Sharp FR. 2007. A proteomic study of serum from children with autism showing differential expression of apolipoproteins and complement proteins. Mol Psychiatry 12(3):292-306. doi:10.1038/sj.mp.4001943 PMID:17189958
• Ye J, Liu H, Kirmiz C, Lebrilla CB, Rocke DM. 2007. On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve. BMC Bioinformatics 8:477. PMID:18076765

2006

• An HJ, Tillinghast JS, Woodruff DL, Rocke DM, Lebrilla CB. 2006. A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins. J Proteome Res 5(10):2800-2808. PMID:17022651
• Dai JJ, Lieu L, Rocke DM. 2006. Dimension reduction for classification with gene expression microarray data. Stat Appl Genet Mol Biol 5(1):1544-6115. PMID:16646870
• Goldberg Z, Rocke DM, Schwietert C, Berglund SR, Santana A, Jones A, Lehmann J, Stern RL, Lu R, Hartmann Siantar CL. 2006. Human in vivo dose response to controlled, low-dose low LET ionizing radiation exposure. Clin Cancer Res 12(12):3723-3729. PMID:16778099
• Lehmann J, Stern RL, Daly TP, Schwietert C, Jones GE, Arnold ML, Hartmann Siantar CL, Rocke DM, Goldberg Z. 2006. Dosimetry for quantitative analysis of the effects of low-dose ionizing radiation in radiation therapy patients. Radiation Research 165(2):240-247. PMID:16435922
• Rea MA, Zhou L, Qin Q, Barrandon Y, Easley KW, Gungner SF, Phillips MA, Holland WS, Gumerlock PH, Rocke DM, Rice RH. 2006. Spontaneous immortalization of human epidermal cells with naturally elevated telomerase. Journal of Investigative Dermatology 126(11):2507-15. PMID:16778798

2005

• Hardin J, Rocke DM. 2005. The distribution of robust distances. Journal of Computational and Graphical Statistics 14(4):928-946.
• Nguyen DV, Rocke DM. 2005. On partial least squares dimension reduction for microarray-based classification: a simulation study. Computational Statistics & Data Analysis 43(3):407-425.
• Purohit PV, Rocke DM, Viant MR, Woodruff DL. 2005. Discrimination models using variance-stabilizing transformation of metabolomic NMR data. OMICS 8(2):118-130. PMID:15268771
• Rocke DM, Goldberg Z, Schwietert C, Santana A. 2005. A method for detection of differential gene expression in the presence of inter-individual variability in response. Bioinformatics 21(21):3990-3992. PMID:16159922
• Zhou L, Rocke DM. 2005. An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics 21(21):3983-3989. doi:10.1093/bioinformatics/bti665 PMID:16159924

2004

• Durbin-Johnson BP, Rocke DM. 2004. Variance-stabilizing transformations for two-color microarrays. Bioinformatics 20(5):660-U190. PMID:15033873
• Rocke DM. 2004. Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol 15(6):703-713. PMID:15561590
• Wilson MD, Rocke DM, Durbin-Johnson BP, Kahn HD. 2004. Detection limits and goodness-of-fit measures for the two-component model of chemical analytical error. Anal Chim Acta 509(2):197-208.
• Wilson MD, Ustin SL, Rocke DM. 2004. Classification of contamination in salt marsh plants using hyperspectral reflectance. IEEE Transactions on Geoscience and Remote Sensing 42:1088-1095.

2003

• Caruso JA, Klaue B, Michalke B, Rocke DM. 2003. Group assessment: elemental speciation. Ecotoxicol Environ Saf 56:32-44. PMID:12915138
• Durbin-Johnson BP, Rocke DM. 2003. Estimation of transformation parameters for microarray data. Bioinformatics 19(11):1360-1367. PMID:12874047
• Geller SC, Hagerman PJ, Gregg JP, Rocke DM. 2003. Transformation and normalization of oligonucleotide microarray data. Bioinformatics 19(14):1817-1823. PMID:14512353
• Hardin J, Rocke DM. 2003. Outlier detection in the multiple cluster setting using the minimum covariance determinant estimator. Computational Statistics & Data Analysis 44(4):625-638.
• Nguyen DV, Rocke DM. 2003. Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics 18(12):1625-1632. PMID:12490447
• Purohit PV, Rocke DM. 2003. Discriminant models for high-throughput proteomics mass spectrometer data. Proteomics 3(9):1699-1703. PMID:12973728
• Rocke DM, Dai JJ. 2003. Sampling and subsampling for cluster analysis in data mining, with applications to sky survey data. Data Mining and Knowledge Discovery 7(2):215-232.
• Rocke DM, Durbin-Johnson BP. 2003. Approximate variance-stabilizing transformations for gene-expression microarray data. Bioinformatics 19(8):966-972. PMID:12761059
• Rocke DM, Durbin-Johnson BP, Wilson MD, Kahn HD. 2003. Modeling uncertainty in the measurement of low-level analytes in environmental analysis. Ecotoxicol Environ Saf 56(1):78-92. PMID:12915142
• Zhao Y, Chen BP, Miao H, Yuan S, Li Y, Hu Y, Rocke DM, Chien S. 2003. Improved significance test for DNA microarray data: temporal effects of shear stress on endothelial genes. Physiol Genomics 12(1):1-11. PMID:12399447

2002

• Durbin-Johnson BP, Hardin J, Hawkins DM, Rocke DM. 2002. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 18Suppl1:S105-S110. PMID:12169537
• Nguyen DV, Rocke DM. 2002. Classification of Acute Leukemia Based on DNA Microarray Gene Expressions Using Partial Least Squares. In: Methods of Microarray Data Analysis. Kluwer Academic, Boston, MA. pp.109-124.
• Nguyen DV, Rocke DM. 2002. Multi-class cancer classification via partial least squares with gene expression profiles. Bioinformatics 18(9):1216-1226. PMID:12217913
• Nguyen DV, Rocke DM. 2002. Tumor classification by partial least squares using gene expression data. Bioinformatics 18(1):39-50. PMID:11836210
• Rocke DM, Woodruff DL. 2002. Computational Connections Between Robust Multivariate Analysis and Clustering. In: COMPSTAT 2002, Proceedings in Computational Staistics. Heidelberg: Physica-Verlag, Berlin, Germany. pp.255-260.

2001

• Jones G, Rocke DM. 2001. Analyte identification in multivariate calibration. Biometrics 57(2):571-576. PMID:11414586
• Rocke DM, Durbin-Johnson BP. 2001. A model for measurement errors for gene expression arrays. Journal of Computational Biology 8(6):557-569.
• Rocke DM, Woodruff DL. 2001. Discussion of multivariate outlier detection and robust covariance matrix estimation. Technometrics 43:300-303.

2000

• Jian D, Rocke DM. 2000. Modeling spatial variation in area source emissions - a poisson regression approach. J Agric Biol Environ Stat 5:7-21.

1999

• Coleman D, Dong X, Hardin J, Rocke DM, Woodruff DL. 1999. Some computational issues in cluster analysis with no a priori metric. Computational Statistics & Data Analysis 31(1):1-12.
• Jones G, Rocke DM. 1999. Bootstrapping in controlled calibration experiments. Technometrics 41:224-233.

1997

• Jones G, Wortberg M, Rocke DM, Hammock BD. 1997. Immunoassay of cross-reacting analytes. In: Immunochemical Technology for Environmental Applications (ACS Symposium Series No. 657). American Chemical Society, Washington, DC. pp.331-342.
• Rocke DM, Jones G. 1997. Optimal design for ELISA and other forms of immunoassay. Technometrics 39(2):162-170.
• Rocke DM, Woodruff DL. 1997. Robust estimation of multivariate location and shape. Journal of Statistical Planning and Inference 57:245-255.

1996

• Jones G, Wortberg M, Hammock BD, Rocke DM. 1996. A procedure for the immunoanalysis of samples containing one or more members of a group of cross-reacting analytes. Anal Chim Acta 336(1-3):175-183.
• Jones G, Wortberg M, Kreissig SB, Hammock BD, Rocke DM. 1996. Application of the bootstrap to calibration experiments. Anal Chem 68(5):763-770. PMID:8779441
• Rocke DM. 1996. Robustness properties of S-estimators of multivariate location and shape in high dimension. The Annals of Statistics 24(3):1327-1345.
• Rocke DM, Woodruff DL. 1996. Identification of outliers in multivariate data. J Am Stat Assoc 91(435):1047-1061.
• Wortberg M, Jones G, Kreissig SB, Rocke DM, Gee SJ, Hammock BD. 1996. An approach to the construction of an immunoarray for differentiating and quantitating cross reacting analytes. Anal Chim Acta 319(3):291-303.

1995

• Jones G, Wortberg M, Kreissig SB, Hammock BD, Rocke DM. 1995. Sources of experimental variation in calibration curves for enzyme-linked immunosorbent assay. Anal Chim Acta 313:197-207.
• Rocke DM. 1995. Optimal design of quantitative immunoassay protocols. In: New Frontiers in Agrochemical Immunoassay. AOAC International, Arlington, VA. pp.251-259.
• Rocke DM, Lorenzato S. 1995. A two-component model for measurement error in analytical chemistry. Technometrics 37(2):176-184.
• Wortberg M, Kreissig SB, Jones G, Rocke DM, Hammock BD. 1995. An immunoarray for the simultaneous determination of multiple triazine herbicides. Anal Chim Acta 304:339-352.