University of California-Davis
Center for Image Processing and Integrated Computing
2343 Academic Surge Building
One Shields Avenue
Davis, CA 95616
Phone: 530-752-0510
Fax: 530-752-2924
Email:
Berglund, Susanne R., David M. Rocke, Jian J. Dai, Chad Schwietert, Alison Santana, Robin L. Stern, Joerg Lehmann, Christine L. Hartmann Siantar, and Zelanna Goldberg. 2008. Transient genome-wide transcriptional response to low-dose ionizing radiation in vivo in humans. International Journal of Radiation Oncology, Biology, Physics. (http://www.sciencedirect.com/science/journal/ 03603016) 70(1):229-34.
Lu, Ruxiaio, Geun-Cheol Lee, Michael A. Shultz, Chris Dardick, Kihong Jung, Robert H. Rice, Jirapa Phetsom, Yi Jia, Zelanna Goldberg, Patrick S. Schnable, Pamela Ronald, and David M. Rocke. 2008. Assessing probe-specific dye and slide biases in two-color microarray data. BMC Bioinformatics. doi:10.1186/1471-2105-9-314(http://dx.doi.org/10.1186/1471-2105-9-314) 9:314.
Xi, Yoanxin and David M. Rocke. 2008. Baseline correction for NMR spectroscopic metabolomics data analysis. BMC Bioinformatics. doi:10.1186/1471-2105-9-324(http://dx.doi.org/10.1186/1471-2105-9-324) 9:324.
2007
Corbett, Blythe A., A.B. Kantor, H. Shulman, W.L. Walker, L. Lit, P. Ashwood, David M. Rocke, and F.R. Sharp. 2007. A Proteomic Study of Serum from Children with Autism Showing Differential Expression of Apolipoproteins and Complement Proteins. Molecular Psychiatry. 12(3):292-306.
Ye, Jingjing, Hao Liu, Crystal Kirmiz, Carlito B. Lebrilla, and David M. Rocke. 2007. On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve. BMC Bioinformatics. 8:477.
2006
An, Hyun Joo, John S. Tillinghast, David L. Woodruff, David M. Rocke, and Carlito B. Lebrilla. 2006. A new computer program (GlycoX) to determine simultaneously the glycosylation sites and oligosaccharide heterogeneity of glycoproteins. Journal of Proteome Research. 5(10):2800-2808.
Dai, Jian J., Linh Lieu, and David M. Rocke. 2006. Dimension Reduction for Classification with Gene Expression Microarray Data. Statistical Applications in Genetics and Molecular Biology. (http://www.bepress.com/sagmb/vol5/iss1/art11/) 5(1):1544-6115.
Goldberg, Zelanna, David M. Rocke, Chad Schwietert, Susanne R. Berglund, Alison Santana, Angela Jones, Joerg Lehmann, Robin L. Stern, Ruxiaio Lu, and Christine L. Hartmann Siantar. 2006. Human in vivo dose response to controlled, low-dose low LET ionizing radiation exposure. Clinical Cancer Research. (http://clincancerres.aacrjournals.org/) 12(12):3723-3729.
Lehmann, Joerg, Robin L. Stern, Thomas P. Daly, Chad Schwietert, Gregory E. Jones, Michelle L. Arnold, Christine L. Hartmann Siantar, David M. Rocke, and Zelanna Goldberg. 2006. Dosimetry for Quantitative Analysis of the Effects of Low-Dose Ionizing Radiation in Radiation Therapy Patients. Radiation Research. (http://www.radres.org/ECOMradres/timssnet/com mon/tnt_InstructionsforAuthors.cfm) 165(2):240-247.
Rea, Miguel A., Lei Zhou, Qin Qin, Yann Barrandon, Karen W. Easley, Sarah F. Gungner, Marjorie A. Phillips, William S. Holland, Paul H. Gumerlock, David M. Rocke, and Robert H. Rice. 2006. Spontaneous immortalization of human epidermal cells with naturally elevated telomerase. Journal of Investigative Dermatology. (http://www.jidonline.org/) 126(9):2507-2515.
Rea, Miguel A., Lei Zhou, Qin Qin, Yann Barrandon, Karen W. Easley, Sarah F. Gungner, Marjorie A. Phillips, William S. Holland, Paul H. Gumerlock, David M. Rocke, and Robert H. Rice. 2006. Spontaneous immortalization of human epidermal cells with naturally elevated telomerase. Journal of Investigative Dermatology. (http://www.jidonline.org/) 126(11):2507-15.
Nguyen, Danh V. and David M. Rocke. 2005. On partial least squares dimension reduction for microarray-based classification: a simulation study. Computational Statistics and Data Analysis. (http://www.sciencedirect.com/science/journal/ 01679473) 43(3):407-425.
Purohit, Parul V., David M. Rocke, Mark R. Viant, and David L. Woodruff. 2005. Discrimination Models using Variance-Stabilizing Transformation of Metabolomic NMR Data. OMICS: A Journal of Integrative Biology. (http://www.liebertpub.com/publication.aspx?pu b_id=43) 8(2):118-130.
Rocke, David M., Zelanna Goldberg, Chad Schwietert, and Alison Santana. 2005. A method for detection of differential gene expression in the presence of inter-individual variability in response. Bioinformatics. (http://bioinformatics.oupjournals.org/) 21(21):3990-3992.
Zhou, Lei and David M. Rocke. 2005. An Expression Index for Affymetrix GeneChips Based on the Generalized Logarithm. Bioinformatics. (http://bioinformatics.oupjournals.org/) 21(21):3983-3989.
2004
Durbin, Blythe P. and David M. Rocke. 2004. Variance-stabilizing transformations for two-color microarrays. Bioinformatics. (http://bioinformatics.oupjournals.org/) 20(5):660-U190.
Nguyen, Danh V. and David M. Rocke. 2004. On partial least squares dimension reduction for microarray-based classification: a simulation study. Computational Statistics and Data Analysis. (http://www.sciencedirect.com/science/journal/ 01679473) 46(3):407-425.
Purohit, Parul V., David M. Rocke, Mark R. Viant, and David L. Woodruff. 2004. Discrimination models using variance-stabilizing transformation of metabolomic NMR data. OMICS: A Journal of Integrative Biology. (http://www.liebertpub.com/publication.aspx?pu b_id=43) 8(2):118-130.
Rocke, David M. 2004. Design and Analysis of Experiments with High Throughput Biological Assay Data. Seminars in Cell and Developmental Biology. 15(6):703-713.
Wilson, Machelle D., David M. Rocke, Blythe P. Durbin, and Henry D. Kahn. 2004. Detection limits and goodness-of-fit measures for the two-component model of chemical analytical error. Analytica Chimica Acta. (http://www.sciencedirect.com/science/journal/ 00032670) 509(2):197-208.
Wilson, Machelle D., Susan L. Ustin, and David M. Rocke. 2004. Classification of Contamination in Salt Marsh Plants Using Hyperspectral Reflectance. IEEE Transactions on Geosciences & Remote Sensing. (http://www.ieee.org/organizations/pubs/transa ctions/tgrs.htm) 42:1088-1095.
2003
Caruso, Joseph A., Bjoern Klaue, B. Michalke, and David M. Rocke. 2003. Group Assessment: Elemental Speciation. Ecotoxicology and Environmental Safety. (http://www.elsevier.com/locate/issn/0147-6513) 56:32-44.
Durbin, Blythe P. and David M. Rocke. 2003. Estimation of transformation parameters for microarray data. Bioinformatics. (http://bioinformatics.oupjournals.org/) 19(11):1360-1367.
Geller, Sue C., Paul Hagerman, Jeff P. Gregg, and David M. Rocke. 2003. Transformation and normalization of oligonucleotide microarray data. Bioinformatics. (http://bioinformatics.oupjournals.org/) 19(14):1817-1823.
Hardin, Johanna and David M. Rocke. 2003. Outlier Detection in the Multiple Cluster Setting using the Minimum Covariance Determinant Estimator. Computational Statistics and Data Analysis. (http://www.sciencedirect.com/science/journal/ 01679473) 44(4):625-638.
Nguyen, Danh V. and David M. Rocke. 2003. Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics. (http://bioinformatics.oupjournals.org/) 18(12):1625-1632.
Purohit, Parul V. and David M. Rocke. 2003. Discriminant Models for High-Throughput Proteomics Mass Spectrometer Data. Proteomics. 3(9):1699-1703.
Rocke, David M. and Jian J. Dai. 2003. Sampling and Subsampling for Cluster Analysis in Data Mining, with Applications to Sky Survery Data. Data Mining and Knowledge Discovery. 7(2):215-232.
Rocke, David M. and Blythe P. Durbin. 2003. Approximate Variance-Stabilizing Transformations for Gene-Expression Microarray Data. Bioinformatics. (http://bioinformatics.oupjournals.org/) 19(8):966-972.
Rocke, David M., Blythe P. Durbin, Machelle D. Wilson, and Henry D. Kahn. 2003. Modeling uncertainty in the measurement of low-level analytes in environmental analysis. Ecotoxicology and Environmental Safety. (http://www.elsevier.com/locate/issn/0147-6513) 56(1):78-92.
Zhao, Yihua, Benjamin PC Chen, Hui Miao, Suli Yuan, Yi-Shuan Li, Yingli Hu, David M. Rocke, and Shu Chien. 2003. Improved significance test for DNA microarray data: temporal effects of shear stress on endothelial genes. Physiological Genomics. (http://physiolgenomics.physiology.org/) 12(1):1-11.
2002
Durbin, Blythe P., Johanna Hardin, Douglas M. Hawkins, and David M. Rocke. 2002. A Variance-Stabilizing Transformation for Gene-Expression Microarray Data. Bioinformatics. (http://bioinformatics.oupjournals.org/) 18(Suppl.1):S105-S110.
Nguyen, Danh V. and David M. Rocke. 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, Danh V. and David M. Rocke. 2002. Multi-Class Cancer Classification via Partial Least Squares with Gene Expression Profiles. Bioinformatics. (http://bioinformatics.oupjournals.org/) 18(9):1216-1226.
Nguyen, Danh V. and David M. Rocke. 2002. Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics. (http://bioinformatics.oupjournals.org/) 18(12):1625-1632.
Nguyen, Danh V. and David M. Rocke. 2002. Tumor Classification by Partial Least Squares using Gene Expression Data. Bioinformatics. (http://bioinformatics.oupjournals.org/) 18(1):39-50.
Rocke, David M. and David L. Woodruff. 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, Geoffrey and David M. Rocke. 2001. Analyte identification in multivariate calibration. Biometrics. (http://stat.tamu.edu/Biometrics/) 57(2):571-576.
Rocke, David M. and Blythe P. Durbin. 2001. A model for measurement errors for gene expression arrays. Journal of Computational Biology. 8(6):557-569.
Rocke, David M. and David L. Woodruff. 2001. Discussion of Multivariate Outlier Detection and Robust Covariance Matrix Estimation. Technometrics. (http://www.jstor.org/journals/00401706.html) 43:300-303.
Coleman, Dan, Xioapeng Dong, Johanna Hardin, David M. Rocke, and David L. Woodruff. 1999. Some computational issues in cluster analysis with no a priori metric. Computational Statistics and Data Analysis. (http://www.sciencedirect.com/science/journal/ 01679473) 31(1):1-12.
Jones, Geoffrey and David M. Rocke. 1999. Bootstrapping in controlled calibration experiments. Technometrics. (http://www.jstor.org/journals/00401706.html) 41:224-233.
1997
Jones, Geoffrey, Monika Wortberg, David M. Rocke, and Bruce D. Hammock. 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, David M. and Geoffrey Jones. 1997. Optimal design for ELISA and other forms of immunoassay. Technometrics. (http://www.jstor.org/journals/00401706.html) 39(2):162-170.
Rocke, David M. and David L. Woodruff. 1997. Robust estimation of multivariate location and shape. Journal of Statistical Planning and Inference. (http://www.elsevier.com/wps/find/journaldescr iption.cws_home/505561/description#descriptio n) 57:245-255.
1996
Jones, Geoffrey, Monika Wortberg, Bruce D. Hammock, and David M. Rocke. 1996. A procedure for the immunoanalysis of samples containing one or more members of a group of cross-reacting analytes. Analytica Chimica Acta. (http://www.sciencedirect.com/science/journal/ 00032670) 336(1-3):175-183.
Jones, Geoffrey, Monika Wortberg, Sabine B. Kreissig, Bruce D. Hammock, and David M. Rocke. 1996. Application of the bootstrap to calibration experiments. Analytical Chemistry. (http://pubs.acs.org/journals/ancham/index.htm l) 68(5):763-770.
Rocke, David M. 1996. Robustness properties of S-estimators of multivariate location and shape in high dimension. Annals Statistics. (http://www.jstor.org/journals/00905364.html) 24(3):1327-1345.
Rocke, David M. and David L. Woodruff. 1996. Identification of outliers in multivariate data. Journal of the American Statistical Association. (http://www.jstor.org/journals/01621459.html) 91(435):1047-1061.
Wortberg, Monika, Geoffrey Jones, Sabine B. Kreissig, David M. Rocke, Shirley J. Gee, and Bruce D. Hammock. 1996. An approach to the construction of an immunoarray for differentiating and quantitating cross reacting analytes. Analytica Chimica Acta. (http://www.sciencedirect.com/science/journal/ 00032670) 319(3):291-303.
1995
Jones, Geoffrey, Monika Wortberg, Sabine B. Kreissig, Bruce D. Hammock, and David M. Rocke. 1995. Sources of experimental variation in calibration curves for enzyme-linked immunosorbent assay. Analytica Chimica Acta. (http://www.sciencedirect.com/science/journal/ 00032670) 313:197-207.
Rocke, David M. 1995. Optimal design of quantitative immunoassay protocols. In: New Frontiers in Agrochemical Immunoassay. AOAC International, Arlington, VA. pp.251-259.
Rocke, David M. and Stefan Lorenzato. 1995. A two-component model for measurement error in analytical chemistry. Technometrics. (http://www.jstor.org/journals/00401706.html) 37(2):176-184.
Wortberg, Monika, Sabine B. Kreissig, Geoffrey Jones, David M. Rocke, and Bruce D. Hammock. 1995. An immunoarray for the simultaneous determination of multiple triazine herbicides. Analytica Chimica Acta. (http://www.sciencedirect.com/science/journal/ 00032670) 304:339-352.
70(1):229-34. 
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