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General Interest

Nature on statistical analysis of microarray data.

Can a Biologist Fix a Radio?, Y. Lazebnik

Bias as a threat to validity of cancer molecular marker research, David F. Ransohoff

Best Practices for Biostatistical Consultation and Collaboration in Academic Health Centers, Susan M. Perkins, Peter Bacchetti, Cynthia S. Davey, Christopher J. Lindsell, Madhu Mazumdar, Robert A. Oster, Peter N. Peduzzi, David M. Rocke, Kyle D. Rudser, Mimi Kim & the Biostatistics, Epidemiology, and Research Design (BERD) Key Function Committee of the Clinical and Translational Science (CTSA) Consortium.
Link to Paper

Unpublished Working Papers

Heterogeneity of Variance in Gene Expression Microarray Data, D.M. Rocke

Some Statistical Tools for Data Mining Applications

Constructive Statistics: Estimators, Algorithms, and Asymptotics

A Synthesis of Outlier Detection and Cluster Identification

A Perspective on Statistical Tools for Data Mining Applications

Presentations

Excess False Positives in Negative-Binomial Based Analysis of Data from RNA-Seq Experiments, UVA, March 2016

Challenges in Experimental Design and Data Analysis for Modern Biological Data, SSR Annual Meeting, July 2016

Reprints

Neonatal Salivary Analysis Reveals Global Gene Expression Changes in the Developing Premature Infant. Maron JL, Johnson KL, Rocke DM, Cohen M, Bianchi DW. Clinical Chemistry, 56: 409-416.

Early Mortality and Cardiorespiratory Failure in Patients with Fibrodysplasia Ossificans Progressiva. Kaplan FS, Zasloff MA, Kitterman JA, Shore EM, Hong CC, Rocke DM. Journal of Bone and Joint Surgery, 92: 686-691.

A Method to Detect Differential Gene Expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Chen Y, Wu R, Felton J, Rocke DM, and Chakicherla A. Biomedical Informatics Insights, 3: 1-10.

A General-Purpose Baseline Estimation Algorithm for Spectroscopic Data. Barkauskas DA and Rocke DM. Analytica Chimica Acta,, 657: 191-197.

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. Li B, Li D, Lau DH, Farwell DG, Luu Q, Rocke DM, Newman K, Courquin J, Purdy JA, and Chen AM. Radiation Oncology, 4: 52.

Bridging the Gap Between Systems Biology and Medicine. Clermont G, Auffray C, Moreau Y, Rocke DM, Dalevi D, Dubhashi D, Marshall D, Raasch P, Dehne F, Provero P, Tegner J, Aronow BJ, Langston MA, and Benson M. Genome Medicine, 1: 88.

Gene Regulation in Parthenocarpic Tomato Fruit. Martinelli F, Uratsu SL, Reagan RL, Chen Y, Tricoli D, Fiehn O, Rocke DM, Gasser CS, Dandekar AM. Journal of Experimental Botany, 60: 3873-3890.

Distinguishing Mouse Strains by Proteomic Anlaysis of Pelage Hair. Rice RH, Rocke DM, Tsai H-S, Lee YJ, Sundberg JP. Journal of Investigative Dermatology, 129: 2120-2125.

IGF-1 Does Not Moderate The Time-Dependent Transcriptional Patterns of Key Homeostatic Genes Induced By Sustained Compression of Bovine Cartilage. Wheeler CA, Jafarzadeh SR, Rocke DM, Grodzinsky AJ. Osteoarthritis and Cartilage, 17: 944-952.

Analysis of MALDI FT-ICR Mass Spectrometry Data: a Time Series Approach. Barkauskas DA, Kronewitter S, Lebrilla CB, Rocke DM. Analytica Chimica Acta, 648: 207-214.

Proteomic Analysis of Low Dose Arsenic and Ionizing Radiation Exposure on Keratinocytes. Berglund SR, Santana A, Li D, Rice RH, Rocke DM, Golberg Z. Proteomics, 9: 1923-1938.

Executive Functioning in Children with Autism Spectrum Disorder, Attention Deficit Hyperactivity Disorder and Typical Development. Corbett BA, Constantine LJ, Hendren R, Rocke D, Ozonoff SA. Psychiatry Research, 166: 210-222.

Papers on Normalization, Variable Selection, Classification, or Clustering of Microarray Data (Editorial). Rocke DM, Ideker T, Troyanskaya O, Quackenbush J, Dopazo J. Bioinformatics, 25: 701-702.

Detecting Glycan Cancer Biomarkers using MALDI FT-ICR mass spectrometry data, DA Barkauskas, HJ An, S Kronewitter, ML de Leoz, S Miyamoto, GS Leiserowitz, CB Lebrilla, and DM Rocke (Bioinformatics, 2009, 25, 251–257).

Stress mediated increases in systemic and local epinephrine impair skin wound healing: potential new indication for beta blockers, RK Sivamani, CE Pullar, CG Manabat-Hidalgo, DM Rocke, RC Carlsen, DG. Greenhalgh, and RR Isseroff (PLOS Medicine, 2009, 6(1): e1000012).

Survival Enhancing Indications for Coronary Artery Bypass Graft Surgery in California, Z Li, RL Kravitz, JP Marcin, PS Romano, DM Rocke, TA. Denton, RG Brindis, J Dai, and EA Amsterdam (BMC Health Services Research, 2008, 8:257).

Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis, Y Xi and DM Rocke (BMC Bioinformatics, 2008, 9:324).

Assessing Probe-Specific Dye and Slide Biases in Two-Color Microarray Data, R Lu, GC Lee, M Shultz, C Dardick, K Jung, J Phetsom, Y Jia, RH Rice, Z Goldberg, PS Schnable, P Ronald and DM Rocke (BMC Bioinformatics, 2008, 9:314).

The CABG Surgery Volume–Outcome Relationship: Temporal Trends and Selection Effects in California, 1998–2004, JP Marcin, Z Li, RL Kravitz, JJ Dai,
DM Rocke, and PS Romano (Health Services Research, 43, 174–192).

Transient Genome-Wide Transcriptional Response to Low-Dose Ionizing Radiation In Vivo in Humans, SR Berglund, DM Rocke, J Dai, CW Schwietert, A Santana, RL Stern, J Lehmann, CL Hartmann Siantar and Z Goldberg (International Journal of Radiation Oncology, Biology, Physics, 2008, 70, 229-234).

On the Analysis of Glycomics Mass Spectrometry Data via the Regularized Area under the ROC Curve, J Ye, H Liu, C. Kirmiz, CB Lebrilla, and DM Rocke, (BMC Bioinformatics, 2007, 8:477).

A Proteomic Study of Serum from Children with Autism Showing Differential Expression of Apolipoproteins and Complement Proteins, BA Corbett, AB Kantor, H Schulman, WL Walker, L Lit, P Ashwood, DM Rocke, and FR Sharp (Molecular Psychiatry, 2007, 12, 292–306).

International Milk Genomics Consortium, JB Germana, FL Schanbacher, Bo Lönnerdal, JF Medrano, MA McGuire, JL McManaman, DM Rocke, TP Smith, MC Neville, P Donnelly, M Lange and R Ward (Trends in Food Science and Technology, 2006, 17, 656–661).

Spontaneous Immortalization of Human Epidermal Cells with Naturally Elevated Telomerase, MA Rea, L Zhou, Q Qin, Y Barrandon, KW Easley, SF Gungner, MA Phillips, WS Holland, PH Gumerlock, DM Rocke, and RH Rice (Journal of Investigative Dermatology, 2006, 126, 2507–2515).

A New Computer Program (GlycoX) To Determine Simultaneously the Glycosylation Sites and Oligosaccharide Heterogeneity of Glycoproteins, HJ An, JS Tillinghast, DL Woodruff, DM Rocke, and CB Lebrilla (Journal of Proteome Research, 2006, 5, 2800–2808).

Human in Vivo Dose-Response to Controlled, Low-Dose, Low Linear Energy Transfer Ionizing Radiation Exposure, Z Goldberg, DM Rocke, C Schweitert, SR Berglund, A Santana, A Jones, J Lehmann, R Stern, R Lu, and C Hartman Siantar (Clinical Cancer Research, 2006, 12, 3723–3729).

Dimension Reduction for Classification with Gene Expression Microarray Data, JJ Dai, L Lieu, and DM Rocke (Statistical Applications in Genetics and Molecular Biology, 2006, 5(1) Article 6).

Dosimetry for Quantitative Analysis of the Effects of Low-Dose Ionizing Radiation in Radiation Therapy Patients, J Lehmann, RL Stern, TP Daly, DM Rocke, CW Schwietert, GE Jones, ML Arnold, CL Hartmann Siantar, and Z Goldberg (Radiation Research, 2006, 165, 240–247).

A Method for Detection of Differential Gene Expression in the Presence of Inter-Individual Variability in Response, DM Rocke, Z Goldberg, C Schwietert, and A Santana (Bioinformatics, 2005, 21, 3990–3992).

An Expression Index for Affymetrix GeneChips Based on the Generalized Logarithm, L Zhou and DM Rocke (Bioinformatics, 2005, 21, 3983–3989).

Iatrogenic Harm Caused By Diagnostic Errors In Fibrodysplasia Ossificans Progressiva, JA Kitterman, S Kantanie, DM Rocke, and FS Kaplan (Pediatrics, 2005, 116, peds.2005–0469).

The Distribution of Robust Distances, J Hardin and DM Rocke (Journal of Computational and Graphical Statistics, 2005, 14, 928–946).

A Robust Testing Procedure for the Equality of Covariance Matrices, S Aslam and DM Rocke (Computational Statistics and Data Analysis, 2005, 49, 864–874).

Design and Analysis of Experiments with High Throughput Biological Assay Data, DM Rocke (Seminars in Cell and Developmental Biology, 2004, 15, 708–713).

Discrimination Models using Variance-Stabilizing Transformation of Metabolomic NMR Data, PV Purohit, DM Rocke, MR Viant, and DL Woodruff (Omics, 2004, 8, 118–130).

Influenza-like Viral Illnesses and Flare-ups of Fibrodysplasia Ossificans Progressiva, RF Scarlett, DM Rocke, S Kantanie, J Patel, EM Shore, and FS Kaplan (Clinical Orthopaedics and Related Research, 2004, 423, 275–279).

On Partial Least Squares Dimension Reduction for Microarray-Based Classification: A Simulation Study, D Nguyen and DM Rocke (Computational Statistics and Data Analysis, 2004, 46, 407–425).

Classification of Contamination in Salt Marsh Plants Using Hyperspectral Data, MD Wilson, SL Ustin, and DM Rocke, (IEEE Transactions on Geoscience and Remote Sensing, 2004, 42, 1088–1095).

Variance Stabilizing Transformations for Two-Color Microarrays, B Durbin and DM Rocke (Bioinformatics, 2004, 20, 660-667).

Detection Limits and Goodness-of-Fit measures for the Two-Component Model of Chemical Analytical Error, M Wilson, DM Rocke, B Durbin, and H Kahn (Analytica Chimica Acta, 2004, 509, 197-208).

A Knowledge-Based Model for Watershed Assessment for Sediment, J Dai and DM Rocke (Environmental Modelling and Software, 2004, 19, 423-433).

Outlier Detection in the Multiple Cluster Setting using the Minimum Covariance Determinant Estimatator, J Hardin and DM Rocke (Computational Statistics and Data Analysis, 2004, 44, 625-638).

The Medical Management of Fibrodysplasia Ossificans Progressiva: Current Treatment Considerations, F.S. Kaplan, E.M. Shore, D.L. Glaser, S. Emerson, et al. (Clin Proc Intl Clin Consort FOP, 2003, 1(2):1-72).

Transformation and Normalization of Oligonucleotide Microarray Data, S.C. Geller, J.P. Gregg, P. Hagerman, and D.M. Rocke (Bioinformatics, 2003, 19, 1817-1823).

Discriminant Models for High-Throughput Proteomics Mass Spectometer Data, P.V. Purohit and D.M. Rocke (Proteomics, 2003, 3, 1699-1703).

Approximate Variance-Stabilizing Transformations for Gene-Expression Microarry Data, D.M. Rocke and B. Durbin (Bioinformatics, 2003, 19, 966-972).

Estimation of Transformation Parameters for Microarray Data, B. Durbin and D.M. Rocke (Bioinformatics, 2003, 19, 1360-1367).

Modeling Uncertainty in Analytical Measures for Analysis of Bioavailability, D.M. Rocke, B. Durbin, M. Wilson, and H. Kahn (Ecotoxicology and Environmental Safety, 2003, 56, 78-92).

Sampling and Subsampling for Cluster Analysis in Data Mining with Applications to Sky Survey (Data Mining and Knowledge Discovery, 2003, 7, 215-232).

Computational Connections Between Robust Multivariate Analysis and Clustering, D.M. Rocke and D.L. Woodruff (COMPSTAT 2002 Proceedings).

Partial Least Squares Proportional Hazard Regression for Application to DNA Microarray Data, D. Nguyen and D.M. Rocke (Bioinformatics, 2002, 18, 1625-1632).

A Variance-Stabilizing Transformation for Gene Expression Microarray Data (Bioinformatics, 2002, 18, S105-S110)

See also Wolfgang Huber's work on microarry data transformation, as well as bioinformatics and molecular genome analysis in general.

Tumor Classification by Partial Least Squares Using Microarray Gene Expression Data (Bioinformatics, 2002, 18, 39-50)

Color Figures for "Tumor Classification by Partial Least Squares Using Microarray Gene Expression Data"

Multi-Class Cancer Classification via Partial Least Squares with Gene Expression Profiles (Bioinformatics, 2002, 18, 1216-1226)

Multivariate Survival Analysis with Doubly-Censored Data: Application to the Assessment of Accutane Treatment for Fibrodysplasia Ossificans Progressiva (Statistics in Medicine, 2002, 21, 2547-2562)

A Model for Measurement Error for Gene Expression Arrays (Journal of Computational Biology, 2001, 8, 557-569)

A Two-Component Model for Measurement Error in Analytical Chemistry, D.M. Rocke and S. Lorenzato (Technometrics, 1995, 37, 176-184).

Transient Genome-Wide Transcriptional Response to Low-Dose Ionizing Radiation In Vivo in Humans, SR Berglund, DM Rocke, J Dai, CW Schwietert, A Santana, RL Stern, J Lehmann, CL Hartmann Siantar and Z Goldberg (International Journal of Radiation Oncology, Biology, Physics, 2008, 70, 229-234). Data (.zip).

On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve, Jingjing Ye, Hao Liu, Crystal Kirmiz, Carlito B. Lebrilla, and David M. Rocke. Data and Supplemental files.

Goldberg et al. Clinical Cancer Research 2006 Supplemental Materials

Nguyen, D.V. and Rocke, D.M.(2002). Partial least squares proportional hazard regression for application to DNA microarray survival data. Bioinformatics, to appear. Article (pdf), Suppl. Figs. (pdf), Suppl. Appendix (pdf), Sample SAS Codes (text)

Nguyen, D.V. and Rocke, D.M. (2002). Multi-class cancer classification via partial least squares using gene expression profiles. Bioinformatics, to appear. Article (pdf), Suppl. Figs. (pdf), Suppl. Appendix (pdf)

Nguyen, D.V. and Rocke, D.M. (2002). Tumor classification by partial least squares using microarray gene expression data. Bioinformatics, 18, 39-50. Article (pdf), Suppl. Figs. (pdf), Sample SAS Codes (text), Errata (text)

Nguyen, D.V. and Rocke, D.M. (2002). Classification of acute leukemia based on DNA microarray gene expr

K.F.(eds), Methods of Microarray Data Analysis. Kluwer Academic Publishers, Boston, pp. 109-124. Article (pdf)

Multivariate Outlier Detection and Cluster Identification, from International Conference on Robust Statistics (ICORS 2002). RealVideo of lecture.

Slides from IMA Talk, September 29, 2003

Data from Geller et al. (2003). Zipped archive of four .cel files.

Slides from PIMS talk in Banff, August 18,2004

Presentation for Autism Research Training Program, May 23, 2005

KFBK Radio Interview on caBIG, May 9, 2005