Contact / Professional Information

• Office: Lund Hall 202-C (435-797-2818)
• E-mail: john.r.stevens@usu.edu
• Mailing address: Department of Mathematics and Statistics, Utah State University, 3900 Old Main Hill, Logan, UT 84322-3900
• I earned my Ph.D. in Statistics from Purdue University under the direction of Rebecca W. Doerge.
• I earned a B.A. in Mathematics from Utah State University and an M.S. in Mathematical Statistics from Purdue University.
• I am a member of the American Statistical Assocation.

Teaching Links

• Stat 5100 Linear Regression and Time Series (Spring 2009)
• Stat 5570/6570 Statistical Bioinformatics (Spring 2009)
• Stat 5810/6810 Biostatistics Methods (Fall 2009)

Research/Professional Interests

• Statistical Bioinformatics / Genomics
• Meta-Analysis
• Applied Statistics in the Biological and Agricultural Sciences
• Statistics Education
• Statistical Consulting

Software

• metahdep: an R package for hierarchical dependence in meta-analysis. Bioconductor, Feb. 2009.
• affyNFM: nested factorial model for Affymetrix data --- tutorial

Publications

• Stevens J.R. and Nicholas G. metahdep: Meta-analysis of hierarchically dependent gene expression studies. Bioinformatics 2009 25(19):2619-2620. (text)
• Aston K.I., Li G.P., Sessions B.R., Davis A.P., Winger Q.A., Rickords L.F., Stevens J.R., and White K.L. Global Gene Expression Analysis of Bovine Somatic Cell Nuclear Transfer Blastocysts and Cotyledons. Molecular Reproduction and Development 2009, 76:471-482. (text)
• Stevens J.R. and Taylor A.M. Hierarchical Dependence in Meta-Analysis. Journal of Educational and Behavioral Statistics 2009 34(1):46-73. (text)
• Cutler A., Cutler D.R., and Stevens J.R. Tree-Based Methods. Chapter 5 in Xiaochun Li and Ronghui Xu, editors, High-Dimensional Data Analysis in Cancer Research, Applied Bioinformatics and Biostatistics in Cancer Research series, Springer, New York, 2009. (info)
• Gowen B.B., Smee D.F., Wong M.-H., Hall J.O., Jung K.-H., Bailey K.W., Stevens J.R., Furuta Y., and Morrey J.D. Treatment of Late Stage Disease in a Model of Arenaviral Hemorrhagic Fever: T-705 Efficacy and Reduced Toxicity Suggests an Alternative to Ribavirin. PLoS ONE 3(11): e3725 (November 2008). (text)
• Stevens J.R., Ganesan B., Desai P., Rajan S., and Weimer B.C. Statistical Issues in the Normalization of Multi-Species Microarray Data. Proceedings of Conference on Applied Statistics in Agriculture 2008. (sample code)
• Kulmatiski A., Beard K.H., Stevens J.R., and Cobbold S.M. Plant-soil feedbacks: A meta-analytical review. Ecology Letters 2008, 11:980–992. (text)
• Hevel J.M., Olson-Buelow L.C., Ganesan B., Stevens J.R., Hardman J.P., and Aust A.E. Novel Functional View of the Crocidolite Asbestos-Treated A549 Human Lung Epithelial Transcriptome Reveals an Intricate Network of Pathways with Opposing Functions. BMC Genomics 2008, 9:376 (text)
• Guttormsen J., Koster M.I., Stevens J.R., Roop D., Williams T., and Winger Q.A. Disruption of Epidermal Specific Gene Expression and Delayed Skin Development in AP-2gamma Mutant Mice. Developmental Biology 2008, 317:187-195. (text)
• Gunaratna N.S., Johnson C.A., and Stevens J.R. Service Learning for Graduate Students through a Student-run Consulting Program. Journal of Statistics Education 2007, 15(2):1-21. (text)
• Ordway J.M., Bedell J.A., Citek R.W., Nunberg A., Garrido A., Kendall R., Stevens J.R., Cao D., Doerge R.W., Korshunova Y., Holemon H., McPherson J.D., Lakey N., Leon J., Martienssen R.A., and Jeddeloh J.A. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 2006, 27(12):2409-2423. (text)
• Stevens J.R. and Schlipalius D.I. Dose-Response Modeling with Marginal Information on a Missing Categorical Covariate. Proceedings of Conference on Applied Statistics in Agriculture 2006, pp. 18-32.
• Cutler A. and Stevens J.R. Random Forests for Microarrays. In Alan Kimmel and Brian Oliver, editors, Methods in Enzymology, Volume 411, DNA Microarrays Part B: Databases and Statistics, pages 422-432. Academic Press, San Diego, 2006.
• Taylor A., Stevens J.R., and Asher J.W. The Effects of Explicit Reading Strategy Training on L2 Reading Comprehension: A Meta-Analysis. In John M. Norris and Lourdes Ortega, editors, Synthesizing Research on Language Learning and Teaching, pages 213-244. John Benjamins, Amsterdam, 2006.
• Stevens J.R. and Doerge R.W. A Bayesian and Covariate Approach to Combine Results from Multiple Microarray Studies. Proceedings of Conference on Applied Statistics in Agriculture 2005, pp. 133-147.
• Stevens J.R. and Doerge R.W. Combining Affymetrix Microarray Results. BMC Bioinformatics 2005, 6:57. (text)
• Stevens J.R. and Deorge R.W. Meta-Analysis Combines Affymetrix Microarray Results Across Laboratories. Comparative and Functional Genomics 2005, 6:116-122. (text)