Dr. John R. Stevens

Associate Professor of Statistics
Department of Mathematics and Statistics
Utah State University

Where is the wisdom we have lost in knowledge?
Where is the knowledge we have lost in information?
-- from T.S. Eliot's "The Rock"

Contact / Professional Information


Teaching Links

  • Stat 5200 Design of Experiments (Fall 2014)

Research/Professional Interests

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

Software

  • RMA-MS: preprocessing multi-species Affymetrix arrays (see 2008 citation below, by Stevens, Ganesan, et al.)
  • metahdep: an R package for hierarchical dependence in meta-analysis. Bioconductor, Feb. 2009.
  • affyNFM: nested factorial model for Affymetrix data --- code
  • SigTree: find significantly responsive branches in a phylogenetic tree

Publications

  1. Saunders G., Fu G., and Stevens J.R. A graphical weighted power improving multiplicity correction approach for SNP selections. Current Genomics 2014, in press.
  2. Kulmatiski A., Anderson-Smith A., Beard K., Doucette-Riise S., Mazzacavallo M., Monal N., Ramirez R., and Stevens J.R. Most soil trophic guilds increase plant growth: a meta-analytical review. Oikos 2014, in press. (abstract)
  3. Rawal S., Bauer M.M., Mendoza K.M., El-Nezami H., Hall J.O., Kim J.E., Stevens J.R., Reed K.M., and Coulombe R.A. Aflatoxicosis Chemoprevention by Probiotic Lactobacillius and its Impact on BG Genes of the Major Histocompatibility Complex. Research in Veterinary Science 2014, in press. (text)
  4. Fu G., Saunders G., and Stevens J.R. Holm multiple correction for large-scale gene-shape association mapping. BMC Genetics 2014 15(Suppl 1):S5. (text)
  5. Cox L., Saunders G., Stevens J.R., and Isom S.C. Gene expression analysis of in vivo- and in vitro- matured porcine metaphase II oocytes. Reproduction, Fertility, and Development 2013 26(1):117-117. (Published poster abstract from International Plant and Animal Genome XXI -- San Diego, CA) (text)
  6. Wu Y., McEwen G.D., Tang M., Yu T., Dimmick J.T., Zhou A., Gilbertson T.A., Coulombe R.A., and Stevens J.R. Sensing biophysical alterations of human lung epithelial cells (A549) in the context of toxicity effects of diesel exhaust particles. Cell Biochemistry and Biophysics 2013, 67(3):1147-1156. (text)
  7. Shah J., Desai P.T., Chen D., Stevens J.R., and Weimer B.C. Pre-adaptation to cold-stress in Salmonella Typhimurium increases survival during subsequent acid-stress exposure. Applied and Environmental Microbiology 2013, 79(23):7281-7289. (text)
  8. Stevens J.R. Statistical Methods in Metabolomics. In B.C. Weimer and C.M. Slupsky, editors, Metabolomics in Food and Nutrition, pp. 44-67. Woodhead, 2013. (info)
  9. Isom S.C., Stevens J.R., Li R., Spollen W., Cox L., Spate L., Murphy C., and Prather R. Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated using a variety of assisted reproductive technologies (ART). Physiological Genomics 2013, 45(14):577-589. (text)
  10. Stevens J.R. and Isom S.C. Gene Set Testing to Characterize Multivariately Differentially Expressed Genes. Proceedings of Conference on Applied Statistics in Agriculture 2012, pp. 125-137.
  11. Stevens J.R. and Nicholas G. Assessing Numerical Dependence in Gene Expression Summaries with the Jackknife Expression Difference. PLoS ONE 2012 7(8):e39570. (text)
  12. Cutler A., Cutler D.R., and Stevens J.R. Random Forests. In Ensemble Machine Learning: Methods and Applications, edited by Cha Zhang and Yunqian Ma. Springer 2012. (info)
  13. Isom S.C., Stevens J.R., Li R., Spollen W., and Prather R.S. Transcriptional profiling by high-throughput sequencing of porcine pre- and peri-implantation embryos. Reproduction, Fertility and Development 2012, 24(1):184-184. (Published poster abstract from Proceedings of the Annual Conference of the International Embryo Transfer Society, Phoenix Arizona, January 2012)(text)
  14. Stevens J.R. Book Review of "Gene Expression Studies Using Affymetrix Microarrays" by Gohlmann and Talloen. Journal of the American Statistical Association 2010 105(491):1279-1280 (text)
  15. Stevens J.R., Bell J.L, Aston K.I., and White K.L. A comparison of probe-level and probeset models for small-sample gene expression data. BMC Bioinformatics 2010 11:281. (text)
  16. Gilbert-Norton L., Wilson R., Stevens J.R., and Beard K.H. A meta-analytic review of corridor effectiveness. Conservation Biology 2010 24(3):660-668. (text; also in Connectivity and Corridors virtual issue; awarded "Outstanding Paper in Landscape Ecology" for 2010 by U.S. International Association for Landscape Ecology)
  17. Aston K.I., Li G.P., Hicks B.A., Sessions B.R., Davis A.P., Rickords L.F., Stevens J.R., and White K.L. Abnormal Levels of Transcript Abundance of Developmentally Important Genes in Various Stages of Preimplantation Bovine Somatic Cell Nuclear Transfer Embryos. Cellular Reprogramming 2010 12(1):23-32. (text)
  18. Stevens J.R. and Nicholas G. metahdep: Meta-analysis of hierarchically dependent gene expression studies. Bioinformatics 2009 25(19):2619-2620. (text)
  19. 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)
  20. Stevens J.R. and Taylor A.M. Hierarchical Dependence in Meta-Analysis. Journal of Educational and Behavioral Statistics 2009 34(1):46-73. (text)
  21. 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)
  22. 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)
  23. 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, pp. 47-62. (sample code)
  24. Kulmatiski A., Beard K.H., Stevens J.R., and Cobbold S.M. Plant-soil feedbacks: A meta-analytical review. Ecology Letters 2008, 11:980992. (text)
  25. 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)
  26. 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)
  27. 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)
  28. 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)
  29. 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. (summary)
  30. 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.
  31. 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.
  32. 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.
  33. Stevens J.R. and Doerge R.W. Combining Affymetrix Microarray Results. BMC Bioinformatics 2005, 6:57. (text)
  34. Stevens J.R. and Deorge R.W. Meta-Analysis Combines Affymetrix Microarray Results Across Laboratories. Comparative and Functional Genomics 2005, 6:116-122. (text)

statistician expert witness Utah statistical expert witness Utah biostatistician expert witness Utah biostatistical expert witness Utah biostatistics expert witness Utah statistics expert witness Utah bioinformatics expert witness Utah