Dr. John R. Stevens

Professor of Statistics
Assistant Head for Graduate Studies
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

Research/Professional Interests

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


  • mvGST: multivariate and directional gene set testing. Bioconductor, Oct. 2014.
  • SigTree: identify and visualize significantly responsive branches in a phylogenetic tree. CRAN, Aug. 2013.
  • affyNFM: nested factorial model for Affymetrix data --- code (see May 2010 citation below, by Stevens, Bell, et al.)
  • metahdep: an R package for hierarchical dependence in meta-analysis. Bioconductor, Feb. 2009.
  • RMA-MS: preprocessing multi-species Affymetrix arrays (see May 2008 citation below, by Stevens, Ganesan, et al.)

Published Works

  1. Stevens J.R., Herrick J.S., Wolff R.K., and Slattery M.L. Power from pairs: assessing the statistical value of paired samples in tests for differential expression. BMC Genomics 2018, 19:953. (text)
  2. Alhojaily S., Stott R., Rutigliano H., Stevens J.R., and Isom S.C. Effects of lactation and negative energy balance on endometrial expression of selected transcripts of Holstein dairy cows at day 7. Journal of Animal Science 2018, 96(suppl3):177-177. (text)
  3. Mullany L.E., Herrick J.S., Sakoda L.C., Samowitz W., Stevens J.R., Wolff R.K., and Slattery M.L. MicroRNA-Messenger RNA Interactions Involving JAK-STAT signaling Genes in Colorectal Cancer. Genes & Cancer 2018, 9(5-6):232-246. (text)
  4. Bishop M.O., Stevens J.R., and Isom S.C. Statistical methods for assessing individual oocyte viability through gene expression profiles. Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture 2017.
  5. Mullany L.E., Herrick J.S., Sakoda L.C., Samowitz W., Stevens J.R., Wolff R.K., and Slattery M.L. MiRNA involvement in cell cycle regulation in colorectal cancer cases. Genes & Cancer 2018, 9(1-2):53-65. (text)
  6. Mullany L.E., Herrick J.S., Wolff R.K., Stevens J.R., Samowitz W., and Slattery M.L. MicroRNA-Transcription Factor Interactions and Their Combined Effect on Target Gene Expression in Colon Cancer Cases. Genes, Chromosomes and Cancer 2018, 57(4):192-202. (text)
  7. Slattery M.L., Mullany L.E., Sakoda L., Samowitz W., Wolff R., Stevens J.R., and Herrick J.S. The NF-kappa-B-signaling pathway in colorectal cancer: associations between dysregulated gene and miRNA expression. Journal of Cancer Research and Clinical Oncology 2018, 114(2):269-283. (text)
  8. Slattery M.L., Mullany L., Sakoda L.C., Samowitz W.S., Wolff R.K., Stevens J.R., and Herrick J.S. Expression of Wnt-Signaling Pathway Genes and their associations with miRNAs in Colorectal Cancer. Oncotarget 2018, 9(5):6075-6085. text
  9. Slattery M.L., Mullany L.E., Sakota L., Wolff R.K., Stevens J.R., Samowitz W., and Herrick J.S. The PI3K/AKT Signaling Pathway: associations of miRNAs with dysregulated gene expression in colorectal cancer. Molecular Carcinogenesis 2018, 57:243-261. (text)
  10. Stevens J.R., Herrick J.S., Wolff R.K., and Slattery M.L. Identifying factors associated with the direction and significance of microRNA tumor-normal expression differences in colorectal cancer. BMC Cancer 2017, 17:707. text
  11. Slattery M.L., Pellatt A.J., Lee F.Y., Herrick J.S., Samowitz W.S., Stevens J.R., Wolff R.K., and Mullany L.E. Infrequently expressed miRNAs influence survival after diagnosis with colorectal cancer. Oncotarget 2017, 8:83845-83859. text
  12. Saunders G., Fu G., and Stevens J.R. A Bivariate Hypothesis Testing Approach for Mapping the Trait-Influential Gene. Scientific Reports 2017, 7:12798. (text)
  13. Pillai S.M., Hoffman M.L., Jones A.K., McFadden K.K., Stevens J.R., Zinn S.A., Reed S.A., and Govoni K.E. Poor maternal nutrition during gestation alters muscle gene expression in fetal offspring. Journal of Animal Science 2017, 95(suppl4):150-150. (text)
  14. Slattery M.L., Herrick J.S., Mullany L.E., Samowitz W., Stevens J.R., Sakoda L., and Wolff R.K. The Co-Regulatory Networks of Tumor Suppressor Genes, Oncogenes, and miRNAs in Colorectal Cancer. Genes, Chromosomes, and Cancer 2017, 56:769-787. (text)
  15. Mullany L.E., Herrick J.S., Wolff R.K., Stevens J.R., Samowitz W., and Slattery M.L. Transcription Factor-microRNA Associations and Their Impact on Colorectal Cancer Survival. Molecular Carcinogenesis 2017, 56(11):2512-2526. (text)
  16. Stevens J.R., Jones T.R., Lefevre M., Ganesan B., and Weimer B.C. SigTree: a microbial community analysis tool to identify and visualize significantly responsive branches in a phylogenetic tree. Computational and Structural Biotechnology Journal 2017, 15:372-378. (text)
  17. Slattery M.L., Herrick J., Stevens J.R., Wolff R.K., and Mullany L.E. An assessment of database-validated microRNA target genes in normal colonic mucosa: Implications for pathway analysis. Cancer Informatics 2017, 16:1176935117716405. (text)
  18. Slattery M.L., Lee F., Pellatt A., Mullany L.E., Stevens J.R., Samowitz W., Wolff R.K., and Herrick J.S. Infrequently expressed miRNAs in colorectal cancer tissue and tumor molecular phenotype. Modern Pathology 2017, 30(8):1152-1169. (text)
  19. Stevens J.R., Al Masud A., and Suyundikov A. A comparison of multiple testing adjustment methods with block-correlation positively-dependent tests. PLOS ONE 2017, 12(4):e0176124. (text)
  20. Mullany L.E., Herrick J.S., Wolff R.K., Stevens J.R., and Slattery M.L. Alterations in microRNA Expression Associated with Alcohol Consumption in Rectal Cancer Subjects. Cancer Causes & Control 2017, 28(6):545-555. (text)
  21. Slattery M.L., Herrick J.S., Wolff R.K., Mullany L.E., Stevens J.R., and Samowitz W. The miRNA landscape of colorectal polyps. Genes, Chromosomes & Cancer 2017, 56(5):347-353. (text)
  22. Slattery M.L., Trivellas A., Pellatt A.J., Mullany L.E., Stevens J.R., Wolff R.K., and Herrick J.S. Genetic variants in the TGF-signaling pathway influence expression of miRNAs in colon and rectal normal mucosa and tumor tissue. Oncotarget 2017, 8(10):16765-16783. (text)
  23. Slattery M.L., Herrick J.S., Mullany L.E., Stevens J.R., and Wolff R.K. Diet and lifestyle factors associated with miRNA expression in colorectal tissue. Pharmacogenomics and Personalized Medicine 2016, 10:1-16. (text)
  24. Belmont P., Stevens J.R., Czuba J.A., Kumarasamy K., and Kelly S.A. Comment on 'Climate and agricultural land use change impacts on streamflow in the upper midwestern United States' by Satish C. Gupta et al. Water Resources Research 2016, 52:7523-7528. (text)
  25. Mullany L.E., Herrick J.S., Wolff R.K., Stevens J.R., and Slattery M.L. Association of cigarette smoking and microRNA expression in rectal cancer: Insight into tumor phenotype. Cancer Epidemiology 2016, 45:98-107. (text)
  26. Slattery M.L., Herrick J., Pellatt D.F., Mullany L.E., Stevens J.R., Wolff E., Hoffman M.D., Wolff R.K., and Samowitz W. Site-specific associations between miRNA expression and survival in colorectal cancer cases. Oncotarget 2016, 7(37):60193-60205. (text)
  27. Polejaeva I., Ranjan R., Davies C.J., Regouski M., Hall J., Olsen A.L., Meng Q., Rutigliano H.M., Dosdall D.J., Angel N.A., Sachse F.B., Seidel T., Thomas A.J., Stott R., Panter K.E., Lee P.M., Van Wettere A.J., Stevens J.R., Wang Z., MacLeod R.S., Marrouche N.F., and White K.L. Increased Susceptibility to Atrial Fibrillation Secondary to Atrial Fibrosis in Transgenic Goats Expressing Transforming Growth Factor-beta1. Journal of Cardiovascular Electrophysiology 2016, 27(10):1220-1229. (text)
  28. Slattery M.L., Herrick J., Mullany L., Wolff E., Hoffman M., Pellatt D., Stevens J.R., and Wolff R.K. Colorectal tumor molecular phenotype and miRNA: expression profiles and prognosis. Modern Pathology 2016, 29:915-927. (text)
  29. Pellat D., Stevens J.R., Wolff R.K., Mullany L.E., Herrick J.S., Samowitz W., and Slattery M.L. Expression profiles of miRNA subsets distinguish human colorectal carcinoma and normal colonic mucosa. Clinical and Translational Gastroenterology 2016, 7:e152. (text)
  30. Slattery M.L., Herrick J., Samowitz W., Pellatt D., Stevens J.R., Mullany L., Wolff E., Hoffman M.D., and Wolff R. MicroRNA profiles in colorectal carcinomas, adenomas, and normal colonic mucosa: variations in miRNA expression and disease progression. Carcinogenesis 2016, 37(3):245-261. (text)
  31. Stevens J.R., Suyundikov A., and Slattery M.L. Accounting for Missing Data in Clinical Research. Journal of the American Medical Association 2016, 315(5):517-518. (text; PMCID)
  32. Suyundikov A., Stevens J.R., Corcoran C., Herrick J., Wolff R.K., and Slattery M.L. Incorporation of subject-level covariates in quantile normalization of miRNA data. BMC Genomics 2015, 16:1045. (text)
  33. Slattery M.L., Herrick J.S., Mullany L.E., Valeri N., Stevens J.R., Caan B.J., Samowitz W., and Wolff R.K. An evaluation and replication of miRNAs with disease stage and colorectal cancer-specific mortality. International Journal of Cancer 2015, 137(2):428-438. (text)
  34. Suyundikov A., Stevens J.R., Corcoran C., Herrick J., Wolff R.K., and Slattery M.L. Accounting for dependence induced by weighted KNN imputation in paired samples, motivated by a colorectal cancer study. PLOS ONE 2015, 10(4): e0119876. (text)
  35. Saunders G., Fu G., and Stevens J.R. A graphical weighted power improving multiplicity correction approach for SNP selections. Current Genomics 2014, 15(5):380-389. (abstract)
  36. 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, 123(12):1409-1419. (text)
  37. Saunders G., Stevens J.R., and Isom S.C. A shortcut for multiple testing on the directed acyclic graph of gene ontology. BMC Bioinformatics 2014, 15:349. (text)
  38. 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, 97(2):274-281. (text)
  39. 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)
  40. 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)
  41. 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)
  42. 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)
  43. 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)
  44. Stevens J.R. Harry Potter's first kiss. Significance 2013, 10(3):46. (Letter to editor; text)
  45. 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)
  46. 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. (text)
  47. 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)
  48. 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)
  49. 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)
  50. 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)
  51. 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)
  52. 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)
  53. 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)
  54. Stevens J.R. and Nicholas G. metahdep: Meta-analysis of hierarchically dependent gene expression studies. Bioinformatics 2009 25(19):2619-2620. (text)
  55. 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)
  56. Stevens J.R. and Taylor A.M. Hierarchical Dependence in Meta-Analysis. Journal of Educational and Behavioral Statistics 2009 34(1):46-73. (text)
  57. 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)
  58. 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)
  59. 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; text)
  60. 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)
  61. 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)
  62. 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)
  63. 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)
  64. 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)
  65. 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. (text)
  66. 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.
  67. 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.
  68. 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. (text)
  69. Stevens J.R. and Doerge R.W. Combining Affymetrix Microarray Results. BMC Bioinformatics 2005, 6:57. (text)
  70. Stevens J.R. and Doerge R.W. Meta-Analysis Combines Affymetrix Microarray Results Across Laboratories. Comparative and Functional Genomics 2005, 6:116-122. (text)

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