John Stevens Ph.D.
Mathematics and Statistics
Department Head | Professor
Contact Information
Office Location: Animal Science (ANSC) 110Phone: (435) 797-2810
Email: john.r.stevens@usu.edu
Additional Information:
Educational Background
Teaching Interests
applied statistical methods
Research Interests
bioinformatics, meta-analysis, applied statistics in agricultural and biomedical sciences
Awards
Presidential Award, 2021
American Society of Agronomy
Researcher of the Year, 2019
Department of Mathematics and Statistics
Researcher of the Year, 2016
Department of Mathematics and Statistics
Editor's Choice Award, 2014
Oikos
Chapter Service Recognition Award, 2014
American Statistical Association, Council of Chapters
Outstanding Paper in Landscape Ecology, 2011
United States Regional Association of the International Association for Landscape Ecology
Teacher of the Year, 2009
Dept. of Math/Stat and College of Science
Publications | Abstracts
- Stevens, J.R, (2022). Using mRNA from cytoplasmic biopsies to assess molecular maturation and developmental potential of bovine oocytes. Reproduction, Fertility, and Development
- Stevens, J.R, (2018). Effects of lactation and negative energy balance on endometrial expression of selected transcripts of Holstein dairy cows at day 7. Journal of Animal Science
- Stevens, J.R, (2017). Poor maternal nutrition during gestation alters muscle gene expression in fetal offspring. Journal of Animal Science
- Cox, L., Saunders, G., Stevens, J.R, Isom, S.C, (2013). Gene expression analysis of in vivo- and in vitro- matured porcine metaphase II oocytes. Reproduction, Fertility, and Development
- Isom, S.C, Stevens, J.R, Li, R., Spollen, W., Prather, R.S, (2012). Transcriptional profiling by high-throughput sequencing of porcine pre- and peri-implantation embryos. Reproduction, Fertility and Development
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
- Stevens, J.R, (2013). Statistical Methods in Metabolomics: Metabolomics in Food and Nutrition. Woodhead Publishing
- Cutler, A., Cutler, D., Stevens, J.R, (2012). Random Forests: Ensemble Machine Learning, Methods and Applications. Springer
- Cutler, A., Cutler, D., Stevens, J.R, (2009). Tree Based Methods: High-Dimensional Data Analysis in Oncology, Applied Bioinformatics and Biostatistics in Cancer Research. Springer
- Stevens, J.R, Taylor, A., Asher, J.W, (2006). The Effects of Explicit Reading Strategy Training on L2 Reading Comprehension: A Meta-Analysis. Synthesizing Research on Language Learning and Teaching
- Stevens, J.R, Cutler, A., (2006). Random Forests for Microarrays: DNA Microarrays, Part B: Databases and Statistics, (Methods in Enzymology). Academic Press
Publications | Book Chapters
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
Publications | Journal Articles
Academic Journal
- Sharp, J.L, Griffiths, E.H, Bridges, W.C, Hanford, K.J, Craig, B.A, Stevens, J.R, (2022). The Academic Collaborative Statistician: Research, Training, and Evaluation. Stat, 11:1, e483.
- Whetten, A., Stevens, J.R, Cann, D., (2021). The implementation of random survival forests in conflict management data: An examination of power sharing and third party mediation in post-conflict countries. PLOS ONE
- Gauvin, M., Pillai, S., Reed, S., Stevens, J.R, Hoffman, M., Jones, A., Zinn, S., Govoni, K., (2020). Poor maternal nutrition during gestation in sheep alters prenatal muscle growth and development in offspring. Journal of Animal Science, 98:1, 1-15.
- Stevens, J.R, Herrick, J.S, Wolff, R.K, Slattery, M.L, (2018). Power from pairs: assessing the statistical value of paired samples in tests for differential expression. BMC Genomics, 19, 953.
- Mullany, L.E, Herrick, J.S, Sakoda, L.C, Samowitz, W., Stevens, J.R, Wolff, R.K, Slattery, M.L, (2018). MicroRNA-Messenger RNA Interactions Involving JAK-STAT signalling Genes in Colorectal Cancer. Genes & Cancer, 9:5-6, 232-246.
- Mullany, L.E, Herrick, J.S, Wolff, R.K, Stevens, J.R, Samowitz, W., Slattery, M.L, (2018). MicroRNA-Transcription Factor Interactions and Their Combined Effect on Target Gene Expression in Colon Cancer Cases. Genes, Chromosomes & Cancer, 57:4, 192-202.
- Slattery, M.L, Mullany, L.E, Sakota, L., Wolff, R.K, Stevens, J.R, Samowitz, W., Herrick, J.S, (2018). The PI3K/AKT Signaling Pathway: associations of miRNAs with dysregulated gene expression in colorectal cancer. Molecular Carcinogenesis, 57, 243-261.
- Slattery, M.L, Mullany, L.E, Sakoda, L.C, Samowitz, W.S, Wolff, R.K, Stevens, J.R, Herrick, J.S, (2018). Expression of Wnt-Signaling Pathway Genes and their associations with miRNAs in Colorectal Cancer. Oncotarget, 9, 6075-6085.
- Mullany, L.E, Herrick, J.S, Sakoda, L.C, Samowitz, W., Stevens, J.R, Wolff, R.K, Slattery, M.L, (2018). MiRNA involvement in cell cycle regulation in colorectal cancer cases. Genes & Cancer, 9:1-2, 53-65.
- Slattery, M.L, Mullany, L.E, Sakoda, L., Samowitz, W., Wolff, R., Stevens, J.R, Herrick, J.S, (2018). The NF-kappa-B-signaling pathway in colorectal cancer: associations between dysregulated gene and miRNA expression. Journal of Cancer Research and Clinical Oncology, 114:2, 269-283.
- Stevens, J.R, Jones, T.R, Lefevre, M., Ganesan, B., Weimer, B.C, (2017). SigTree: a microbial community analysis tool to identify and visualize significantly responsive branches in a phylogenetic tree. Computational and Structural Biotechnology Journal, 15, 372-378.
- Slattery, M.L, Herrick, J.S, Mullany, L.E, Samowitz, W., Stevens, J.R, Sakoda, L., Wolff, R.K, (2017). The Co-Regulatory Networks of Tumor Suppressor Genes, Oncogenes, and miRNAs in Colorectal Cancer. Genes, Chromosomes & Cancer, 56, 769-787.
- Mullany, L.E, Herrick, J.S, Wolff, R.K, Stevens, J.R, Samowitz, W., Slattery, M.L, (2017). Transcription Factor-microRNA Associations and Their Impact on Colorectal Cancer Survival. Molecular Carcinogenesis, 56:11, 2512-2526.
- Stevens, J.R, Herrick, J.S, Wolff, R.K, Slattery, M.L, (2017). Identifying factors associated with the direction and significance of microRNA tumor-normal expression differences in colorectal cancer. BMC Cancer, 17, 707.
- Saunders, G., Fu, G., Stevens, J.R, (2017). A Bivariate Hypothesis Testing Approach for Mapping the Trait-Influential Gene. Scientific Reports, 7, 12798.
- Slattery, M.L, Pellatt, A.J, Lee, F.Y, Herrick, J.S, Samowitz, W., Stevens, J.R, Wolff, R.K, (2017). Infrequently expressed miRNAs influence survival after diagnosis with colorectal cancer. Oncotarget, 8, 83845-83859.
- Slattery, M.L, Herrick, J.S, Stevens, J.R, Wolff, R.K, Mullany, L.E, (2017). An assessment of database-validated microRNA target genes in normal colonic mucosa: Implications for pathway analysis. Cancer Informatics, 16, 1176935117716405.
- Slattery, M.L, Lee, F., Pellat, A., Mullany, L.E, Stevens, J.R, Samowitz, W., Wolff, R.K, (2017). Infrequently expressed miRNAs in colorectal cancer tissue and tumor molecular phenotype. Modern Pathology, 30:8, 1152-1169.
- Stevens, J.R, Masud, A.A, Suyundikov, A., (2017). A Comparison of Multiple Testing Adjustment Methods with Block-Correlation Positively-Dependent Tests. PLOS ONE, 12:4, e0176124.
- Mullany, L.E, Herrick, J.S, Wolff, R.K, Stevens, J.R, Slattery, M.L, (2017). Alterations in microRNA Expression Associated with Alcohol Consumption in Rectal Cancer Subjects. Cancer Causes & Control, 28:6, 545-555.
- Slattery, M.L, Herrick, J.S, Wolff, R.K, Mullany, L.E, Stevens, J.R, Samowitz, W., (2017). The miRNA landscape of colorectal polyps. Genes, Chromosomes & Cancer, 56:5, 347-353.
- Slattery, M.L, Trivellas, A., Pellatt, A.J, Mullany, L.E, Stevens, J.R, Wolff, R.K, Herrick, J.S, (2017). Genetic variants in the TGFβ-signaling pathway influence expression of miRNAs in colon and rectal normal mucosa and tumor tissue. Oncotarget, 8:10, 16765-16783.
- Mullany, L.E, Herrick, J.S, Wolff, R.K, Stevens, J.R, Slattery, M.L, (2016). Association of cigarette smoking and microRNA expression in rectal cancer: Insight into tumor phenotype. Cancer Epidemiology, 45, 98-107.
- Slattery, M.L, Herrick, J.S, Mullany, L.E, Stevens, J.R, Wolff, R.K, (2016). Diet and lifestyle factors associated with miRNA expression in colorectal tissue.. Pharmacogenomics and Personalized Medicine, 10, 1-16.
- Polejaeva, I., Ranjan, R., Davies, C., Regouski, M., Hall, J., Olsen, A., Meng, Q., Rutigliano, H., Dosdall, D., Angel, N., Sachse, F., Seidel, T., Thomas, A., Stott, R., Panter, K., Lee, P., Van Wettere, A., Stevens, J.R, Wang, Z., MacLeod, R., Marrouche, N.F, White, K., (2016). Increased Susceptibility to Atrial Fibrillation Secondary to Myocardial Fibrosis in Transgenic Goats Expressing Transforming Growth Factor-β1 in the Heart. Journal of Cardiovascular Electrophysiology, 27, 1220-1229.
- Polejaeva, I., Ranjan, R., Davies, C., Regouski, M., Hall, J., Olsen, A.L, Meng, Q., Rutigliano, H., Dosdall, D., Angel, N., Sachse, F., Seidel, T., Thomas, A., Stott, R.D, Panter, K., Lee, P., Van Wettere, A., Stevens, J.R, Wang, Z., MacLeod, R., Marrouche, N., White, K.L, (2016). Increased Susceptibility to Atrial Fibrillation Secondary to Atrial Fibrosis in Transgenic Goats Expressing Transforming Growth Factor-β1. Journal of Cardiovascular Electrophysiology. , 27:10, 1220-1229.
- Belmont, P., Stevens, J.R, Czuba, J.A, Kumarasamy, K., Kelly, S.A, (2016). 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, 52, 7523-7528.
- Slattery, M.L, Herrick, J.S, Mullany, L.E, Wolff, E., Hoffman, M.D, Pellatt, D.F, Stevens, J.R, Wolff, R.K, (2016). Colorectal tumor molecular phenotype and miRNA: expression profiles and prognosis. Modern Pathology, 29, 915-927.
- Slattery, M.L, Herrick, J.S, Pellatt, D.F, Mullany, L.E, Stevens, J.R, Wolff, E., Hoffman, M.D, Wolff, R.K, Samowitz, W., (2016). Site-specific associations between miRNA expression and survival in colorectal cancer cases. Oncotarget, 7:37, 60193-60205.
- Pellatt, D.F, Stevens, J.R, Wolff, R.K, Mullany, L.E, Herrick, J.S, Samowitz, W., Slattery, M.L, (2016). Expression profiles of miRNA subsets distinguish human colorectal carcinoma and normal colonic mucosa. Clinical and Translational Gastroenterology, 7:e152
- Slattery, M.L, Herrick, J., Samowitz, W., Pellatt, D., Stevens, J.R, Mullany, L., Wolff, E., Hoffman, M.D, Wolff, R.K, (2016). MicroRNA profiles in colorectal carcinomas, adenomas, and normal colonic mucosa: variations in miRNA expression and disease progression. Carcinogenesis, 37:3, 245-261.
- Suyundikov, A., Stevens, J.R, Corcoran, C., Herrick, J., Wolff, R.K, Slattery, M.L, (2015). Incorporation of subject-level covariates in quantile normalization of miRNA data. BMC Genomics, 16:1045
- Slattery, M.L, Herrick, J.S, Mullany, L.E, Valeri, N., Stevens, J.R, Caan, B.J, Samowitz, W., Wolff, R.K, (2015). An evaluation and replication of miRNAs with disease stage and colorectal cancer-specific mortality. International Journal of Cancer, 137:2, 428-438.
- Suyundikov, A., Stevens, J.R, Corcoran, C., Herrick, J., Wolff, R.K, Slattery, M.L, (2015). Accounting for dependence induced by weighted KNN imputation of paired tumor-normal colorectal cancer miRNA data. PLOS ONE, 10:4, e0119876.
- Saunders, G., Fu, G., Stevens, J.R, (2014). A Graphical Weighted Power Improving Multiplicity Correction Approach for SNP Selections. Current Genomics, 15:5, 380-389.
- Saunders, G., Stevens, J.R, Isom, S.C, (2014). A shortcut for multiple testing on the directed acyclic graph of gene ontology. BMC Bioinformatics, 15, 349.
- Kulmatiski, A., Anderson-Smith, A., Beard, K.H, Doucette-Riis, S., Mazzacavallo, M., Nolan, N.E, Ramirez, R., Stevens, J.R, (2014). Most soil trophic guilds increase plant growth: a meta-analytical review. Oikos, 123:2, 1409-1419. doi: 10.1111/oik.01767
- Saunders, G., Stevens, J.R, Isom, S., (2014). A shortcut for multiple testing on the directed acyclic graph of Gene Ontology. BMC Bioinformatics, 15:349, doi: DOI: 10.1186/s12859-014-0349-3
- Rawal, S., Bauer, M.M, Mendoza, K.M, El-Nezami, H., Hall, J., Kim, J.E, Stevens, J.R, Reed, K.M, Coulombe, Jr, R.A, (2014). Aflatoxicosis chemoprevention by probiotic Lactobacillius and lack of effect on the major histocompatibility complex.. Research in veterinary science, 97:2, 274-281. doi: doi:10.1016/j.rvsc.2014.06.008
- Fu, G., Saunders, G., Stevens, J.R, (2014). Holm multiple correction for large-scale gene-shape association mapping. BMC Genetics, 15:Suppl 1, S5.
- Shaw, J., Desai, P.T, Chen, D., Stevens, J.R, Weimer, B.C, (2013). Pre-adaptation to cold-stress in Salmonella Typhimurium increases survival during subsequent acid-stress exposure. Applied and Environmental Microbiology, 79:23, 7281-7289. doi: 10.1128/AEM.02621-13
- Wu, Y., McEwen, G.D, Tang, M., Yu, T., Dimmick, J.T, Zhou, A., Gilbertson, T.A, Coulombe, R.A, Stevens, J.R, (2013). Sensing biophysical alterations of human lung epithelial cells (a549) in the context of toxicity effects of diesel exhaust particles. Cell biochemistry and biophysics, 67:3, 1147-56.
- Wu, Y., McEwen, G., Tang, M., Dimmick, J., Gilbertson, T.A, Zhou, A., Coulombe, R.A, Stevens, J.R, (2013). Sensing Biophysical Alterations of Human Lung Cells (A549) in the Context of Toxicity Effects of Diesel Exhaust Particles. , 67:3, 1147-1156. doi: doi: 10.1007/s12013-013-9618-4
- Isom, S.C, Stevens, J.R, Li, R., Spollen, W., Cox, L., Spate, L., Murphy, C., Prather, R., (2013). Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated using a variety of assisted reproductive technologies (ART). Physiological Genomics, 45:14, 577-589. doi: 10.1152/physiolgenomics.00094.2012
- Isom, S., Stevens, J.R, Li, R., Spollen, W., Cox, L., Spate, L., Murphy, C., Prather, R., (2013). Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated using a variety of assisted reproductive technologies (ART). Physiol Genomics, 45:14, 577-589. doi: 10.1152/physiolgenomics.00094.2012
- Stevens, J.R, Nicholas, G., (2012). Assessing Numerical Dependence in Gene Expression Summaries with the Jackknife Expression Difference. PLoS ONE, 7:8, e39570.
- Aston, K.I, Li, G.P, Hicks, B.A, Sessions, B.R, Davis, A.P, Winger, Q.A, Rickords, L.F, Stevens, J.R, White, K.L, (2010). Global gene expression analysis of bovine somatic cell nuclear transfer blastocyst and cotyledons. Mol Reprod Dev, 76, 471-482.
- Gilbert-Norton, L., Wilson, R., Stevens, J.R, Beard, K.H, (2010). A Meta-Analytic Review of Corridor Effectiveness. Conservation Biology, 24:3, 660-668. doi: 10.1111/j.1523-1739.2010.01450.x
- Stevens, J.R, Bell, J.L, Aston, K.I, White, K.L, (2010). A Comparison of Probe-Level and Probeset Models for Small-Sample Gene Expression Data. BMC Bioinformatics, 11:281
- Aston, K.I, Li, G.P, Hicks, B.A, Sessions, B.R, Davis, A.P, Rickords, L.F, Stevens, J.R, White, K.L, (2010). Abnormal Levels of Transcript Abundance of Developmentally Important Genes in Various Stages of Preimplantation Bovine Somatic Cell Nuclear Transfer. Cellular Reprogamming, 12:1, 23-32.
- Stevens, J.R, Nicholas, G., (2009). Metahdep: Meta-analysis of hierarchically dependent gene expression studies. Bioinformatics, 25(19), 2619-2620.
- Aston, K.I, Li, G.P, Hicks, B.A, Sessions, B.R, Davis, A.P, Winger, Q.A, Rickords, L.F, Stevens, J.R, White, K.L, (2009). Global Gene Expression Analysis of Bovine Somatic Cell Nuclear Transfer Blastocysts and Cotyledons. Molecular Reproduction and Development, 76, 471-482.
- Stevens, J.R, Taylor, A.M, (2009). Hierarchical Dependence in Meta-Analysis. Journal of Educational and Behavioral Statistics, 34(1), 46-73.
- Gowen, B.B, Smee, D.F, Wong, M.H, Hall, J.O, Jung, K.H, Bailey, K.W, Stevens, J.R, Furuta, Y., Morrey, J.D, (2008). 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.
- Kulmatiski, A., Beard, K.H, Stevens, J.R, Cobbold, S.M, (2008). Plant-soil feedbacks: A meta-analytical review. Ecology Letters, 11:9, 980-992.
- Hevel, J.M, Olson-Buelow, L.C, Ganesan, B., Stevens, J.R, Hardman, J.P, Aust, A.E, (2008). Novel Functional View of the Crocidolite Asbestos-Treated Human Lung Transcriptome Illustrates Intricate Network of Pathways with Opposing Functions.. BMC Genomics, 9, 376.
- Kulmatiski, A., Beard, K.H, Stevens, J.R, Cobbold, S.M, (2008). Plant-soil feedbacks: A meta-analytical review. Ecology Letters, 11, 980-992.
- Guttormsen, J., Koster, M.I, Stevens, J.R, Roop, D., Williams, T., Winger, Q.A, (2008). Disruption of epidermal specific gene expression and delayed skin development in AP-2gamma mutant mice. Developmental Biology, 317, 187-195.
- Gunaratna, N.S, Johnson, C.A, Stevens, J.R, (2007). Service Learning for Graduate Students through a Student-run Consulting Program. Journal of Statistics Education, 15(2), 1-21.
- 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, Jeddeloh, J.A, (2006). Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis, 27(12), 2409-2423.
- Stevens, J.R, Doerge, R.W, (2005). Combining Affymetrix Microarray Results. BMC Bioinformatics, 6, 57.
Professional Journal
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
Publications | MultiMedia
Software
- Stevens, J.R, Mecham, D.S, (2014). mvGST: multivariate and directional gene set testing. Bioconductor
- Stevens, J.R, Jones, T.R, (2013). SigTree: identify and visualize significantly responsive branches in a phylogenetic tree. CRAN (The Comprehensive R Archive Network)
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
Publications | Other
Other
- Craig, B.A, Dixon, P., Gbur, E.E, Koehler, K.J, Nettleton, D., Stroup, W.W, Zhu, J., Bridges, W.C, Macchiavelli, R.E, Madden, L., Bello, N.M, Dai, X., Davis, J.W, Duke, S., Durham, S., Goad, C.L, Keuler, N., Kramer, M.H, Lee-Bartlett, J.A, Momen, B., Osborne, J.A, Paton, N.D, Rendahl, A., Sharp, J., Stevens, J.R, Tempelman, R.J, Yandell, B.S, Yeater, K.M, (2018). Statistics as a Scientific Discipline and Practical Implications for the Evaluation of Faculty Excellence. American Statistical Association
- Stevens, J.R, Suyundikov, A., Slattery, M.L, (2016). Accounting for Missing Data in Clinical Research. Journal of the American Medical Association
- Stevens, J.R, (2013). Harry Potter's first kiss. Significance *
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.