John Stevens Ph.D.

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An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.

Publications | Book Chapters

• 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

An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.

Publications | Journal Articles

Academic Journal

• Rutigliano, H.M, Morgado, K.P, Stevens, J.R, Davies, C.J, Polejaeva, I.R, (2025). Bovine trophoblast-derived extracellular vesicles modulate the gene expression profile of peripheral leukocytes. Animal Reproduction Science, 283, 108025.
• Rutigliano, H.M, Stevens, J.R, Polejaeva, I.A, Davies, C.J, (2025). Bovine trophoblast-derived extracellular vesicles modulate the gene expression profile of peripheral leukocytes. Animal Reproduction Science, 283:108025, 1-14. doi: https://doi.org/10.1016/j.anireprosci.2025.108025
• Crookston, B., Bowman, M., Stevens, J.R, Veum, K., Yost, M., (2023). Microbial respiration gives early indication of soil health improvement following cover crops. The Journal of Soil and Water Conservation, 78:3, 1-10.
• 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.

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.