My Bibliography

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Ampofo ET, Seamon E, Ridenhour BJ. Using Geographically Weighted Random Forests to Analyze County-level Diabetes Prevalence in the USA. Medical Research Archives. 2026 April; 14(4).

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Phan TA, Ridenhour BJ, Remien CH. Resilience of a stochastic generalized Lotka-Volterra model for microbiome studies. Math Biosci Eng. 2025 May 14;22(6):1517-1550. doi: 10.3934/mbe.2025056. PubMed PMID: 40676982; PubMed Central PMCID: PMC13221212.

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Narum S, Stalder T, Ridenhour B, Coats ER. SARS-CoV-2 surveillance of wastewater in small rural communities identifies lack of vaccine coverage as influence of omicron outbreak. Water Res. 2025 Sep 1;283:123818. doi: 10.1016/j.watres.2025.123818. Epub 2025 May 12. PubMed PMID: 40381278.

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Castañeda-Barba S, Ridenhour BJ, Top EM, Stalder T. Detection of rare plasmid hosts using a targeted Hi-C approach. ISME Commun. 2025 Jan;5(1):ycae161. doi: 10.1093/ismeco/ycae161. eCollection 2025 Jan. PubMed PMID: 40161467; PubMed Central PMCID: PMC11950669.

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Meadows T, Coats ER, Narum S, Top EM, Ridenhour BJ, Stalder T. Epidemiological model can forecast COVID-19 outbreaks from wastewater-based surveillance in rural communities. Water Res. 2025 Jan 1;268(Pt A):122671. doi: 10.1016/j.watres.2024.122671. Epub 2024 Oct 20. PubMed PMID: 39488168; PubMed Central PMCID: PMC11614685.

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Reveles KR, Hickmott AJ, Strey KA, Mustoe AC, Arroyo JP, Power ML, Ridenhour BJ, Amato KR, Ross CN. Developing the Common Marmoset as a Translational Geroscience Model to Study the Microbiome and Healthy Aging. Microorganisms. 2024 Apr 25;12(5). doi: 10.3390/microorganisms12050852. Review. PubMed PMID: 38792682; PubMed Central PMCID: PMC11123169.

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Moxley TA, Johnson-Leung J, Seamon E, Williams C, Ridenhour BJ. Application of elastic net regression for modeling COVID-19 sociodemographic risk factors. PLoS One. 2024;19(1):e0297065. doi: 10.1371/journal.pone.0297065. eCollection 2024. PubMed PMID: 38277346; PubMed Central PMCID: PMC10817220.

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Ferguson JM, González-González A, Kaiser JA, Winzer SM, Anast JM, Ridenhour B, Miura TA, Parent CE. Hidden variable models reveal the effects of infection from changes in host survival. PLoS Comput Biol. 2023 Feb;19(2):e1010910. doi: 10.1371/journal.pcbi.1010910. eCollection 2023 Feb. PubMed PMID: 36812266; PubMed Central PMCID: PMC9987815.

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Metzger GA, Ridenhour BJ, France M, Gliniewicz K, Millstein J, Settles ML, Forney LJ, Stalder T, Top EM. Biofilms preserve the transmissibility of a multi-drug resistance plasmid. NPJ Biofilms Microbiomes. 2022 Dec 9;8(1):95. doi: 10.1038/s41522-022-00357-1. PubMed PMID: 36481746; PubMed Central PMCID: PMC9732292.

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Slanzon GS, Ridenhour BJ, Parrish LM, Trombetta SC, Moore DA, Sischo WM, McConnel CS. Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves. PLoS One. 2022;17(10):e0276638. doi: 10.1371/journal.pone.0276638. eCollection 2022. PubMed PMID: 36269743; PubMed Central PMCID: PMC9586405.

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Mokhtari EB, Ridenhour BJ. Filtering ASVs/OTUs via mutual information-based microbiome network analysis. BMC Bioinformatics. 2022 Sep 16;23(1):380. doi: 10.1186/s12859-022-04919-0. PubMed PMID: 36114453; PubMed Central PMCID: PMC9482178.

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Hsueh BY, Severin GB, Elg CA, Waldron EJ, Kant A, Wessel AJ, Dover JA, Rhoades CR, Ridenhour BJ, Parent KN, Neiditch MB, Ravi J, Top EM, Waters CM. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nat Microbiol. 2022 Aug;7(8):1210-1220. doi: 10.1038/s41564-022-01162-4. Epub 2022 Jul 11. PubMed PMID: 35817890; PubMed Central PMCID: PMC9830645.

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Ridenhour BJ, Sarathchandra D, Seamon E, Brown H, Leung FY, Johnson-Leon M, Megheib M, Miller CR, Johnson-Leung J. Effects of trust, risk perception, and health behavior on COVID-19 disease burden: Evidence from a multi-state US survey. PLoS One. 2022;17(5):e0268302. doi: 10.1371/journal.pone.0268302. eCollection 2022. PubMed PMID: 35594254; PubMed Central PMCID: PMC9122183.

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Slanzon GS, Ridenhour BJ, Moore DA, Sischo WM, Parrish LM, Trombetta SC, McConnel CS. Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease. PLoS One. 2022;17(1):e0262317. doi: 10.1371/journal.pone.0262317. eCollection 2022. PubMed PMID: 34982792; PubMed Central PMCID: PMC8726473.

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Remien CH, Eckwright MJ, Ridenhour BJ. Structural identifiability of the generalized Lotka-Volterra model for microbiome studies. R Soc Open Sci. 2021 Jul;8(7):201378. doi: 10.1098/rsos.201378. eCollection 2021 Jul. PubMed PMID: 34295510; PubMed Central PMCID: PMC8292772.

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Van Leuven JT, Gonzalez AJ, Ijezie EC, Wixom AQ, Clary JL, Naranjo MN, Ridenhour BJ, Miller CR, Miura TA. Rhinovirus Reduces the Severity of Subsequent Respiratory Viral Infections by Interferon-Dependent and -Independent Mechanisms. mSphere. 2021 Jun 30;6(3):e0047921. doi: 10.1128/mSphere.00479-21. Epub 2021 Jun 23. PubMed PMID: 34160242; PubMed Central PMCID: PMC8265665.

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Baumgaertner B, Ridenhour BJ, Justwan F, Carlisle JE, Miller CR. Risk of disease and willingness to vaccinate in the United States: A population-based survey. PLoS Med. 2020 Oct;17(10):e1003354. doi: 10.1371/journal.pmed.1003354. eCollection 2020 Oct. PubMed PMID: 33057373; PubMed Central PMCID: PMC7561115.

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Lee JA, Riazi S, Nemati S, Bazurto JV, Vasdekis AE, Ridenhour BJ, Remien CH, Marx CJ. Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations. PLoS Genet. 2019 Nov;15(11):e1008458. doi: 10.1371/journal.pgen.1008458. eCollection 2019 Nov. PubMed PMID: 31710603; PubMed Central PMCID: PMC6858071.

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Witkin SS, Moron AF, Ridenhour BJ, Minis E, Hatanaka A, Sarmento SGP, Franca MS, Carvalho FHC, Hamamoto TK, Mattar R, Sabino E, Linhares IM, Rudge MVC, Forney LJ. Vaginal Biomarkers That Predict Cervical Length and Dominant Bacteria in the Vaginal Microbiomes of Pregnant Women. mBio. 2019 Oct 22;10(5). doi: 10.1128/mBio.02242-19. PubMed PMID: 31641087; PubMed Central PMCID: PMC6805993.

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Nunn KL, Ridenhour BJ, Chester EM, Vitzthum VJ, Fortenberry JD, Forney LJ. Vaginal Glycogen, Not Estradiol, Is Associated With Vaginal Bacterial Community Composition in Black Adolescent Women. J Adolesc Health. 2019 Jul;65(1):130-138. doi: 10.1016/j.jadohealth.2019.01.010. Epub 2019 Mar 14. PubMed PMID: 30879880; PubMed Central PMCID: PMC6589382.

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Gliniewicz K, Schneider GM, Ridenhour BJ, Williams CJ, Song Y, Farage MA, Miller K, Forney LJ. Comparison of the Vaginal Microbiomes of Premenopausal and Postmenopausal Women. Front Microbiol. 2019;10:193. doi: 10.3389/fmicb.2019.00193. eCollection 2019. PubMed PMID: 30837959; PubMed Central PMCID: PMC6382698.

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France MT, Ridenhour BJ, Forney LJ. Effects of spatial structure and reduced growth rates on evolution in bacterial populations.. In: Rampelotto PH, editor. Grand Challenges in Biology and Biotechnology Berlin: Springer International Publishing; 2018. Chapter 8; p.175-197.

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Ridenhour BJ, Ridenhour JR. Stability of equilibria in quantitative genetic models based on modified-gradient systems. J Biol Dyn. 2018 Dec;12(1):39-50. doi: 10.1080/17513758.2017.1400598. PubMed PMID: 29157143.

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Ridenhour BJ, Brooker SL, Williams JE, Van Leuven JT, Miller AW, Dearing MD, Remien CH. Modeling time-series data from microbial communities. ISME J. 2017 Nov;11(11):2526-2537. doi: 10.1038/ismej.2017.107. Epub 2017 Aug 8. PubMed PMID: 28786973; PubMed Central PMCID: PMC5649163.

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VanLeuven JT, Ridenhour BJ, Gonzalez AJ, Miller CR, Miura TA. Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses. PLoS One. 2017;12(6):e0178408. doi: 10.1371/journal.pone.0178408. eCollection 2017. PubMed PMID: 28575086; PubMed Central PMCID: PMC5456070.

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Ridenhour BJ, Metzger GA, France M, Gliniewicz K, Millstein J, Forney LJ, Top EM. Persistence of antibiotic resistance plasmids in bacterial biofilms. Evol Appl. 2017 Jul;10(6):640-647. doi: 10.1111/eva.12480. eCollection 2017 Jul. PubMed PMID: 28616070; PubMed Central PMCID: PMC5469168.

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Ridenhour BJ. Coevolutionary fitness landscapes. In: Kliman RM, editor. Encyclopedia of Evolutionary Biology Cambridge: Academic Press; 2016. p.299-304. 2132p.

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Ridenhour BJ, Top EM. Plasmid Driven Evolution of Bacteria. In: Kliman RM, editor. Encyclopedia of Evolutionary Biology Cambridge: Academic Press; 2016. p.301-306. 2132p.

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Nardin LG, Miller CR, Ridenhour BJ, Krone SM, Joyce P, Baumgaertner BO. Planning horizon affects prophylactic decision-making and epidemic dynamics. PeerJ. 2016;4:e2678. doi: 10.7717/peerj.2678. eCollection 2016. PubMed PMID: 27843714; PubMed Central PMCID: PMC5103819.

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Ridenhour BJ, Cramer MJ. Differentiation of white-footed mice (Peromyscus leucopus) and deer mice (Peromyscus maniculatus) of the Upper Midwest using PCR melt curve analysis. Conservation Genetics Resources. 2015 September; 7(1):29-31. doi: 10.1007/s12686-014-0324-3.

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Ridenhour BJ. Coevolution. In: Losos J, editor. Oxford Bibliographies Online Evolutionary Biology ed. New York: Oxford University of Press; 2014.

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Turner KG, Smith MJ, Ridenhour BJ. Whirling disease dynamics: an analysis of intervention strategies. Prev Vet Med. 2014 Mar 1;113(4):457-68. doi: 10.1016/j.prevetmed.2013.12.008. Epub 2013 Dec 30. PubMed PMID: 24439792.

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Ridenhour B, Kowalik JM, Shay DK. Unraveling R0: considerations for public health applications. Am J Public Health. 2014 Feb;104(2):e32-41. doi: 10.2105/AJPH.2013.301704. Epub 2013 Dec 12. PubMed PMID: 24328646; PubMed Central PMCID: PMC3935673.

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Ridenhour BJ, Campitelli MA, Kwong JC, Rosella LC, Armstrong BG, Mangtani P, Calzavara AJ, Shay DK. Effectiveness of inactivated influenza vaccines in preventing influenza-associated deaths and hospitalizations among Ontario residents aged ≥ 65 years: estimates with generalized linear models accounting for healthy vaccinee effects. PLoS One. 2013;8(10):e76318. doi: 10.1371/journal.pone.0076318. eCollection 2013. PubMed PMID: 24146855; PubMed Central PMCID: PMC3797825.

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Ridenhour BJ, Nuismer SL. A quantitative genetic approach for predicting ecological change in biological communities. Theoretical ecology. 2013; 7(2):137-148. doi: 10.1007/s12080-013-0206-4.

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Ridenhour B, Nuismer S. Perspective. In: Ohgushi T, Schmitz O, Holt R, Ohgushi T, Schmitz O, Holt R, editors. Trait-Mediated Indirect Interactions [Internet] Cambridge: Cambridge University Press; 2012. Chapter Chapter Eleven; 207-220p. Available from: https://www.cambridge.org/core/product/identifier/CBO9780511736551A022/type/book_part.

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Thompson WW, Ridenhour BL, Barile JP, Shay DK. Time-series analyses of count data to estimate the burden of seasonal infectious diseases. Epidemiology. 2012 Nov;23(6):839-42; discussion 843-4. doi: 10.1097/EDE.0b013e31826cc1df. PubMed PMID: 23038110.

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Ridenhour BJ, Braun A, Teyrasse T, Goldsman D. Controlling the spread of disease in schools. PLoS One. 2011;6(12):e29640. doi: 10.1371/journal.pone.0029640. Epub 2011 Dec 29. PubMed PMID: 22242138; PubMed Central PMCID: PMC3248433.

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Burkhardt A, Ridenhour BJ, Delph LF, Bernasconi G. The contribution of a pollinating seed predator to selection on Silene latifolia females. J Evol Biol. 2012 Mar;25(3):461-72. doi: 10.1111/j.1420-9101.2011.02436.x. Epub 2011 Dec 13. PubMed PMID: 22168583.

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Nuismer SL, Gomulkiewicz R, Ridenhour BJ. When is correlation coevolution?. Am Nat. 2010 May;175(5):525-37. doi: 10.1086/651591. PubMed PMID: 20307203.

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Kölliker M, Ridenhour BJ, Gaba S. Antagonistic parent-offspring co-adaptation. PLoS One. 2010 Jan 6;5(1):e8606. doi: 10.1371/journal.pone.0008606. PubMed PMID: 20066041; PubMed Central PMCID: PMC2797617.

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Shay DK, Ridenhour BJ. Can we "hedge" against the development of antiviral resistance among pandemic influenza viruses?. PLoS Med. 2009 Jun 30;6(6):e1000103. doi: 10.1371/journal.pmed.1000103. Epub 2009 Jun 30. PubMed PMID: 19564898; PubMed Central PMCID: PMC2694987.

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Nuismer SL, Ridenhour BJ. The contribution of parasitism to selection on floral traits in Heuchera grossulariifolia. J Evol Biol. 2008 Jul;21(4):958-65. doi: 10.1111/j.1420-9101.2008.01551.x. Epub 2008 May 28. PubMed PMID: 18507700.

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Ridenhour BJ, Storfer AT. Geographically variable selection in Ambystoma tigrinum virus (Iridoviridae) throughout the western USA. J Evol Biol. 2008 Jul;21(4):1151-9. doi: 10.1111/j.1420-9101.2008.01537.x. Epub 2008 Apr 25. PubMed PMID: 18444995.

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Storfer A, Alfaro ME, Ridenhour BJ, Jancovich JK, Mech SG, Parris MJ, Collins JP. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic. Ecol Lett. 2007 Nov;10(11):1075-83. doi: 10.1111/j.1461-0248.2007.01102.x. Epub 2007 Sep 10. PubMed PMID: 17850337.

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Nuismer SL, Ridenhour BJ, Oswald BP. Antagonistic coevolution mediated by phenotypic differences between quantitative traits. Evolution. 2007 Aug;61(8):1823-34. doi: 10.1111/j.1558-5646.2007.00158.x. PubMed PMID: 17683426.

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Ridenhour BJ, Brodie, Jr.,Edmund,D, Brodie III ED. Patterns of genetic differentiation in Thamnophis and Taricha from the Pacific Northwest. Journal of Biogeography. 2007 April; 34(4):724-735. doi: 10.1111/j.1365-2699.2006.01642.x.

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Giordano AR, Ridenhour BJ, Storfer A. The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym). Mol Ecol. 2007 Apr;16(8):1625-37. doi: 10.1111/j.1365-294X.2006.03223.x. PubMed PMID: 17402978.

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Gomulkiewicz R, Drown DM, Dybdahl MF, Godsoe W, Nuismer SL, Pepin KM, Ridenhour BJ, Smith CI, Yoder JB. Dos and don'ts of testing the geographic mosaic theory of coevolution. Heredity (Edinb). 2007 May;98(5):249-58. doi: 10.1038/sj.hdy.6800949. Epub 2007 Mar 7. Review. PubMed PMID: 17344805.

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Ridenhour BJ, Nuismer SL. Polygenic traits and parasite local adaptation. Evolution. 2007 Feb;61(2):368-76. doi: 10.1111/j.1558-5646.2007.00029.x. PubMed PMID: 17348946.