Please contact me for reprints of any of my articles that are not freely available to you! My CV can be downloaded at the bottom.
Castaneda-Barba, S., B. J. Ridenhour, E. M. Top, and T. Stalder. Detection of rare plasmid hosts using a targeted Hi-C approach. ISME Communications In press.
Meadows, T., E. R. Coats, S. Narum, E. M. Top, B. J. Ridenhour, and T. Stalder. 2025. Epidemiological model can forecast COVID-19 outbreaks from wastewater-based surveillance in rural communities. Water Research 268:122671. Link.
Reveles, K. R., A. J. Hickmott, K. A. Strey, A. C. Mustoe, J. P. Arroyo, M. L. Power, B. J. Ridenhour, K. R. Amato, and C. N. Ross. 2024. Developing the common marmoset as a translational geroscience model to study the microbiome and healthy aging. Microorganisms 12:852. Link.
Moxley, T. A., J. Johnson-Leung, E. Seamon, C. Williams, and B. J. Ridenhour. 2024. Applications of elastic net regression for modeling COVID-19 sociodemographic risk factors. PLoS One 19:e0297065. Link.
Ferguson, J., A. González-González, J. Kaiser, S. Winzer, J. Anast, B. J. Ridenhour, T. A. Miura, and C. E. Parent. 2023. Hidden variable models reveal the effects of infection from changes in host survival. PLoS Computational Biology 19:e1010910. Link.
Metzger G., B. J. Ridenhour, M. France, K. Gliniewicz, J. Millstein, M. L. Settles, L. Forney, T. Stalder, and E. Top. 2022. Biofilms preserve the transmissibility of a multi-drug resistance plasmid. npj Biofilms and Microbiomes 8:95. Link.
Slanzon, G.S., B. J. Ridenhour, L. M. Parrish, S. C. Trombetta, D. A. Moore, W. M. Sischo, and C. S. McConnel. 2022. Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves. PLoS One 17: e0276638. Link.
Bayat-Mokhtari, E. and B. J. Ridenhour. 2022. Filtering ASVs/OTUs via mutual information-based microbiome network analysis. BMC Bioinformatics 23:380. Link.
Ridenhour, B. J., D. Sarathchandra, E. Seamon, H. Brown, F.-Y. Leung, M. Johnson-Leon, M. Megheib, C. R. Miller, and J. Johnson-Leung. 2022. Effects of trust, risk perception, and health behavior on COVID-19 disease burden: Evidence from a multi-state US survey. PLoS One 17:e0268302. Link.
Hsueh, B. Y., G. B. Severin, C. A. Elg, E. J. Waldron, A. Kant, A. J. Wessel, J. A. Dover, C. R. Rhoades, B. J. Ridenhour, K. N. Parent, M. B. Neiditch, J. Ravi, E. M. Top, and C. M. Waters. 2022. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nature Microbiology 7:1210-1220. Link.
Slanzon, G. S., B. J. Ridenhour, D. A. Moore, W. M. Sischo, L. M. Parrish, S. C. Trombetta, and C. S. McConnel. 2022. Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease. PLoS One 17: e0262317. Link.
Van Leuven, J. T., A. J. Gonzalez, E. C. Ijezie, A. Q. Wixom, J. L. Clary, M. N., Naranjo, B. J. Ridenhour, C. R. Miller, and T. A. Miura. 2021. Rhinovirus reduces the severity of subsequent respiratory viral infections by interferon-dependent and -independent mechanisms. mSphere 6:e00479-21. Link.
Remien, C. H., M. J. Eckwright, and B. J. Ridenhour. 2021. Structural identifiability of the generalized Lotka-Volterra model for microbiome studies. Royal Society Open Science 8:201378. Link.
Baumgaertner, B., B. J. Ridenhour, F. Justwan, J. E. Carlisle, and C. R. Miller. 2020. Risk of disease and willingness to vaccinate in the United States: A population-based survey. PLoS Medicine 17:e1003354. Link.
Witkin S., A. Moron, B. J. Ridenhour, E. Minis, A. Hatanaka, S. Sarmento, M. Franca, F. Carvalho, T. Hamamoto, R. Mattar, E. Sabino, I. Linhares, M. Rudge, and L. J. Forney. 2019. Vaginal biomarkers that predict cervical length and dominant bacteria in the vaginal microbiome of pregnant women. mBio 10:e02242-19. Link.
Lee, J. A., S. Riazi, S. H. Nemati, J. V. Bazurto, A. E. Vasdekis, B. J. Ridenhour, C. H. Remien, and C. J. Marx. 2019. Microbial phenotypic heterogeneity in response to a metabolic toxin: continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations. PLoS Genetics 15: e1008458. Link.
Nunn, K. L., B. J. Ridenhour, E. M. Chester, V. J. Vitzthum, J. D. Fortenberry, and L. J. Forney. 2019. Vaginal glycogen, not estradiol, is associated with vaginal bacterial community composition in black adolescent women. Journal of Adolescent Health 65:130-138. Link.
Gliniewicz K., G. M. Schneider, B. J. Ridenhour, C. J. Williams, Y. Song, M. A. Farage, K. Miller, and L. J. Forney. 2019. Comparison of the vaginal microbiomes of premenopausal and postmenopausal women. Frontier in Microbiology 10:193. Link.
Ridenhour, B. J. and J. R. Ridenhour. 2018. Stability of equilibria in quantitative genetic models based on modified-gradient systems. Journal of Biological Dynamics 12:39-50. Link.
France, M. T., B. J. Ridenhour, and L. J. Forney. 2018. Effects of spatial structure and reduced growth rates on evolution in bacterial populations. In Grand Challenges in Biology and Biotechnology: Molecular Mechanisms of Microbial Evolution. Ed: Pabulo H. Rampelotto. Springer International Publishing: Berlin. Link.
Ridenhour, B. J., S. L. Brooker, J. E. Williams, J. T. Van Leuven, A. W. Miller, M. D. Dearing, and C. H. Remien. 2017. Modeling time-series data from microbial communities. ISMEJ 11:2526-2537. Link.
Ridenhour, B. J., G. A. Metzger, M. France, K. Gliniewicz, J. Millstein, L. J. Forney, and E. M. Top. 2017. Persistence of antibiotic resistance plasmids in bacterial biofilms. Evolutionary Applications 10:640-647. Link.
J. T. Van Leuven, B. J. Ridenhour, C. R. Miller, and T. A. Miura. 2017. Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses. PLoS One 12:e0178408. Link.
Nardin, L. G., C. R. Miller, B. J. Ridenhour, S. M. Krone, P. Joyce, and B. O. Baumgaertner. 2016. Planning horizon affects prophylactic decision-making and epidemic dynamics. PeerJ 4:e2678. Link.
Ridenhour, B. J. 2016. Coevolutionary fitness landscapes. In The Encyclopedia of Evolutionary Biology. Ed: Richard M. Kliman. Academic Press: Oxford. pp. 299–304. Link.
Ridenhour, B. J. and E. M. Top. 2016. Plasmid driven evolution of bacteria. In The Encyclopedia of Evolutionary Biology. Ed: Richard M. Kliman. Academic Press: Oxford. pp. 301–306. Link.
Ridenhour, B. J.and M. J. Cramer. 2015. Differentiation of white-footed mice (Peromyscus leucopus) and deer mice (Peromyscus maniculatus) of the Upper Midwest using PCR melt curve analysis. Conservation Genetics Resource 7:29–31. Link.
Turner, K. G., M. J. Smith, and B. J. Ridenhour. 2014. Whirling disease dynamics: an analysis of intervention strategies. Preventive Veterinary Medicine 113:457–468. Link.
Ridenhour, B. J., J. M. Kowalik, and D. K. Shay. 2014. Unravelling R0: Considerations for public health applications. American Journal of Public Health 104:e32–e41.
Link.
Ridenhour, B. J.and S. L. Nuismer. 2014. A quantitative genetic approach to predicting change in biological communities. Theoretical Ecology 7:137–148. Link.
Ridenhour, B. J. 2014. Coevolution. In Oxford Bibliographies in Evolutionary Biology. Ed: J. Losos. New York: Oxford University Press. Link.
Ridenhour, B. J., M. A. Campitelli, J. C. Kwong, L. C. Rosella, B. G. Armstrong, P. Mangtani, A. J. Calzavara, and D. K. Shay. 2013. 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 8:e76318. Link.
Ridenhour, B. J.and S. L. Nuismer. 2012. Trait-mediated indirect interactions and the coevolutionary process. In Ecology and Evolution of Trait-mediated Indirect Interactions: Linking Evolution, Community, and Ecosystem. Eds: T. Ohgushi, O. Schmitz, and R. Holt. New York: Cambridge University Press. pp. 207–220. Link.
Thompson, W. W., B. J. Ridenhour, J. P. Barile, and D. K. Shay. 2012. Time-series analyses of count data to estimate the burden of infectious diseases. Epidemiology 23:839–842. Link.
Burkhardt, A., B. J. Ridenhour, L. F. Delph, and G. Bernasconi. 2012. The contribution of a pollinating seed predator to selection on Silene latifolia females. Journal of Evolutionary Biology 25:461–472. Link.
Ridenhour, B. J., A. Braun, T. Teyrasse, and D. Goldsman. 2011. Controlling the spread of disease in schools. PLoS One 6: e29640. Link.
Nuismer, S. L., R. Gomulkiewicz, and B. J. Ridenhour. 2010. When is correlation coevolution? American Naturalist 175: 525–537. Link.
Kölliker, M., B. J. Ridenhour, and S. Gaba. 2010. Antagonistic parent-offspring coadaptation. PLoS One 5: e8606. Link.
Shay, D. K. and B. J. Ridenhour. 2009. Can we ”hedge” against the development of antiviral resistance among pandemic influenza viruses? PLoS Medicine 6: e1000103. Link.
Ridenhour, B. J. and A. T. Storfer. 2008. Geographically variable selection in Ambystoma tigrinum Virus (Iridoviridae) throughout the Western United States. Journal of Evolutionary Biology 21:958–965. Link.
Nuismer, S. L. and B. J. Ridenhour. 2008. The contribution of parasitism to selection on floral traits in Heuchera grossulariifolia. Journal of Evolutionary Biology 21:1151–1159. Link.
Storfer, A., M. E. Alfaro, B. J. Ridenhour, J. K. Jancovich, S. G. Mech, M. J. Parris, and J. P. Collins. 2007. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic. Ecology Letters 10:1075–1083. Link.
Nuismer, S. L., B. J. Ridenhour, and B. Oswald. 2007. Antagonistic coevolution mediated by phenotypic differences between quantitative traits. Evolution 61:1823–1834. Link.
Ridenhour, B. J., E. D. Brodie, Jr., and E. D. Brodie III. 2007. Patterns of genetic differentiation in Thamnophis and Taricha from the Pacific Northwest. Journal of Biogeography 34:724–735. Link.
Gomulkiewicz, R., D. M. Drown, M. F. Dybdahl, W. Godsoe, S. L. Nuismer, K. M. Pepin, B. J. Ridenhour, C. I. Smith, and J. B. Yoder. 2007. Dos and don’ts of testing the geographic mosaic theory of coevolution. Heredity 98:249–258. Link.
Giordano, A. R., B. J. Ridenhour, and A. Storfer. 2007. Tests of the influences of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactylum). Molecular Ecology 16:1625-1637. Link.
Ridenhour, B. J. 2005. Identification of selective sources: partitioning selection based on interactions. American Naturalist 166:12–25. Link.
Freedberg, S., M. A. Ewert, M. Neiman, B. Ridenhour, and C. E. Nelson. 2005. Nesting fidelity and molecular evidence for natal homing in the freshwater turtle, Graphemes kohnii. Proceedings of the Royal Society: B5.4 272:1345–1350. Link.
Ridenhour, B. J., E. D. Brodie, Jr., and E. D. Brodie III. 2004. Resistance of neonates and field-collected garter snakes (Thamnophis spp.) to tetrodotoxin. Journal of Chemical Ecology 30:143–154. Link.
Brodie, E. D. III and B. J. Ridenhour. 2003. Reciprocal selection at the phenotypic interface of coevolution. Integrative and Comparative Biology 43:408–419. Link.
Brodie, E. D., Jr., B. J. Ridenhour, and E. D. Brodie III. 2002. The evolutionary response of predators to dangerous prey: Hotspots and coldspots in the geographic mosaic of coevolution between garter snakes and newts. Evolution 56:2067–2082. Link.
Ridenhour, B. J., E. D. Brodie, Jr., and E. D. Brodie III. 1999. Effects of repeated injections of tetrodotoxin on growth and resistance in the garter snake Thamnophis sirtalis. Copeia 1999:531–535. Link.
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