Peer reviewed journal articles
Valles, S., Rivers, A. R., 2019. Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range. Virus Genes. 55, 368-380. doi:10.1007/s11262-019-01652-4
Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J., Brown, C.T., Callahan, B.J., Caraballo-Rodríguez, A.M., Chase, J., Cope, E., Silva, R. Da, Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B., Kang, K. Bin, Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G., Lee, J., Ley, R., Liu, Y.-X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B.D., McDonald, D., McIver, L.J., Melnik, A. V, Metcalf, J.L., Morgan, S.C., Morton, J., Naimey, A.T., Navas-Molina, J.A., Nothias, L.F., Orchanian, S.B., Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Michael S Robeson, I., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S.J., Spear, J.R., Swafford, A.D., Thompson, L.R., Torres, P.J., Trinh, P., Tripathi, A., Turnbaugh, P.J., Ul-Hasan, S., Hooft, J.J. van der, Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., Hippel, M. von, Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C.H., Willis, A.D., Xu, Z.Z., Zaneveld, J.R., Zhang, Y., Zhu, Q., Knight, R., Caporaso, J.G., 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. doi:10.7287/peerj.preprints.27295v2
Rivers, A.R., Weber, K.C., Gardner, T.G., Liu, S., Armstrong, S.D., 2018. ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research 7, 1418. doi:10.12688/f1000research.15704.1
Lamit, L.J., Romanowicz, K.J., Potvin, L.R., Rivers, A.R., Singh, K., Lennon, J.T., Tringe, S.G., Kane, E.S., Lilleskov, E.A., 2017. Patterns and drivers of fungal community depth stratification in Sphagnum peat. FEMS Microbiol. Ecol. 93, 1–21. doi:10.1093/femsec/fix082
Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T.B.K., Schulz, F., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., Tringe, S.G., Ivanova, N.N., Copeland, A., Clum, A., Becraft, E.D., Malmstrom, R.R., Birren, B., Podar, M., Bork, P., Weinstock, G.M., Garrity, G.M., Dodsworth, J.A., Yooseph, S., Sutton, G., Glöckner, F.O., Gilbert, J.A., Nelson, W.C., Hallam, S.J., Jungbluth, S.P., Ettema, T.J.G., Tighe, S., Konstantinidis, K.T., Liu, W.-T., Baker, B.J., Rattei, T., Eisen, J.A., Hedlund, B., McMahon, K.D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G.W., Rinke, C., Kyrpides, N.C., Schriml, L., Garrity, G.M., Hugenholtz, P., Sutton, G., Yilmaz, P., Meyer, F., Glöckner, F.O., Gilbert, J.A., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D.H., Eren, A.M., Schriml, L., Banfield, J.F., Hugenholtz, P., Woyke, T., 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731. doi:10.1038/nbt.3893
Paez-Espino, D., Chen, I.-M.A., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V.M., Nielsen, T., Huntemann, M., K. Reddy, T.B., Pavlopoulos, G.A., Sullivan, M.B., Campbell, B.J., Chen, F., McMahon, K., Hallam, S.J., Denef, V., Cavicchioli, R., Caffrey, S.M., Streit, W.R., Webster, J., Handley, K.M., Salekdeh, G.H., Tsesmetzis, N., Setubal, J.C., Pope, P.B., Liu, W.-T., Rivers, A.R., Ivanova, N.N., Kyrpides, N.C., 2017. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 45, D457–D465. doi:10.1093/nar/gkw1030
Rivers, A.R., Burns, A.S., Chan, L.-K., Moran, M.A., 2016. Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3. Front. Microbiol. 7. doi:10.3389/fmicb.2016.00380
Moran, M.A., Satinsky, B., Gifford, S.M., Luo, H., Rivers, A., Chan, L.-K., Meng, J., Durham, B.P., Shen, C., Varaljay, V.A., Smith, C.B., Yager, P.L., Hopkinson, B.M., 2013. Sizing up metatranscriptomics. ISME J. 7, 237–43. doi:10.1038/ismej.2012.94
Kemp, D.W., Rivers, A.R., Kemp, K.M., Lipp, E.K., Porter, J.W., Wares, J.P., 2015. Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata. PLoS One 10, e0143790. doi:10.1371/journal.pone.0143790
Beier, S., Rivers, A.R., Moran, M.A., Obernosterer, I., 2015. The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater. Environ. Microbiol. 17, 3466–3480. doi:10.1111/1462-2920.12434
Beier, S., Rivers, A.R., Moran, M.A., Obernosterer, I., 2015. Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures. ISME J. 9, 1141–51. doi:10.1038/ismej.2014.206
Rivers, A.R., Smith, C.B., Moran, M.A., 2014. An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3. Stand. Genomic Sci. 9, 11. doi:10.1186/1944-3277-9-11
Rivers, A.R., Rose, A.L., Webb, E.A., 2013. An online calculator for marine phytoplankton iron culturing experiments. J. Phycol. 49, 1017–1021. doi:10.1111/jpy.12107
Rivers, A.R., Sharma, S., Tringe, S.G., Martin, J., Joye, S.B., Moran, M.A., 2013. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J. 19, 1–15. doi:10.1038/ismej.2013.129 Rivers, A.R., Jakuba, R.W., Webb, E.A., 2009. Iron stress genes in marine Synechococcus and the development of a flow cytometric iron stress assay. Environ. Microbiol. 11, 382–396. doi:10.1111/j.1462-2920.2008.01778.x
Teske, A., Edgcomb, V., Rivers, A., Thompson, J., de Alvin, V.G., Molyneaux, S., Wirsen, C., 2009. A molecular and physiological survey of a diverse collection of hydrothermal vent Thermococcus and Pyrococcus isolates. Extremophiles 13, 905–915. doi:10.1007/s00792-009-0278-7
Rivers, A.R., Jakuba, R.W., Webb, E.A., 2009. Iron stress genes in marine Synechococcus and the development of a flow cytometric iron stress assay. Environ. Microbiol. 11, 382–396. doi:10.1111/j.1462-2920.2008.01778.x
McIntyre, P.B., Michel, E., France, K., Rivers, A., Hakizimana, P., Cohen, A.S., 2005. Individual- and Assemblage-Level Effects of Anthropogenic Sedimentation on Snails in Lake Tanganyika. Conserv. Biol. 19, 171–181. doi:10.1111/j.1523-1739.2005.00456.x