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(2016) Spring bloom of the raphidophycean <i>Heterosigma akashiwo<\/i> in the Golden Horn Estuary at the northeast of Sea of Marmara. Ege J Fish Aquat               33: 201\u2013207.","DOI":"10.12714\/egejfas.2016.33.3.03"},{"key":"15","doi-asserted-by":"crossref","unstructured":"Endo, H., Ogata, H., and Suzuki, K. (2018) Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean. Sci Rep               8: 10916.","DOI":"10.1038\/s41598-018-29039-9"},{"key":"16","doi-asserted-by":"crossref","unstructured":"Eren, A.M., Esen, \u00d6.C., Quince, C., Vineis, J.H., Morrison, H.G., Sogin, M.L., et al. (2015) Anvi\u2019o: an advanced anal\u00adysis and visualization platform for \u2018omics data. PeerJ               3: e1319.","DOI":"10.7717\/peerj.1319"},{"key":"17","doi-asserted-by":"crossref","unstructured":"Fang, Y., Meng, L., Xia, J., Gotoh, Y., Hayashi, T., Nagasaki, K., et al. 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Nat Commun               15: 7536.","DOI":"10.1038\/s41467-024-51936-z"},{"key":"73","doi-asserted-by":"crossref","unstructured":"Yutin, N., Wolf, Y.I., Raoult, D., and Koonin, E.V. (2009) Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J               6: 223.","DOI":"10.1186\/1743-422X-6-223"},{"key":"74","doi-asserted-by":"crossref","unstructured":"Zhou, Z., Tran, P.Q., Martin, C., Rohwer, R.R., Baker, B.J., and Anantharaman, K. (2025) Unravelling viral ecology and evolution over 20 years in a freshwater lake. Nat Microbiol               10: 231\u2013245.","DOI":"10.1038\/s41564-024-01876-7"},{"key":"75","doi-asserted-by":"crossref","unstructured":"Zwart, M.P., and Elena, S.F. (2015) Matters of size: genetic bottlenecks in virus infection and their potential impact on evolution. 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