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English Information

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Authors
# Name
1 Mariana Gabas(mlouiseg@usp.br)
2 Arthur Barrios Solano(arthur.barrios@usp.br)
3 João Setubal(setubal@iq.usp.br)

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Reference
# Reference
1 An, S.-Q., Potnis, N., Dow, M., V orhölter, F.-J., He, Y . -Q., Becker, A., Teper, D., Li, Y ., Wang, N., Bleris, L., & Tang, J.-L. (2019). Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiology Reviews, 44(1), 1–32
2 Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., Kuchin, K., Karasikov, M., Lyons, A., Mak, L., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y ., Ng, A., & Nikolayeva, O. (2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, 0(0)
3 Elena Schmitz, J., & Rahmann, S. (2025). A comprehensive review and evaluation of species richness estimation. Briefings in Bioinformatics, 26(2)
4 Gotelli, N.J. and Colwell, R.K. (2011) Chapter 4. Estimating Species Richness. In: Magurran, A.E. and McGill, B.J., Eds., Biological Diversity: Frontiers in Measurement and Assessment, Oxford University Press, New York, 39-54
5 Magurran A. E. (2007). Species abundance distributions over time. Ecology letters, 10(5), 347–354
6 Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., Dodsworth, J. A., Hedlund, B. P., Tsiamis, G., Sievert, S. M., Liu, W. -T., Eisen, J. A., Hallam, S. J., Kyrpides, N. C., Stepanauskas, R., & Rubin, E. M. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499(7459), 431–437
7 ‌ Roumpeka, D. D., Wallace, R. J., Escalettes, F., Fotheringham, I., & Watson, M. (2017). A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. Frontiers in Genetics, 8
8 Seemann T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxford, England), 30(14), 2068–2069
9 Solano, A., & Setubal, J. (2024). A computational pipeline for species- and strain-level classification of metagenomic sequences. In Proceedings of the 17th Brazilian Symposium on Bioinformatics, pp. 155-166. Porto Alegre: SBC
10 Steen, A. D., Crits-Christoph, A., Carini, P., DeAngelis, K. M., Fierer, N., Lloyd, K. G., & Cameron Thrash, J. (2019). High proportions of bacteria and archaea across most biomes remain uncultured. The ISME Journal, 13(12), 3126–3130
11 Sunagawa, S., Acinas, S. G., Bork, P., Bowler, C., Eveillard, D., Gorsky, G., Guidi, L., Iudicone, D., Karsenti, E., Lombard, F., Ogata, H., Pesant, S., Sullivan, M. B., Wincker, P., & de Vargas, C. (2020). Tara Oceans: towards global ocean ecosystems biology. Nature Reviews Microbiology, 18
12 Tettelin, H., Riley, D., Cattuto, C., & Medini, D. (2008). Comparative genomics: the bacterial pan-genome. Current opinion in microbiology, 11(5), 472–477
13 Tonkin-Hill, G., MacAlasdair, N., Ruis, C., Weimann, A., Horesh, G., Lees, J. A., Gladstone, R. A., Lo, S., Beaudoin, C., Floto, R. A., Frost, S. D. W., Corander, J., Bentley, S. D., & Parkhill, J. (2020). Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biology, 21(1)