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Commit 7a121bd4 authored by Adriana Monserrat Salazar Puente's avatar Adriana Monserrat Salazar Puente
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<section id= "References" class="page-section">
<h2>References</h2>
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<p>Fu, H., Elena, R. C., & Marquez, P. H. (2019). The roles of small RNAs: Insights from bacterial quorum sensing. ExRNA, 1(1), 32<a href="https://doi.org/10.1186/s41544-019-0027-8" target="blank">https://doi.org/10.1186/s41544-019-0027-8</a></p>
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<p>Hofacker, I. L. (2008). The Vienna RNA Websuite. Nucleic Acids Research, 36(Web Server), W70–W74. <a href="https://doi.org/10.1093/nar/gkn188"target="blank">https://doi.org/10.1093/nar/gkn188</a></p>
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<p>Kucharík, M., Hofacker, I. L., Stadler, P. F., & Qin, J. (2014). Basin Hopping Graph: A computational framework to characterize RNA folding landscapes. Bioinformatics, 30(14), 2009–2017. <a href="https://doi.org/10.1093/bioinformatics/btu156" target="blank">https://doi.org/10.1093/bioinformatics/btu156</a></p>
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<p>Kumar, K., Chakraborty, A., & Chakrabarti, S. (2021). PresRAT: A server for identification of bacterial small-RNA sequences and their targets with probable binding region. RNA Biology, 18(8), 1152–1159.<a href="https://doi.org/10.1080/15476286.2020.1836455" target="blank">https://doi.org/10.1080/15476286.2020.1836455</a></p>
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<p>Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011). ViennaRNA Package 2.0. Algorithms for Molecular Biology, 6(1), 26. <a href="https://doi.org/10.1186/1748-7188-6-26" target="blank">https://doi.org/10.1186/1748-7188-6-26 </a></p>
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<p>Tafer, H., Ameres, S. L., Obernosterer, G., Gebeshuber, C. A., Schroeder, R., Martinez, J., & Hofacker, I. L. (2008). The impact of target site accessibility on the design of effective siRNAs. Nature Biotechnology, 26(5), 578–583. <a href="https://doi.org/10.1038/nbt1404" target="blank">https://doi.org/10.1038/nbt1404</a></p>
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<p>Trotta, E. (2014). On the Normalization of the Minimum Free Energy of RNAs by Sequence Length. PLoS ONE, 9(11), e113380.<a href=" https://doi.org/10.1371/journal.pone.0113380" target="blank"> https://doi.org/10.1371/journal.pone.0113380</a></p>
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<p>Vazquez-Anderson, J., Mihailovic, M. K., Baldridge, K. C., Reyes, K. G., Haning, K., Cho, S. H., Amador, P., Powell, W. B., & Contreras, L. M. (2017). Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions. Nucleic Acids Research, 45(9), 5523–5538. <a href="https://doi.org/10.1093/nar/gkx115" target="blank">https://doi.org/10.1093/nar/gkx115</a></p>
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<p>Woodson, S. A. (2010). Compact Intermediates in RNA Folding. Annual Review of Biophysics, 39(1), 61–77.<a href="https://doi.org/10.1146/annurev.biophys.093008.131334" target="blank">https://doi.org/10.1146/annurev.biophys.093008.131334</a></p>
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<p>Yoo, S. M., Na, D., & Lee, S. Y. (2013). Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli. Nature Protocols, 8(9), 1694–1707. <a href="https://doi.org/10.1038/nprot.2013.105" target="blank">https://doi.org/10.1038/nprot.2013.105</a></p>
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<p>Zhu, L. P., Song, S. Z., & Yang, S. (2021). Gene repression using synthetic small regulatory RNA in Methylorubrum extorquens. Journal of Applied Microbiology, 131(6), 2861–2875. <a href="https://doi.org/10.1111/jam.15159" target="blank">https://doi.org/10.1111/jam.15159"</a></p>
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