References
- Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature Medicine, 26(4), 450–452. https://doi.org/https://doi.org/10.1038/s41591-020-0820-9
- Baine, I., & Hui, P. (2019). Practical applications of DNA genotyping in diagnostic pathology. Expert Review of Molecular Diagnostics, 19(2), 175–188. https://doi.org/https://doi.org/10.1080/14737159.2019.1568874
- Balakirev, E. S., Chechetkin, V. R., Lobzin, V. V., & Ayala, F. J. (2003). DNA polymorphism in the β-esterase gene cluster of Drosophila melanogaster. Genetics, 164(2), 533–544. PMID: 12807774
- Balakirev, E. S., Chechetkin, V. R., Lobzin, V. V., & Ayala, F. J. (2005). Entropy and GC content in the beta-esterase gene cluster of the Drosophila melanogaster subgroup . Molecular Biology and Evolution, 22(10), 2063–2072. https://doi.org/https://doi.org/10.1093/molbev/msi197
- Balakirev, E. S., Chechetkin, V. R., Lobzin, V. V., & Ayala, F. J. (2014). Computational methods of identification of pseudogenes based on functionality: Entropy and GC content. Methods in Molecular Biology (Clifton, N.J.), 1167, 41–62. https://doi.org/https://doi.org/10.1007/978-1-4939-0835-6_4
- Boeva, V., Regnier, M., Papatsenko, D., & Makeev, V. (2006). Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics (Oxford, England), 22(6), 676–684. https://doi.org/https://doi.org/10.1093/bioinformatics/btk032
- Butler, J. (2011). Advanced topics in forensic DNA typing: Methodology. Elsevier Academic Press.
- Cagliani, R., Forni, D., Clerici, M., & Sironi, M. (2020). Computational inference of selection underlying the evolution of the novel coronavirus, severe acute respiratory syndrome coronavirus 2. Journal of Virology, 94(12), e00411–e00420. https://doi.org/https://doi.org/10.1128/JVI.00411-20
- Chang, C., Hou, M., Chang, C., Hsiao, C., & Huang, T. (2014). The SARS coronavirus nucleocapsid protein-forms and functions. Antiviral Research, 103, 39–50. https://doi.org/https://doi.org/10.1016/j.antiviral.2013.12.009
- Chang, C. K., Hsu, Y. L., Chang, Y. H., Chao, F. A., Wu, M. C., Huang, Y. S., Hu, C. K., & Huang, T. H. (2009). Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: Implications for ribonucleocapsid protein packaging. Journal of Virology, 83(5), 2255–2264. https://doi.org/https://doi.org/10.1128/JVI.02001-08
- Chang, C-K., Lo, S.-C., Wang, Y.-S., & Hou, M.-H. (2016). Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discovery Today, 21(4), 562–572. https://doi.org/https://doi.org/10.1016/j.drudis.2015.11.015
- Chechetkin, V. R. (2011). Spectral sum rules and search for periodicities in DNA sequences. Physics Letters A, 375(16), 1729–1732. https://doi.org/https://doi.org/10.1016/j.physleta.2011.03.007
- Chechetkin, V. R., & Lobzin, V. V. (1996). Levels of ordering in coding and non-coding regions of DNA sequences. Physics Letters A, 222(5), 354–360. https://doi.org/https://doi.org/10.1016/0375-9601(96)00672-X
- Chechetkin, V. R., & Lobzin, V. V. (2017). Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique. Journal of Theoretical Biology, 426, 162–179. https://doi.org/https://doi.org/10.1016/j.jtbi.2017.05.033
- Chechetkin, V. R., & Lobzin, V. V. (2019). Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences. Journal of Biomolecular Structure & Dynamics, 37(9), 2322–2338. https://doi.org/https://doi.org/10.1080/07391102.2018.1479660
- Chechetkin, V. R., & Lobzin, V. V. (2020a). Detection of large-scale noisy multi-periodic patterns with discrete double Fourier transform. Fluctuation and Noise Letters, 19(02), 2050019. https://doi.org/https://doi.org/10.1142/S0219477520500194
- Chechetkin, V. R., & Lobzin, V. V. (2020b). Detection of large-scale noisy multi-periodic patterns with discrete double Fourier transform. II. Study of correlations between patterns. Fluctuation and Noise Letters, 20(1), 2150003. https://doi.org/https://doi.org/10.1142/S0219477521500036
- Chechetkin, V. R., & Turygin, A. Y. (1994). On the spectral criteria of disorder in non-periodic sequences: Application to inflation models, symbolic dynamics and DNA sequences. Journal of Physics A: Mathematical and General, 27(14), 4875–4898. https://doi.org/https://doi.org/10.1088/0305-4470/27/14/016
- Chechetkin, V. R., & Turygin, A. Y. (1995). Search of hidden periodicities in DNA sequences. Journal of Theoretical Biology, 175, 477–494. https://doi.org/https://doi.org/10.1006/jtbi.1995.0155
- Chen, C. Y., Chang, C. K., Chang, Y. W., Sue, S. C., Bai, H. I., Riang, L., Hsiao, C. D., & Huang, T. H. (2007). Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA. Journal of Molecular Biology, 368(4), 1075–1086. https://doi.org/https://doi.org/10.1016/j.jmb.2007.02.069
- Dufva, M. (Ed.). (2009). DNA microarrays for biomedical research: Methods and protocols. Springer Humana Press. https://doi.org/https://doi.org/10.1007/978-1-59745-538-1
- Feng, W., Zong, W., Wang, F., & Ju, S. (2020). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A review. Molecular Cancer, 19(1), 100. https://doi.org/https://doi.org/10.1186/s12943-020-01218-1
- Filipovska, A., & Rackham, O. (2012). Modular recognition of nucleic acids by PUF, TALE and PPR proteins. Molecular Biosystems, 8(3), 699–708. https://doi.org/https://doi.org/10.1039/c2mb05392f
- Forster, P., Forster, L., Renfrew, C., & Forster, M. (2020). Phylogenetic network analysis of SARS-CoV-2 genomes. Proceedings of the National Academy of Sciences of the United States of America, 117(17), 9241–9243. https://doi.org/https://doi.org/10.1073/pnas.2004999117
- Fosmire, J. A., Hwang, K., & Makino, S. (1992). Identification and characterization of a coronavirus packaging signal. Journal of Virology, 66(6), 3522–3530. https://doi.org/https://doi.org/10.1128/JVI.66.6.3522-3530.1992
- Fung, T. S., & Liu, D. X. (2019). Human coronavirus: Host-pathogen interaction. Annual Review of Microbiology, 73, 529–557. https://doi.org/https://doi.org/10.1146/annurev-micro-020518-115759
- Grover, A., & Sharma, P. C. (2016). Development and use of molecular markers: Past and present. Critical Reviews in Biotechnology, 36(2), 290–302. https://doi.org/https://doi.org/10.3109/07388551.2014.959891
- Gui, M., Liu, X., Guo, D., Zhang, Z., Yin, C., Chen, Y., & Xiang, Y. (2017). Electron microscopy studies of the coronavirus ribonucleoprotein complex. Protein & Cell, 8(3), 219–224. https://doi.org/https://doi.org/10.1007/s13238-016-0352-8
- Hall, T. M. (2016). De-coding and re-coding RNA recognition by PUF and PPR repeat proteins. Current Opinion in Structural Biology, 36, 116–121. https://doi.org/https://doi.org/10.1016/j.sbi.2016.01.010
- Hurst, K. R., Ye, R., Goebel, S. J., Jayaraman, P., & Masters, P. S. (2010). An interaction between the nucleocapsid protein and a component of the replicase-transcriptase complex is crucial for the infectivity of coronavirus genomic RNA. Journal of Virology, 84(19), 10276–10288. https://doi.org/https://doi.org/10.1128/JVI.01287-10
- Karlin, S., & Altschul, S. F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National Academy of Sciences of the United States of America, 87(6), 2264–2268. https://doi.org/https://doi.org/10.1073/pnas.87.6.2264
- Kayser, M. (2017). Forensic use of Y-chromosome DNA: A general overview. Human Genetics, 136(5), 621–635. https://doi.org/https://doi.org/10.1007/s00439-017-1776-9
- Kramps, T., & Elbers, K. (Eds.). (2017). RNA vaccines. In Methods and protocols. Springer Humana Press. https://doi.org/https://doi.org/10.1007/978-1-4939-6481-9
- Kuo, L., Hurst-Hess, K. R., Koetzner, C. A., & Masters, P. S. (2016). Analyses of coronavirus assembly interactions with interspecies membrane and nucleocapsid protein chimeras. Journal of Virology, 90(9), 4357–4368. https://doi.org/https://doi.org/10.1128/JVI.03212-15
- Lin, S.-M., Lin, S.-C., Hsu, J.-N., Chang, C-K., Chien, C.-M., Wang, Y.-S., Wu, H.-Y., Jeng, U.-S., Kehn-Hall, K., & Hou, M.-H. (2020). Structure-based stabilization of non-native protein-protein interactions of coronavirus nucleocapsid proteins in antiviral drug design. Journal of Medicinal Chemistry, 63(6), 3131–3141. https://doi.org/https://doi.org/10.1021/acs.jmedchem.9b01913
- Lobzin, V. V., & Chechetkin, V. R. (2000). Order and correlations in genomic DNA sequences. The spectral approach. Physics-Uspekhi, 43(1), 55–78. https://doi.org/https://doi.org/10.1070/PU2000v043n01ABEH000611
- Lunde, B. M., Moore, C., & Varani, G. (2007). RNA-binding proteins: Modular design for efficient function. Nature Reviews. Molecular Cell Biology, 8(6), 479–490. https://doi.org/https://doi.org/10.1038/nrm2178
- MacLean, O. A., Orton, R. J., Singer, J. B., & Robertson, D. L. (2020). No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution, 6(1), veaa034. https://doi.org/https://doi.org/10.1093/ve/veaa034
- Macneughton, M. R., Davies, H. A., & Nermut, M. V. (1978). Ribonucleoprotein-like structures from coronavirus particles. Journal of General Virology, 39(3), 545–549. https://doi.org/https://doi.org/10.1099/0022-1317-39-3-545
- Madhugiri, R., Fricke, M., Marz, M., & Ziebuhr, J. (2016). Coronavirus cis-acting RNA elements. Advances in Virus Research, 96, 127–163. https://doi.org/https://doi.org/10.1016/bs.aivir.2016.08.007
- Maier, H. J., Bickerton, E., & Britton, P. (Eds.). (2015). Coronaviruses. In Methods and protocols. Springer Humana Press. https://doi.org/https://doi.org/10.1007/978-1-4939-2438-7
- Marhon, S. A., & Kremer, S. C. (2011). Gene prediction based on DNA spectral analysis: A literature review. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 18(4), 639–676. https://doi.org/https://doi.org/10.1089/cmb.2010.0184
- Marple, S. L., Jr. (1987). Digital spectral analysis with applications. Prentice-Hall.
- Masters, P. S. (2019). Coronavirus genomic RNA packaging. Virology, 537, 198–207. https://doi.org/https://doi.org/10.1016/j.virol.2019.08.031
- McBride, R., van Zyl, M., & Fielding, B. C. (2014). The coronavirus nucleocapsid is a multifunctional protein. Viruses, 6(8), 2991–3018. https://doi.org/https://doi.org/10.3390/v6082991
- Min, W.-P., & Ichim, T. (Eds.). (2010). RNA interference. In From biology to clinical applications. Springer Humana Press. https://doi.org/https://doi.org/10.1007/978-1-60761-588-0
- Narayanan, K., & Makino, S. (2001). Cooperation of an RNA packaging signal and a viral envelope protein in coronavirus RNA packaging. Journal of Virology, 75(19), 9059–9067. https://doi.org/https://doi.org/10.1128/JVI.75.19.9059-9067.2001
- Neuman, B. W., & Buchmeier, M. J. (2016). Supramolecular architecture of the coronavirus particle. Advances in Virus Research, 96, 1–27. https://doi.org/https://doi.org/10.1016/bs.aivir.2016.08.005
- Saxena, S. (Ed.). (2020). Coronavirus disease 2019 (COVID-19). In Medical virology: From pathogenesis to disease control. Springer. https://doi.org/https://doi.org/10.1007/978-981-15-4814-7_13
- Solovyev, A. G., & Makarov, V. V. (2016). Helical capsids of plant viruses: Architecture with structural lability. The Journal of General Virology, 97(8), 1739–1754. https://doi.org/https://doi.org/10.1099/jgv.0.000524
- Stockley, P. G., White, S. J., Dykeman, E., Manfield, I., Rolfsson, O., Patel, N., Bingham, R., Barker, A., Wroblewski, E., Chandler-Bostock, R., Weiß, E. U., Ranson, N. A., Tuma, R., & Twarock, R. (2016). Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid. Bacteriophage, 6(1), e1157666. https://doi.org/https://doi.org/10.1080/21597081.2016.1157666
- Stubbs, G., & Kendall, A. (2012). Helical viruses. Advances in Experimental Medicine and Biology, 726, 631–658. https://doi.org/https://doi.org/10.1007/978-1-4614-0980-9_28
- Subirana, J. A., & Messeguer, X. (2019). Satellites in the prokaryote world. BMC Evolutionary Biology, 19(1), 181. https://doi.org/https://doi.org/10.1186/s12862-019-1504-2
- Suvorova, Y. M., Korotkova, M. A., & Korotkov, E. V. (2014). Comparative analysis of periodicity search methods in DNA sequences. Computational Biology and Chemistry, 53, 43–48. https://doi.org/https://doi.org/10.1016/j.compbiolchem.2014.08.008
- Sznajder, L. J., & Swanson, M. S. (2019). Short tandem repeat expansions and RNA-mediated pathogenesis in myotonic dystrophy. International Journal of Molecular Sciences, 20(13), 3365. https://doi.org/https://doi.org/10.3390/ijms20133365
- Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., Duan, Y., Zhang, H., Wang, Y., Qian, Z., Cui, J., & Lu, J. (2020). On the origin and continuing evolution of SARS-CoV-2. National Science Review, 7(6), 1012–1023. https://doi.org/https://doi.org/10.1093/nsr/nwaa036
- Tilocca, B., Soggiu, A., Sanguinetti, M., Musella, V., Britti, D., Bonizzi, L., Urbani, A., & Roncada, R. (2020). Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses. Microbes and Infection, 22(4–5), 188–194. https://doi.org/https://doi.org/10.1016/j.micinf.2020.04.002
- Twarock, R., Bingham, R. J., Dykeman, E. C., & Stockley, P. G. (2018). A modelling paradigm for RNA virus assembly. Current Opinion in Virology, 31, 74–81. https://doi.org/https://doi.org/10.1016/j.coviro.2018.07.003
- Verheije, M. H., Hagemeijer, M. C., Ulasli, M., Reggiori, F., Rottier, P. J., Masters, P. S., & de Haan, C. A. (2010). The coronavirus nucleocapsid protein is dynamically associated with the replication-transcription complexes. Journal of Virology, 84(21), 11575–11579. https://doi.org/https://doi.org/10.1128/JVI.00569-10
- Woo, J., Lee, E. Y., Lee, M., Kim, T., & Cho, Y.-E. (2019). An in vivo cell-based assay for investigating the specific interaction between the SARS-CoV N-protein and its viral RNA packaging sequence . Biochemical and Biophysical Research Communications, 520(3), 499–506. https://doi.org/https://doi.org/10.1016/j.bbrc.2019.09.115
- Xie, M., & Chen, Q. (2020). Insight into 2019 novel coronavirus - An updated interim review and lessons from SARS-CoV and MERS-CoV. International Journal of Infectious Diseases: IJID: Official Publication of the International Society for Infectious Diseases, 94, 119–124. https://doi.org/https://doi.org/10.1016/j.ijid.2020.03.071
- Yadav, R., Imran, M., Dhamija, P., Suchal, K., & Handu, S. (2020). Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1778536
- Ziebuhr, J. (Ed.). (2016). Coronaviruses. Elsevier Academic Press. https://doi.org/https://doi.org/10.1016/bs.aivir.2016.08.005
- Zubkov, A. M., & Mikhailov, V. G. (1974). Limit distributions of random variables associated with long duplications in a sequence of independent trials. Theory of Probability & Its Applications, 19(1), 172–179. https://doi.org/https://doi.org/10.1137/1119017