References
- Abe, T, Akazawa, Y, Toyoda, A, Niki, H and Baba, T. 2020. Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes. Frontiers in microbiology, 11: 1486. DOI: 10.3389/fmicb.2020.01486
- Abe, T, Kanaya, S, Kinouchi, M, Ichiba, Y, Kozuki, T and Ikemura, T. 2003. Informatics for unveiling hidden genome signatures. Genome research, 13: 693–702. DOI: 10.1101/gr.634603
- Benvenuto, D, Giovanetti, M, Salemi, M, Prosperi, M, De Flora, C, Junior Alcantara, LC, Angeletti, S and Ciccozzi, M. 2020. The global spread of 2019-nCoV: a molecular evolutionary analysis. Pathogens and global health, 114: 64–67. DOI: 10.1080/20477724.2020.1725339
- Elbe, S and Buckland-Merrett, G. 2017. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global challenges (Hoboken, NJ), 1: 33–46. DOI: 10.1002/gch2.1018
- Gorbalenya, AE, Baker, SC, Baric, RS, de Groot, RJ, Drosten, C, Gulyaeva, AA, Haagmans, BL, Lauber, C, Leontovich, AM, Neuman, BW, et al. 2020. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature microbiology, 5: 536–544. DOI: 10.1038/s41564-020-0695-z
- Hadfield, J, Megill, C, Bell, SM, Huddleston, J, Potter, B, Callender, C, Sagulenko, P, Bedford, T and Neher, RA. 2018. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics (Oxford, England), 34: 4121–4123. DOI: 10.1093/bioinformatics/bty407
- Han, AX, Parker, E, Scholer, F, Maurer-Stroh, S and Russell, CA. 2019. Phylogenetic Clustering by Linear Integer Programming (PhyCLIP). Molecular Biology and Evolution, 36: 1580–1595. DOI: 10.1093/molbev/msz053
- Hu, B, Guo, H, Zhou, P and Shi, ZL. 2021. Characteristics of SARS-CoV-2 and COVID-19. Nature reviews Microbiology, 19: 141–154. DOI: 10.1038/s41579-020-00459-7
- Ikemura, T, Iwasaki, Y, Wada, K, Wada, Y and Abe, T. 2021. AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome. Genes Genet Syst. (in press). DOI: 10.1101/2021.05.23.445371
- Ikemura, T, Wada, K, Wada, Y, Iwasaki, Y and Abe, T. 2020. Unsupervised explainable AI for simultaneous molecular evolutionary study of forty thousand SARS-CoV-2 genomes. bioRxiv. DOI: 10.1101/2020.10.11.335406
- Iwasaki, Y, Abe, T and Ikemura, T. 2021. Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes. BMC Microbiol, 21: 89. DDOI: 10.1186/s12866-021-02158-6
- Iwasaki, Y, Abe, T, Wada, K, Itoh, M and Ikemura, T. 2011. Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case. DNA research, 18: 125–136. DOI: 10.1093/dnares/dsr005
- Iwasaki, Y, Abe, T, Wada, Y, Wada, K and Ikemura, T. 2013. Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains. BMC infectious diseases, 13: 386. DOI: 10.1186/1471-2334-13-386
- Kanaya, S, Kinouchi, M, Abe, T, Kudo, Y, Yamada, Y, Nishi, T, Mori, H and Ikemura, T. 2001. Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene, 276: 89–99. DOI: 10.1016/S0378-1119(01)00673-4
- Karlin, S, Campbell, AM and Mrazek, J. 1998. Comparative DNA analysis across diverse genomes. Annual review of genetics, 32: 185–225. DOI: 10.1146/annurev.genet.32.1.185
- Kirby, T. 2021. New variant of SARS-CoV-2 in UK causes surge of COVID-19. The Lancet Respiratory medicine, 9: e20–e21. DOI: 10.1016/S2213-2600(21)00005-9
- Kohonen, T. 1990. The self-organizing map. Proceedings of the IEEE, 78: 1464–1480. DOI: 10.1109/5.58325
- Kohonen, T, Oja, E, Simula, O, Visa, A and Kangas, J. 1996. Engineering applications of the self-organizing map. Proceedings of the IEEE, 84: 1358–1384. DOI: 10.1109/5.537105
- Kumar, S, Stecher, G, Li, M, Knyaz, C and Tamura, K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol, 35: 1547–1549. DOI: 10.1093/molbev/msy096
- Mangeat, B, Turelli, P, Caron, G, Friedli, M, Perrin, L and Trono, D. 2003. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature, 424: 99–103. DOI: 10.1038/nature01709
- Mercatelli, D and Giorgi, FM. 2020. Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Frontiers in microbiology, 11: 1800. DOI: 10.3389/fmicb.2020.01800
- Qiu, Y, Abe, T, Nakao, R, Satoh, K and Sugimoto, C. 2019. Viral population analysis of the taiga tick, Ixodes persulcatus, by using Batch Learning Self-Organizing Maps and BLAST search. The Journal of veterinary medical science, 81: 401–410. DOI: 10.1292/jvms.18-0483
- Simmonds, P. 2020. Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories. mSphere, 5. DOI: 10.1128/mSphere.00408-20
- Sun, J, He, WT, Wang, L, Lai, A, Ji, X, Zhai, X, Li, G, Suchard, MA, Tian, J, Zhou, J, et al. 2020. COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives. Trends in molecular medicine, 26: 483–495. DOI: 10.1016/j.molmed.2020.02.008
- Tang, X, Wu, C, Li, X, Song, Y, Yao, X, Wu, X, Duan, Y, Zhang, H, Wang, Y, Qian, Z, et al. 2020. On the origin and continuing evolution of SARS-CoV-2. National Science Review, 7: 1012–1023. DOI: 10.1093/nsr/nwaa036
- Wada, K, Wada, Y and Ikemura, T. 2020. Time-series analyses of directional sequence changes in SARS-CoV-2 genomes and an efficient search method for candidates for advantageous mutations for growth in human cells. Gene: X, 5: 100038. DOI: 10.1016/j.gene.2020.100038
- Wang, R, Chen, J, Gao, K, Hozumi, Y, Yin, C and Wei, GW. 2021. Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Communications biology, 4: 228. DOI: 10.1038/s42003-021-01754-6
- World Health Organization. 2020. Coronavirus Disease (COVID-2019). Situation Reports. URL:
https://www.who.int/emergencies/diseases/novel-coronavirus-2019 .