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nlp_final_sars-cov-2_spike_mutations_prediction

using CNN+NLTK(NLP) and data from GISAID. (Senior year 1st-semester final project)

https://github.com/kanzakimoe/nlp_final_sars-cov-2_spike_mutations_prediction

Science Score: 18.0%

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Repository

using CNN+NLTK(NLP) and data from GISAID. (Senior year 1st-semester final project)

Basic Info
  • Host: GitHub
  • Owner: KanzakiMoe
  • License: gpl-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 37.1 KB
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  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed over 3 years ago
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Readme License Citation

README.md

NLPFINALSARS-COV-2spikemutations_prediction

using CNN+NLTK(NLP) and data from GISAID. (Senior year 1st-semester final project)

Please get data from GISAID.org

We sincerely thank all data contributors, i.e., the authors and their originating laboratories responsible for obtaining specimens, and the submitting laboratories responsible for generating gene sequences and relay data to be shared through the GISAID program on which this study is based.

Owner

  • Name: KanzakiMoe
  • Login: KanzakiMoe
  • Kind: user
  • Location: Taichung

Citation (citations.txt) 

Kullappan, M., Mary, U., Ambrose, J. M., Veeraraghavan, V. P., & Surapaneni, K. M. (2021). Elucidating the role of N440K mutation in SARS-CoV-2 spike–ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. Journal of Biomolecular Structure and Dynamics, 1-18.
Magazine, N., Zhang, T., Wu, Y., McGee, M. C., Veggiani, G., & Huang, W. (2022). Mutations and evolution of the SARS-CoV-2 spike protein. Viruses, 14(3), 640.
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A., Gayed, S., Jahun, A., ... & Gupta, R. K. (2021). SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592(7853), 277-282.
Shrestha, L. B., Foster, C., Rawlinson, W., Tedla, N., & Bull, R. A. (2022). Evolution of the SARS‐CoV‐2 omicron variants BA. 1 to BA. 5: Implications for immune escape and transmission. Reviews in Medical Virology, 32(5), e2381.
Cao, Y., Jian, F., Wang, J., Yu, Y., Song, W., Yisimayi, A., ... & Xie, X. S. (2022). Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Nature, 1-3.
Qu, P., Evans, J. P., Zheng, Y. M., Carlin, C., Saif, L. J., Oltz, E. M., ... & Liu, S. L. (2022). Evasion of neutralizing antibody responses by the SARS-CoV-2 BA. 2.75 variant. Cell host & microbe, 30(11), 1518-1526.
Wang, Q., Iketani, S., Li, Z., Liu, L., Guo, Y., Huang, Y., ... & Ho, D. D. (2022). Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell.
Shen, L., Triche, T. J., Bard, J. D., Biegel, J. A., Judkins, A. R., & Gai, X. (2021). Spike Protein NTD mutation G142D in SARS-CoV-2 Delta VOC lineages is associated with frequent back mutations, increased viral loads, and immune evasion. MedRxiv.
Wilhelm, A., Toptan, T., Pallas, C., Wolf, T., Goetsch, U., Gottschalk, R., ... & Widera, M. (2021). Antibody-mediated neutralization of authentic SARS-CoV-2 B. 1.617 variants harboring L452R and T478K/E484Q. Viruses, 13(9), 1693.
Shen, L., Bard, J. D., Triche, T. J., Judkins, A. R., Biegel, J. A., & Gai, X. (2021). Rapidly emerging SARS-CoV-2 B. 1.1. 7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Emerging Microbes & Infections, 10(1), 1293-1299.
Wang, Q., Iketani, S., Li, Z., Liu, L., Guo, Y., Huang, Y., ... & Ho, D. D. (2022). Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell.
Mathema, B., Chen, L., Wang, P., Cunningham, M. H., Mediavilla, J. R., Chow, K. F., ... & Kreiswirth, B. N. (2022). Genomic Epidemiology and Serology Associated with a SARS-CoV-2 R. 1 Variant Outbreak in New Jersey. Mbio, 13(5), e02141-22.
Haslwanter, D., Dieterle, M. E., Wec, A. Z., O’brien, C. M., Sakharkar, M., Florez, C., ... & Jangra, R. K. (2021). A combination of receptor-binding domain and N-terminal domain neutralizing antibodies limits the generation of SARS-CoV-2 spike neutralization-escape mutants. Mbio, 12(5), e02473-21.
Romero, P. E., Dávila-Barclay, A., Salvatierra, G., González, L., Cuicapuza, D., Solís, L., ... & Tsukayama, P. (2021). The emergence of SARS-CoV-2 variant lambda (C. 37) in South America. Microbiology spectrum, 9(2), e00789-21.
Wang, Q., Iketani, S., Li, Z., Guo, Y., Yeh, A. Y., Liu, M., ... & Ho, D. D. (2022). Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA. 2.75. Cell Host & Microbe, 30(11), 1512-1517.
Wang, Q., Li, Z., Ho, J., Guo, Y., Yeh, A. Y., Mohri, H., ... & Ho, D. D. (2022). Resistance of SARS-CoV-2 omicron subvariant BA. 4.6 to antibody neutralisation. The Lancet Infectious Diseases, 22(12), 1666-1668.
Grabowski, F., Kochańczyk, M., & Lipniacki, T. (2021). L18F substrain of SARS-CoV-2 VOC-202012/01 is rapidly spreading in England. MedRxiv.
Washington, N. L., White, S., Barrett, K. M. S., Cirulli, E. T., Bolze, A., & Lu, J. T. (2020). S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US. MedRxiv.
Collier, D. A., De Marco, A., Ferreira, I. A., Meng, B., Datir, R., & Walls, A. C. (2021). SARS-CoV-2 B. 1.1. 7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. MedRxiv.
Zahradník, J., Marciano, S., Shemesh, M., Zoler, E., Harari, D., Chiaravalli, J., ... & Schreiber, G. (2021). SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nature microbiology, 6(9), 1188-1198.
Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., ... & Xie, X. S. (2022). Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature, 602(7898), 657-663.
Kimura, I., Yamasoba, D., Nasser, H., Zahradnik, J., Kosugi, Y., Wu, J., ... & Sato, K. (2022). SARS-CoV-2 spike S375F mutation characterizes the Omicron BA. 1 variant. bioRxiv.
Zhang, W., Shi, K., Geng, Q., Ye, G., Aihara, H., & Li, F. (2022). Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant. Proceedings of the National Academy of Sciences, 119(44), e2206509119.

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