Future Pandemics: Primer Set Design and Analysis for Specific Viruses and Variants
This study presents an innovative approach using artificial intelligence (AI) to design primers for the rapid and accurate detection of viruses (e.g. mpox and SARS-CoV-2). Leveraging evolutionary algorithms, we developed primer sets with high specificity and sensitivity, validated in silico and in laboratory settings.
Perez-Romero, C. A., Mendoza-Maldonado, L., Tonda, A., Coz, E., Tabeling, P., Vanhomwegen, J., MacSharry, J., Szafran, J., Bobadilla-Morales, L., Corona-Rivera, A., Claassen, E., Garssen, J., Kraneveld, A. D., & Lopez-Rincon, A. (2023). An Innovative AI-based primer design tool for precise and accurate detection of SARS-CoV-2 variants of concern. Scientific Reports, 13(1), Article 15782. https://doi.org/10.1038/s41598-023-42348-y
Lopez-Rincon, A., Tonda, A., Mendoza-Maldonado, L., Mulders, D. G. J. C., Molenkamp, R., Perez-Romero, C. A., Claassen, E., Garssen, J., & Kraneveld, A. D. (2021). Classification and specific primer design for accurate detection of SARS-CoV-2 using deep learning. Scientific Reports, 11(1), 1-11. Article 947. https://doi.org/10.1038/s41598-020-80363-5
Mouhrim, N., Tonda, A., Rodríguez-Guerra, I., Kraneveld, A. D., & Rincon, A. L. (2022). An evolutionary approach to the discretization of gene expression profiles to predict the severity of COVID-19. In J. E. Fieldsend (Ed.), GECCO '22: Proceedings of the Genetic and Evolutionary Computation Conference Companion (pp. 731-734). Association for Computing Machinery (ACM). https://doi.org/10.1145/3520304.3529001
https://dspace.library.uu.nl/bitstream/handle/1874/424189/3520304.3529001.pdf?sequence=1
Rincon, A. L., Romero, C. A. P., Maldonado, L. M., Claassen, E., Garssen, J., Kraneveld, A. D., & Tonda, A. (2021). Design of specific primer sets for SARS-CoV-2 variants using evolutionary algorithms. In F. Chicano (Ed.), GECCO '21: Proceedings of the Genetic and Evolutionary Computation Conference (pp. 982-990). Association for Computing Machinery (ACM). https://doi.org/10.1145/3449639.3459359
Awards
- 2022: Silver Medal Award at the HUMIES Awards for Human-Competitive Results. Project: Detection of SARS-CoV-2 with EAs. Genetic and Evolutionary Computation Conference (GECCO) conference.
General Public:
- L. Heida, Genetische code sars-cov-2 snel op te sporen via deep-learning, Engineeringnet, 2021.https://engineeringnet.be/nl/nieuws/item/17833
- M. Koopmans, Koopmans: ‘britse variant kan zich snel uitbreiden in nederland’, NRC, 2021.https://www.nrc.nl/nieuws/2021/01/07/koopmans-britse-variant-kan-zich-snel-uitbreiden-in-nederland-a4026637
- UDLAP, Egresado udlap hace investigación sobre covid-19, e-Consulta, 2021.https://www.e-consulta.com/nota/2021-07-13/universidades/egresado-udlap-hace-investigacion-sobre-covid-19
- J. Spinhoven, A. Lopez-Rincon, and A. Kraneveld, Corona-onderzoek: Geen tijd te verliezen, het belang van open science tijdens een pandemie, Surf Magazine, 2020, pp. 18–19
https://www.surf.nl/files/2020-12/201001-surf-magazine_2020-nr04.pdf