{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:09:40Z","timestamp":1778058580113,"version":"3.51.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,10,5]],"date-time":"2021-10-05T00:00:00Z","timestamp":1633392000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Silico Trial for Vaccine Development","award":["777123"],"award-info":[{"award-number":["777123"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The COVID-19 pandemic has highlighted the need to come out with quick interventional solutions that can now be obtained through the application of different bioinformatics software to actively improve the success rate. Technological advances in fields such as computer modeling and simulation are enriching the discovery, development, assessment and monitoring for better prevention, diagnosis, treatment and scientific evidence generation of specific therapeutic strategies. The combined use of both molecular prediction tools and computer simulation in the development or regulatory evaluation of a medical intervention, are making the difference to better predict the efficacy and safety of new vaccines. An integrated bioinformatics pipeline that merges the prediction power of different software that act at different scales for evaluating the elicited response of human immune system against every pathogen is proposed. As a working example, we applied this problem solving protocol to predict the cross-reactivity of pre-existing vaccination interventions against SARS-CoV-2.<\/jats:p>","DOI":"10.1093\/bib\/bbab403","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T11:20:51Z","timestamp":1631100051000},"source":"Crossref","is-referenced-by-count":28,"title":["A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets"],"prefix":"10.1093","volume":"23","author":[{"given":"Giulia","family":"Russo","sequence":"first","affiliation":[{"name":"Department of Drug and Health Sciences, University of Catania, Catania, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina","family":"Di Salvatore","sequence":"additional","affiliation":[{"name":"Department of Drug and Health Sciences, University of Catania, Catania, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppe","family":"Sgroi","sequence":"additional","affiliation":[{"name":"Department of Drug and Health Sciences, University of Catania, Catania, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppe Alessandro","family":"Parasiliti Palumbo","sequence":"additional","affiliation":[{"name":"Department of Drug and Health Sciences, University of Catania, Catania, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pedro A","family":"Reche","sequence":"additional","affiliation":[{"name":"Department of Drug and Health Sciences, University of Catania, Catania, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1668-3320","authenticated-orcid":false,"given":"Francesco","family":"Pappalardo","sequence":"additional","affiliation":[{"name":"Department of Drug and Health Sciences, University of Catania, Catania, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,10,5]]},"reference":[{"key":"2022011921123546800_ref1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/s41577-021-00522-1","article-title":"The first 12 months of COVID-19: a timeline of immunological insights","volume":"21","author":"Carvalho","year":"2021","journal-title":"Nat Rev Immunol"},{"key":"2022011921123546800_ref2","doi-asserted-by":"crossref","first-page":"111769","DOI":"10.1016\/j.fct.2020.111769","article-title":"SARS-CoV-2 pathophysiology and its clinical implications: an integrative overview of the pharmacotherapeutic management of COVID-19","volume":"146","author":"Tsatsakis","year":"2020","journal-title":"Food Chem Toxicol"},{"key":"2022011921123546800_ref3","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.2217\/fmb-2020-0110","article-title":"Pathogenesis, clinical manifestations and complications of coronavirus disease 2019 (COVID-19)","volume":"15","author":"Kordzadeh-Kermani","year":"2020","journal-title":"Future Microbiol"},{"key":"2022011921123546800_ref4","doi-asserted-by":"crossref","first-page":"5475","DOI":"10.3390\/ijms21155475","article-title":"SARS-CoV-2 and the nervous system: from clinical features to molecular mechanisms","volume":"21","author":"Pennisi","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2022011921123546800_ref5","volume-title":"Science","author":"Davies","year":"2021"},{"key":"2022011921123546800_ref6","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/s41586-021-03412-7","article-title":"Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies","volume":"593","author":"Collier","year":"2021","journal-title":"Nature"},{"key":"2022011921123546800_ref7","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/s41418-020-00720-9","article-title":"COVID-19 Commission of Accademia Nazionale dei Lincei R. 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