{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:10:57Z","timestamp":1772165457555,"version":"3.50.1"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"S17","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,12,14]],"date-time":"2020-12-14T00:00:00Z","timestamp":1607904000000},"content-version":"vor","delay-in-days":13,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>In silico trials are showing to be powerful weapons in predicting immune responses of potential candidate vaccines. Here, UISS has been extended to be used as an in silico trial platform to speed-up and drive the discovery pipeline of vaccine against SARS-CoV-2.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-020-03872-0","type":"journal-article","created":{"date-parts":[[2020,12,13]],"date-time":"2020-12-13T20:02:38Z","timestamp":1607889758000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform"],"prefix":"10.1186","volume":"21","author":[{"given":"Giulia","family":"Russo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marzio","family":"Pennisi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Epifanio","family":"Fichera","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Santo","family":"Motta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppina","family":"Raciti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Viceconti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Pappalardo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,12,14]]},"reference":[{"key":"3872_CR1","unstructured":"World Health Organization. Novel Coronavirus (2019-nCoV) situation reports. 2020."},{"key":"3872_CR2","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","volume":"579","author":"F Wu","year":"2020","unstructured":"Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265\u20139.","journal-title":"Nature"},{"key":"3872_CR3","doi-asserted-by":"publisher","first-page":"66","DOI":"10.15698\/cst2020.04.216","volume":"4","author":"D Raoult","year":"2020","unstructured":"Raoult D, Zumla A, Locatelli F, Ippolito G, Kroemer G. Coronavirus infections: epidemiological, clinical and immunological features and hypotheses. Cell Stress. 2020;4:66\u201375.","journal-title":"Cell Stress"},{"key":"3872_CR4","doi-asserted-by":"publisher","first-page":"S88","DOI":"10.1038\/nm1143","volume":"10","author":"JSM Peiris","year":"2004","unstructured":"Peiris JSM, Guan Y, Yuen KY. Severe acute respiratory syndrome. Nat Med. 2004;10:S88\u201397.","journal-title":"Nat Med"},{"key":"3872_CR5","doi-asserted-by":"publisher","first-page":"210","DOI":"10.3201\/eid1002.030730","volume":"10","author":"J Wu","year":"2004","unstructured":"Wu J, Xu F, Zhou W, Feikin DR, Lin C-Y, He X, et al. Risk factors for SARS among persons without known contact with SARS patients, Beijing, China. Emerg Infect Dis. 2004;10:210\u20136. https:\/\/doi.org\/10.3201\/eid1002.030730.","journal-title":"Emerg Infect Dis"},{"key":"3872_CR6","doi-asserted-by":"publisher","first-page":"244","DOI":"10.3390\/v12020244","volume":"12","author":"J Xu","year":"2020","unstructured":"Xu J, Zhao S, Teng T, Abdalla AE, Zhu W, Xie L, et al. Systematic comparison of two animal-to-human transmitted human coronaviruses: SARS-CoV-2 and SARS-CoV. Viruses. 2020;12:244.","journal-title":"Viruses"},{"key":"3872_CR7","doi-asserted-by":"publisher","first-page":"105924","DOI":"10.1016\/j.ijantimicag.2020.105924","volume":"55","author":"CC Lai","year":"2020","unstructured":"Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges. Int J Antimicrob Agents. 2020;55:105924.","journal-title":"Int J Antimicrob Agents"},{"key":"3872_CR8","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa449","author":"X Chen","year":"2020","unstructured":"Chen X, Zhao B, Qu Y, Chen Y, Xiong J, Feng Y, et al. Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely associated with drastically elevated interleukin 6 (IL-6) level in critically ill COVID-19 patients. medRxiv. 2020. https:\/\/doi.org\/10.1093\/cid\/ciaa449.","journal-title":"medRxiv"},{"key":"3872_CR9","doi-asserted-by":"publisher","first-page":"2202","DOI":"10.1172\/JCI137647","volume":"130","author":"SF Pedersen","year":"2020","unstructured":"Pedersen SF, Ho Y-C. SARS-CoV-2: a storm is raging. J Clin Investig. 2020;130:2202\u20135. https:\/\/doi.org\/10.1172\/JCI137647.","journal-title":"J Clin Investig"},{"key":"3872_CR10","doi-asserted-by":"publisher","first-page":"5475","DOI":"10.3390\/ijms21155475","volume":"21","author":"M Pennisi","year":"2020","unstructured":"Pennisi M, Lanza G, Falzone L, Fisicaro F, Ferri R, Bella R. SARS-CoV-2 and the nervous system: from clinical features to molecular mechanisms. Int J Mol Sci. 2020;21:5475.","journal-title":"Int J Mol Sci"},{"key":"3872_CR11","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1007\/s11886-020-01327-9","volume":"22","author":"MR Aryal","year":"2020","unstructured":"Aryal MR, Gosain R, Donato A, Pathak R, Bhatt VR, Katel A, et al. Venous thromboembolism in COVID-19: towards an ideal approach to thromboprophylaxis, screening, and treatment. Curr Cardiol Rep. 2020;22:52.","journal-title":"Curr Cardiol Rep"},{"key":"3872_CR12","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.3390\/cancers12082237","volume":"12","author":"S Vivarelli","year":"2020","unstructured":"Vivarelli S, Falzone L, Grillo CM, Scandurra G, Torino F, Libra M. Cancer management during covid-19 pandemic: Is immune checkpoint inhibitors-based immunotherapy harmful or beneficial? Cancers. 2020;12:2237.","journal-title":"Cancers"},{"key":"3872_CR13","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1016\/j.cmi.2020.03.025","volume":"26","author":"MR Capobianchi","year":"2020","unstructured":"Capobianchi MR, Rueca M, Messina F, Giombini E, Carletti F, Colavita F, et al. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy. Clin Microbiol Infect. 2020;26:954\u20136.","journal-title":"Clin Microbiol Infect"},{"key":"3872_CR14","doi-asserted-by":"publisher","first-page":"e1003565","DOI":"10.1371\/journal.ppat.1003565","volume":"9","author":"EC Smith","year":"2013","unstructured":"Smith EC, Blanc H, Vignuzzi M, Denison MR. Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics. PLoS Pathog. 2013;9:e1003565.","journal-title":"PLoS Pathog"},{"key":"3872_CR15","doi-asserted-by":"publisher","first-page":"271.e8","DOI":"10.1016\/j.cell.2020.02.052","volume":"181","author":"M Hoffmann","year":"2020","unstructured":"Hoffmann M, Kleine-Weber H, Schroeder S, Kr\u00fcger N, Herrler T, Erichsen S, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020;181:271.e8-280.e8.","journal-title":"Cell"},{"key":"3872_CR16","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1056\/NEJMc2001737","volume":"382","author":"L Zou","year":"2020","unstructured":"Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z, et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med. 2020;382:1177\u20139. https:\/\/doi.org\/10.1056\/NEJMc2001737.","journal-title":"N Engl J Med"},{"key":"3872_CR17","first-page":"1","volume":"52","author":"KF Amanat Fatima","year":"2020","unstructured":"Amanat Fatima KF. SARS-CoV-2 vaccines: status report. Cell. 2020;52:1\u20137.","journal-title":"Cell"},{"key":"3872_CR18","doi-asserted-by":"publisher","first-page":"102743","DOI":"10.1016\/j.ebiom.2020.102743","volume":"55","author":"E Kim","year":"2020","unstructured":"Kim E, Erdos G, Huang S, Kenniston TW, Balmert SC, Carey CD, et al. Microneedle array delivered recombinant coronavirus vaccines: immunogenicity and rapid translational development. EBioMedicine. 2020;55:102743.","journal-title":"EBioMedicine"},{"key":"3872_CR19","doi-asserted-by":"publisher","first-page":"623","DOI":"10.3390\/jcm9030623","volume":"9","author":"J Pang","year":"2020","unstructured":"Pang J, Wang MX, Ang IYH, Tan SHX, Lewis RF, Chen JI-P, et al. Potential rapid diagnostics, vaccine and therapeutics for 2019 novel coronavirus (2019-nCoV): a systematic review. J Clin Med. 2020;9:623.","journal-title":"J Clin Med"},{"key":"3872_CR20","doi-asserted-by":"publisher","first-page":"2657","DOI":"10.3390\/ijms21072657","volume":"21","author":"Y-F Tu","year":"2020","unstructured":"Tu Y-F, Chien C-S, Yarmishyn AA, Lin Y-Y, Luo Y-H, Lin Y-T, et al. A review of SARS-CoV-2 and the ongoing clinical trials. Int J Mol Sci. 2020;21:2657.","journal-title":"Int J Mol Sci"},{"key":"3872_CR21","first-page":"1","volume":"4","author":"AA Rabaan","year":"2020","unstructured":"Rabaan AA, Al-ahmed SH, Sah R, Tiwari R, Iqbal M, Patel SK, et al. SARS-CoV-2\/COVID-19 and advances in developing potential therapeutics and vaccines to counter this emerging pandemic virus\u2014a review. Ann Clin Microbiol Antimicrob. 2020;4:1\u201346.","journal-title":"Ann Clin Microbiol Antimicrob"},{"key":"3872_CR22","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1089\/dna.2007.0616","volume":"26","author":"AN Zakhartchouk","year":"2007","unstructured":"Zakhartchouk AN, Viswanathan S, Moshynskyy I, Petric M, Babiuk LA. Optimization of a DNA vaccine against SARS. DNA Cell Biol. 2007;26:721\u20136.","journal-title":"DNA Cell Biol"},{"key":"3872_CR23","doi-asserted-by":"publisher","first-page":"153","DOI":"10.3390\/vaccines8020153","volume":"8","author":"J Zhang","year":"2020","unstructured":"Zhang J, Zeng H, Gu J, Li H, Zheng L, Zou Q. Progress and prospects on vaccine development against SARS-CoV-2. Vaccines. 2020;8:153.","journal-title":"Vaccines"},{"key":"3872_CR24","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1038\/s41541-020-0170-0","volume":"5","author":"W Shang","year":"2020","unstructured":"Shang W, Yang Y, Rao Y, Rao X. The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines. NPJ Vaccines. 2020;5:18.","journal-title":"NPJ Vaccines"},{"key":"3872_CR25","doi-asserted-by":"crossref","unstructured":"Chen X, Li R, Pan Z, Qian C, Yang Y, You R, et al. Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin converting enzyme 2 receptor; 2020.","DOI":"10.1101\/2020.04.06.20055475"},{"key":"3872_CR26","doi-asserted-by":"publisher","DOI":"10.31219\/osf.io\/sbgy3","author":"PA Reche","year":"2020","unstructured":"Reche PA. Cross-reactive immunity from combination DTP vaccines could protect against COVID-19. OSF Prepr. 2020. https:\/\/doi.org\/10.31219\/osf.io\/sbgy3.","journal-title":"OSF Prepr"},{"key":"3872_CR27","doi-asserted-by":"publisher","first-page":"1699","DOI":"10.1093\/bib\/bby043","volume":"20","author":"F Pappalardo","year":"2019","unstructured":"Pappalardo F, Russo G, Tshinanu FM, Viceconti M. In silico clinical trials: concepts and early adoptions. Brief Bioinform. 2019;20:1699\u2013708. https:\/\/doi.org\/10.1093\/bib\/bby043.","journal-title":"Brief Bioinform"},{"key":"3872_CR28","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2020.01.011","author":"M Viceconti","year":"2020","unstructured":"Viceconti M, Pappalardo F, Rodriguez B, Horner M, Bischoff J, Musuamba Tshinanu F. In silico trials: Verification, validation and uncertainty quantification of predictive models used in the regulatory evaluation of biomedical products. Methods. 2020. https:\/\/doi.org\/10.1016\/j.ymeth.2020.01.011.","journal-title":"Methods"},{"key":"3872_CR29","doi-asserted-by":"publisher","first-page":"2465","DOI":"10.1038\/s41598-018-20737-y","volume":"8","author":"A Carlier","year":"2018","unstructured":"Carlier A, Vasilevich A, Marechal M, de Boer J, Geris L. In silico clinical trials for pediatric orphan diseases. Sci Rep. 2018;8:2465. https:\/\/doi.org\/10.1038\/s41598-018-20737-y.","journal-title":"Sci Rep"},{"key":"3872_CR30","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1002\/psp4.12018","volume":"4","author":"J Cosgrove","year":"2015","unstructured":"Cosgrove J, Butler J, Alden K, Read M, Kumar V, Cucurull-Sanchez L, et al. Agent-based modeling in systems pharmacology. CPT Pharmacometr Syst Pharmacol. 2015;4:615\u201329.","journal-title":"CPT Pharmacometr Syst Pharmacol"},{"key":"3872_CR31","doi-asserted-by":"publisher","first-page":"7280","DOI":"10.1073\/pnas.082080899","volume":"99","author":"E Bonabeau","year":"2002","unstructured":"Bonabeau E. Agent-based modeling: methods and techniques for simulating human systems. Proc Natl Acad Sci USA. 2002;99:7280\u20137.","journal-title":"Proc Natl Acad Sci USA"},{"key":"3872_CR32","doi-asserted-by":"publisher","first-page":"2672","DOI":"10.1093\/bioinformatics\/btw293","volume":"32","author":"F Pappalardo","year":"2016","unstructured":"Pappalardo F, Fichera E, Paparone N, Lombardo A, Pennisi M, Russo G, et al. A computational model to predict the immune system activation by citrus-derived vaccine adjuvants. Bioinformatics. 2016;32:2672\u201380. https:\/\/doi.org\/10.1093\/bioinformatics\/btw293.","journal-title":"Bioinformatics"},{"key":"3872_CR33","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1186\/s12859-017-1961-9","volume":"18","author":"M Pennisi","year":"2017","unstructured":"Pennisi M, Russo G, Ravalli S, Pappalardo F. Combining agent based-models and virtual screening techniques to predict the best citrus-derived vaccine adjuvants against human papilloma virus. BMC Bioinform. 2017;18:544. https:\/\/doi.org\/10.1186\/s12859-017-1961-9.","journal-title":"BMC Bioinform"},{"key":"3872_CR34","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1186\/s12859-019-3045-5","volume":"20","author":"M Pennisi","year":"2019","unstructured":"Pennisi M, Russo G, Sgroi G, Bonaccorso A, Parasiliti Palumbo GA, Fichera E, et al. Predicting the artificial immunity induced by RUTI\u00ae vaccine against tuberculosis using universal immune system simulator (UISS). BMC Bioinform. 2019;20:504. https:\/\/doi.org\/10.1186\/s12859-019-3045-5.","journal-title":"BMC Bioinform"},{"key":"3872_CR35","doi-asserted-by":"publisher","first-page":"586","DOI":"10.3390\/cells9030586","volume":"9","author":"F Pappalardo","year":"2020","unstructured":"Pappalardo F, Russo G, Pennisi M, Parasiliti Palumbo GA, Sgroi G, Motta S, et al. The potential of computational modeling to predict disease course and treatment response in patients with relapsing multiple sclerosis. Cells. 2020;9:586. https:\/\/doi.org\/10.3390\/cells9030586.","journal-title":"Cells"},{"key":"3872_CR36","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1080\/14737159.2020.1757437","volume":"20","author":"A Tahamtan","year":"2020","unstructured":"Tahamtan A, Ardebili A. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Expert Rev Mol Diagn. 2020;20:453\u20134.","journal-title":"Expert Rev Mol Diagn"},{"key":"3872_CR37","doi-asserted-by":"publisher","first-page":"957","DOI":"10.3892\/ijmm.2020.4673","volume":"46","author":"L Falzone","year":"2020","unstructured":"Falzone L, Musso N, Gattuso G, Bongiorno D, Palermo CI, Scalia G, et al. Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection. Int J Mol Med. 2020;46:957\u201364.","journal-title":"Int J Mol Med"},{"key":"3872_CR38","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1038\/s41467-020-16256-y","volume":"11","author":"C Wang","year":"2020","unstructured":"Wang C, Li W, Drabek D, Okba NMA, van Haperen R, Osterhaus ADME, et al. A human monoclonal antibody blocking SARS-CoV-2 infection. Nat Commun. 2020;11:2251. https:\/\/doi.org\/10.1038\/s41467-020-16256-y.","journal-title":"Nat Commun"},{"key":"3872_CR39","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/s41586-020-2180-5","volume":"581","author":"J Lan","year":"2020","unstructured":"Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020;581:215\u201320.","journal-title":"Nature"},{"key":"3872_CR40","doi-asserted-by":"publisher","first-page":"2514","DOI":"10.1093\/bioinformatics\/btv172","volume":"31","author":"F Gullo","year":"2015","unstructured":"Gullo F, van der Garde M, Russo G, Pennisi M, Motta S, Pappalardo F, et al. Computational modeling of the expansion of human cord blood CD133+ hematopoietic stem\/progenitor cells with different cytokine combinations. Bioinformatics. 2015;31:2514\u201322. https:\/\/doi.org\/10.1093\/bioinformatics\/btv172.","journal-title":"Bioinformatics"},{"key":"3872_CR41","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.plrev.2016.05.012","volume":"17","author":"MA Ragusa","year":"2016","unstructured":"Ragusa MA, Russo G. ODEs approaches in modeling fibrosis. Phys Life Rev. 2016;17:112\u20133. https:\/\/doi.org\/10.1016\/j.plrev.2016.05.012.","journal-title":"Phys Life Rev"},{"key":"3872_CR42","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.jtbi.2010.01.009","volume":"263","author":"NL Komarova","year":"2010","unstructured":"Komarova NL, Wodarz D. ODE models for oncolytic virus dynamics. J Theor Biol. 2010;263:530\u201343. https:\/\/doi.org\/10.1016\/j.jtbi.2010.01.009.","journal-title":"J Theor Biol"},{"key":"3872_CR43","doi-asserted-by":"publisher","first-page":"1492","DOI":"10.1109\/TCBB.2017.2733529","volume":"15","author":"G Russo","year":"2017","unstructured":"Russo G, Pennisi M, Boscarino R, Pappalardo F. Continuous petri nets and microRNA analysis in melanoma. IEEE\/ACM Trans Comput Biol Bioinform. 2017;15:1492\u20139. https:\/\/doi.org\/10.1109\/TCBB.2017.2733529.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"3872_CR44","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bby118","author":"F Liu","year":"2018","unstructured":"Liu F, Heiner M, Gilbert D. Fuzzy petri nets for modelling of uncertain biological systems. Brief Bioinform. 2018. https:\/\/doi.org\/10.1093\/bib\/bby118.","journal-title":"Brief Bioinform"},{"key":"3872_CR45","doi-asserted-by":"publisher","first-page":"1750072","DOI":"10.1142\/S1793524517500723","volume":"10","author":"C Bianca","year":"2017","unstructured":"Bianca C, Br\u00e9zin L. Modeling the antigen recognition by B-cell and T-cell receptors through thermostatted kinetic theory methods. Int J Biomath. 2017;10:1750072.","journal-title":"Int J Biomath"},{"key":"3872_CR46","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1140\/epjp\/i2015-15159-4","volume":"130","author":"C Bianca","year":"2015","unstructured":"Bianca C, Riposo J. Mimic therapeutic actions against keloid by thermostatted kinetic theory methods. Eur Phys J Plus. 2015;130:159.","journal-title":"Eur Phys J Plus"},{"key":"3872_CR47","doi-asserted-by":"publisher","first-page":"7755","DOI":"10.1158\/0008-5472.CAN-10-0701","volume":"70","author":"A Palladini","year":"2010","unstructured":"Palladini A, Nicoletti G, Pappalardo F, Murgo A, Grosso V, Stivani V, et al. In silico modeling and in vivo efficacy of cancer-preventive vaccinations. Cancer Res. 2010;70:7755\u201363. https:\/\/doi.org\/10.1158\/0008-5472.CAN-10-0701.","journal-title":"Cancer Res"},{"issue":"Suppl 7","key":"3872_CR48","doi-asserted-by":"publisher","first-page":"S13","DOI":"10.1186\/1471-2105-11-S7-S13","volume":"11","author":"M Pennisi","year":"2010","unstructured":"Pennisi M, Pappalardo F, Palladini A, Nicoletti G, Nanni P, Lollini P-L, et al. Modeling the competition between lung metastases and the immune system using agents. BMC Bioinform. 2010;11(Suppl 7):S13. https:\/\/doi.org\/10.1186\/1471-2105-11-S7-S13.","journal-title":"BMC Bioinform"},{"key":"3872_CR49","doi-asserted-by":"publisher","first-page":"e26523","DOI":"10.1371\/journal.pone.0026523","volume":"6","author":"F Pappalardo","year":"2011","unstructured":"Pappalardo F, Forero IM, Pennisi M, Palazon A, Melero I, Motta S. SimB16: modeling induced immune system response against B16-melanoma. PLoS ONE. 2011;6:e26523. https:\/\/doi.org\/10.1371\/journal.pone.0026523.","journal-title":"PLoS ONE"},{"key":"3872_CR50","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1093\/bioinformatics\/btn306","volume":"24","author":"F Pappalardo","year":"2008","unstructured":"Pappalardo F, Musumeci S, Motta S. Modeling immune system control of atherogenesis. Bioinformatics. 2008;24:1715\u201321. https:\/\/doi.org\/10.1093\/bioinformatics\/btn306.","journal-title":"Bioinformatics"},{"key":"3872_CR51","doi-asserted-by":"publisher","first-page":"3176","DOI":"10.3389\/fimmu.2018.03176","volume":"9","author":"TA Patente","year":"2019","unstructured":"Patente TA, Pinho MP, Oliveira AA, Evangelista GCM, Bergami-Santos PC, Barbuto JAM. Human dendritic cells: their heterogeneity and clinical application potential in cancer immunotherapy. Front Immunol. 2019;9:3176. https:\/\/doi.org\/10.3389\/fimmu.2018.03176.","journal-title":"Front Immunol"},{"key":"3872_CR52","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1002\/jmv.25681","volume":"92","author":"Y Chen","year":"2020","unstructured":"Chen Y, Liu Q, Guo D. Emerging coronaviruses: genome structure, replication, and pathogenesis. J Med Virol. 2020;92:418\u201323. https:\/\/doi.org\/10.1002\/jmv.25681.","journal-title":"J Med Virol"},{"key":"3872_CR53","doi-asserted-by":"publisher","first-page":"4412","DOI":"10.1182\/blood-2009-11-255935","volume":"115","author":"D Matheoud","year":"2010","unstructured":"Matheoud D, Perie L, Hoeffel G, Vimeux L, Parent I, Maranon C, et al. Cross-presentation by dendritic cells from live cells induces protective immune responses in vivo. Blood. 2010;115:4412\u201320. https:\/\/doi.org\/10.1182\/blood-2009-11-255935.","journal-title":"Blood"},{"key":"3872_CR54","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/S0140-6736(20)30183-5","volume":"395","author":"C Huang","year":"2020","unstructured":"Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395:497\u2013506. https:\/\/doi.org\/10.1016\/S0140-6736(20)30183-5.","journal-title":"Lancet"},{"key":"3872_CR55","doi-asserted-by":"publisher","first-page":"1266","DOI":"10.3201\/eid2606.200516","volume":"26","author":"J Harcourt","year":"2020","unstructured":"Harcourt J, Tamin A, Lu X, Kamili S, Sakthivel SK, Murray J, et al. Severe acute respiratory syndrome coronavirus 2 from patient with 2019 novel coronavirus disease, United States. Emerg Infect Dis. 2020;26:1266\u201373. https:\/\/doi.org\/10.3201\/eid2606.200516.","journal-title":"Emerg Infect Dis"},{"key":"3872_CR56","doi-asserted-by":"publisher","first-page":"2019","DOI":"10.1016\/S1473-3099(20)30232-2","volume":"2019","author":"Y Liu","year":"2020","unstructured":"Liu Y, Yan L-M, Wan L, Xiang T-X, Le A, Liu J-M, et al. Viral dynamics in mild and severe cases of COVID-19. Lancet Infect Dis. 2020;2019:2019\u201320. https:\/\/doi.org\/10.1016\/S1473-3099(20)30232-2.","journal-title":"Lancet Infect Dis"},{"key":"3872_CR57","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/s41591-020-0819-2","volume":"26","author":"I Thevarajan","year":"2020","unstructured":"Thevarajan I, Nguyen THO, Koutsakos M, Druce J, Caly L, van de Sandt CE, et al. Breadth of concomitant immune responses prior to patient recovery: a case report of non-severe COVID-19. Nat Med. 2020;26:453\u20135. https:\/\/doi.org\/10.1038\/s41591-020-0819-2.","journal-title":"Nat Med"},{"issue":"1026\u20131039","key":"3872_CR58","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1016\/j.cell.2018.12.028","volume":"176","author":"AC Walls","year":"2019","unstructured":"Walls AC, Xiong X, Park Y-J, Tortorici MA, Snijder J, Quispe J, et al. Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell. 2019;176(1026\u20131039):e15. https:\/\/doi.org\/10.1016\/j.cell.2018.12.028.","journal-title":"Cell"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-03872-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-020-03872-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-03872-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,13]],"date-time":"2020-12-13T20:03:02Z","timestamp":1607889782000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-020-03872-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12]]},"references-count":58,"journal-issue":{"issue":"S17","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["3872"],"URL":"https:\/\/doi.org\/10.1186\/s12859-020-03872-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.05.06.080630","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12]]},"assertion":[{"value":"29 October 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 November 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 December 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"527"}}