Viral Pandemics Group Publications Page

Publications From the Viral Pandemics Group and Group Members

  1. JM Sasso, BJB Ambrose, R Tenchov, RS Datta, MT Basel, RK DeLong, QA Zhou. The Progress and Promise of RNA Medicine─An Arsenal of Targeted Treatments. J Med Chem. 2022 May 9. doi: 10.1021/acs.jmedchem.2c00024. Epub ahead of print. PMID: 35533054.

  2. Fain, B, and H.M. Dobrovolny, GPU acceleration and data fitting: Agent-based models of viral infections can now be parameterized in hours, Journal of Computational Science, https://doi.org/10.1016/j.jocs.2022.101662

  3. Dale Larie, Gary An, Robert Chase Cockrell, Preparing for the next COVID: Deep Reinforcement Learning trained Artificial Intelligence discovery of multi-modal immunomodulatory control of systemic inflammation in the absence of effective anti-microbials http://dx.doi.org/10.1101/2022.02.17.480940
  4. Gary An, Specialty Grand Challenge: What it will take to cross the Valley of Death: Translational Systems Biology, “True” Precision Medicine, Medical Digital Twins, Artificial Intelligence and In Silico Clinical trials (Provisionally accepted, pending final quality checks) https://www.frontiersin.org/articles/10.3389/fsysb.2022.901159/ful
  5. Pinky, L., and H.M, Dobrovolny, Epidemiological consequences of viral interference: A mathematical modeling study of two interacting viruses, Frontiers in Microbiology 13:822606, March 2022, https://www.frontiersin.org/articles/10.3389/fmicb.2022.830423/full
  6. Rita M C de Almeida, Gilberto L Thomas, James A Glazier, Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection, NAR Genomics and Bioinformatics, Volume 4, Issue 1, March 2022, lqac020, https://doi.org/10.1093/nargab/lqac020
  7. Karr J, Malik-Sheriff RS, Osborne J, Gonzalez-Parra G, Forgoston E, Bowness R, Liu Y, Thompson R, Garira W, Barhak J, Rice J, Torres M, Dobrovolny HM, Tang T, Waites W, Glazier JA, Faeder JR and Kulesza A (2022) Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility. Front. Syst. Biol. 2:822606. doi: 10.3389/fsysb.2022.822606
  8. Ferrari Gianlupi, J.; Mapder, T.; Sego, T.J.; Sluka, J.P.; Quinney, S.K.; Craig, M.; Stratford, R.E., Jr.; Glazier, J.A. "Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2". Viruses 2022, 14, 605. https://doi.org/10.3390/v14030605
  9. Larie D, An G, Cockrell RC. "Preparing for the next COVID: Deep Reinforcement Learning trained Artificial Intelligence discovery of multi-modal immunomodulatory control of systemic inflammation in the absence of effective anti-microbials." Preprint, Feb. 18, 2022. https://www.biorxiv.org/content/10.1101/2022.02.17.480940v1.
  10. Waites W, Cavaliere M, Danos V, Datta R, Eggo RM, Hallett TB, Manheim D,  Panovska-Griffiths J, Russell TW, Zarnitsyna VI. "Compositional modelling of immune response and virus transmission dynamics." https://arxiv.org/abs/2111.02510.
  11. Sego TJ, Mochan ED, Ermentrout GB, Glazier JA. "A multiscale multicellular spatiotemporal model of local influenza infection and immune response." J Theor Biol. 2021 Sep 27;532:110918. doi: 10.1016/j.jtbi.2021.110918. Epub ahead of print. PMID: 34592264; PMCID: PMC8478073.
  12. Sego TJ, Aponte-Serrano JO, Gianlupi JF, Glazier JA. "Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection". BMC Biol. 2021 Sep 8;19(1):196. PMID: 34496857. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01115-z
  13. Veronika I Zarnitsyna, Juliano Ferrari Gianlupi, Amit Hagar, TJ Sego, James A Glazier. "Advancing therapies for viral infections using mechanistic computational models of the dynamic interplay between the virus and host immune response." Current Opinion in Virology, 50, October 2021, Pages 103-109. https://authors.elsevier.com/a/1ddta6hO9tQJED
  14. Cockrell, C.; An, G. "Comparative Computational Modeling of the Bat and Human Immune Response to Viral Infection with the Comparative BiologyImmune Agent Based Model." Viruses 2021, 13, 1620. https://doi.org/10.3390/v13081620.
  15. Sarah M Bartsch, Patrick T Wedlock, Kelly J O’Shea, Sarah N Cox, Ulrich Strych, Jennifer B Nuzzo, Marie C Ferguson, Maria Elena Bottazzi, Sheryl S Siegmund, Peter J Hotez, Bruce Y Lee, Lives and Costs Saved by Expanding and Expediting Coronavirus Disease 2019 Vaccination, The Journal of Infectious Diseases, Volume 224, Issue 6, 15 September 2021, Pages 938–948, https://academic.oup.com/jid/article/224/6/938/6267841
  16. Laubenbacher R, Sluka JP, Glazier JA. Using digital twins in viral infection. Science. 2021 Mar 12;371(6534):1105-1106. doi: 10.1126/science.abf3370. PMID: 33707255. https://science-sciencemag-org.proxyiub.uits.iu.edu/content/371/6534/1105
  17. Masison, J., J. Beezley, Y. Mei, H. a. L. Ribeiro, A. C. Knapp, L. Sordo Vieira, B. Adhikari,  Y. Scindia, M. Grauer, B. Helba,W. Schroeder, B. Mehrad,  R. Laubenbacher. A Modular Computational Framework for Medical Digital Twins. Proceedings of the National Academy of Sciences 118, no. 20 (May 18, 2021). https://doi.org/10.1073/pnas.2024287118
  18. Sego TJ, Aponte-Serrano JO, Ferrari Gianlupi J, Heaps SR, Breithaupt K, Brusch L, Osborne JM, Quardokus EM, Plemper RK, Glazier JA. A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness, bioRxiv 2020.04.27.064139; doi: https://doi.org/10.1101/2020.04.27.064139
  19. Getz M, Wang Y, An G, Becker A, Cockrell C, Collier N, Craig M, Davis CL, Faeder J, Ford Versypt AN, Ferrari Gianlupi J, Glazier JA, Hamis S, Heiland R, Hillen T, Hou D, Aminul Islam M, Jenner A, Kurtoglu F, Liu B, Macfarlane F, Maygrundter P, Morel PA, Narayanan A, Ozik J, Pienaar E, Rangamani P, Shoemaker JE, Smith AM, Macklin P. Rapid community-driven development of a SARS-CoV-2 tissue simulator, bioRxiv 2020.04.02.019075; doi: https://doi.org/10.1101/2020.04.02.019075
  20. de Almeida RMC, Thomas GL, Glazier JA, Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection, bioRxiv 2020.06.16.155267; doi: https://doi.org/10.1101/2020.06.16.155267
  21. Jessie B, Dobrovolny HM, The role of syncytia during viral infections, 2021, Journal of Theoretical Biology, 525:110749, doi:10.1016/j.jtbi.2021.110749
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