My research focuses on development, analysis and validation of mathematical models that describe immune system responses to viral diseases such as human immunodeficiency virus, hepatitis B virus, dengue virus and equine infectious anemia virus. Besides modeling virus-host interactions, I am investigating possible homeostatic mechanisms that regulate lymphocyte population size and T cell receptor diversity, the immune deficiencies that lead to diabetes, and the use of dynamical systems to model archeological data. The mathematical questions associated with my research range from the study of existence and positivity of solutions of systems of ordinary and delayed differential equations, to conducting local and global stability analysis of steady state solutions, to determining conditions for the emergence of bi-stable solutions, to optimization techniques involved in data fitting, to analysis of the sensitivity of models to changes in parameters and errors in data measurements, and finally, to questions regarding model validation. Biologically, I aim to determine the individual and combined contributions of cellular and antibody immune responses in protection against viral infections, the host-virus mechanisms responsible for transitions from acute to chronic disease, and the determination of the values of unknown parameters.
National Institutes of Health, National Institute of General Medical Sciences
People: Achla Marathe, Stanca Ciupe, Jiangzhuo Chen, Kaja Abbas, Gloria Kang
2014 – 2020 Continue Reading Systems Analysis of Social Pathways of Epidemics to Reduce Health Disparities
Persinger RD, Kuchinsky SC, Cereghino C, Murphy QM, Liyanage YR, Tuncer N, Ciupe SM, Duggal NK. (2026). North American Culex pipiens mosquitoes are competent for Usutu virus transmission. Npj viruses, 4(1)
Afrin N, Ciupe SM, Conway JM, Gulbudak H. (2025). Bistability between acute and chronic states in a Model of Hepatitis B Virus Dynamics. Mathematical biosciences
Castellano K, Saucedo O, Ciupe SM. (2025). Investigation of a two-patch within-host model of hepatitis B viral infection. ArXiv
Tuncer N, Martcheva M, Ciupe SM. (2025). Structural and practical identifiability of within-host models of virus dynamics - a review. Current opinion in systems biology, (42)
Phan T, Brozak S, Pell B, Ciupe SM, Ke R, Ribeiro RM, Gitter A, Mena KD, Perelson AS, Kuang Y, Wu F. (2025). Post-recovery viral shedding shapes wastewater-based epidemiological inferences. Communications medicine, 5(1)
Heitzman-Breen N, Golden J, Wang Y, Weger-Lucarelli J, Ciupe SM. (2025). The role of nutrition in virus dynamics in vector-borne viral infections. Journal of theoretical biology
Tuncer N, Liyanage YR, Murphy QM, Persinger RD, Duggal NK, Ciupe SM. (2025). From Bird Viremia to Bird Surveillance: Identifiability in a Multiscale Vector-Borne Model of Usutu Virus Infection. bioRxiv : the preprint server for biology
Castellano S, Saucedo S, Ciupe SM. (2025). Investigation of a Two-Patch Within-Host Model of Hepatitis B Viral Infection. Bulletin of mathematical biology, 87(12)
Murphy QM, Lewis GK, Sajadi MM, Forde JE, Ciupe SM. (2024). Understanding antibody magnitude and durability following vaccination against SARS-CoV-2. Mathematical biosciences, (376)
Tehrani ZR, Habibzadeh P, Flinko R, Chen H, Abbasi A, Yared JA, Ciupe SM, Lewis GK, Sajadi MM. (2024). Deficient Generation of Spike-Specific Long-Lived Plasma Cells in the Bone Marrow After Severe Acute Respiratory Syndrome Coronavirus 2 Infection. The Journal of infectious diseases, 230(1)
Phan T, Brozak S, Pell B, Ciupe SM, Ke R, Ribeiro RM, Gitter A, Mena KD, Perelson AS, Kuang Y, Wu F. (2023). Prolonged viral shedding from noninfectious individuals confounds wastewater-based epidemiology. medRxiv : the preprint server for health sciences
Ciupe SM, Boribong BP, Kadelka S, Jones CN. (2021). Bistable Mathematical Model of Neutrophil Migratory Patterns After LPS-Induced Epigenetic Reprogramming. Frontiers in genetics, (12)
Forde JE, Ciupe SM. (2021). Modeling the Influence of Vaccine Administration on COVID-19 Testing Strategies. Viruses, 13(12)
Forde JE, Ciupe SM. (2021). Quantification of the Tradeoff between Test Sensitivity and Test Frequency in a COVID-19 Epidemic-A Multi-Scale Modeling Approach. Viruses, 13(3)
Ciupe SM, Vaidya NK, Forde JE. (2021). Early events in hepatitis B infection: the role of inoculum dose. Proceedings. Biological sciences, 288(1944)
Kadelka S, Dahari H, Ciupe SM. (2021). Understanding the antiviral effects of RNAi-based therapy in HBeAg-positive chronic hepatitis B infection. Scientific reports, 11(1)
Erwin S, Childs LM, Ciupe SM. (2020). Mathematical model of broadly reactive plasma cell production. Scientific reports, 10(1)
Kaderali L, Theis F, Ganusov VV, Ciupe SM, Mehr R, Ribeiro RM, Hernandez-Vargas EA. (2019). Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine. Frontiers in microbiology, (9)
Kadelka S, Ciupe SM. (2019). Mathematical investigation of HBeAg seroclearance. Mathematical biosciences and engineering : MBE, 16(6)
Ciupe SM. (2018). Modeling the dynamics of hepatitis B infection, immunity, and drug therapy. Immunological reviews, 285(1)
Nikin-Beers R, Blackwood JC, Childs LM, Ciupe SM. (2018). Unraveling within-host signatures of dengue infection at the population level. Journal of theoretical biology, (446)
Kadelka S, Boribong BP, Li L, Ciupe SM. (2018). Modeling the Bistable Dynamics of the Innate Immune System. Bulletin of mathematical biology, 81(1)
Ciupe SM, Miller CJ, Forde JE. (2018). A Bistable Switch in Virus Dynamics Can Explain the Differences in Disease Outcome Following SIV Infections in Rhesus Macaques. Frontiers in microbiology, (9)
Ciupe SM, Heffernan JM. (2017). In-host modeling. Infectious Disease Modelling, 2(2)
Dorratoltaj N, Nikin-Beers R, Ciupe SM, Eubank SG, Abbas KM. (2017). Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models. PeerJ, (5)
Nikin-Beers R, Ciupe SM. (2018). Modelling original antigenic sin in dengue viral infection. Mathematical medicine and biology : a journal of the IMA, 35(2)
Carracedo Rodriguez A, Chung M, Ciupe SM. (2017). Understanding the Complex Patterns Observed during Hepatitis B Virus Therapy. Viruses, 9(5)
Erwin S, Ciupe SM. (2017). Germinal center dynamics during acute and chronic infection. Mathematical biosciences and engineering : MBE, 14(3)
Verma M, Erwin S, Abedi V, Hontecillas R, Hoops S, Leber A, Bassaganya-Riera J, Ciupe SM. (2017). Modeling the Mechanisms by Which HIV-Associated Immunosuppression Influences HPV Persistence at the Oral Mucosa. PloS one, 12(1)
Leber A, Abedi V, Hontecillas R, Viladomiu M, Hoops S, Ciupe S, Caughman J, Andrew T, Bassaganya-Riera J. (2016). Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection. Journal of theoretical biology, (398)
Nikin-Beers R, Ciupe SM. (2015). The role of antibody in enhancing dengue virus infection. Mathematical biosciences, (263)
Ciupe SM, Ribeiro RM, Perelson AS. (2014). Antibody responses during hepatitis B viral infection. PLoS computational biology, 10(7)
Ciupe SM. (2015). Mathematical model of multivalent virus-antibody complex formation in humans following acute and chronic HIV infections. Journal of mathematical biology, 71(3)
Ciupe SM, Schwartz EJ. (2014). Understanding virus-host dynamics following EIAV infection in SCID horses. Journal of theoretical biology, (343)
Ciupe SM, Devlin BH, Markert ML, Kepler TB. (2013). Quantification of total T-cell receptor diversity by flow cytometry and spectratyping. BMC immunology, (14)
Forde J, Volpe JM, Ciupe SM. (2012). Latently infected cell activation: a way to reduce the size of the HIV reservoir?. Bulletin of mathematical biology, 74(7)
Ciupe SM, Hews S. (2012). Mathematical models of e-antigen mediated immune tolerance and activation following prenatal HBV infection. PloS one, 7(7)
Ciupe SM, De Leenheer P, Kepler TB. (2011). Paradoxical suppression of poly-specific broadly neutralizing antibodies in the presence of strain-specific neutralizing antibodies following HIV infection. Journal of theoretical biology, 277(1)
Ciupe SM, Devlin BH, Markert ML, Kepler TB. (2009). The dynamics of T-cell receptor repertoire diversity following thymus transplantation for DiGeorge anomaly. PLoS computational biology, 5(6)
Nelson P, Smith N, Ciupe S, Zou W, Omenn GS, Pietropaolo M. (2009). Modeling dynamic changes in type 1 diabetes progression: quantifying beta-cell variation after the appearance of islet-specific autoimmune responses. Mathematical biosciences and engineering : MBE, 6(4)
Ciupe SM, Ribeiro RM, Nelson PW, Dusheiko G, Perelson AS. (2007). The role of cells refractory to productive infection in acute hepatitis B viral dynamics. Proceedings of the National Academy of Sciences of the United States of America, 104(12)
Ciupe SM, Ribeiro RM, Nelson PW, Perelson AS. (2007). Modeling the mechanisms of acute hepatitis B virus infection. Journal of theoretical biology, 247(1)
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