{"id":19,"date":"2012-09-05T11:22:25","date_gmt":"2012-09-05T15:22:25","guid":{"rendered":"https:\/\/people.clas.ufl.edu\/template\/?page_id=19"},"modified":"2026-06-16T10:43:27","modified_gmt":"2026-06-16T14:43:27","slug":"publications","status":"publish","type":"page","link":"https:\/\/people.clas.ufl.edu\/pilyugin\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n
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Publications<\/h1>\n\n\n\n
  • P. C. Perera, S. S. Pilyugin, L. Davis and T. Gedeon (2026), Effect of transcriptional delay on ribosome abundance control, Journal of Mathematical Biology, 93:2.
    \nhttps:\/\/doi.org\/10.1007\/s00285-026-02420-3. <\/span><\/li>\n
  • H. B. Taboe, S. S. Pilyugin and C. N. Ngonghala (2025), Revealing hidden drivers of Lassa fever through a
    \nmodel-informed approach for reproducing and predicting disease dynamics and guiding control strategies, Scientific Reports, 15:33786.
    \nDOI: 10.1038\/s41598-025-01176-y.<\/span><\/li>\n
  • X. Duan and S. S. Pilyugin (2025), A chemostat model with variable dilution rate due to \nbiofilm growth, SIAM J. Appl. Math. 85 (5), pp. 2295-2317.
    DOI: 10.1137\/24M1704890.<\/span><\/li>\n
  • H. B. Taboe, S. S. Pilyugin and C. N. Ngonghala (2024), Resolve Lassa fever persistence:
    \nA compartmental model with environmental virus-host-vector interaction, Research Square,
    \nDOI: 10.21203\/rs.3.rs-5248593\/v1.<\/span><\/li>\n
  • X. Duan and S. S. Pilyugin (2024), A chemostat model with variable dilution rate due to \nbiofilm growth, arXiv: 2411.05213.<\/span><\/li>\n
  • J. K.E.O. Todd-Brown, J.R. Holmquist, M.L. Vahsen, J. Hicks, S. S. Pilyugin and J.T. Morris \n(2024), Cohort Marsh Equilibrium Model (CMEM): History, mathematics, and implementation, JGR Biosciences, DOI: 10.1029\/2023JG0007823.<\/span><\/li>\n
  • J. M. Flynn and S. S. Pilyugin (2022), Using restart sequences to determine beneficial first passage under restart, \tarXiv:2204.07422.<\/span><\/li>\n
  • J. M. Flynn and S. S. Pilyugin (2021), First passage with restart in discrete time: with applications to biased random walks on the half-line, arXiv:2108.11508v2.<\/span><\/li>\n
  • J. Jiao, L. Riotte-Lambert, S. S. Pilyugin, M. A. Gil and C. W. Osenberg (2020), Mobility and its sensitivity to fitness differences determine consumer\u2013resource distributions, R. Soc. Open Sci. 7: 200247. http:\/\/dx.doi.org\/10.1098\/rsos.200247.<\/span><\/li>\n
  • M. Binder and S. S. Pilyugin (2019), Stability analysis of a deterministic model of Zika\/Dengue co-circulation, Int. J. Biomath. 12 (4), 1950045 (39 pages), DOI: 10.1142\/S1793524519500451.<\/span><\/li>\n
  • J. Jiao, S. S. Pilyugin, L. Riotte-Lambert and C. W. Osenberg (2018), Habitat-dependent movement rate can determine the efficacy of marine protected areas, Ecology, 99 (11), pp. 2485-2495, https:\/\/doi.org\/10.1002\/ecy.2477.<\/span><\/li>\n
  • S. Khonthapagdee and S. S. Pilyugin (2017), Crowding and light limitation affect phytoplankton competition for nitrogen, Journal of Biological Systems 25 (4), 743-765.<\/span><\/li>\n
  • J. Jiao, S. S. Pilyugin, and C. Osenberg (2016), Random movement of predators can eliminate trophic cascades in marine protected areas, Ecosphere, DOI: 10.1002\/ecs2.1421.<\/span><\/li>\n
  • E. Milliken and S. S. Pilyugin (2016), A model of infectious salmon anemia virus with viral diffusion between wild and farmed patches, Discrete and Continuous Dynamical Systems B 21(6), 1869 – 1893.<\/span><\/li>\n
  • C. J. Browne and S. S. Pilyugin (2016), Minimizing R_0 for in-host model with periodic combination antiviral therapy, Discrete and Continuous Dynamical Systems B 21(10), 3301-3314.<\/span><\/li>\n
  • S. S. Pilyugin, Jan Medlock, P. De Leenheer (2016), The effectiveness of marine protected areas for predator and prey with varying mobility, Theoretical Population Biology 110, 63-77.<\/span><\/li>\n
  • J. Jiao, S. S. Pilyugin, C. Osenberg (2016), Random movement of predators can eliminate trophic cascades in marine protected areas, Ecosphere, in press.
    \n<\/span><\/li>\n
  • C. J. Littles, S. S. Pilyugin, T. K. Frazer (2016), A combined inverse method and multivariate approach for exploring population trends of Florida manatees, Marine Mammal Science 32 (1), 122-140.<\/span><\/li>\n
  • E. Milliken and S. S. Pilyugin (2016), A model of infectious salmon anemia virus with viral diffusion between wild and farmed patches, Discrete and Continuous Dynamical Systems B, in press.<\/span><\/li>\n
  • K. Jacobsen and S. S. Pilyugin (2015), Analysis of a mathematical model for tumor therapy with a fusogenic oncolytic virus, Math. Biosci. (270): 169-182.<\/span><\/li>\n
  • G. V. Beznoussenko, S. S. Pilyugin, W. J. C Geertz, M. M. Kozlov, K. N J. Burger, A. Luini, J. Derganc, and A. A. Mironov (2015), Trans-membrane area asymmetry controls the shape of cellular organelles, International Journal of Molecular Science, 16(3), 5299-5333. <\/li>\n
  • A. Handel, V. Akin, S. S. Pilyugin, V. Zarnitsyna, and R. Antia (2014), How sticky should a virus be? The impact of virus binding and release on transmission fitness using influenza as an example,\u00a0J. R. Soc. Interface. 2014 11 20131083; doi:10.1098\/rsif.2013.1083. <\/li>\n
  • H. Pourbashash, S. S. Pilyugin, C. McCluskey, and P. De Leenheer (2013), Global analysis of within host virus models with cell-to-cell viral transmission, to appear in DCDS-B.\u00a0<\/li>\n
  • K. Jacobsen, J. Stupiansky, and S. S. Pilyugin (2013), Mathematical modeling of citrus groves infected by Huanglongbing, Math. Biosci. Eng. 10 (3), pp. 705-728.\u00a0<\/li>\n
  • C. J. Browne and S. S. Pilyugin (2013), A within-host virus model with age-structured infected cell component, DCDS – B 18 (8), pp. 1999-2017.\u00a0<\/li>\n
  • C. J. Browne and S. S. Pilyugin (2012), Periodic multidrug therapy in a within-host virus model, Bull. Math. Biol., PMID: 21822766.<\/li>\n
  • S. F. Ellermeyer and S. S. Pilyugin (2011), A size-structured model of bacterial growth and reproduction, J. Biol. Dyn., DOI:10.1080\/17513758.2010.535127.\u00a0<\/li>\n
  • P. De Leenheer, J. Dockery, T. Gedeon, and S. S. Pilyugin (2010), The chemostat with lateral gene transfer, J. Biol. Dyn. 4 (6), pp. 607-620.\u00a0<\/li>\n
  • P. De Leenheer, J. Dockery, T. Gedeon, and S. S. Pilyugin (2010), Senescence and antibiotic resistance in an age-structured population model, J. Math. Biol. 61 (4), pp. 475-499.\u00a0<\/li>\n
  • J. T. Noel, S. S. Pilyugin, and A. Narang (2009), The diffusive influx and carrier efflux have a strong effect on the bistability of the lac operon in Escherichia coli, J. Theor. Biol. 256 (1), pp. 14-28.\u00a0<\/li>\n
  • A. Handel, A. Yates, S. S. Pilyugin, and R. Antia (2009), Sharing the burden: Antigen transport and firebreaks in immune responses, J. Royal Soc. -Interface 6 (34), pp. 447-454.\u00a0<\/li>\n
  • P. De Leenheer and S. S. Pilyugin (2008), Multi-strain virus dynamics with mutations: A global analysis, Math. Med. and Biol. 25 (4), pp. 285-322.\u00a0<\/li>\n
  • A. Narang and S. S. Pilyugin (2008), Bistability of the lac operon during growth of\u00a0Escherichia coli<\/i>\u00a0on lactose and lactose + glucose, Bull. Math. Biol. 70 (4), pp. 1032-1064.\u00a0<\/li>\n
  • P. De Leenheer, W. S. Keeran, and S. S. Pilyugin (2008), Feedback-mediated coexistence and oscillations in the chemostat, DCDS – B 9 (2), pp. 321-351.\u00a0<\/li>\n
  • P. De Leenheer and S. S. Pilyugin (2008), Immune response to a malaria infection: Properties of a mathematical model, J. Biological Dynamics 2 (2), pp. 102-120.\u00a0<\/li>\n
  • A. Handel, S. S. Pilyugin, A. Yates, and R. Antia (2007), The importance of gap junctions during immune responses, Theor. Immunol. 28 (11), pp. 463-466.\u00a0<\/li>\n
  • W. S. Keeran, P. De Leenheer, and S. S. Pilyugin (2007), Circular and elleptic orbits in a feedback-mediated chemostat, DCDS – B 7(4), pp. 779-792.<\/li>\n
  • M. Martcheva, S. S. Pilyugin, and R. D. Holt (2007), Subthreshold and superthreshold coexistence of pathogen variants: The impact of age-structure, Math. Biosci. 207, pp. 58-77.\u00a0<\/li>\n
  • A. Narang and S. S. Pilyugin (2007), Bacterial gene regulation in diauxic and non-diauxic growth, J. Theor. Biol. 244, pp. 326-348.<\/li>\n
  • A. Meyer-Baese and S. S. Pilyugin (2006), Stability analysis of an unsupervised neural network with feedforward and feedback dynamics, Neurocomputing Letters 70, pp. 603-606.\u00a0<\/li>\n
  • M. Martcheva and S. S. Pilyugin (2006), The role of coinfection in multi-disease dynamics, SIAM J. Appl. Math. 66 (3), pp. 843-872.<\/li>\n
  • M. Martcheva and S. S. Pilyugin (2006), An epidemic model structured by host immunity, J. Biol. Sys. 14 (2), pp. 185-203.<\/li>\n
  • P. De Leenheer and S. S. Pilyugin (2006), Feedback-mediated oscillatory coexistence in the chemostat, Lecture Notes in Control and Information Sciences 341, pp. 97-104.<\/li>\n
  • V. V. Ganusov, S. S. Pilyugin, R. Ahmed, and R. Antia (2006), How does cross-reactive stimulation affect the longevity of CD8+ T cell memory?, PLoS Comp. Biol. 2(6), e55 DOI: 10.1371\/journal.pcbi.0020055.\u00a0<\/li>\n
  • S. S. Pilyugin, V. V. Ganusov, R. DeBoer, R. Antia, K. Murali-Krishna, and R. Ahmed (2005), Quantifying cell turnover using CFSE data, J. Immun. Meth., 298, pp. 183-200.<\/li>\n
  • S. Gupta, S. S. Pilyugin, and A. Narang (2005), The dynamics of single-substrate continuous cultures: The role of ribosomes, J. Theor. Biol. 232, pp. 467-490.<\/li>\n
  • A. Narang and S. S. Pilyugin (2005), Toward an integrated physiological theory of microbial growth: From subcellular variables to population dynamics, Math. Biosci. Eng. 2 (1), pp. 169-206.<\/span><\/li>\n
  • S. S. Pilyugin, G. T. Reeves, and A. Narang (2004), Predicting stability of mixed microbial cultures from single species experiments: 1. Phenomenological model, Math. Biosci. 192, pp. 85-109.<\/li>\n
  • S. S. Pilyugin, G. T. Reeves, and A. Narang (2004), Predicting stability of mixed microbial cultures from single species experiments: 2. Physiological model, Math. Biosci. 192, pp. 111-136.<\/li>\n
  • J. Arino, S. S. Pilyugin, and G. S. K. Wolkowicz (2003), Considerations on yield, nutrient uptake, cellular growth, and competition in chemostat models, Can. Appl. Math. Quart. 11 (2), pp. 107-142.<\/li>\n
  • A. Mayer-Baese, S. S. Pilyugin, A. Wismuller, and S. Foo (2004), Local exponential stability of competitive neural networks with different time scales, Eng. Appl. Art. Intel. 17, 227-232.<\/li>\n
  • G. T. Reeves, A. Narang, and S. S. Pilyugin (2004), Growth of mixed cultures on mixtures of substitutable substrates: The operating diagram for a structured mode, J. Theor. Biol. 226 (2), pp. 143-157.<\/li>\n
  • S. S. Pilyugin and P. Waltman (2003), Divergence criterion for generic planar systems, SIAM J. Appl. Math. 64 (1), pp. 81-93.\u00a0<\/li>\n
  • S. S. Pilyugin, V. V. Ganusov, K. Murali-Krishna, R. Ahmed, and R. Antia (2003), The rescaling method for quantifying the turnover of cell populations, J. Theor. Biol. 225, pp. 275-283.\u00a0<\/li>\n
  • A. Meyer-Baese, S. S. Pilyugin, and Y. Chen (2003), Global exponential stability of competitive neural networks with different time scales, IEEE Trans. Neur. Net., 14 (3), pp. 716-719.<\/li>\n
  • J. Shoemaker, G. T. Reeves, S. Gupta, S. S. Pilyugin, T. Egli, and A. Narang (2003), The dynamics of single-substrate continuous cultures: The role of transport enzymes, J. Theor. Biol. 222, pp. 307-322.<\/li>\n
  • R. Antia, C. Bergstrom, S. S. Pilyugin, S. M. Kaech, and R. Ahmed (2003), Models of CD8+ responses: 1. What is the antigen-independent proliferation program? J. Theor. Biol. 221, pp. 585-598.\u00a0<\/li>\n
  • A. Meyer-Baese and S. S. Pilyugin (2003), Global asymptotic stability of a class of dynamical neural networks, International Journal of Neural Systems 13 (1), pp. 47-53.\u00a0<\/li>\n
  • S. S. Pilyugin and P. Waltman (2003), Multiple limit cycles in the chemostat with variable yield, Math. Biosci. 182, pp. 151-166.\u00a0<\/li>\n
  • S. F. Ellermyer, S. S. Pilyugin, and R. Redheffer (2001), Persistence criteria for a chemostat with variable nutrient input, J. Diff. Eqns. 171, pp. 132-147.\u00a0<\/li>\n
  • S. S. Pilyugin and R. Antia (2000), Modeling immune responses with handling time, Bull. Math. Biol. 62, pp. 869-890.\u00a0<\/li>\n
  • S. S. Pilyugin and P. Waltman (1999), The simple chemostat with wall growth, SIAM J. Appl. Math. 59 (5), pp. 1552-1572.<\/li>\n
  • S. S. Pilyugin and P. Waltman (1999), Competition in the unstirred chemostat with periodic input and washout, SIAM J. Appl. Math. 59 (4), pp. 1157-1177.<\/li>\n
  • R. Antia, S. S. Pilyugin, and R. Ahmed (1998), Models of immune memory: One the role of cross-reactive stimulation, competition and homeostasis in maintaining immune memory, Proc. Natl. Acad. Sci. USA 95, pp. 14926-14931.\u00a0<\/li>\n
  • S. S. Pilyugin, J. Mittler, and R. Antia (1997), Modeling T-cell proliferation: An investigation of consequences of the Hayflick limit, J. Theor. Biol. 186 (1), pp. 117-129.<\/li><\/ul>\n\n\n\n\t\t\t<\/div>\n\t\t<\/div>\n\t<\/div>\n<\/section>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":311,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"featured_post":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-19","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/pages\/19","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/users\/311"}],"replies":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/comments?post=19"}],"version-history":[{"count":10,"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/pages\/19\/revisions"}],"predecessor-version":[{"id":1638,"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/pages\/19\/revisions\/1638"}],"wp:attachment":[{"href":"https:\/\/people.clas.ufl.edu\/pilyugin\/wp-json\/wp\/v2\/media?parent=19"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}