Publications

2025

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• Cawiding, O.R., Jeon, S., Tubera-Panes, D., de los Reyes V, A.A. & Kim, J.K.  Disentangling climate’s dual role in dengue dynamics: A multiregion causal analysis study. Science Advances 11(7): eadq1901 (2025)

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• Lee, J., Mendoza, R., Mendoza, V.M.P. & Jung, E. Differential evolution with spherical search algorithm for nonlinear engineering and infectious disease optimization problems. Applied Soft Computing 168: 112446 (2025)

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• Villejo, E.J.V. & Talabis, D.A.S.J. Weakly Reversible Realizations of Biochemical Systems Theory (BST) Models. MATCH Commun Math Comput Chem 93(3): 631-687 (2025)

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• Hernandez, B.S., Lubenia, P.V.N. & Mendoza, E.R. Equilibria Decomposition-Based Comparison of Reaction Networks of Wnt Signaling. MATCH Commun Math Comput Chem 93(2): 291-318 (2025)

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• Hernandez, B.S., Lubenia, P.V.N. & Mendoza, E.R. Embedding-Based Comparison of Reaction Networks of Wnt Signaling. MATCH Commun Math Comput Chem 93(1): 223-245 (2025)

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2024

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• Pilario, K.E., Escober, E.J., de los Reyes V, A. & Espino, M.P. Robust prediction of chlorophyll-A from nitrogen and phosphorus content in Philippine and global lakes using fine-tuned, explainable machine learning. Environmental Challenges 17: 101056 (2024)

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• Mata, M.A.E., Escosio, R.A.S., Rosero, E.V.G.A., Viernes, J.P.T., Añonuevo, L.E., Hernandez, B.S., Addawe, J.M., Addawe, R.C., Pilar-Arceo, C.P.C., Mendoza, V.M.P. & de los Reyes V, A.A.  Analyzing the dynamics of COVID-19 transmission in select regions of the Philippines: A modeling approach to assess the impact of various tiers of community quarantines. Heliyon 10(21): e39330 (2024)

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• Abas, C.L., Velasco, A.C. & Arceo, C. Application of a reaction-based water quality model to the total dissolved solids concentration of the Pasig River. PeerJ 12:e18076 (2024)

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• Alamin, A.J.L.J., Hernandez, B.S. Positive steady states of a class of power law systems with independent decompositions. Journal of Mathematical Chemistry 62, 1647–1666 (2024)

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• Song, Y.M., Jeong, J., de los Reyes V, A.A., Lim, D., Cho, C.H., Yeom, J.W., Lee, T., Lee, J.B., Lee, H.J. & Kim, J.K. Causal dynamics of sleep, circadian rhythm, and mood symptoms in patients with major depression and bipolar disorder: insights from longitudinal wearable device data. EBioMedicine 103:105094 (2024)

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• Lim, Y., Ko, Y., Mendoza, V.M.,  Mendoza, R., Lee, J. & Jung, E. Optimal Non-Pharmaceutical Interventions Considering Limited Healthcare System Capacity and Economic Costs in the Republic of Korea. Mathematical Modelling of Natural Phenomena, 19(6) (2024)

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• Lee, D.,  de los Reyes V, A.A. & Kim, Y. Optimal strategies of oncolytic virus-bortezomib therapy via the apoptotic, necroptotic, and oncolysis signaling network. Mathematical Biosciences and Engineering, 21(3): 3876-3909 (2024)

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• Villareal, K.A.M., Hernandez, B.S., & Lubenia, P.V.N. Derivation of steady state parametrizations of chemical reaction networks with n independent and identical subnetworks, MATCH Commun Math Comput Chem 91(2): 337-365 (2024)

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2023​

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• Castillo, R. C. J., Mendoza, V. M., Lope, J. E., & Mendoza, R. Modeling Infectious Disease Trend using Sobolev Polynomials. Communication in Biomathematical Sciences, 6(2), 100-107 (2023)

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• Escosio, R.A.S.,  Cawiding, O.R., Hernandez, B.S., Mendoza, R.G., Mendoza, V.M.P., Mohammad, R.Z., Pilar-Arceo, C.P.C., Salonga, P.K.N., Suarez, F.L.E., Sy, P.W., Vergara, T.H.M. & de los Reyes V, A.A.  A model-based strategy for the COVID-19 vaccine roll-out in the Philippines. Journal of Theoretical Biology 573, 111596 (2023)

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• Hernandez, B.S. & Buendicho, K.D.E.  A network-based parametrization of positive steady states of power-law kinetic systems. Journal of Mathematical Chemistry (2023)​

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• Pino, R., Mendoza, V.M.P., Enriquez, E.A., Velasco, A.C. & Mendoza, R.  An optimization model with simulation for optimal regional allocation of COVID-19 vaccines. Healthcare Analytics 4, 100244 (2023)​

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• ​Ko, Y., Mendoza, V.M.P., Mendoza, R., Seo Y., Lee, J.,& Jung, E.  Risk estimation of lifted mask mandates and emerging variants using mathematical model. Heliyon 9, e16841 (2023)​

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• Malaguit, J.C., Mendoza, V.M.P., Tubay, J.M. & Mata, M.A.E.  Identifying patterning behavior in a plant infestation of insect pests. Mathematical Biosciences 362, 109032 (2023)​

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• Hong, H, Hernandez, B.S., Kim, J. & Kim, J.K. Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics. SIAM Journal on Applied Mathematics 83:3, 1025-1048  (2023)

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• Monica, T., Tubay, J. & de los Reyes V, A.A. Quantitative assessment of a dual epidemic caused by tuberculosis and HIV  in the Philippines. Bulletin of Mathematical Biology 85, 56 (2023)

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• Lee, J., Mendoza, R., Mendoza, V.M.P., Lee, J., Seo, Y. & Jung, E.  Modelling the effects of social distancing, antiviral therapy, and booster shots on mitigating Omicron spread. Scientific Reports 13, 6914 (2023)​

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• Gavina, B.L.A., de los Reyes V, A.A., Olufsen, M.S., Lenhart, S. & Ottesen, J.T. Toward an optimal contraception dosing strategy. PLoS Computational Biology 19(4): e1010073 (2023)

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• Hernandez, B.S., Lubenia, P.V.N., Johnston, M.D. & Kim, J.K. A framework for deriving analytic long-term behavior of biochemical reaction networks. PLoS Computational Biology 19(4): e1011039 (2023)

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• Añonuevo, L.E., Lachica, Z.P.T., Amistas, D.A., Lato, J.I.E., Boniato, H.L.C., Catalan, J.M.G., Pasion, R.J.F., Yumang, A.P., Almocera, A.E.S., Arcede, J.P., Mata, M.A.E. & de los Reyes V, A.A. Transmission dynamics and baseline epidemiological parameter estimates of Coronavirus disease 2019 pre-vaccination: Davao City, Philippines. PLoS ONE 18(4): e0283068 (2023)

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• Campos, H. J., Raza, M. N., Arcede, J. P., Martinez, J. G., & L., R. Vaccination and Variants: A COVID-19 Multi-Strain Model Evolution for the Philippines. Frontiers in Applied Mathematics and Statistics, 9, 1029018 (2023).

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• Caga-anan, R. L., Macalisang, J. M., Dalisay, J. L., Raza, M. N., Martinez, J. G., & Arcede, J. P. Optimal Vaccination Control for COVID-19 in a Metapopulation Model: A Case of the Philippines. Frontiers in Applied Mathematics and Statistics, 9, 1154634 (2023).

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2022

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• Hernandez, B.S. & Mendoza, E.R. Positive equilibria of power law kinetics on networks with independent linkage classes. J Math Chem (2022). ​

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• Escosio R.A.S. & Mendoza, R. A modified accelerated gradient descent using an n-dimensional golden section search for escaping saddle points. Proceedings of the 8th International Conference on Control and Optimization with Industrial Applications, Vol. 1, 24-26 August 2022, Baku, Azerbaijan, pp. 153-155

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• Mendoza, V.M.P., Mendoza, R., Ko, Y., Lee, J. & Jung, E. Managing bed capacity and timing of interventions: a COVID-19 model considering behavior and underreporting. AIMS Mathematics, 8(1): 2201-2225 (2023)

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• Ko, Y., Mendoza, V.M.P., Mendoza, R., Seo, Y., Lee, J. & Jung, E., Estimation of monkeypox spread in a non-endemic country considering contact tracing and self-reporting: a stochastic modeling study. J Med Virol, 1-11 (2022)

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• Cabanilla, K.I., Enriquez, E.A., Velasco, A.C., Mendoza, V.M.P. &Mendoza, R. Optimal selection of COVID-19 vaccination sites in the Philippines at the municipal level. PeerJ, 10:e14151 (2022)

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• Mendoza, V.M., Mendoza, R., Lee, J. & Jung, E. Adjusting non-pharmaceutical interventions based on hospital bed capacity using a multi-operator differential evolution. AIMS Mathematics, 7(11): 19922-19953 (2022)

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• ​Ko, Y., Mendoza, V.M., Mendoza, R., Seo, Y., Lee, J., Lee, J., Kwon, D. & Jung, E., Multi-Faceted Analysis of COVID-19 Epidemic in Korea Considering Omicron Variant: Mathematical Modeling-Based Study, J Korean Med Sci, 37(26):e209 (2022)

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• Ko, Y., Mendoza, V.M., Seo, Y., Lee, J., Kim, Y., Kwon, D. & Jung, E., Quantifying the effects of non-pharmaceutical and pharmaceutical interventions against COVID-19 epidemic in the Republic of Korea: Mathematical model-based approach considering age groups and the Delta variant, Math Model Nat Phenom 17(39) (2022)

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• Hernandez, B.S. & Mendoza, E.R. Weakly reversible CF-decompositions of chemical kinetic systems, J Math Chem (2022)

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• de los Reyes V, A.A. & Kim, Y. Optimal regulation of tumour-associated neutrophils in cancer progression, R. Soc. Open Sci. 9: 210705 (2022)

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• Hernandez, B.S., Amistas, D.A., De la Cruz, R.J.L., Fontanil, L.L., de los Reyes V, A.A, & Mendoza, E.R. Independent, incidence independent and weakly reversible decompositions of chemical reaction networks, MATCH Commun Math Comput Chem 87(2): 367-396 (2022)

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2021

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• Ignacio, N., Liwag, R., Addawe, R. Spatiotemporal Analysis of Typhoid Cases in Baguio City, Philippines. In: Mohd, M.H., Misro, M.Y., Ahmad, S., Nguyen Ngoc, D. (eds) Modelling, Simulation and Applications of Complex Systems. CoSMoS 2019. Springer Proceedings in Mathematics & Statistics, vol 359. Springer, Singapore (2021)

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• Salonga, P.K.N., Mendoza, V.M.P., Mendoza, R.G., & Belizario Jr, V.Y. A mathematical model of the dynamics of lymphatic filariasis in Caraga Region, the Philippines. R. Soc. Open Sci. 8: 201965 (2021)

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• Calderon, P.G.B., Palma, Lean V., Kappel, F., & de los Reyes V, A.A. Control, Sensitivity and Identification of a Cardiovascular-Respiratory System Model. In: Mohd M.H., Misro M.Y., Ahmad S., Nguyen Ngoc D. (eds) Modelling, Simulation and Applications of Complex Systems. CoSMoS 2019. Springer Proceedings in Mathematics & Statistics, vol 359. Springer, Singapore. 151-173 (2021)

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• Hernandez, B.S. & De la Cruz, R.J.L. Independent decompositions of chemical reaction networks, Bull Math Biol 83, 1–23 (2021)

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• Hernandez, B.S. & Mendoza, E.R. Positive equilibria of Hill-type kinetic systems, J Math Chem 59, 840–870 (2021)

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• Aspirin, A.P., de los Reyes V, A. A. & Kim, Y. Polytherapeutic strategies with oncolytic virus–bortezomib and adjuvant NK cells in cancer treatment. J R Soc Interface 18: 20200669 (2021)

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• ​Magpantay, D. M., Hernandez, B. S., de los Reyes V, A. A., Mendoza, E. R. & Nocon, E. G. A Computational Approach to Multistationarity in Poly-PL Kinetic Systems, MATCH Commun Math Comput Chem 85(3): 605-634 (2021)

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• Hernandez, B. S. Analysis of Equilibria Properties of Chemical Reaction Networks with Independent Decompositions for Classes of Kinetics, MATCH Commun Math Comput Chem 85(3): 577-604 (2021)

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• Caga-anan, R., Raza, M., Labrador, G., Metillo, E., Castillo, P., & Mammeri, Y. Effect of Vaccination to COVID-19 Disease Progression and Herd Immunity. Computational and Mathematical Biophysics, 9(1), 262-272 (2021).

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​2020

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• ​Estadilla, C.D.S. & de los Reyes V, A.A. Optimal strategies for mitigating the HIV/AIDS epidemic in the Philippines. Math Meth Applied Sci 43: 10690-10710 (2020)

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• Jamilla, C.U., Mendoza, R.G. & Mendoza, V.M.P. Explicit solution of a Lotka-Sharpe-McKendrick system involving neutral delay differential equations using the r-Lambert W function. Math Biosci Eng 17(5): 5686-5708 (2020)

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• Jamilla, C.U., Mendoza, R.G., & Mező, I. Solutions of neutral delay differential equations using a generalized Lambert W function. Applied Mathematics and Computation, 382:125334 (2020)

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• Alota, C.P., Pilar-Arceo, C.P.C. & de los Reyes V, A.A. An edge-based model of SEIR epidemics on static random networks. Bull Math Biol 82, 96 (2020)

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• Kim, S., de los Reyes V, A.A. & Jung, E. Country-specific intervention strategies for top three TB burden countries using mathematical model. PLoS ONE 15(4): e0230964 (2020)

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• Cajayon, R.C., Lucilo, J.A., Pilar-Arceo, C.P.C. & Mendoza, E.R. Comparison of Two Nature-inspired Algorithms for Parameter Estimation of S-system Models. Philipp J Sci 149 (1): 63-78 (2020)

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• Hernandez, B. S. On the Independence of Fundamental Decompositions of Power-Law Kinetic Systems. MATCH Commun Math Comput Chem 84(1): 57-84 (2020) ​

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• Hernandez, B.S., Mendoza, E.R. & de los Reyes V, A.A. Fundamental Decompositions and Multistationarity of Power-Law Kinetic Systems. MATCH Commun Math Comput Chem 83(2): 403-434 (2020)

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• Hernandez, B.S., Mendoza, E.R. & de los Reyes V, A.A. A computational approach to multistationarity of power-law kinetic systems. J Math Chem 58, 56–87 (2020)

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​2019

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• Villar, J.J.S., Lubenia, P.V.N, Mendoza, E.R. & Pilar-Arceo, C.P.C. Structural Stability Analysis of Models of Dopamine Synthesis and D1 Receptor Trafficking in RPT Cells using CRNT. Philipp J Sci 148 (3): 523-533 (2019)

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• Pilar-Arceo, C.P.C., Jose, E.C., Lao, A.R. & Mendoza, E.R. Chemical Reaction Networks: Filipino Contributions to Their Theory and Its Applications. Philipp J Sci 148(2): 249-261

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• ​Jung, E., de los Reyes V, A.A., Pumares, K.J.A. & Kim, Y. Strategies in regulating glioblastoma singling pathways and anti-invasion therapy. PLoS ONE 14(4): e0215547 (2019)

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• Almocera, A.E.S, Hsu, S.B. & Sy, P.W. Extinction and uniform persistence in a microbial food web with mycoloop: limiting behavior of a population model with parasitic fungi. Math Biosci Eng 16(1): 516-537 (2019)

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2018

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• de los Reyes V, A.A. & Escaner IV, J.M.L. Dengue in the Philippines: model and analysis of parameters affecting transmission. J Biol Dyn 12:1, 894-912 (2018) 

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• Paguio, V.M.E., Kappel, F. & Kotanko, P. A model of vascular refilling with inflammation. Math Biosci 303: 101-114 (2018)

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• ​Jung, E., de los Reyes V, A.A., Pumares, K.J.A. & Kim, Y. Strategies in regulating glioblastoma singling pathways and anti-invasion therapy. PLoS ONE 14(4): e0215547 (2018)

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• Pilar-Arceo, C.P.P., Jose, E.C., Lao, A.R. & Mendoza, E.R. Reactant subspaces and kinetics of chemical reaction networks. J Math Chem 56: 395-422 (2018)

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• Talabis, D.A.S.J., Arceo, C.P.P. & Mendoza, E.R. Positive equilibria of a class of power-law kinetics. J Math Chem 56: 358-394 (2018)

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2017

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• ​Calderon, P.G.B., Habib, M., Kappel, F. & de los Reyes V, A.A. Control aspects of the human cardiovascular-respiratory system under a nonconstant workload. Math Biosci 289: 142-152 (2017) 

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• Nazareno, A. L. & Hernandez, B.S. A mathematical model of the interaction of abscisic acid, ethylene and methyl jasmonate on stomatal closure in plants. PLoS ONE 12(2): e0171065 (2017)

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• Arceo, C.P.P., Jose, E.C., Lao, A.R. & Mendoza, E.R. Reaction networks and kinetics of biochemical systems. Math Biosci 283: 13-29

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2016

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• ​de los Reyes V, A.A., Fuertinger, D. H., Kappel, F., Meyring-Woesten, A., Thijssen, S. & Kotanko, P. A physiologically based model of vascular refilling during ultrafiltration in hemodialysis. J Theor Biol 390: 146-155 (2016)

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2015

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• Arceo, C.P.P., Jose, E.C., Marin-Sanguino, A. & Mendoza, E.R. Chemical reaction network approaches to biochemical systems theory. Math Biosci 269: 135-152 (2015)

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• ​de los Reyes V, A.A., Jung, E., & Kim, Y. Optimal strategies of eradicating glioblastoma cells after conventional surgery. J R Soc Interface 12: 20141392 (2015)

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• de los Reyes V, A.A. Dynamics of a cardiovascular model obtaining measurable pulsatile pressure output. World J Model Simul 11(1):20-32 (2015)

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2014

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• ​de los Reyes V, A.A., Jung, E. & Kappel, F. Stabilizing control for a pulsatile cardiovascular mathematical model. Bull Math Biol 76(6):1306-1332 (2014)