Using PyBioNetFit to Leverage Qualitative and Quantitative Data in Biological Model Parameterization and Uncertainty Quantification. Miller, E.F., Mallela, A., Neumann, J., Lin, Y.T., Hlavacek, W.S., and Posner, R.G. (2025), Frontiers in Immunology
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Structural hormesis in protein aggregation: A minimal mechanistic model. Mallela, A. and Schnell, S. (2026), Journal of the Royal Society Interface
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Strategies of cooperation and defection in five large language models. Pal, S., Mallela, A., Hilbe, C., Pracher, L., Wei, C., Fu, F., Schnell, S., and Nowak, M.A. (2026), aRxiv preprint
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Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. Mathis, S.M., Webber, A.E., Basu, A., et al. (2024), Nature Communications, 15:6289
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Impacts of vaccination and Severe Acute Respiratory Syndrome Coronavirus 2 variants Alpha and Delta on Coronavirus Disease 2019 transmission dynamics in four metropolitan areas of the United States. Mallela, A., Chen, Y., Lin, Y.T., Miller, E.F., Neumann, J., He, Z., Nelson, K.E., Posner, R.G., and Hlavacek, W.S. (2024), Bulletin of Mathematical Biology, 86(3):31
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Differential contagiousness of respiratory disease across the United States. Mallela, A., Lin, Y.T., and Hlavacek, W.S. (2023), Epidemics, 45:100718
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Quantification of early nonpharmaceutical interventions aimed at slowing transmission of Coronavirus Disease 2019 in the Navajo Nation and surrounding states. Miller, E.F., Neumann, J., Chen, Y., Mallela, A., Lin, Y.T., Hlavacek, W.S., and Posner, R.G. (2023), PLOS Global Public Health, 3(6):e0001490
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Optimal management of stochastic invasion in a metapopulation with Allee effects. Mallela, A. and Hastings, A. (2022), Journal of Theoretical Biology, 549:111221
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The United States COVID-19 Forecast Hub dataset. Cramer, E.Y., Huang, Y., Wang, Y., et al. (2022), Scientific Data, 9(462):1-15
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Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit. Neumann, J., Lin, Y.T., Mallela, A., Miller, E.F., Colvin, J., Duprat, A.T., Chen, Y., Hlavacek, W.S., and Posner, R.G. (2022), Bioinformatics, 38(6):1770-1772
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Bayesian inference of state-level COVID-19 basic reproduction numbers across the United States. Mallela, A., Neumann, J., Miller, E.F., Chen, Y., Posner, R.G., Lin, Y.T., and Hlavacek, W.S. (2022), Viruses, 14(1):157
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Tipping cascades in a multi-patch system with noise and spatial coupling. Mallela, A. and Hastings, A. (2021), Bulletin of Mathematical Biology, 83(11):1-27
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Robustness and the evolution of length control strategies in the T3SS and flagellar hook. Nariya, M.K., Mallela, A., Shi, J.J., and Deeds, E.J. (2021), Biophysical Journal, 120(17):3820-3830
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The role of stochasticity in noise-induced tipping cascades: A master equation approach. Mallela, A. and Hastings, A. (2021), Bulletin of Mathematical Biology, 83(5):1-20
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Daily forecasting of regional epidemics of Coronavirus disease with Bayesian uncertainty quantification. Lin, Y.T., Neumann, J., Miller, E.F., Posner, R.G., Mallela, A., Safta, C., Ray, J., Thakur, G., Chinthavali, S., and Hlavacek, W.S. (2021), Emerging Infectious Diseases, 27(3):767
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Crosstalk and ultrasensitivity in protein degradation pathways. Mallela, A., Nariya, M.K., and Deeds, E.J. (2020), PLOS Computational Biology, 16(12):e1008492
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Optimal Control applied to a SEIR model of 2019-nCoV with social distancing. Mallela, A. (2020), medRxiv preprint
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HIV-TB co-infection treatment: modeling and optimal control theory perspectives. Mallela, A., Lenhart, S., Vaidya, N.K. (2016), Journal of Computational and Applied Mathematics, 307:143-161
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