Publications

Multi-season evaluation and analysis of categorical trend forecasts of influenza hospital admissions in the United States

Multi-season evaluation and analysis of categorical trend forecasts of influenza hospital admissions in the United States. Davis, J.T., Kaur, G., Hines, A., et al. (2026), medRxiv preprint
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Large language models instantiate evolutionarily robust strategies of cooperation

Large language models instantiate evolutionarily robust strategies of cooperation. Pal, S., Mallela, A., Pracher, L., Wei, C., Fu, F., Schnell, S., and Nowak, M.A. (2026), PNAS Nexus
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Using PyBioNetFit to Leverage Qualitative and Quantitative Data in Biological Model Parameterization and Uncertainty Quantification

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. (2026), Frontiers in Immunology
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Structural hormesis in protein aggregation: A minimal mechanistic model

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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Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations

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

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

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 (Arizona, Colorado, New Mexico, and Utah)

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

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

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

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

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

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

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 point cascades: a master equation approach

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, United States

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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Abhishek Mallela