This repository is an Example using GitHub Actions [egga] for the Advanced Programming with R class. The project consists of a quarto document updated once a week or whenever there’s a push or pull request. It performs a search on PubMed looking for the latest papers about Agent-Based Models. The last update was on 2025-01-26 00:47:14.
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Early COVID-19 Pandemic Preparedness: Informing Public Health Interventions and Hospital Capacity Planning Through Participatory Hybrid Simulation Modeling.
Tian Y, Basran J, McDonald W, Osgood ND.
Int J Environ Res Public Health. 2024 Dec 30;22(1):39. doi: 10.3390/ijerph22010039.
The objective was to use simulation modeling to guide the implementation of public health measures and short-term hospital capacity planning to mitigate the disease burden from March to June 2020. We developed a hybrid simulation model combining System Dynamics (SD) …
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Critical mobility in policy making for epidemic containment.
Moreno López JA, Mateo D, Hernando A, Meloni S, Ramasco JJ.
Sci Rep. 2025 Jan 24;15(1):3055. doi: 10.1038/s41598-025-86759-5.
Nonetheless, quantitative knowledge on the relationship between mobility-contagions and, consequently, on the efficiency of containment measures remains elusive. Here we introduce an agent-based model with a simple interaction between mobility and contacts. D …
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Updates to HIV transmission rate estimates along the HIV care continuum in the United States, 2019.
Baxter A, Gopalappa C, Islam MH, Viguerie A, Lyles C, Johnson AS, Khurana N, Farnham PG.
J Acquir Immune Defic Syndr. 2025 Jan 23. doi: 10.1097/QAI.0000000000003623. Online ahead of print.
METHODS: We updated Progression and Transmission of HIV 3.0, an agent-based simulation model, to estimate 2019 HIV transmission rates and distribution of transmissions by the HIV care continuum, race/ethnicity, transmission group, and age group. …
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Pharmacodynamics of interspecies interactions in polymicrobial infections.
Herzberg C, van Hasselt JGC.
NPJ Biofilms Microbiomes. 2025 Jan 21;11(1):20. doi: 10.1038/s41522-024-00621-6.
Here, we investigated how interspecies interactions in a multi-species bacterial community affect the pharmacodynamic response to antimicrobial treatment. To this end, we developed an in silico model which combined agent-based modeling with ordinary di …
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Connectome-based biophysical models of pathological protein spreading in neurodegenerative diseases.
Ren P, Cui X, Liang X.
PLoS Comput Biol. 2025 Jan 21;21(1):e1012743. doi: 10.1371/journal.pcbi.1012743. eCollection 2025 Jan.
To elucidate this dynamic process in vivo from a computational perspective, researchers have proposed three connectome-based biophysical models to simulate the spread of pathological proteins: the Network Diffusion Model, the Epidemic Spreading Model, and the …
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An agent-based model facilitating stakeholder engagement in management of estuaries along the Texas Gulf Coast (USA).
Wang HH, Banerjee P, Ragland CJ, Grant WE, Peterson TR.
MethodsX. 2024 Dec 20;14:103121. doi: 10.1016/j.mex.2024.103121. eCollection 2025 Jun.
We describe an agent-based model purposed for social learning, which was developed by stakeholders, with the technical assistance of professional modelers, to facilitate stakeholder involvement in modeling issues related to the development of an …
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Predictors of evacuation behavior: dataset on respondents’ route choice and web interaction.
Snopková D, Tancoš M, Herman L, Juřík V.
Sci Data. 2025 Jan 20;12(1):116. doi: 10.1038/s41597-025-04440-y.
Empirical data on human evacuation behavior are invaluable for adjusting and training computational algorithms that simulate evacuation processes, including agent-based modeling. We provide a dataset on human decision-making during evacuations from virtual bu …
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Effects of improved partner notification on the transmission of HIV and N. gonorrhoea among men who have sex with men: a modelling study.
Reitsema M, Wallinga J, van Benthem BHB, Op de Coul ELM, Van Sighem A, Schim van der Loeff M, Xiridou M.
Sex Transm Infect. 2025 Jan 20:sextrans-2023-055772. doi: 10.1136/sextrans-2023-055772. Online ahead of print.
We investigated the effects of improving PN on the transmission of HIV and Neisseria gonorrhoeae (NG) among MSM in the Netherlands. Methods We developed an agent-based model that describes the transmission of HIV and NG among MSM. In the baseline scenario, 14 …
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Fibrotic extracellular matrix preferentially induces a partial Epithelial-Mesenchymal Transition phenotype in a 3-D agent based model of fibrosis.
Kim KP, Lemmon CA.
Math Biosci. 2025 Jan 18:109375. doi: 10.1016/j.mbs.2025.109375. Online ahead of print.
As such, we sought to develop a 3-D computational model of epithelial spheroids that captured both EMT signaling dynamics and TGF-beta1-FN tethering dynamics. We have incorporated the bi-stable EMT switch model developed by Tian et al. (2013) into a 3-D multicellula …
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Evolutionary analysis of a coupled epidemic-voluntary vaccination behavior model with immunity waning on complex networks.
Meng X, Fan Y, Qiao Y, Lin J, Cai Z, Si S.
Risk Anal. 2025 Jan 18. doi: 10.1111/risa.17699. Online ahead of print.
The evolutionary model of voluntary vaccination strategy is integrated into the SIRSV model to characterize the impact of vaccination behavior on the infectious disease transmission. …The results indicate that the thresholds obtained from the agent-based …
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