Latest papers on Agent-Based Modeling in PubMed

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 2026-11-08 00:06:36.

1. SwimmingIndividuals: A high-performance agent-based model for marine ecosystems.

   Woodstock MS, Mattern JP, Wu Z, Britten GL.

   PLoS Comput Biol. 2026 Nov 6;22(11):e1013610. doi: 10.1371/journal.pcbi.1013610. Online ahead of print.

   Because they are based on established theory, mechanistic models are essential for projecting ecological responses to novel conditions. Yet mechanistic agent-based model (ABM) applications have often been limited by computational constraints. …We dem …

2. Application of Mechanistic Modeling to Support Dose-Relevant Decision Making for CAR-T Cell Therapy in Oncology: A Systematic Scoping Review.

   Odujinrin D, McClelland G.

   Clin Transl Sci. 2026 Nov;19(11):e70756. doi: 10.1111/cts.70756.

   Eligible studies reported original CK/PD, PK/PD, QSP, PBPK/PD, stochastic, or agent-based models for dose-relevant application or regimen optimization. Nineteen studies met the inclusion criteria (13 mechanistic and 6 semi-mechanistic models) spanning …

3. Understanding African swine fever dynamics in South Korean pig farms through agent-based modeling and spatiotemporal analysis of farm outbreaks.

   Tanveer M, Hirwa F, Ntakiyisumba E, Won G.

   Front Vet Sci. 2026 Oct 22;13:1945299. doi: 10.3389/fvets.2026.1945299. eCollection 2026.

   African swine fever continues to pose a major threat to the swine industry in South Korea since 2019, with increased farm outbreaks in 2026. This study applied agent-based modeling and spatiotemporal outbreak analysis to characterize ASF dynamics at within-fa …

4. How AI threat perception relates to post-adoptive AI agent engagement: the dual paths of self-efficacy and defensive motivation.

   Yang G, Feng M, Yang W.

   Front Psychol. 2026 Oct 22;17:1887571. doi: 10.3389/fpsyg.2026.1887571. eCollection 2026.

   INTRODUCTION: As AI evolves into agent-based forms, AI threat perception has become a defining workplace concern. Informed by Cognitive Appraisal Theory and Protection Motivation Theory, this cross-sectional study investigates how AI threat perception relates to pos …

5. HydroGuard: a controlled release hydrogel-phage delivery system to combat catheter-associated urinary tract infections.

   Rao S, McLean R, Zakir Hussain A.

   Front Syst Biol. 2026 Oct 22;6:1923468. doi: 10.3389/fsysb.2026.1923468. eCollection 2026.

   Agent-based biofilm simulations captured emergent spatial dynamics under nutrient, flow, and pH constraints, while a coupled predator-prey model investigated phage-bacteria population dynamics within the degrading GelMA matrix. …By integrating synthetic bio …

6. Agent-based modelling of late-stage mechanical loading of femur defects in prematurely ageing PolgA mice.

   Kendall JJ, Ledoux C, Marques FC, Kuhn GA, Schulte FA, Müller R.

   Front Bioeng Biotechnol. 2026 Oct 21;14:1879777. doi: 10.3389/fbioe.2026.1879777. eCollection 2026.

   To test this hypothesis, we developed a micro-Multiphysics Agent-based (micro-MPA) model of the remodelling phase during bone regeneration. We employed a hierarchical grid-search to calibrate the model based on bone volume fraction using weekly time-la …

7. Agent-Based Modelling of Microbialite Formation Through Sedimentation and Precipitation Dynamics.

   Rodgers N, Fogret L, van Zuilen M, Cleaves HJ, Rajamani S, McMahon S.

   Geobiology. 2026 Nov-Dec;24(6):e70071. doi: 10.1111/gbi.70071.

   In this work, we present an agent-based model of microbialite formation using a fast, open-source, high-level microbialite modelling framework, written in Julia. …Further exploration and extension of our model may offer new approaches to resol …

8. Pooled testing for SARS-CoV-2 surveillance in schools: evaluation of transmission control, testing resources, and educational disruption.

   Colosi E, Calmon L, Fässli M, Koch KN, Bielicki JA, Colizza V.

   Int J Infect Dis. 2026 Nov 4:109233. doi: 10.1016/j.ijid.2026.109233. Online ahead of print.

   METHODS: We analyzed data from the pooled testing program implemented in 62 primary schools in Basel-Landschaft, Switzerland, during the Fall-Winter 2021 Delta wave. We fitted an agent-based transmission model informed by pooled and individual testing results …

9. Big Data and Artificial Intelligence in Sleep Medicine: Opportunities and Obstacles.

   Maghsoudi A, Ong JL, Razjouyan J, Sharafkhaneh A.

   Sleep Med Clin. 2026 Dec;21(4):619-631. doi: 10.1016/j.jsmc.2026.08.017. Epub 2026 Sep 28.

   It outlines the evolution from traditional rule-based sleep staging to advanced machine learning, deep learning, and emerging foundation and agent-based models. The article highlights diverse data sources and discusses the challenges of data quality, harmoniz …

10. Computational Models of the Foreign Body Response: A Focus on Biomaterial Properties.

    Marradi M, Riccio J, van Griensven M, Presotto L, Chirico G, Carlier A.

    J Biomed Mater Res A. 2026 Nov;114(11):e70181. doi: 10.1002/jbm.a.70181.

    Existing approaches, including ordinary differential equation (ODE), partial differential equation (PDE), and agent-based (AB) models, have provided important insights into inflammatory signaling, macrophage dynamics, fibrosis progression, and capsule formati …

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