Bibliography

Cogno N, Axenie C, Bauer R, Vavourakis V. Recipes for calibration and validation of agent-based models in cancer biomedicine. October 30th 2023 ArXiv. https://arxiv.org/abs/2310.20031

de Montigny J, Sernagor E, Bauer R. Retinal self-organization: a model of retinal ganglion cells and starburst amacrine cells mosaic formation. Open Biol. 2023 Apr;13(4):220217. DOI: 10.1098/rsob.220217

Breitwieser L, Hesam A, Rademakers F, Luna JG, and Mutlu O. High-Performance and Scalable Agent-Based Simulation with BioDynaMo. In Proceedings of the 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming (PPoPP '23). Association for Computing Machinery, New York, NY, USA, 174–188. DOI: 10.1145/3572848.3577480

Demetriades M, Zivanovic M, Hadjicharalambous M, Ioannou E, Ljujic B, Vucicevic K, Ivosevic Z, Dagovic A, Milivojevic N, Kokkinos O, Bauer R, and Vavourakis V. Interrogating and Quantifying In Vitro Cancer Drug Pharmacodynamics via Agent-Based and Bayesian Monte Carlo Modelling.  Pharmaceutics 2022;14(4):749 DOI: 10.3390/pharmaceutics14040749 

Gazeli K, Hadjicharalambous M, Ioannou E, Gazeli O, Lazarou C, Anastassiou C, Svarnas P, Vavourakis V, Georghiou GE. Interrogating an in silico model to determine helium plasma jet and chemotherapy efficacy against B16F10 melanoma cells. Appl. Phys. Lett. 2022;120:054101 DOI: 10.1063/5.0077694

Cogno N, Bauer R, Durante M. A 3D Agent-Based Model of Lung Fibrosis.  Symmetry. 2022;14(1):90. DOI: 10.3390/sym14010090 

Breitwieser L, Hesam A, de Montigny J, Vavourakis V, Iosif A, Jennings J, Kaiser M, Manca M, Di Meglio A, Al-Ars Z, Rademakers F, Mutlu O, Bauer R. BioDynaMo: a modular platform for high-performance agent-based simulation. Bioinformatics. 2022;38(2):453–60. doi: 10.1093/bioinformatics/btab649. PMID: 34529036; PMCID: PMC8723141.

Hesam A, Breitwieser L, Rademakers F, Al-Ars Z. GPU Acceleration of 3D Agent-Based Biological Simulations. arXiv:2105.00039

de Montigny J, Sernagor E, Bauer R. Retinal self-organization: a model of RGC and SAC mosaic formation. bioRXive DOI: 10.1101/2021.10.22.465398 

de Montigny J, Iosif A, Breitwieser L, Manca M, Bauer R, Vavourakis V. An in silico hybrid continuum-/agent-based procedure to modelling cancer development: Interrogating the interplay amongst glioma invasion, vascularity and necrosis. Methods. DOI: 10.1016/j.ymeth.2020.01.006 

(code and supplementary material available here)

Bauer R. Computational Neuroscience and Cryonics: Strangers that are just friends waiting to happen. Cryonics 2020 Vol.41 Issue 2 pages:9-13

Breitwieser L, Hesam A, de Montigny J, Vavourakis V, Iosif A, Jennings J, Kaiser M, Manca M, Di Meglio A, Al-Ars Z, Rademakers F, Mutlu O, Bauer R. BioDynaMo: an agent-based simulation platform for scalable computational biology research. bioRxiv doi: 10.1101/2020.06.08.139949

Gonzalez-de-Aledo P, Vladimirov A, Manca M, Baugh J, Asai R, Kaiser M, Bauer R. An optimization approach for agent-based computational models of biological development. Advances in Engineering Software. 2018;121:262-275 DOI: 10.1016/j.advengsoft.2018.03.010

Nguyen N. Distributed BioDynaMo. CERN openlab Report 2018

Bauer R, Breitwieser L, Di Meglio A, Johard L, Kaiser M, Manca M, Mazzara M, Rademakers F, Talanov M, Tchitchigin AD. The BioDynaMo Project: Experience Report. in "Advanced Research on Biologically Inspired Cognitive Architectures" DOI: 10.4018/978-1-5225-1947-8.ch006 available on ArXiv

Breitwieser L, Bauer R, Di Meglio A, Johard L, Kaiser M, Manca M, Mazzara M, Rademakers F, Talanov M. The BioDynaMo Project: Creating a Platform for Large-Scale Reproducible Biological Simulations. arXiv:1608.04967

Sabitov A, Gafarov F, Kugurakova V, Abramov V. The Implementation of Growth Guidance Factor Diffusion via Octree Spatial Structures for Neuronal Systems Simulation. HCC 2017: Human Centered Computing pp 158-163 DOI: 10.1007/978-3-319-74521-3_18

Sayfullin S, Akhmetov F, Mazzara M, Mustafin R, Rivera V. Gene Expression for Simulation of Biological Tissue. 2018 32nd International Conference on Advanced Information Networking and Applications Workshops (WAINA), Krakow, 2018, pp. 232-239, doi: 10.1109/WAINA.2018.00092.

Hesam AS. Faster than the Speed of Life: Accelerating Developmental BiologySimulations with GPUs and FPGAs. Master Thesis in Computer Engineering at TU Delft CE-MS-2018-24

Breitwieser LJ. BioDynaMo: A New Platform forLarge-Scale Biological Simulation. Software Engineering and Management Master's Thesis at Graz University of Technology (2016)

Breitwieser L, Bauer R, Di Meglio A, Johard L, Kaiser M, Manca M, Mazzara M, Rademakers F, Talanov M.  The BioDynaMo project: Creating a platform for large-scale reproducible biological simulations. CEUR Workshop Proceedings 2016 vol 1686