BioDynaMo is a general purpose agent-based modeling software platform, and it took inspiration from an older software called CX3D. We want to give an overview over impactful publications based on CX3D because of the relevance of the agent-based modelling approach.


  • Roman Bauer et al. Creative destruction: a basic computational model of cortical layer formation. In: Cerebral Cortex, 31(7), 2021. DOI: 10.1093/cercor/bhab003.


  • Pegah Kassraian-Fard et al. A generative growth model for thalamocortical axonal branching in primary visual cortex. In: PLoS computational biology, 16(2), 2020. DOI: 10.1371/journal.pcbi.1007315.


  • Roman Bauer and Marcus Kaiser. Nonlinear growth: an origin of hub organization in complex networks. In: Royal Society open science, 4(3), 2017. DOI: 10.1098/rsos.160691.
  • Roman Bauer and Marcus Kaiser. Organisational principles of connectomes: changes during evolution and development. In: Brain Evolution by Design (pp. 387-401), Springer, 2017. DOI: 10.1007/978-4-431-56469-0_17.


  • Roman Bauer et al. Developmental origin of patchy axonal connectivity in the neocortex: a computational model. In: Cerebral cortex, 24(2), 2014. DOI: 10.1093/cercor/bhs327.
  • Roman Bauer et al. Developmental self-construction and-configuration of functional neocortical neuronal networks. In: PLoS computational biology, 10(12), 2014. DOI: 10.1371/journal.pcbi.1003994.
  • Roman Bauer et al. A computational model incorporating neural stem cell dynamics reproduces glioma incidence across the lifespan in the human population. In: PLoS one, 9(11), 2014. DOI: 10.1371/journal.pone.0111219.


  • Frederic Zubler et al. Simulating cortical development as a self constructing process: a novel multi-scale approach combining molecular and physical aspects. In: PLoS computational biology, 9(8), 2013. DOI: 10.1371/journal.pcbi.1003173.
  • Roman Bauer. Self-construction and-configuration of functional neuronal networks. Doctoral dissertation, ETH Zurich, 2013. DOI: 10.3929/ethz-a-009988668.


  • Rene Brun and Fons Rademakers. ROOT — An object oriented data analysis framework. In: Nuclear Instruments and Methods in Physics Research, 389, 1997. DOI: 10.1016/S0168-9002(97)00048-X.