Advancing microbial sciences by individual-based modelling

FL Hellweger, RJ Clegg, JR Clark, CM Plugge… - Nature Reviews …, 2016 - nature.com
Remarkable technological advances have revealed ever more properties and behaviours of
individual microorganisms, but the novel data generated by these techniques have not yet …

Agent-based models in cellular systems

J Pleyer, C Fleck - Frontiers in Physics, 2023 - frontiersin.org
This mini-review discusses agent-based models as modeling techniques for studying
pattern formation of multi-cellular systems in biology. We introduce and compare different …

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

E Bauer, J Zimmermann, F Baldini… - PLoS computational …, 2017 - journals.plos.org
Recent advances focusing on the metabolic interactions within and between cellular
populations have emphasized the importance of microbial communities for human health …

Agent-based modeling of microbial communities

K Nagarajan, C Ni, T Lu - ACS synthetic biology, 2022 - ACS Publications
Microbial communities are complex living systems that populate the planet with diverse
functions and are increasingly harnessed for practical human needs. To deepen the …

Pathways to cellular supremacy in biocomputing

L Grozinger, M Amos, TE Gorochowski… - Nature …, 2019 - nature.com
Synthetic biology uses living cells as the substrate for performing human-defined
computations. Many current implementations of cellular computing are based on the …

A systematic literature review of agents applied in healthcare

D Isern, A Moreno - Journal of medical systems, 2016 - Springer
Intelligent agents and healthcare have been intimately linked in the last years. The intrinsic
complexity and diversity of care can be tackled with the flexibility, dynamics and reliability of …

Agent-based modelling in synthetic biology

TE Gorochowski - Essays in biochemistry, 2016 - portlandpress.com
Biological systems exhibit complex behaviours that emerge at many different levels of
organization. These span the regulation of gene expression within single cells to the use of …

A mechanistic Individual-based Model of microbial communities

PG Jayathilake, P Gupta, B Li, C Madsen, O Oyebamiji… - PloS one, 2017 - journals.plos.org
Accurate predictive modelling of the growth of microbial communities requires the credible
representation of the interactions of biological, chemical and mechanical processes …

[HTML][HTML] Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor

M Wang, X Chen, X Liu, Y Fang, X Zheng, T Huang… - Cell Reports, 2022 - cell.com
Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a
community, functionally specialized strains can perform different yet complementary steps …

Integrating systems and synthetic biology to understand and engineer microbiomes

PA Leggieri, Y Liu, M Hayes, B Connors… - Annual Review of …, 2021 - annualreviews.org
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly
limitless chemical transformations could be harnessed to benefit agriculture, medicine, and …