A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

I Dukovski, D Bajić, JM Chacón, M Quintin, JCC Vila… - Nature protocols, 2021 - nature.com
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …

The complex genetic basis and multilayered regulatory control of yeast pseudohyphal growth

A Kumar - Annual Review of Genetics, 2021 - annualreviews.org
Eukaryotic cells are exquisitely responsive to external and internal cues, achieving precise
control of seemingly diverse growth processes through a complex interplay of regulatory …

[KSIĄŻKA][B] Mechanisms of morphogenesis

JA Davies - 2023 - books.google.com
Mechanisms of Morphogenesis, Third Edition offers a bottom-up discussion of mechanisms
of cell and tissue morphogenesis in a diverse array of organisms, including prokaryotes …

An off-lattice discrete model to characterise filamentous yeast colony morphology

K Li, JEF Green, H Tronnolone, AKY Tam… - PLOS Computational …, 2024 - journals.plos.org
We combine an off-lattice agent-based mathematical model and experimentation to explore
filamentous growth of a yeast colony. Under environmental stress, Saccharomyces …

Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa

N Luo, S Wang, J Lu, X Ouyang, L You - Molecular systems biology, 2021 - embopress.org
Branching pattern formation is common in many microbes. Extensive studies have focused
on addressing how such patterns emerge from local cell–cell and cell–environment …

Morphology and size of bacterial colonies control anoxic microenvironment formation in porous media

G Ceriotti, SM Borisov, JS Berg… - Environmental Science & …, 2022 - ACS Publications
Bacterial metabolisms using electron acceptors other than oxygen (eg, methanogenesis and
fermentation) largely contribute to element cycling and natural contaminant attenuation …

Integrative analysis of yeast colony growth

T Gaizer, J Juhász, B Pillér, H Szakadáti… - Communications …, 2024 - nature.com
Yeast colonies are routinely grown on agar plates in everyday experimental settings to
understand basic molecular processes, produce novel drugs, improve health, and so on …

Nutrient-limited growth with non-linear cell diffusion as a mechanism for floral pattern formation in yeast biofilms

A Tam, JEF Green, S Balasuriya, EL Tek… - Journal of theoretical …, 2018 - Elsevier
Previous experiments have shown that mature yeast mat biofilms develop a floral
morphology, characterised by the formation of petal-like structures. In this work, we …

Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies

K Hitomi, J Weng, BW Ying - Frontiers in Microbiology, 2022 - frontiersin.org
Colony growth is a common phenomenon of structured populations dispersed in nature;
nevertheless, studies on the spatial distribution of colonies are largely insufficient. Here, we …

A thin-film extensional flow model for biofilm expansion by sliding motility

A Tam, JEF Green, S Balasuriya… - … of the Royal …, 2019 - royalsocietypublishing.org
In the presence of glycoproteins, bacterial and yeast biofilms are hypothesized to expand by
sliding motility. This involves a sheet of cells spreading as a unit, facilitated by cell …