Browsing by Author "Varela, Pedro L."
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- Author Correction: Human Sexual Cycles are Driven by Culture and Match Collective MoodsPublication . Wood, Ian B.; Varela, Pedro L.; Bollen, Johan; Rocha, Luis M.; Gonçalves-Sá, JoanaA correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
- EpiLog: A software for the logical modelling of epithelial dynamicsPublication . Varela, Pedro L.; Ramos, Camila V.; Monteiro, Pedro T.; Chaouiya, ClaudineCellular responses are governed by regulatory networks subject to external signals from surrounding cells and to other micro-environmental cues. The logical (Boolean or multi-valued) framework proved well suited to study such processes at the cellular level, by specifying qualitative models of involved signalling pathways and gene regulatory networks. Here, we describe and illustrate the main features of EpiLog, a computational tool that implements an extension of the logical framework to the tissue level. EpiLog defines a collection of hexagonal cells over a 2D grid, which embodies a mono-layer epithelium. Basically, it defines a cellular automaton in which cell behaviours are driven by associated logical models subject to external signals. EpiLog is freely available on the web at http://epilog-tool.org. It is implemented in Java (version ≥1.7 required) and the source code is provided at https://github.com/epilog-tool/epilog under a GNU General Public License v3.0.
- Impact of changing cell-cell communication network in models of epithelial pattern formationPublication . Varela, Pedro L.; Monteiro, Pedro T.; Chaouiya, ClaudineWhen modelling multi-cellular systems, one has to account for cell-cell signalling in addition to the molecular networks driving cell behaviours. Here, we aim at exploring how the topology of the cell-cell communication network impacts the behaviour of the whole multicellular system. More precisely, we focus on epithelial pattern formation, on which our question can be rephrased in terms of cell sizes and shapes. Relying on a logical modelling framework, and using a simple lateral inhibition model over a population of epithelial cells, we assess the model behaviours considering a variety of communication networks. This study suggests that reasonable deviations from a fixed grid (with regular hexagonal shaped cells) do not change much the resulting patterns. We further explore the impact of cell shapes and show that characteristics such as network regularity and number of shared neighbours of contacting cells are relevant to qualify such deviations.