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Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…
Ecological systems show a variety of characteristic patterns of biodiversity in space and time. It is a challenge for theory to find models that can reproduce and explain the observed patterns. Since the advent of island biogeography these…
We propose here to interpret and model peculiar plant morphologies (cushions, tussocks) observed in the Andean altiplano as localized structures. Such structures resulting in a patchy, aperiodic aspect of the vegetation cover are…
RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…
Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…
We describe a hybrid agent-based model and simulation of urban morphogenesis. It consists of a cellular automata grid coupled to a dynamic network topology. The inherently heterogeneous properties of urban structure and function are taken…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
A major challenge in plant developmental biology is to understand how plant growth is coordinated by interacting hormones and genes. To meet this challenge, it is important to not only use experimental data, but also formulate a…
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
The dynamic stability of the Boolean networks representing a model for the gene transcriptional regulation (Kauffman model) is studied by calculating analytically and numerically the Hamming distance between two evolving configurations.…
Spatial models for areal data are often constructed such that all pairs of adjacent regions are assumed to have near-identical spatial autocorrelation. In practice, data can exhibit dependence structures more complicated than can be…
The adoption of agroecological practices will be crucial to address the challenges of climate change and biodiversity loss. Such practices favor the cultivation of plants in complex mixtures with layouts differing from the monoculture…
Nonuniform spatial distributions of vegetation in scarce environments consist of either gaps, bands often called tiger bush or patches that can be either self-organized or spatially localized in space. When the level of aridity is…
Do ecosystems primarily reflect evolutionary history or current environment? Predicting land-atmosphere exchange hinges on this unresolved question. Plant traits adapt to particular environments over evolutionary timescales, yet their…
Random Boolean networks (RBNs) are models of genetic regulatory networks. It is useful to describe RBNs as self-organizing systems to study how changes in the nodes and connections affect the global network dynamics. This article reviews…
Nature offers remarkable examples of complex photonic architectures such as those responsible for the iridescent colors of butterfly wings that emerge spontaneously during growth, well before any centralized control takes place. Arising…
We consider two mathematical dynamical models of gene regulatory networks (GRNs) and obtain results on robust synchronization on these dynamical models based on the existing theoretical results in the coupled cell network formalism. We also…
How far is neuroepithelial cell proliferation in the developing central nervous system a deterministic process? Or, to put it in a more precise way, how accurately can it be described by a deterministic mathematical model? To provide tracks…