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Many models of genome rearrangement involve operations (e.g. inversions and translocations) that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…
Starting from the hypothesis that both physics, in particular space-time and the physical vacuum, and the corresponding mathematics are discrete on the Planck scale we develop a certain framework in form of a class of ' cellular networks'…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
Identifiability of phylogenetic models is a necessary condition to ensure that the model parameters can be uniquely determined from data. Mixture models are phylogenetic models where the probability distributions in the model are convex…
Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species. The architecture of these webs seems to pervade some of their robust and fragile behaviour. Recent work indicates that there is…
Cellular response to environmental and internal signals can be modeled by dynamical gene regulatory networks (GRN). In the literature, three main classes of gene network models can be distinguished: (i) non-quantitative (or data-based)…
Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…