Related papers: Phylogenetic tree reconstruction from genome-scale…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
Evolutionary mechanism in a self-organized system cause some functional changes that force to adapt new conformation of the interaction pattern between the components of that system. Measuring the structural differences one can retrace the…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…