Related papers: Phylogenetics and the human microbiome
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
The human niche represents the intersection of biological, ecological, cultural, and technological processes that have co-evolved to shape human adaptation and societal complexity. This paper explores the human niche through the lens of…
Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…
This paper shows that differentiating the lifetimes of two phenotypes independently from their fertility can lead to a qualitative change in the equilibrium of a population: since survival and reproduction are distinct functional aspects of…
Population stratification is a problem encountered in several areas of biology and public health. We tackle this problem by mapping a population and its elements attributes into a hypergraph, a natural extension of the concept of graph or…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
Our planet is experiencing an accelerated process of change associated to a variety of anthropogenic phenomena. The future of this transformation is uncertain, but there is general agreement about its negative unfolding that might threaten…
Machine learning (ML) is poised to drive innovations in clinical microbiomics, such as in disease diagnostics and prognostics. However, the successful implementation of ML in these domains necessitates the development of reproducible,…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Bioconvection, a phenomenon arising from the collective motion of motile microorganisms, plays a crucial role in shaping microbial distributions, fluid dynamics, and bloom formation in aquatic environments. While extensive research has…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
The interpretation of recent environmental genomics data exposes the far-reaching influence of horizontal gene transfer, and is changing our basic concepts of organism, species and evolution itself.
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…