Computational characterization of multiple Gag-like human proteins
In a genome-wide analysis, we have identified 85 human genes encoding 103 protein
isoforms that resemble retroviral Gag proteins. These genes were domesticated from …
isoforms that resemble retroviral Gag proteins. These genes were domesticated from …
Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been
viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life …
viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life …
Grad-seq guides the discovery of ProQ as a major small RNA-binding protein
The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA)
classes has been greatly facilitated by the advent of next-generation RNA sequencing …
classes has been greatly facilitated by the advent of next-generation RNA sequencing …
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe
The farming way of life originated in the Near East some 11,000 years ago and had reached
most of the European continent 5000 years later. However, the impact of the agricultural …
most of the European continent 5000 years later. However, the impact of the agricultural …
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however,
the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we …
the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we …
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin
Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina,(
Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens …
Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens …
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
Background In recent years, model based approaches such as maximum likelihood have
become the methods of choice for constructing phylogenies. A number of authors have …
become the methods of choice for constructing phylogenies. A number of authors have …
Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes)
Production of massive DNA sequence data sets is transforming phylogenetic inference, but
best practices for analyzing such data sets are not well established. One uncertainty is …
best practices for analyzing such data sets are not well established. One uncertainty is …
Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges
DP Faith, AM Baker - Evolutionary bioinformatics, 2006 - journals.sagepub.com
Biodiversity conservation addresses information challenges through estimations
encapsulated in measures of diversity. A quantitative measure of phylogenetic …
encapsulated in measures of diversity. A quantitative measure of phylogenetic …
A cell atlas of the chick retina based on single-cell transcriptomics
Retinal structure and function have been studied in many vertebrate orders, but molecular
characterization has been largely confined to mammals. We used single-cell RNA …
characterization has been largely confined to mammals. We used single-cell RNA …