Microbial genome analysis: the COG approach
For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a
popular tool for microbial genome annotation and comparative genomics. Initially created for …
popular tool for microbial genome annotation and comparative genomics. Initially created for …
A biologist's guide to Bayesian phylogenetic analysis
Bayesian methods have become very popular in molecular phylogenetics due to the
availability of user-friendly software for running sophisticated models of evolution. However …
availability of user-friendly software for running sophisticated models of evolution. However …
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
Abstract eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at
different taxonomic levels, each with integrated and summarized functional annotations …
different taxonomic levels, each with integrated and summarized functional annotations …
Insights into land plant evolution garnered from the Marchantia polymorpha genome
The evolution of land flora transformed the terrestrial environment. Land plants evolved from
an ancestral charophycean alga from which they inherited developmental, biochemical, and …
an ancestral charophycean alga from which they inherited developmental, biochemical, and …
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more
OMA is an established resource to elucidate evolutionary relationships among genes from
currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise …
currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise …
A multidimensional systems biology analysis of cellular senescence in aging and disease
RA Avelar, JG Ortega, R Tacutu, EJ Tyler, D Bennett… - Genome biology, 2020 - Springer
Background Cellular senescence, a permanent state of replicative arrest in otherwise
proliferating cells, is a hallmark of aging and has been linked to aging-related diseases …
proliferating cells, is a hallmark of aging and has been linked to aging-related diseases …
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Background A major bottleneck in our understanding of the molecular underpinnings of life
is the assignment of function to proteins. While molecular experiments provide the most …
is the assignment of function to proteins. While molecular experiments provide the most …
Discovery of human signaling systems: pairing peptides to G protein-coupled receptors
The peptidergic system is the most abundant network of ligand-receptor-mediated signaling
in humans. However, the physiological roles remain elusive for numerous peptides and …
in humans. However, the physiological roles remain elusive for numerous peptides and …
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
Current methods for inference of phylogenetic trees require running complex pipelines at
substantial computational and labor costs, with additional constraints in sequencing …
substantial computational and labor costs, with additional constraints in sequencing …
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
Abstract The Orthologous Matrix (OMA) is a leading resource to relate genes across many
species from all of life. In this update paper, we review the recent algorithmic improvements …
species from all of life. In this update paper, we review the recent algorithmic improvements …