Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements

A novel insect-infecting virga/nege-like virus group and its pervasive endogenization into insect genomes

(2017) Hideki Kondo et al.   VIRUS RESEARCH

Co-option of endogenous viral sequences for host cell function

(2017) John A .Frank et al.   Current Opinion in Virology

Time-Dependent Rate Phenomenon in Viruses

(2016) Pakorn Aiewsakun et al.   JOURNAL OF VIROLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity

(2016) Ana Carolina M. Junqueira et al.   Scientific Reports

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

The bornavirus-derived human protein EBLN1 promotes efficient cell cycle transit, microtubule organisation and genome stability

(2016) Katie N. Myers et al.   Scientific Reports

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

(2015) Helen Attrill et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Endogenous viruses: Connecting recent and ancient viral evolution

(2015) Pakorn Aiewsakun et al.   VIROLOGY

Most partial domains in proteins are alignment and annotation artifacts

(2015) Deborah A Triant et al.   GENOME BIOLOGY

Deep Recombination: RNA and ssDNA Virus Genes in DNA Virus and Host Genomes

(2015) Kenneth M. Stedman   Annual Review of Virology

The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes

(2015) Shuangmei Ding et al.   PLoS One

Simultaneous Bayesian Estimation of Alignment and Phylogeny under a Joint Model of Protein Sequence and Structure

(2014) Joseph L. Herman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inhibition of Borna disease virus replication by an endogenous bornavirus-like element in the ground squirrel genome

(2014) K. Fujino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently "Orphan" Viral Proteins

(2013) D. B. Kuchibhatla et al.   JOURNAL OF VIROLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

(2013) Simon Roux et al.   Nature Communications

A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

(2012) Geoffrey S Diemer et al.   Biology Direct

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

(2012) T. W. Whon et al.   JOURNAL OF VIROLOGY

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

(2012) C. J. Challis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Remote Sequence Homology in Disordered Proteins: Discovery of Conserved Motifs in the N-Termini of Mononegavirales phosphoproteins

(2012) David Karlin et al.   PLoS One

Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny

(2012) Jessica A. Thomas et al.   SYSTEMATIC BIOLOGY

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution

(2011) Aare Abroi et al.   BIOESSAYS

Co-divergence and host-switching in the evolution of tobamoviruses

(2011) A. H. Stobbe et al.   JOURNAL OF GENERAL VIROLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Episodic radiations in the fly tree of life

(2011) B. M. Wiegmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-Retroviral Fossils in Vertebrate Genomes

(2011) Masayuki Horie et al.   Viruses-Basel

Endogenous Viral Elements in Animal Genomes

(2010) Aris Katzourakis et al.   PLoS Genetics

Virgaviridae: a new family of rod-shaped plant viruses

(2009) Michael J. Adams et al.   ARCHIVES OF VIROLOGY

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Evolutionary Capture of Viral and Plasmid DNA by Yeast Nuclear Chromosomes

(2009) A. Carolin Frank et al.   EUKARYOTIC CELL

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS