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

The Evolutionary Dynamics of Bluetongue Virus

(2010) Giovanna Carpi et al.   JOURNAL OF MOLECULAR EVOLUTION

Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes

(2010) H. Liu et al.   JOURNAL OF VIROLOGY

Discovery and Characterization of Mammalian Endogenous Parvoviruses

(2010) A. Kapoor et al.   JOURNAL OF VIROLOGY

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes: the Parvoviridae and Circoviridae Are More than 40 to 50 Million Years Old

(2010) V. A. Belyi et al.   JOURNAL OF VIROLOGY

Analysis of Host–Parasite Incongruence in Papillomavirus Evolution Using Importance Sampling

(2010) Seena D. Shah et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Evolutionary History of Archaeal MCM Helicases: A Case Study of Vertical Evolution Combined with Hitchhiking of Mobile Genetic Elements

(2010) M. Krupovic et al.   MOLECULAR BIOLOGY AND EVOLUTION

Endogenous non-retroviral RNA virus elements in mammalian genomes

(2010) Masayuki Horie et al.   NATURE

Mimivirus: the emerging paradox of quasi-autonomous viruses

(2010) Jean-Michel Claverie et al.   TRENDS IN GENETICS

Endogenous Viral Elements in Animal Genomes

(2010) Aris Katzourakis et al.   PLoS Genetics

Unexpected Inheritance: Multiple Integrations of Ancient Bornavirus and Ebolavirus/Marburgvirus Sequences in Vertebrate Genomes

(2010) Vladimir A. Belyi et al.   PLoS Pathogens

Friendly Viruses

(2009) Mariana Varela et al.   Annals of the New York Academy of Sciences

The origin, evolution and structure of the protein world

(2009) Gustavo Caetano-Anollés et al.   BIOCHEMICAL JOURNAL

Genomic and structural aspects of protein evolution

(2009) Cyrus Chothia et al.   BIOCHEMICAL JOURNAL

The evolution of novel fungal genes from non-retroviral RNA viruses

(2009) Derek J Taylor et al.   BMC BIOLOGY

Discrete–continuous duality of protein structure space

(2009) Ruslan I Sadreyev et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The evolutionary biology of poxviruses

(2009) Austin L. Hughes et al.   INFECTION GENETICS AND EVOLUTION

Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses

(2009) S. Duffy et al.   JOURNAL OF GENERAL VIROLOGY

Viruses are essential agents within the roots and stem of the tree of life

(2009) Luis P. Villarreal et al.   JOURNAL OF THEORETICAL BIOLOGY

Virology in the 21st Century

(2009) L. W. Enquist et al.   JOURNAL OF VIROLOGY

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Photosystem I gene cassettes are present in marine virus genomes

(2009) Itai Sharon et al.   NATURE

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Compelling reasons why viruses are relevant for the origin of cells

(2009) Eugene V. Koonin et al.   NATURE REVIEWS MICROBIOLOGY

Reasons to include viruses in the tree of life

(2009) Nagendra R. Hegde et al.   NATURE REVIEWS MICROBIOLOGY

There is no such thing as a tree of life (and of course viruses are out!)

(2009) Didier Raoult   NATURE REVIEWS MICROBIOLOGY

Six comments on the ten reasons for the demotion of viruses

(2009) Jesús Navas-Castillo   NATURE REVIEWS MICROBIOLOGY

Viral genomes are part of the phylogenetic tree of life

(2009) Ethan B. Ludmir et al.   NATURE REVIEWS MICROBIOLOGY

Ten good reasons not to exclude giruses from the evolutionary picture

(2009) Jean-Michel Claverie et al.   NATURE REVIEWS MICROBIOLOGY

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Nature of the protein universe

(2009) M. Levitt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms

(2009) M. Boyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of template-based models in CASP8 with standard measures

(2009) Domenico Cozzetto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The origin of viruses

(2009) Patrick Forterre et al.   RESEARCH IN MICROBIOLOGY

Extremely High Mutation Rate of a Hammerhead Viroid

(2009) S. Gago et al.   SCIENCE

Probing the “Dark Matter” of Protein Fold Space

(2009) William R. Taylor et al.   STRUCTURE

New dimensions of the virus world discovered through metagenomics

(2009) David M. Kristensen et al.   TRENDS IN MICROBIOLOGY

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

(2008) Gustavo Caetano-Anolles   Frontiers in Bioscience-Landmark

The virophage as a unique parasite of the giant mimivirus

(2008) Bernard La Scola et al.   NATURE

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS

The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture

(2008) Adrian J. Gibbs et al.   PLoS One