The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes

Functional Characterization of a Conserved Archaeal Viral Operon Revealing Single-Stranded DNA Binding, Annealing and Nuclease Activities

(2015) Yang Guo et al.   JOURNAL OF MOLECULAR BIOLOGY

Origins and evolution of viruses of eukaryotes: The ultimate modularity

(2015) Eugene V. Koonin et al.   VIROLOGY

Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase

(2014) Darius Kazlauskas et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Unique genome replication mechanism of the archaeal virus AFV1

(2014) Mery Pina et al.   MOLECULAR MICROBIOLOGY

Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages

(2014) Frazer J Rixon et al.   Current Opinion in Virology

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery

(2014) Kira S. Makarova et al.   Frontiers in Microbiology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

(2013) N. Philippe et al.   SCIENCE

Poxvirus DNA Replication

(2013) B. Moss   Cold Spring Harbor Perspectives in Biology

Helicase Loading at Chromosomal Origins of Replication

(2013) S. P. Bell et al.   Cold Spring Harbor Perspectives in Biology

A virocentric perspective on the evolution of life

(2013) Eugene V Koonin et al.   Current Opinion in Virology

The major role of viruses in cellular evolution: facts and hypotheses

(2013) Patrick Forterre et al.   Current Opinion in Virology

Two distinct SSB protein families in nucleo-cytoplasmic large DNA viruses

(2012) Darius Kazlauskas et al.   BIOINFORMATICS

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Structure of a topoisomerase II–DNA–nucleotide complex reveals a new control mechanism for ATPase activity

(2012) Bryan H Schmidt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Herpes Simplex Viruses: Mechanisms of DNA Replication

(2012) S. K. Weller et al.   Cold Spring Harbor Perspectives in Biology

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus

(2011) Aurore Gorlas et al.   ENVIRONMENTAL MICROBIOLOGY

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

(2011) M. Krupovic et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

All tangled up: how cells direct, manage and exploit topoisomerase function

(2011) Seychelle M. Vos et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size

(2011) Darius Kazlauskas et al.   NUCLEIC ACIDS RESEARCH

How a DNA Polymerase Clamp Loader Opens a Sliding Clamp

(2011) B. A. Kelch et al.   SCIENCE

Identification of a bifunctional primase–polymerase domain of corynephage BFK20 replication protein gp43

(2011) Nora Halgasova et al.   VIRUS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Comparative Analysis of the Mosaic Genomes of Tailed Archaeal Viruses and Proviruses Suggests Common Themes for Virion Architecture and Assembly with Tailed Viruses of Bacteria

(2010) Mart Krupovič et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of a Domain of the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus Single-Strand DNA-Binding Protein LEF-3 Essential for Viral DNA Replication

(2010) M. Yu et al.   JOURNAL OF VIROLOGY

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

Nucleases: diversity of structure, function and mechanism

(2010) Wei Yang   QUARTERLY REVIEWS OF BIOPHYSICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity

(2009) Natalya Yutin et al.   Biology Direct

DNA Ligases: Progress and Prospects

(2009) Stewart Shuman   JOURNAL OF BIOLOGICAL CHEMISTRY

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

(2009) P. Forterre et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

(2009) Natalya Yutin et al.   Virology Journal

The MCM complex: (just) a replicative helicase?

(2008) Alessandro Costa et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases

(2008) Lakshminarayan M Iyer et al.   Biology Direct

Vaccinia Virus DNA Ligase Recruits Cellular Topoisomerase II to Sites of Viral Replication and Assembly

(2008) Y.-C. J. Lin et al.   JOURNAL OF VIROLOGY