Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

(2013) Mircea Podar et al.   Biology Direct

Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability

(2013) Miao Pan et al.   EXTREMOPHILES

Why Are There So Many Diverse Replication Machineries?

(2013) Patrick Forterre   JOURNAL OF MOLECULAR BIOLOGY

Novel Interaction of the Bacterial-Like DnaG Primase with the MCM Helicase in Archaea

(2013) Robert J. Bauer et al.   JOURNAL OF MOLECULAR BIOLOGY

The effects of model choice and mitigating bias on the ribosomal tree of life

(2013) Erica Lasek-Nesselquist et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Gene similarity networks provide tools for understanding eukaryote origins and evolution

(2013) D. Alvarez-Ponce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The archaeal DnaG protein needs Csl4 for binding to the exosome and enhances its interaction with adenine-rich RNAs

(2013) Linlin Hou et al.   RNA Biology

Archaeology of Eukaryotic DNA Replication

(2013) K. S. Makarova et al.   Cold Spring Harbor Perspectives in Biology

Specificity and Function of Archaeal DNA Replication Initiator Proteins

(2013) Rachel Y. Samson et al.   Cell Reports

Essential Developmental, Genomic Stability, and Tumour Suppressor Functions of the Mouse Orthologue of hSSB1/NABP2

(2013) Wei Shi et al.   PLoS Genetics

The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes

(2012) Kira S Makarova et al.   Biology Direct

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

Phylogenomics of Prokaryotic Ribosomal Proteins

(2012) Natalya Yutin et al.   PLoS One

A congruent phylogenomic signal places eukaryotes within the Archaea

(2012) T. A. Williams et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Genetic and Biochemical Identification of a Novel Single-Stranded DNA-Binding Complex in Haloferax volcanii

(2012) Amy Stroud et al.   Frontiers in Microbiology

DNA replication: archaeal oriGINS

(2011) Stephen D Bell   BMC BIOLOGY

Molecular machines in archaeal DNA replication

(2011) Thomas R Beattie et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Phylogeny and evolution of the Archaea: one hundred genomes later

(2011) Celine Brochier-Armanet et al.   CURRENT OPINION IN MICROBIOLOGY

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Thermococcus kodakarensis encodes three MCM homologs but only one is essential

(2011) Miao Pan et al.   NUCLEIC ACIDS RESEARCH

Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism

(2011) Agnieszka Skowyra et al.   NUCLEIC ACIDS RESEARCH

Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales

(2011) S. Paytubi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

(2011) Lionel Guy et al.   TRENDS IN MICROBIOLOGY

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY 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

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

Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins

(2010) Nicolas Soler et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon

(2010) Amber L. Hartman et al.   PLoS One

Evolution of DNA Replication Protein Complexes in Eukaryotes and Archaea

(2010) Nicholas Chia et al.   PLoS One

Enigmatic, ultrasmall, uncultivated Archaea

(2010) B. J. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Isolation of the anaerobic thermoacidophilic crenarchaeote Acidilobus saccharovorans sp. nov. and proposal of Acidilobales ord. nov., including Acidilobaceae fam. nov. and Caldisphaeraceae fam. nov.

(2009) M. I. Prokofeva et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

(2009) P. G. Foster et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogeny of prokaryotes: does it exist and why should we care?

(2009) Simonetta Gribaldo et al.   RESEARCH IN MICROBIOLOGY

DNA Polymerases at the Replication Fork in Eukaryotes

(2008) Bruce Stillman   MOLECULAR CELL

Single-stranded DNA-binding protein hSSB1 is critical for genomic stability

(2008) Derek J. Richard et al.   NATURE

Extra-chromosomal elements and the evolution of cellular DNA replication machineries

(2008) Adam T. McGeoch et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The archaebacterial origin of eukaryotes

(2008) C. J. Cox et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation

(2008) Jonathan Berthon et al.   GENOME BIOLOGY