Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life

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

(2014) Kasie Raymann et al.   Genome Biology and Evolution

Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?

(2014) Hemalatha Golaconda Ramulu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Phylogenomic Data Support a Seventh Order of Methylotrophic Methanogens and Provide Insights into the Evolution of Methanogenesis

(2013) Guillaume Borrel et al.   Genome Biology and Evolution

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

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

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens

(2012) Kristina Paul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

(2012) Josselin Bodilis et al.   PLoS One

Phylogenomics of Prokaryotic Ribosomal Proteins

(2012) Natalya Yutin et al.   PLoS One

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

Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

(2011) M. Groussin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The archaeal cell envelope

(2011) Sonja-Verena Albers et al.   NATURE REVIEWS MICROBIOLOGY

The Genome Sequence of the Crenarchaeon Acidilobus saccharovorans Supports a New Order, Acidilobales, and Suggests an Important Ecological Role in Terrestrial Acidic Hot Springs

(2010) A. V. Mardanov et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Archaea — timeline of the third domain

(2010) Ricardo Cavicchioli   NATURE REVIEWS MICROBIOLOGY

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

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

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes

(2010) S. Kelly et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Fervidicoccus fontis gen. nov., sp. nov., an anaerobic, thermophilic crenarchaeote from terrestrial hot springs, and proposal of Fervidicoccaceae fam. nov. and Fervidicoccales ord. nov.

(2009) A. A. Perevalova et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Search for Primitive Methanopyrus Based on Genetic Distance Between Val- and Ile-tRNA Synthetases

(2009) Zhiliang Yu et al.   JOURNAL OF MOLECULAR EVOLUTION

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

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

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

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

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

When DNA replication and protein synthesis come together

(2009) Jonathan Berthon et al.   TRENDS IN BIOCHEMICAL SCIENCES

SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis

(2008) Martin Kostka et al.   BMC BIOINFORMATICS

Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov.

(2008) S. Sakai et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY

A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene

(2008) Agnès Mihajlovski et al.   RESEARCH IN MICROBIOLOGY

Tracking microbial biodiversity through molecular and genomic ecology

(2007) Purificación López-García et al.   RESEARCH IN MICROBIOLOGY