Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota

(2019) Luke J. McKay et al.   Nature Microbiology

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

(2018) Panagiotis S. Adam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

(2017) Panagiotis S Adam et al.   ISME Journal

Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea

(2017) Shawn E. McGlynn   MICROBES AND ENVIRONMENTS

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

(2017) Anja Spang et al.   SCIENCE

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

(2017) Peer H. A. Timmers et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea

(2017) Dipti D Nayak et al.   eLife

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments

(2017) Nina Dombrowski et al.   Microbiome

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

(2017) Dimitry Y. Sorokin et al.   Nature Microbiology

Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments

(2017) Luke J. McKay et al.   Scientific Reports

Methanogenesis and the Wood–Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association

(2016) Guillaume Borrel et al.   Genome Biology and Evolution

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

(2016) Kiley W Seitz et al.   ISME Journal

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

(2016) Masaru Konishi Nobu et al.   ISME Journal

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Thermophilic archaea activate butane via alkyl-coenzyme M formation

(2016) Rafael Laso-Pérez et al.   NATURE

The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea

(2016) Kaiyuan Zheng et al.   SCIENCE

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

(2016) Inka Vanwonterghem et al.   Nature Microbiology

The physiology and habitat of the last universal common ancestor

(2016) Madeline C. Weiss et al.   Nature Microbiology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

The two-domain tree of life is linked to a new root for the Archaea

(2015) Kasie Raymann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

(2015) Jie Li et al.   Scientific Reports

A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea

(2015) Arslan Arshad et al.   Frontiers in Microbiology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

(2014) Guillaume Borrel et al.   BMC GENOMICS

Elucidating the Process of Activation of Methyl-Coenzyme M Reductase

(2014) D. Prakash et al.   JOURNAL OF BACTERIOLOGY

Metagenomes from two microbial consortia associated with Santa Barbara seep oil

(2014) Erik R. Hawley et al.   Marine Genomics

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

The prokaryotic Mo/W-bisPGD enzymes family: A catalytic workhorse in bioenergetic

(2013) Stéphane Grimaldi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

SyntTax: a web server linking synteny to prokaryotic taxonomy

(2013) Jacques Oberto   BMC BIOINFORMATICS

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

Early bioenergetic evolution

(2013) F. L. Sousa et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis

(2013) F. Sarmiento et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Role of syntrophic microbial communities in high-rate methanogenic bioreactors

(2012) Alfons J. M. Stams et al.   WATER SCIENCE AND TECHNOLOGY

More Than 200 Genes Required for Methane Formation from H2and CO2and Energy Conservation Are Present inMethanothermobacter marburgensisandMethanothermobacter thermautotrophicus

(2011) Anne-Kristin Kaster et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt 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

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group

(2009) Anke Meyerdierks et al.   ENVIRONMENTAL MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Molecular mechanism of energy conservation in polysulfide respiration

(2008) Mika Jormakka et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review

(2008) Burak Demirel et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY