Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion

(2016) Inka Vanwonterghem et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

(2016) Cassandre Sara Lazar et al.   ENVIRONMENTAL MICROBIOLOGY

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

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

Long-Term Incubation Reveals Methanogenic Biodegradation of C5 and C6 iso-Alkanes in Oil Sands Tailings

(2015) Tariq Siddique et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

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

(2015) P. N. Evans et al.   SCIENCE

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

(2015) Dongwan D. Kang et al.   PeerJ

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia)

(2015) Alexey S Rozanov et al.   BMC GENOMICS

New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

(2014) Kristina Lang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

An Expanded Genomic Representation of the Phylum Cyanobacteria

(2014) Rochelle M. Soo et al.   Genome Biology and Evolution

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

(2014) Inka Vanwonterghem et al.   ISME Journal

CDD: NCBI's conserved domain database

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

Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses

(2014) William P. Hocking et al.   Frontiers in Microbiology

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens

(2013) Cornelia Welte et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

(2013) Jianyi Yang et al.   BIOINFORMATICS

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane

(2013) Amelia-Elena Rotaru et al.   Energy & Environmental Science

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Stratification of Archaea in the Deep Sediments of a Freshwater Meromictic Lake: Vertical Shift from Methanogenic to Uncultured Archaeal Lineages

(2012) Guillaume Borrel et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Phylogenetic diversity of microbial communities associated with the crude-oil, large-insoluble-particle and formation-water components of the reservoir fluid from a non-flooded high-temperature petroleum reservoir

(2011) Hajime Kobayashi et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2Storage

(2010) Rudolf K. Thauer et al.   Annual Review of Biochemistry

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Efficient use of accessibility in microRNA target prediction

(2010) Ray M. Marín et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge

(2009) Y. Yashiro et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Methanogenic archaea: ecologically relevant differences in energy conservation

(2008) Rudolf K. Thauer et al.   NATURE REVIEWS MICROBIOLOGY