Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species

Methyl/alkyl‐coenzyme M reductase‐based anaerobic alkane oxidation in archaea

(2020) Yinzhao Wang et al.   ENVIRONMENTAL MICROBIOLOGY

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Diversity, ecology and evolution of Archaea

(2020) Brett J. Baker et al.   Nature Microbiology

Anaerobic degradation of paraffins by thermophilic Actinobacteria under methanogenic conditions

(2020) Yifan Liu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

(2019) Joel A. Boyd et al.   ISME Journal

Expanding anaerobic alkane metabolism in the domain of Archaea

(2019) Yinzhao Wang et al.   Nature Microbiology

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

(2019) Guillaume Borrel et al.   Nature Microbiology

Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep

(2019) Song-Can Chen et al.   NATURE

Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes

(2019) Rudolf K. Thauer   BIOCHEMISTRY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

(2019) Kerrin Mendler et al.   NUCLEIC ACIDS RESEARCH

Asgard archaea capable of anaerobic hydrocarbon cycling

(2019) Kiley W. Seitz et al.   Nature Communications

Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’ (JS1) inferred from genomics

(2019) Yi-Fan Liu et al.   ISME Journal

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils

(2019) Shiping Wei et al.   EXTREMOPHILES

Anaerobic Degradation of Non-Methane Alkanes by “Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico

(2019) Rafael Laso-Pérez et al.   mBio

Preferential degradation of long-chain alkyl substituted hydrocarbons in heavy oil under methanogenic conditions

(2019) Lei Cheng et al.   ORGANIC GEOCHEMISTRY

Methanogenesis

(2018) Zhe Lyu et al.   CURRENT BIOLOGY

Development of a duplex droplet digital PCR assay for absolute quantitative detection of "Candidatus Liberibacter asiaticus"

(2018) Vijayanandraj Selvaraj et al.   PLoS One

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The controls on the composition of biodegraded oils in the deep subsurface – Part 4. Destruction and production of high molecular weight non-hydrocarbon species and destruction of aromatic hydrocarbons during progressive in-reservoir biodegradation

(2017) Thomas B.P. Oldenburg et al.   ORGANIC GEOCHEMISTRY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment

(2016) Ralf Rabus et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Thermophilic archaea activate butane via alkyl-coenzyme M formation

(2016) Rafael Laso-Pérez et al.   NATURE

Methane production from coal by a single methanogen

(2016) D. Mayumi et al.   SCIENCE

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   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

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

(2014) Q.-L. Qin et al.   JOURNAL OF BACTERIOLOGY

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

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

Progressive Degradation of Crude Oil n-Alkanes Coupled to Methane Production under Mesophilic and Thermophilic Conditions

(2014) Lei Cheng et al.   PLoS One

Syntrophic biodegradation of hydrocarbon contaminants

(2013) Lisa M Gieg et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA-SIP Reveals That Syntrophaceae Play an Important Role in Methanogenic Hexadecane Degradation

(2013) Lei Cheng et al.   PLoS One

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Isolation and Characterization of Methanothermobacter crinale sp. nov., a Novel Hydrogenotrophic Methanogen from the Shengli Oil Field

(2011) Lei Cheng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Methanogenic toluene metabolism: community structure and intermediates

(2011) S. Jane Fowler et al.   ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Methanogenesis in Marine Sediments

(2008) James G. Ferry et al.   Annals of the New York Academy of Sciences

Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil

(2008) J. Peng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Methanogenic archaea: ecologically relevant differences in energy conservation

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