Diverse anaerobic methane‐ and multi‐carbon alkane‐metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment

Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia

(2018) Viola Krukenberg et al.   ENVIRONMENTAL MICROBIOLOGY

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

(2018) Nina Dombrowski et al.   Nature Communications

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

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

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

(2017) Nina Dombrowski et al.   Microbiome

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

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

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Thermophilic archaea activate butane via alkyl-coenzyme M formation

(2016) Rafael Laso-Pérez et al.   NATURE

Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California

(2016) Luke McKay et al.   Environmental Microbiology Reports

A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments

(2016) Vengadesh Perumal Natarajan et al.   Frontiers in Microbiology

Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin

(2016) Frederick Dowell et al.   Frontiers in Microbiology

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He 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

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2015) P. N. Evans et al.   SCIENCE

Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers

(2014) Mark A. Lever et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)

(2013) Adrien Vigneron et al.   ISME Journal

Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways

(2013) Feng-Ping Wang et al.   ISME Journal

Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses

(2013) Jun Meng et al.   ISME Journal

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

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

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

(2013) Mohamed F. Haroon et al.   NATURE

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps

(2012) Ulrike Jaekel et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments

(2011) Jennifer F Biddle et al.   ISME Journal

Thermophilic anaerobic oxidation of methane by marine microbial consortia

(2011) Thomas Holler et al.   ISME Journal

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Anaerobic Oxidation of Methane: Progress with an Unknown Process

(2009) Katrin Knittel et al.   Annual Review of Microbiology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

(2009) Anke Meyerdierks et al.   ENVIRONMENTAL MICROBIOLOGY

Mutagenesis of the C1 Oxidation Pathway in Methanosarcina barkeri: New Insights into the Mtr/Mer Bypass Pathway

(2008) P. V. Welander et al.   JOURNAL OF BACTERIOLOGY