Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost

Microbial diversity involved in iron and cryptic sulfur cycling in the ferruginous, low-sulfate waters of Lake Pavin

(2019) Jasmine S. Berg et al.   PLoS One

Structure and Mechanisms of F-Type ATP Synthases

(2019) Werner Kühlbrandt   Annual Review of Biochemistry

Asgard archaea capable of anaerobic hydrocarbon cycling

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

Characterisation of the Carpinus betulus L. Phyllomicrobiome in Urban and Forest Areas

(2019) Valeria Imperato et al.   Frontiers in Microbiology

Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages

(2019) Robert E. Danczak et al.   PLoS One

Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates

(2018) Oliver Müller et al.   ENVIRONMENTAL MICROBIOLOGY

Methanotrophy across a natural permafrost thaw environment

(2018) Caitlin M Singleton et al.   ISME Journal

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Inverted signaling by bacterial chemotaxis receptors

(2018) Shuangyu Bi et al.   Nature Communications

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Climate-driven thaw of permafrost preserved glacial landscapes, northwestern Canada

(2017) Steven V. Kokelj et al.   GEOLOGY

Microbial survival strategies in ancient permafrost: insights from metagenomics

(2017) Rachel Mackelprang et al.   ISME Journal

On the Origin and Distribution of Antibiotic Resistance: Permafrost Bacteria Studies

(2017) S. Z. Mindlin et al.   Molecular Genetics Microbiology and Virology

Corrigendum: Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Potential microbial contamination during sampling of permafrost soil assessed by tracers

(2017) Toke Bang-Andreasen et al.   Scientific Reports

Permafrost Meta-Omics and Climate Change

(2016) Rachel Mackelprang et al.   Annual Review of Earth and Planetary Sciences

MOCAT2: a metagenomic assembly, annotation and profiling framework

(2016) Jens Roat Kultima et al.   BIOINFORMATICS

Thiosulfate oxidation by Thiomicrospira thermophila : metabolic flexibility in response to ambient geochemistry

(2016) J. L. Houghton et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

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

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

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

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

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

Structural and Molecular Basis for Resistance to Aminoglycoside Antibiotics by the Adenylyltransferase ANT(2″)-Ia

(2015) Georgina Cox et al.   mBio

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

(2015) Morten Schostag et al.   Frontiers in Microbiology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Dongwan D. Kang et al.   PeerJ

The impacts of recent permafrost thaw on land–atmosphere greenhouse gas exchange

(2014) Daniel J Hayes et al.   Environmental Research Letters

Fluoroquinolones and qnr Genes in Sediment, Water, Soil, and Human Fecal Flora in an Environment Polluted by Manufacturing Discharges

(2014) Carolin Rutgersson et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The sodium pumping NADH:quinone oxidoreductase (Na+-NQR), a unique redox-driven ion pump

(2014) Blanca Barquera   JOURNAL OF BIOENERGETICS AND BIOMEMBRANES

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

(2014) Jie Deng et al.   MOLECULAR ECOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The microbial ecology of permafrost

(2014) Janet K. Jansson et al.   NATURE REVIEWS MICROBIOLOGY

Discovery of a novel methanogen prevalent in thawing permafrost

(2014) Rhiannon Mondav et al.   Nature Communications

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

(2014) Antje Gittel et al.   Frontiers in Microbiology

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

(2014) Akihiro Koyama et al.   Frontiers in Microbiology

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

(2014) Michael Imelfort et al.   PeerJ

Metagenomic Profiles of Antibiotic Resistance Genes (ARGs) between Human Impacted Estuary and Deep Ocean Sediments

(2013) Baowei Chen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Bacterial genome replication at subzero temperatures in permafrost

(2013) Steven J Tuorto et al.   ISME Journal

Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1

(2013) Nadia C S Mykytczuk et al.   ISME Journal

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile

(2013) David A. Lipson et al.   PLoS One

The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

(2013) David D. Myrold et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics

(2013) David Emerson et al.   Frontiers in Microbiology

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms

(2012) Alexander Tveit et al.   ISME Journal

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic

(2011) Roland C. Wilhelm et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Metabolic regulation of Escherichia coli and its phoB and phoR genes knockout mutants under phosphate and nitrogen limitations as well as at acidic condition

(2011) Lolo Marzan et al.   Microbial Cell Factories

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Genome Sequence of Psychrobacter arcticus 273-4, a Psychroactive Siberian Permafrost Bacterium, Reveals Mechanisms for Adaptation to Low-Temperature Growth

(2010) H. L. Ayala-del-Rio et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard

(2010) Arwyn Edwards et al.   ISME Journal

The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses

(2010) Etienne Yergeau et al.   ISME Journal

Soil organic carbon pools in the northern circumpolar permafrost region

(2009) C. Tarnocai et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Vulnerability of Permafrost Carbon to Climate Change: Implications for the Global Carbon Cycle

(2008) Edward A. G. Schuur et al.   BIOSCIENCE

Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic

(2008) Blaire Steven et al.   ENVIRONMENTAL MICROBIOLOGY

Desulfosporosinus hippei sp. nov., a mesophilic sulfate-reducing bacterium isolated from permafrost

(2008) A. Vatsurina et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY