Genome-centric view of carbon processing in thawing permafrost

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

(2018) Joel A Boyd et al.   NUCLEIC ACIDS RESEARCH

Atmospheric trace gases support primary production in Antarctic desert surface soil

(2017) Mukan Ji et al.   NATURE

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis

(2016) Anastasia A. Ivanova et al.   MOLECULAR ECOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Microbial diversity drives multifunctionality in terrestrial ecosystems

(2016) Manuel Delgado-Baquerizo et al.   Nature Communications

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

(2016) Eric R. Johnston et al.   Frontiers in Microbiology

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

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

Climate change and the permafrost carbon feedback

(2015) E. A. G. Schuur et al.   NATURE

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

(2015) Jenni Hultman et al.   NATURE

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS 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

Metatranscriptomic Analysis of Arctic Peat Soil Microbiota

(2014) Alexander T. Tveit et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Methane dynamics regulated by microbial community response to permafrost thaw

(2014) Carmody K. McCalley et al.   NATURE

Humic substances as fully regenerable electron acceptors in recurrently anoxic environments

(2014) Laura Klüpfel et al.   Nature Geoscience

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The microbial ecology of permafrost

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

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production

(2014) S. B. Hodgkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a novel methanogen prevalent in thawing permafrost

(2014) Rhiannon Mondav et al.   Nature Communications

Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective

(2014) William Kricka et al.   Frontiers in Microbiology

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

Glycerol fermentation to hydrogen by Thermotoga maritima: Proposed pathway and bioenergetic considerations

(2013) B.T. Maru et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Genetic analysis of D-xylose metabolism pathways in Gluconobacter oxydans 621H

(2013) Minhua Zhang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Solid-phase organic matter reduction regulates anaerobic decomposition in bog soil

(2013) Jason K. Keller et al.   Ecosphere

The use of underloaded C 18 solid-phase extraction plates increases reproducibility of analysis of tryptic peptides from unfractionated human plasma

(2012) Xiaofeng Guo et al.   ANALYTICAL BIOCHEMISTRY

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

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

(2012) Alexander Tveit et al.   ISME Journal

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

pH controls over anaerobic carbon mineralization, the efficiency of methane production, and methanogenic pathways in peatlands across an ombrotrophic–minerotrophic gradient

(2012) Rongzhong Ye et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

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

The Effects of Permafrost Thaw on Soil Hydrologic, Thermal, and Carbon Dynamics in an Alaskan Peatland

(2011) Jonathan A. O’Donnell et al.   ECOSYSTEMS

Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat

(2011) Timofey A. Pankratov et al.   ENVIRONMENTAL MICROBIOLOGY

Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics

(2011) Philippe N Bertin et al.   ISME Journal

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

(2011) Daniel McDonald et al.   ISME Journal

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Permafrost carbon-climate feedbacks accelerate global warming

(2011) C. D. Koven et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Permafrost-thaw-induced land-cover change in the Canadian subarctic: implications for water resources

(2010) W.L. Quinton et al.   HYDROLOGICAL PROCESSES

Reduction of iron (III) and humic substances plays a major role in anaerobic respiration in an Arctic peat soil

(2010) David A. Lipson et al.   JOURNAL OF GEOPHYSICAL RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

(2009) Alfons J. M. Stams et al.   NATURE REVIEWS MICROBIOLOGY

Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach

(2008) Debora F Rodrigues et al.   BMC GENOMICS

Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2

(2008) M. Baani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA