Host-linked soil viral ecology along a permafrost thaw gradient

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

Permafrost Meta-Omics and Climate Change

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

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland

(2016) Suzanne B. Hodgkins et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11

(2016) Lindsey M Solden et al.   ISME Journal

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming

(2016) Kai Xue et al.   Nature Climate Change

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

(2016) Gareth Trubl et al.   PeerJ

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

(2016) Rebecca A. Daly et al.   Nature Microbiology

Soil incubations reproduce field methane dynamics in a subarctic wetland

(2015) Suzanne B. Hodgkins et al.   BIOGEOCHEMISTRY

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

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Methane dynamics regulated by microbial community response to permafrost thaw

(2014) Carmody K. McCalley et al.   NATURE

Metagenomic scaffolds enable combinatorial lignin transformation

(2014) C. R. Strachan 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

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

(2013) Joanne B. Emerson et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

(2012) Joanne B. Emerson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt 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

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2011) Rachel Mackelprang et al.   NATURE

Structure and function of chitinases from glycoside hydrolase family 19

(2011) Wimal Ubhayasekera   POLYMER INTERNATIONAL

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

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

NCBI Reference Sequences: current status, policy and new initiatives

(2008) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE

A Sparse PLS for Variable Selection when Integrating Omics Data

(2008) Kim-Anh Lê Cao et al.   Statistical Applications in Genetics and Molecular Biology

Sparse principal component analysis via regularized low rank matrix approximation

(2007) Haipeng Shen et al.   JOURNAL OF MULTIVARIATE ANALYSIS