Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil

Diversity and Host Interactions among Virulent and Temperate Baltic Sea Flavobacterium Phages

(2020) Emelie Nilsson et al.   Viruses-Basel

Author Correction: Aeolian transport of viable microbial life across the Atacama Desert, Chile: Implications for Mars

(2020) Armando Azua-Bustos et al.   Scientific Reports

Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community

(2020) Gherman Uritskiy et al.   ENVIRONMENTAL MICROBIOLOGY

Phages Actively Challenge Niche Communities in Antarctic Soils

(2020) Oliver K. I. Bezuidt et al.   mSystems

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

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils

(2020) Krishnakali Roy et al.   Frontiers in Microbiology

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

(2020) Paraskevi Mara et al.   ISME Journal

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases

(2019) Marco Di Salvo et al.   BMC BIOINFORMATICS

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application

(2019) Yuting Li et al.   Viruses-Basel

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Aeolian Dispersal of Bacteria Associated With Desert Dust and Anthropogenic Particles Over Continental and Oceanic Surfaces

(2019) Teruya Maki et al.   JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES

Soil Viruses: A New Hope

(2019) Joanne B. Emerson   mSystems

A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages

(2019) Paula Szymczak et al.   Scientific Reports

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

A Review on Viral Metagenomics in Extreme Environments

(2019) Sonia Dávila-Ramos et al.   Frontiers in Microbiology

Investigating microbial associations from sequencing survey data with co‐correspondence analysis

(2019) Benjamin Alric et al.   Molecular Ecology Resources

Deposition rates of viruses and bacteria above the atmospheric boundary layer

(2018) Isabel Reche et al.   ISME Journal

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Transitory microbial habitat in the hyperarid Atacama Desert

(2018) Dirk Schulze-Makuch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

The Actinobacterial WhiB-like (Wbl) Family of Transcription Factors

(2018) Matthew J. Bush   MOLECULAR MICROBIOLOGY

Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions

(2018) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Xerotolerant bacteria: surviving through a dry spell

(2017) Pedro H. Lebre et al.   NATURE REVIEWS MICROBIOLOGY

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes

(2017) Abraham G. Moller et al.   PeerJ

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

(2017) Benjamin Bolduc et al.   PeerJ

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

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

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

A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells

(2017) Svetlana Fridman et al.   Nature Microbiology

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community

(2016) Alexander Crits-Christoph et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria

(2016) Rohit Ghai et al.   ISME Journal

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

(2016) Nathan A. Ahlgren et al.   NUCLEIC ACIDS RESEARCH

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

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

The Significance of Mutualistic Phages for Bacterial Ecology and Evolution

(2016) Nancy Obeng et al.   TRENDS IN MICROBIOLOGY

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

(2016) David Burstein et al.   Nature Communications

Diversity and Ecology of Viruses in Hyperarid Desert Soils

(2015) Olivier Zablocki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Filamentous Bacteriophage Promote Biofilm Assembly and Function

(2015) Patrick R. Secor et al.   Cell Host & Microbe

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

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

Discovery and microbial content of the driest site of the hyperarid Atacama Desert, Chile

(2015) Armando Azua-Bustos et al.   Environmental Microbiology Reports

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Phage and bacteria support mutual diversity in a narrowing staircase of coexistence

(2014) Jan O Haerter et al.   ISME Journal

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

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

The bacteria and bacteriophages from a Mesquite Flats site of the Death Valley desert

(2013) Eric Prestel et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Quorum sensing: How bacteria can coordinate activity and synchronize their response to external signals?

(2012) Zhi Li et al.   PROTEIN SCIENCE

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal

(2011) Diane McDougald et al.   NATURE REVIEWS MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Insights into the function of the WhiB-like protein of mycobacteriophage TM4 - a transcriptional inhibitor of WhiB2

(2010) Jan Rybniker et al.   MOLECULAR MICROBIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Photosystem I gene cassettes are present in marine virus genomes

(2009) Itai Sharon et al.   NATURE

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

phiSITE: database of gene regulation in bacteriophages

(2009) Lubos Klucar et al.   NUCLEIC ACIDS RESEARCH

The biofilm life cycle and virulence of Pseudomonas aeruginosa are dependent on a filamentous prophage

(2008) Scott A Rice et al.   ISME Journal

An examination of the bacteriophages and bacteria of the Namib desert

(2008) Eric Prestel et al.   JOURNAL OF MICROBIOLOGY