Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems

Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters

(2016) Bradley B Tolar et al.   ISME Journal

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Two distinct pools of B12analogs reveal community interdependencies in the ocean

(2016) Katherine R. Heal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low genome content diversity of marine planktonic Thaumarchaeota

(2016) Haiwei Luo et al.   Environmental Microbiology Reports

The Epigenomic Landscape of Prokaryotes

(2016) Matthew J. Blow et al.   PLoS Genetics

The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger

(2015) Willm Martens-Habbena et al.   ENVIRONMENTAL MICROBIOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation

(2015) Barbara Bayer et al.   ISME Journal

Factors influencing nitrification rates and the abundance and transcriptional activity of ammonia-oxidizing microorganisms in the dark northeast Pacific Ocean

(2015) Jason M. Smith et al.   LIMNOLOGY AND OCEANOGRAPHY

Genomic and proteomic characterization of “CandidatusNitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

(2015) Alyson E. Santoro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vitro analysis of phosphorothioate modification of DNA reveals substrate recognition by a multiprotein complex

(2015) Bo Cao et al.   Scientific Reports

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

(2015) Jennifer B. Glass et al.   Frontiers in Microbiology

Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006

(2015) Matthew Ouellette et al.   Frontiers in Microbiology

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions

(2015) Cheryl-Emiliane T. Chow et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds

(2014) Laura E. Lehtovirta-Morley et al.   FEMS MICROBIOLOGY ECOLOGY

Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota

(2014) Philippe Deschamps et al.   Genome Biology and Evolution

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Connecting thermal physiology and latitudinal niche partitioning in marine Synechococcus

(2014) Justine Pittera et al.   ISME Journal

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

(2014) Jacob A Cram et al.   ISME Journal

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production

(2014) Andrew C Doxey et al.   ISME Journal

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

(2014) Brandon K. Swan et al.   PLoS One

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

(2014) W. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

(2014) Bo Cao et al.   Nature Communications

Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean

(2014) Estelle Pedneault et al.   Scientific Reports

DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks

(2014) Rui Gan et al.   Scientific Reports

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

(2013) K. Vasu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

Correction: A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Genome Sequence of "Candidatus Nitrosopumilus salaria" BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary

(2012) A. C. Mosier et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Role for urea in nitrification by polar marine Archaea

(2012) L. Alonso-Saez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat

(2012) Steven J. Biller et al.   Frontiers in Microbiology

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea

(2011) Mart Krupovic et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine

(2011) Benjamin J. Tully et al.   ENVIRONMENTAL MICROBIOLOGY

Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

(2011) Rika E. Anderson et al.   FEMS MICROBIOLOGY ECOLOGY

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

(2011) Alyson E Santoro et al.   ISME Journal

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

DNA phosphorothioation is widespread and quantized in bacterial genomes

(2011) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

(2010) Alyson E. Santoro et al.   ENVIRONMENTAL MICROBIOLOGY

Dur3 is the major urea transporter in Candida albicans and is co-regulated with the urea amidolyase Dur1,2

(2010) D. H. M. L. P. Navarathna et al.   MICROBIOLOGY-SGM

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella

(2010) Tiegang Xu et al.   NUCLEIC ACIDS RESEARCH

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus

(2009) Tiegang Xu et al.   BMC MICROBIOLOGY

Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses

(2009) Asuncion Martinez et al.   ENVIRONMENTAL MICROBIOLOGY

Functional analysis ofspfDgene involved in DNA phosphorothioation inPseudomonas fluorescensPf0-1

(2009) Fen Yao et al.   FEBS LETTERS

Urea distribution and uptake in the Atlantic Ocean between 50°N and 50°S

(2008) SC Painter et al.   MARINE ECOLOGY PROGRESS SERIES

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY