Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

Phage hunters: Computational strategies for finding phages in large-scale ‘omics datasets

(2018) Bonnie L. Hurwitz et al.   VIRUS RESEARCH

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

(2017) Nathan A. Ahlgren et al.   ENVIRONMENTAL MICROBIOLOGY

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

(2017) Alyson E. Santoro et al.   LIMNOLOGY AND OCEANOGRAPHY

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

Multiple origins of viral capsid proteins from cellular ancestors

(2017) Mart Krupovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico “Dead Zone”

(2017) J. Cameron Thrash et al.   mBio

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

(2017) Mario López-Pérez et al.   PLoS Genetics

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone

(2017) Clara A. Fuchsman et al.   Frontiers in Microbiology

Putative archaeal viruses from the mesopelagic ocean

(2017) Dean R. Vik et al.   PeerJ

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

(2017) Benjamin J. Tully et al.   PeerJ

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

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

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux 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

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

(2016) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

(2015) Anastasis Oulas et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia and nitrite oxidation in the Eastern Tropical North Pacific

(2015) Xuefeng Peng et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Genomic potential for arsenic efflux and methylation varies among global Prochlorococcus populations

(2015) Jaclyn K Saunders et al.   ISME Journal

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

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

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

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

Archaeal viruses and bacteriophages: comparisons and contrasts

(2014) Maija K. Pietilä et al.   TRENDS IN MICROBIOLOGY

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

The Wonderful World of Archaeal Viruses

(2013) David Prangishvili   Annual Review of Microbiology

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

Seasonal variation in the metratranscriptomes of a Thaumarchaeota population from SE USA coastal waters

(2013) James T Hollibaugh et al.   ISME Journal

New insights into hydrothermal vent processes in the unique shallow-submarine arc-volcano, Kolumbo (Santorini), Greece

(2013) Stephanos P. Kilias et al.   Scientific Reports

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

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

(2012) Y. Peng et al.   BIOINFORMATICS

Phylogenomics of T4 cyanophages: lateral gene transfer in the ‘core’ and origins of host genes

(2012) J. Cesar Ignacio-Espinoza et al.   ENVIRONMENTAL MICROBIOLOGY

ArchaealamoA gene diversity points to distinct biogeography of ammonia-oxidizingCrenarchaeotain the ocean

(2012) Eva Sintes et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Mart Krupovic et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

(2010) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

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

Cyanobacterial psbA gene family: optimization of oxygenic photosynthesis

(2009) Paula Mulo et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California

(2008) J Michael Beman et al.   ISME Journal