Genome‐resolved viral ecology in a marine oxygen minimum zone

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

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

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

(2020) Paraskevi Mara et al.   ISME Journal

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

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

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Scientists’ warning to humanity: microorganisms and climate change

(2019) Ricardo Cavicchioli et al.   NATURE REVIEWS MICROBIOLOGY

Stable aerobic and anaerobic coexistence in anoxic marine zones

(2019) Emily J. Zakem et al.   ISME Journal

Microbial niches in marine oxygen minimum zones

(2018) Anthony D. Bertagnolli et al.   NATURE REVIEWS MICROBIOLOGY

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

(2018) Nathan A. Ahlgren et al.   ISME Journal

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Decline in global oceanic oxygen content during the past five decades

(2017) Sunke Schmidtko et al.   NATURE

Putative archaeal viruses from the mesopelagic ocean

(2017) Dean R. Vik et al.   PeerJ

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

(2017) Benjamin Bolduc et al.   PeerJ

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Effect of the oxygen minimum zone on the second chlorophyll maximum

(2017) J Cepeda-Morales   CIENCIAS MARINAS

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

(2016) Maria Hauser et al.   BIOINFORMATICS

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

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

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

Bacterial diversity and community composition from seasurface to subseafloor

(2015) Emily A Walsh 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

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

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Simon Roux et al.   eLife

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

(2013) Jennifer R Brum et al.   ISME Journal

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

(2013) J. Michael Beman et al.   Nature Communications

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Widespread functional anoxia in the oxygen minimum zone of the Eastern South Pacific

(2012) Bo Thamdrup et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone

(2012) Jessica A. Bryant et al.   ECOLOGY

Oxygen minimum zones harbour novel viral communities with low diversity

(2012) Noriko Cassman et al.   ENVIRONMENTAL MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

Microbial oceanography of anoxic oxygen minimum zones

(2012) O. Ulloa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline

(2012) Melissa B. Duhaime et al.   VIROLOGY

Middepth circulation of the eastern tropical South Pacific and its link to the oxygen minimum zone

(2011) Rena Czeschel et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor

(2011) Niels Peter Revsbech et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Microbial Nitrogen Cycling Processes in Oxygen Minimum Zones

(2010) Phyllis Lam et al.   Annual Review of Marine Science

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

Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific

(2010) Paris Lavin et al.   Environmental Microbiology Reports

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

(2009) Daniel L. Rabosky   ECOLOGY LETTERS

Phylogenetic Diversity of Sequences of Cyanophage Photosynthetic Gene psbA in Marine and Freshwaters

(2008) C. Chenard et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific

(2008) Heike Stevens et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygen minimum zones in the eastern tropical Atlantic and Pacific oceans

(2008) Johannes Karstensen et al.   PROGRESS IN OCEANOGRAPHY

Oxygen minimum zones (OMZs) in the modern ocean

(2008) A. Paulmier et al.   PROGRESS IN OCEANOGRAPHY

Expanding Oxygen-Minimum Zones in the Tropical Oceans

(2008) L. Stramma et al.   SCIENCE