The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

Microbial dynamics of elevated carbon flux in the open ocean’s abyss

(2021) Kirsten E. Poff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

(2021) Silvia G. Acinas et al.   Communications Biology

Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria

(2020) Jimmy H. W. Saw et al.   mBio

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Tara Oceans: towards global ocean ecosystems biology

(2020) Shinichi Sunagawa et al.   NATURE REVIEWS MICROBIOLOGY

In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes

(2020) Kento Tominaga et al.   Frontiers in Microbiology

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics

(2020) Shunan Cao et al.   Microbiome

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets

(2020) Yi Yue et al.   BMC BIOINFORMATICS

Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean

(2020) Frank O. Aylward et al.   mSystems

Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

(2019) Benjamin J. Tully   Nature Communications

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

(2019) Ella T. Sieradzki et al.   Nature Communications

Marine biofilms constitute a bank of hidden microbial diversity and functional potential

(2019) Weipeng Zhang et al.   Nature Communications

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones

(2019) Xin Sun et al.   ISME Journal

Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean

(2019) Dominique Boeuf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic and seasonal variations among aquatic phages infecting the Baltic Sea Gammaproteobacteria Rheinheimera sp. BAL341

(2019) E. Nilsson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes

(2019) Karen Krüger et al.   ISME Journal

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

(2019) Brent Nowinski et al.   Scientific Data

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics

(2019) Maria G. Pachiadaki et al.   CELL

Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics

(2019) Jose M. Haro-Moreno et al.   Frontiers in Microbiology

Long-term stability and Red Queen-like strain dynamics in marine viruses

(2019) J. Cesar Ignacio-Espinoza et al.   Nature Microbiology

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Potential for primary productivity in a globally-distributed bacterial phototroph

(2018) E. D. Graham et al.   ISME Journal

A strong link between marine microbial community composition and function challenges the idea of functional redundancy

(2018) Pierre E. Galand et al.   ISME Journal

Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean

(2018) Yingdong Li et al.   Frontiers in Microbiology

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

(2018) Jose M. Haro-Moreno et al.   Microbiome

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

Deep mitochondrial origin outside the sampled alphaproteobacteria

(2018) Joran Martijn et al.   NATURE

Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum

(2018) Eric W. Getz et al.   mBio

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea

(2018) Johannes Alneberg et al.   Scientific Data

Marine microbial metagenomes sampled across space and time

(2018) Steven J. Biller et al.   Scientific Data

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

(2018) Christian Rinke et al.   ISME Journal

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

New insights into marine group III Euryarchaeota, from dark to light

(2017) Jose M Haro-Moreno et al.   ISME Journal

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

The MAR databases: development and implementation of databases specific for marine metagenomics

(2017) Terje Klemetsen et al.   NUCLEIC ACIDS RESEARCH

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

(2017) Kristin Bergauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

(2017) Maria G. Pachiadaki et al.   SCIENCE

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

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

(2017) Benjamin J. Tully et al.   PeerJ

A compendium of multi-omic sequence information from the Saanich Inlet water column

(2017) Alyse K. Hawley et al.   Scientific Data

Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera

(2017) Samuel T. Wilson et al.   Nature Microbiology

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

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

Environmental drivers of a microbial genomic transition zone in the ocean’s interior

(2017) Daniel R. Mende et al.   Nature Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

(2017) Yosuke Nishimura et al.   mSphere

MOCAT2: a metagenomic assembly, annotation and profiling framework

(2016) Jens Roat Kultima et al.   BIOINFORMATICS

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

(2016) Mohamed F. Haroon et al.   Scientific Data

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

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

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

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

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

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

(2014) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R

(2013) Eric Pante et al.   PLoS One

Ocean Science: The power of plankton

(2012) Paul Falkowski   NATURE

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

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE