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

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

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

(2018) Alina Pushkarev et al.   NATURE

Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi

(2018) Maliheh Mehrshad et al.   Microbiome

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

(2017) Maliheh Mehrshad et al.   ISME Journal

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

(2017) Beate M Slaby et al.   ISME Journal

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

(2017) Meinhard Simon et al.   ISME Journal

Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments

(2017) Miho Hirai et al.   MICROBES AND ENVIRONMENTS

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) J. Cameron Thrash et al.   mBio

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

(2017) Zachary Landry et al.   mBio

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

(2017) Ramunas Stepanauskas et al.   Nature Communications

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms

(2016) Takaaki Kubota et al.   Frontiers in Microbiology

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

(2015) Jacob H. Munson-McGee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Dongwan D. Kang et al.   PeerJ

Chemical and enzymatic fractionation of cell walls from Fucales: insights into the structure of the extracellular matrix of brown algae

(2014) Estelle Deniaud-Bouët et al.   ANNALS OF BOTANY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The novel strainFusarium proliferatumLE1 (RCAM02409) produces α-L-fucosidase and arylsulfatase during the growth on fucoidan

(2014) Svetlana V. Shvetsova et al.   JOURNAL OF BASIC MICROBIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

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

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

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

Systematic removal of neutral sugars within dissolved organic matter across ocean basins

(2011) Stuart J. Goldberg et al.   GEOPHYSICAL RESEARCH LETTERS

Net removal of major marine dissolved organic carbon fractions in the subsurface ocean

(2011) Dennis A. Hansell et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Dissolved Organic Matter in the Ocean: A Controversy Stimulates New Insights

(2011) Dennis Hansell et al.   OCEANOGRAPHY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

(2010) Nianzhi Jiao et al.   NATURE REVIEWS MICROBIOLOGY

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean

(2009) Martha Schattenhofer et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal dynamics of dissolved combined neutral sugars and the quality of dissolved organic matter in the Northwestern Sargasso Sea

(2008) Stuart J. Goldberg et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic

(2008) Marta M. Varela et al.   ENVIRONMENTAL MICROBIOLOGY