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

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities

(2018) Tyler P. Barnum et al.   ISME Journal

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

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

Microbial metatranscriptomes from the thermally stratified Gulf of Aqaba/Eilat during summer

(2017) Dan R. Miller et al.   Marine Genomics

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

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

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

(2017) Pedro J. Cabello-Yeves et al.   Frontiers in Microbiology

Microorganisms and ocean global change

(2017) David A. Hutchins et al.   Nature Microbiology

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

Global genetic capacity for mixotrophy in marine picocyanobacteria

(2016) Alexis P Yelton et al.   ISME Journal

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

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

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

(2016) Jarone Pinhassi et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea

(2016) Mario López-Pérez et al.   Frontiers in Microbiology

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

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

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages

(2015) Haiwei Luo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

Genomes of Planktonic Acidimicrobiales : Widening Horizons for Marine Actinobacteria by Metagenomics

(2015) Carolina Megumi Mizuno et al.   mBio

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution

(2015) Dominique Boeuf et al.   Database-The Journal of Biological Databases and Curation

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Master recyclers: features and functions of bacteria associated with phytoplankton blooms

(2014) Alison Buchan et al.   NATURE REVIEWS MICROBIOLOGY

Prochlorococcus: the structure and function of collective diversity

(2014) Steven J. Biller et al.   NATURE REVIEWS MICROBIOLOGY

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

(2014) Ari J. S. Ferreira et al.   PLoS One

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Ecology of marine Bacteroidetes: a comparative genomics approach

(2013) Beatriz Fernández-Gómez et al.   ISME Journal

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

(2013) Janine Kamke et al.   ISME Journal

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Prochlorococcus can use the Pro1404 transporter to take up glucose at nanomolar concentrations in the Atlantic Ocean

(2013) M. d. C. Munoz-Marin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria

(2013) I. Gushchin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters

(2013) M. Hugoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

(2013) Rohit Ghai et al.   Scientific Reports

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

(2012) Y. Peng et al.   BIOINFORMATICS

Spatio-temporal behaviour of the deep chlorophyll maximum in Mediterranean Sea: Development of a stochastic model for picophytoplankton dynamics

(2012) G. Denaro et al.   Ecological Complexity

Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

(2012) Aitor Gonzaga et al.   Genome Biology and Evolution

Expression patterns reveal niche diversification in a marine microbial assemblage

(2012) Scott M Gifford et al.   ISME Journal

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

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

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Seasonality in Ocean Microbial Communities

(2012) S. J. Giovannoni et al.   SCIENCE

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

(2012) V. Iverson et al.   SCIENCE

Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade

(2012) J. Grote et al.   mBio

Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

(2012) Mario López-Pérez et al.   Scientific Reports

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Differential photoinhibition of bacterial and archaeal ammonia oxidation

(2011) Stephanie N. Merbt et al.   FEMS MICROBIOLOGY LETTERS

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing

(2010) Rohit Ghai et al.   ISME Journal

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

(2010) Yanmei Shi et al.   ISME Journal

Major bacterial contribution to the ocean reservoir of detrital organic carbon and nitrogen

(2010) Karl Kaiser et al.   LIMNOLOGY AND OCEANOGRAPHY

Inter-annual recurrence of archaeal assemblages in the coastal NW Mediterranean Sea (Blanes Bay Microbial Observatory)

(2010) Pierre E. Galand et al.   LIMNOLOGY AND OCEANOGRAPHY

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

Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre

(2009) K. T. Konstantinidis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of ribosomal RNA genes in metagenomic fragments

(2009) Ying Huang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic

(2009) Federico Baltar et al.   ENVIRONMENTAL MICROBIOLOGY

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria

(2009) Shi Yan et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

(2008) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Proteorhodopsins: an array of physiological roles?

(2008) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

New substrates for TonB-dependent transport: do we only see the ‘tip of the iceberg’?

(2008) Kristine Schauer et al.   TRENDS IN BIOCHEMICAL SCIENCES