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

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

(2018) Tom O. Delmont et al.   PeerJ

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

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation

(2017) Wei Xie et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2017) J. Cameron Thrash et al.   mBio

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

(2017) Benjamin J. Tully et al.   PeerJ

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

(2017) Elaina D. Graham et al.   PeerJ

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

(2017) Adriana Alberti et al.   Scientific Data

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

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

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

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

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

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom

(2016) David M. Needham et al.   Nature Microbiology

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

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

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter

(2015) William D Orsi et al.   ISME Journal

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

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

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

(2015) A. Murat Eren et al.   PeerJ

The ocean sampling day consortium

(2015) Anna Kopf et al.   GigaScience

Open science resources for the discovery and analysis of Tara Oceans data

(2015) Stéphane Pesant et al.   Scientific Data

ATP synthases from archaea: The beauty of a molecular motor

(2014) Gerhard Grüber et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

ITEP: An integrated toolkit for exploration of microbial pan-genomes

(2014) Matthew N Benedict et al.   BMC GENOMICS

Mannosylglycerate: structural analysis of biosynthesis and evolutionary history

(2014) Nuno Borges et al.   EXTREMOPHILES

Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota

(2014) Philippe Deschamps et al.   Genome Biology and Evolution

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

Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling

(2013) Brett J Baker et al.   ISME Journal

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2013) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

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

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation

(2012) K. Schlegel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) V. Iverson et al.   SCIENCE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH