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

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

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

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Genomes of Abundant and Widespread Viruses from the Deep Ocean

(2016) Carolina Megumi Mizuno et al.   mBio

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre

(2015) Jessica A Bryant et al.   ISME Journal

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Microbial community transcriptional networks are conserved in three domains at ocean basin scales

(2015) Frank O. Aylward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics

(2015) Matteo Ramazzotti et al.   Frontiers in Genetics

Estimating the compensation irradiance in the ocean: The importance of accounting for non-photosynthetic uptake of inorganic carbon

(2014) Edward A. Laws et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Reductive genome evolution at both ends of the bacterial population size spectrum

(2014) Bérénice Batut et al.   NATURE REVIEWS MICROBIOLOGY

Prochlorococcus: the structure and function of collective diversity

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

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

The significance of nitrogen cost minimization in proteomes of marine microorganisms

(2011) Joseph J Grzymski et al.   ISME Journal

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

(2011) Chris L Dupont et al.   ISME Journal

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

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

Prochlorococcus: Advantages and Limits of Minimalism

(2009) Frédéric Partensky et al.   Annual Review of Marine Science

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS