Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean

(2014) B. E. Pedler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microspatial gene expression patterns in the Amazon River Plume

(2014) B. M. Satinsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters

(2013) Fernando Unrein et al.   ISME Journal

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

(2013) Kevin L Vergin et al.   ISME Journal

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pattern and synchrony of gene expression among sympatric marine microbial populations

(2013) E. A. Ottesen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relationship between Abundance and Specific Activity of Bacterioplankton in Open Ocean Surface Waters

(2012) Dana E. Hunt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Global distribution of a wild alga revealed by targeted metagenomics

(2012) Alexandra Z. Worden et al.   CURRENT BIOLOGY

Basin-scale patterns in the abundance of SAR11 subclades, marine Actinobacteria (OM1), members of the Roseobacter clade and OCS116 in the South Atlantic

(2012) Robert M. Morris et al.   ENVIRONMENTAL MICROBIOLOGY

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

(2012) Lisa Zeigler Allen et al.   ISME Journal

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

(2012) Ryan A Lesniewski et al.   ISME Journal

Expression patterns reveal niche diversification in a marine microbial assemblage

(2012) Scott M Gifford et al.   ISME Journal

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

(2012) V. Iverson et al.   SCIENCE

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

(2011) Frank J. Stewart et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Chris L Dupont et al.   ISME Journal

The green ribbon: Multiscale physical control of phytoplankton productivity and community structure over a narrow continental shelf

(2011) Andrew J. Lucas et al.   LIMNOLOGY AND OCEANOGRAPHY

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Assimilation of upwelled nitrate by small eukaryotes in the Sargasso Sea

(2011) Sarah E. Fawcett et al.   Nature Geoscience

GenBank

(2011) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration

(2011) Laura Steindler et al.   PLoS One

The Phylogenetic Diversity of Metagenomes

(2011) Steven W. Kembel et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu 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

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

Quantitative analysis of a deeply sequenced marine microbial metatranscriptome

(2010) Scott M Gifford et al.   ISME Journal

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

Characterization of Prochlorococcus clades from iron-depleted oceanic regions

(2010) D. B. Rusch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

(2010) Terry C. Hazen et al.   SCIENCE

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

(2009) D. A. Walsh et al.   SCIENCE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY