Metagenomic covariation along densely sampled environmental gradients in the Red Sea

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages

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

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

The transport of nutrient-rich Indian Ocean water through the Red Sea and into coastal reef systems

(2015) James H. Churchill et al.   JOURNAL OF MARINE RESEARCH

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

(2014) L. W. Kelly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

(2013) Libusha Kelly et al.   ISME Journal

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

(2013) Luke R. Thompson et al.   Ecology and Evolution

Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea

(2012) David Kamanda Ngugi et al.   PLoS One

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment

(2012) Juan F. Villarreal-Chiu   Frontiers in Microbiology

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Potential for phosphite and phosphonate utilization by Prochlorococcus

(2011) Roi Feingersch et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Exploration of community traits as ecological markers in microbial metagenomes

(2011) ALBERT BARBERÁN et al.   MOLECULAR ECOLOGY

Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea

(2011) DAVID KAMANDA NGUGI et al.   MOLECULAR ECOLOGY

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

One Carbon Metabolism in SAR11 Pelagic Marine Bacteria

(2011) Jing Sun et al.   PLoS One

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

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

(2010) Rohit Ghai et al.   ISME Journal

Ecosystem-specific selection pressures revealed through comparative population genomics

(2010) M. L. Coleman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses

(2009) Asuncion Martinez et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community genomics in eastern Mediterranean Sea surface waters

(2009) Roi Feingersch et al.   ISME Journal

Ecological Genomics of Marine Picocyanobacteria

(2009) D. J. Scanlan et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Large Scale Comparative Proteomics of a Chloroplast Clp Protease Mutant Reveals Folding Stress, Altered Protein Homeostasis, and Feedback Regulation of Metabolism

(2009) Boris Zybailov et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE