Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column

Decline in global oceanic oxygen content during the past five decades

(2017) Sunke Schmidtko et al.   NATURE

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium

(2016) Vega Shah et al.   ISME Journal

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

(2016) William D Orsi et al.   ISME Journal

NC10 bacteria in marine oxygen minimum zones

(2016) Cory C Padilla et al.   ISME Journal

Deciphering ocean carbon in a changing world

(2016) Mary Ann Moran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

(2016) Ping Hu et al.   mBio

Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions

(2016) Matthias Winkel et al.   Frontiers in Microbiology

Ocean Acidification Accelerates the Growth of Two Bloom-Forming Macroalgae

(2016) Craig S. Young et al.   PLoS One

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

(2015) Laura A. Hug et al.   ENVIRONMENTAL 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

Genomic potential for arsenic efflux and methylation varies among global Prochlorococcus populations

(2015) Jaclyn K Saunders et al.   ISME Journal

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

(2015) Masaru K Nobu et al.   ISME Journal

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

(2015) Jennifer B. Glass et al.   Frontiers in Microbiology

Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone

(2015) Molly T. Carolan et al.   Frontiers in Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle

(2013) Jody J Wright et al.   ISME Journal

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

(2013) Sangita Ganesh et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Physiological and Metabolic Effects of Carbon Monoxide Oxidation in the Model Marine Bacterioplankton Ruegeria pomeroyi DSS-3

(2012) Michael Cunliffe   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Free-living and aggregate-associated Planctomycetes in the Black Sea

(2012) Clara A. Fuchsman et al.   FEMS MICROBIOLOGY ECOLOGY

Isolation of an aerobic sulfur oxidizer from the SUP05/Arctic96BD-19 clade

(2012) Katharine T Marshall et al.   ISME Journal

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

(2012) Elke Allers 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

Anammox and denitrification in the oxygen minimum zone of the eastern South Pacific

(2012) Tage Dalsgaard et al.   LIMNOLOGY AND OCEANOGRAPHY

Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria

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

Microbial oceanography of anoxic oxygen minimum zones

(2012) O. Ulloa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton

(2011) Elizabeth A Ottesen et al.   ISME Journal

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Biotransformation and Volatilization of Arsenic by Three Photosynthetic Cyanobacteria

(2011) X.-X. Yin et al.   PLANT PHYSIOLOGY

Activity of abundant and rare bacteria in a coastal ocean

(2011) B. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy 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

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

(2010) Yanmei Shi et al.   ISME Journal

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

(2010) Robert M Morris et al.   ISME Journal

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

(2010) D. E. Canfield et al.   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

Temporal changes in bacterial rRNA and rRNA genes in Delaware (USA) coastal waters

(2009) BJ Campbell et al.   AQUATIC MICROBIAL ECOLOGY

Selenoproteins in Archaea and Gram-positive bacteria

(2009) Tilmann Stock et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

(2009) Elena Zaikova et al.   ENVIRONMENTAL MICROBIOLOGY

Denitrification as the dominant nitrogen loss process in the Arabian Sea

(2009) B. B. Ward et al.   NATURE

Molybdenum cofactors, enzymes and pathways

(2009) Günter Schwarz et al.   NATURE

Revising the nitrogen cycle in the Peruvian oxygen minimum zone

(2009) P. Lam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

(2009) D. A. Walsh et al.   SCIENCE

Simulated 21st century's increase in oceanic suboxia by CO2-enhanced biotic carbon export

(2008) Andreas Oschlies et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Molybdoproteomes and Evolution of Molybdenum Utilization

(2008) Yan Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH

Design and testing of ‘genome-proxy’ microarrays to profile marine microbial communities

(2007) Virginia I. Rich et al.   ENVIRONMENTAL MICROBIOLOGY