Going Deeper: Metagenome of a Hadopelagic Microbial Community

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages

(2010) C. Andrews-Pfannkoch et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics

(2010) Toshi Nagata et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

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

(2010) Rohit Ghai et al.   ISME Journal

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

(2010) Achim Quaiser et al.   ISME Journal

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

(2010) Wei Xie et al.   ISME Journal

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

(2010) Christopher L Hemme et al.   ISME Journal

Genome Sequence of Lentisphaera araneosa HTCC2155T, the Type Species of the Order Lentisphaerales in the Phylum Lentisphaerae

(2010) J. C. Thrash et al.   JOURNAL OF BACTERIOLOGY

Genomic and functional adaptation in surface ocean planktonic prokaryotes

(2010) Shibu Yooseph et al.   NATURE

Autotrophic carbon fixation in archaea

(2010) Ivan A. Berg et al.   NATURE REVIEWS MICROBIOLOGY

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

(2010) Nianzhi Jiao et al.   NATURE REVIEWS MICROBIOLOGY

Role of macroscopic particles in deep-sea oxygen consumption

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

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

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

Life cycle analysis of the model organism Rhodopirellula baltica SH 1T by transcriptome studies

(2010) Patricia Wecker et al.   Microbial Biotechnology

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

(2010) David M. Tanenbaum et al.   Standards in Genomic Sciences

CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea

(2009) A.-B. Martin-Cuadrado et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

Bacterial diversity in surface sediments from the Pacific Arctic Ocean

(2009) Huirong Li et al.   EXTREMOPHILES

Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing

(2009) Pierre E Galand et al.   ISME Journal

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

Complete Genome Sequence of Robiginitalea biformata HTCC2501

(2009) H.-M. Oh et al.   JOURNAL OF BACTERIOLOGY

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

(2009) Konstantinos Liolios et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Community composition of the marine bacterioplankton in Kongsfjorden (Spitsbergen) as revealed by 16S rRNA gene analysis

(2009) Yinxin Zeng et al.   POLAR BIOLOGY

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria

(2009) E. Poiata et al.   RNA

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation

(2008) Pierre E. Galand et al.   ENVIRONMENTAL MICROBIOLOGY

Source/process apportionment of major and trace elements in sinking particles in the Sargasso sea

(2008) S. Huang et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Genomic patterns of recombination, clonal divergence and environment in marine microbial populations

(2008) Konstantinos T Konstantinidis et al.   ISME Journal

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

(2008) Ana-Belen Martin-Cuadrado et al.   ISME Journal

Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter

(2008) Elena Ivars-Martinez et al.   ISME Journal

The Transporter Classification Database: recent advances

(2008) M. H. Saier et al.   NUCLEIC ACIDS RESEARCH

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea Iron Reducing Bacterium Shewanella piezotolerans WP3

(2008) Fengping Wang et al.   PLoS One

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

(2008) J. F. Biddle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA