Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
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Title
Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
Authors
Keywords
Photic zone, Deep chlorophyll maximum, Mediterranean, Stratification, Stenobathic
Journal
Microbiome
Volume 6, Issue 1, Pages -
Publisher
Springer Nature
Online
2018-07-10
DOI
10.1186/s40168-018-0513-5
References
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Note: Only part of the references are listed.- Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities
- (2018) Tyler P. Barnum et al. ISME Journal
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- (2017) Jose M Haro-Moreno et al. ISME Journal
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- (2017) Dan R. Miller et al. Marine Genomics
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- (2017) Mario López-Pérez et al. PLoS Genetics
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- Microorganisms and ocean global change
- (2017) David A. Hutchins et al. Nature Microbiology
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- (2016) Matthew L Bendall et al. ISME Journal
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- (2016) Alexis P Yelton et al. ISME Journal
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- (2016) Minoru Kanehisa et al. JOURNAL OF MOLECULAR BIOLOGY
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- (2016) Jarone Pinhassi et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
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- (2016) Sudhir Kumar et al. MOLECULAR BIOLOGY AND EVOLUTION
- MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
- (2016) Daniel H. Huson et al. PLoS Computational Biology
- Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea
- (2016) Mario López-Pérez et al. Frontiers in Microbiology
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages
- (2015) Haiwei Luo et al. MOLECULAR BIOLOGY AND EVOLUTION
- Marine microbial community dynamics and their ecological interpretation
- (2015) Jed A. Fuhrman et al. NATURE REVIEWS MICROBIOLOGY
- KEGG as a reference resource for gene and protein annotation
- (2015) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- Genomic and proteomic characterization of “CandidatusNitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean
- (2015) Alyson E. Santoro et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2015) Carolina Megumi Mizuno et al. mBio
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- (2014) Benjamin Buchfink et al. NATURE METHODS
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- (2014) Alison Buchan et al. NATURE REVIEWS MICROBIOLOGY
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- (2014) Steven J. Biller et al. NATURE REVIEWS MICROBIOLOGY
- Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses
- (2014) Ari J. S. Ferreira et al. PLoS One
- Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
- (2014) N. Kashtan et al. SCIENCE
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- (2013) Janine Kamke et al. ISME Journal
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- (2013) Mads Albertsen et al. NATURE BIOTECHNOLOGY
- The carbohydrate-active enzymes database (CAZy) in 2013
- (2013) Vincent Lombard et al. NUCLEIC ACIDS RESEARCH
- Ribosomal Database Project: data and tools for high throughput rRNA analysis
- (2013) James R. Cole et al. NUCLEIC ACIDS RESEARCH
- Prochlorococcus can use the Pro1404 transporter to take up glucose at nanomolar concentrations in the Atlantic Ocean
- (2013) M. d. C. Munoz-Marin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria
- (2013) I. Gushchin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
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- (2013) M. Hugoni et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
- (2013) Rohit Ghai et al. Scientific Reports
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- (2012) Y. Peng et al. BIOINFORMATICS
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- (2012) G. Denaro et al. Ecological Complexity
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- (2012) Aitor Gonzaga et al. Genome Biology and Evolution
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- (2012) Scott M Gifford et al. ISME Journal
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- dbCAN: a web resource for automated carbohydrate-active enzyme annotation
- (2012) Yanbin Yin et al. NUCLEIC ACIDS RESEARCH
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- (2012) S. J. Giovannoni et al. SCIENCE
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- (2009) Ying Huang et al. BIOINFORMATICS
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- (2009) H. Li et al. BIOINFORMATICS
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- (2009) Federico Baltar et al. ENVIRONMENTAL MICROBIOLOGY
- 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
- Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria
- (2009) Shi Yan et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
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- (2008) Ana-Belen Martin-Cuadrado et al. ISME Journal
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- (2008) Jed A. Fuhrman et al. NATURE REVIEWS MICROBIOLOGY
- New substrates for TonB-dependent transport: do we only see the ‘tip of the iceberg’?
- (2008) Kristine Schauer et al. TRENDS IN BIOCHEMICAL SCIENCES
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