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922 research outcomes, page 1 of 93
  • publication . Preprint . 2017
    Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota Identified by Genome-Centric Metagenomics
    Open Access English
    Authors:
    Alon Philosof; Natalya Yutin; José Flores-Uribe; Itai Sharon; Eugene V. Koonin; Oded Béjà;
    Persistent Identifiers

    doi: 10.1101/101196

    Publisher: Cold Spring Harbor Laboratory
    Project: EC | PHOTOPHAGE (321647), EC | PHOTO.COMM (317184), TARA | Tara Oceans (2)

    AbstractMarine Group II Euryarchaeota (MGII) are among the most abundant microbes in the oceanic surface waters. So far, however, representatives of MGII have not been cultivated, and no viruses infecting these organisms have been described. Here we present complete gen...

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  • publication . Article . Preprint . 2018
    Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
    Open Access
    Authors:
    Lucas Czech; Alexandros Stamatakis;
    Persistent Identifiers

    doi: 10.1371/journal.pone.0217050 , 10.5445/ir/1000095849 , 10.1101/346353

    pmc: PMC6538146

    pmid: 31136592

    Publisher: Public Library of Science (PLoS)
    Country: Germany
    Project: TARA | Tara Oceans (2)

    1AbstractThe exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutionary provenance of anonymous sequenc...

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  • publication . Article . 2017
    Pan-Arctic optical characteristics of colored dissolved organic matter: Tracing dissolved organic carbon in changing Arctic waters using satellite ocean color data
    Open Access English
    Authors:
    Matsuoka, Atsushi; Boss, Emmanuel; Babin, Marcel; Karp-Boss, Lee; Hafez, Mark; Chekalyuk, Alex; Proctor, Christopher W.; Werdell, P. Jeremy; Bricaud, Annick;
    Persistent Identifiers

    doi: 10.1016/j.rse.2017.08.009

    Publisher: HAL CCSD
    Country: France
    Project: TARA | Tara Oceans (2)

    International audience; Light absorption of the colored fraction of dissolved organic matter (CDOM) is a dominant optical component of the Arctic Ocean (AO). Here we show Pan-Arctic characteristics of CDOM light absorption for various Arctic regions covering both coasta...

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  • publication . Preprint . 2020
    Inferring Multiple Metagenomic Association Networks based on Variation of Environmental Factors
    Open Access English
    Authors:
    Yuqing Yang; Xin Wang; Kaikun Xie; Congmin Zhu; Ning Chen; Ting Chen;
    Persistent Identifiers

    doi: 10.1101/2020.03.04.976423

    Publisher: Cold Spring Harbor Laboratory
    Project: TARA | Tara Oceans (2)

    AbstractIdentifying significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose, but they assume that associations are static, neglecting the fact that relationsh...

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  • publication . Preprint . 2019
    Pangenomics reveal diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria
    Open Access
    Authors:
    Saw, Jimmy H.W.; Nunoura, Takuro; Hirai, Miho; Takaki, Yoshihiro; Parsons, Rachel; Michelsen, Michelle; Longnecker, Krista; Kujawinski, Elizabeth B.; Stepanauskas, Ramunas; Landry, Zachary; ...
    Persistent Identifiers

    doi: 10.1101/692848

    Publisher: bioRxiv
    Project: TARA | Tara Oceans (2), NSF | Collaborative research: U... (1441717), NSF | MRI: Acquisition of genom... (1335810), NSF | Dissolved Organic Matter ... (1154320)

    AbstractIt has been hypothesized that abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylumChloroflexievolved specialized metabolism for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathway...

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  • publication . Preprint . Article . 2019
    Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
    Open Access English
    Authors:
    Cuadrat, Rafael R. C.; Sorokina, Maria; Andrade, Bruno G.; Goris, Tobias; Dávila, Alberto M. R.;
    Persistent Identifiers

    doi: 10.1101/765446

    Country: Brazil
    Project: TARA | Tara Oceans (2)

    Submitted by Sandra Infurna (sandra.infurna@ioc.fiocruz.br) on 2020-05-29T14:22:18Z No. of bitstreams: 1 AlbertoDÀvila_etal_IOC_2019.pdf: 399391 bytes, checksum: 13383d1bc270738ef6c0bb3ae6a1f84c (MD5) Approved for entry into archive by Sandra Infurna (sandra.infurna@ioc...

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  • publication . Conference object . 2015
    Simka: fast kmer-based method for estimating the similarity between numerous metagenomic datasets
    English
    Authors:
    Benoit, Gaëtan; Peterlongo, Pierre; Lavenier, Dominique; Lemaitre, Claire;
    Publisher: HAL CCSD
    Country: France
    Project: TARA | Tara Oceans (2)

    International audience; Comparative metagenomics aims to provide high-level information based on DNA material sequenced from different environments. The purpose is mainly to estimate proximity between two or more environmental sites at the genomic level. One way to esti...

  • publication . Article . 2020
    Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition
    Open Access
    Authors:
    Alicia S. Arroyo; Romain Iannes; Eric Bapteste; Iñaki Ruiz-Trillo;
    Persistent Identifiers

    doi: 10.1093/gbe/evaa117

    handle: 10261/236387

    pmc: PMC7533066

    pmid: 32533833

    Publisher: Oxford University Press
    Country: France
    Project: TARA | Tara Oceans (2)

    The Holozoa clade comprises animals and several unicellular lineages (choanoflagellates, filastereans, and teretosporeans). Understanding their full diversity is essential to address the origins of animals and other evolutionary questions. However, they are poorly known...

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  • publication . Preprint . 2021
    Restructuring of genomic provinces of surface ocean plankton under climate change
    Open Access English
    Authors:
    Paul Frémont; Marion Gehlen; Mathieu Vrac; Jade Leconte; Tom O. Delmont; Patrick Wincker; Daniele Iudicone; Olivier Jaillon;
    Persistent Identifiers

    doi: 10.1101/2020.10.20.347237

    Publisher: HAL CCSD
    Country: France
    Project: TARA | Tara Oceans (2)

    AbstractThe impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here, niche theory is applied to plankton metagenomes of 6 size fractions, from viruses to meso-zooplankton, sampled during the Tara Ocea...

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  • publication . Article . Other literature type . 2019
    Microplastics in Mediterranean Sea: A protocol to robustly assess contamination characteristics.
    Open Access English
    Authors:
    Kedzierski, Mikaël; Villain, Jonathan; Falcou-Préfol, Mathilde; Kerros, Marie Emmanuelle; Henry, Maryvonne; Pedrotti, Maria Luiza; Bruzaud, Stéphane;
    Persistent Identifiers

    doi: 10.1371/journal.pone.0212088

    pmc: PMC6370211

    pmid: 30742663

    Publisher: Public Library of Science (PLoS)
    Country: France
    Project: TARA

    International audience; The study of microplastic pollution involves multidisciplinary analyses on a large number of microplastics. Therefore, providing an overview of plastic pollution is time consuming and, despite high throughput analyses, remains a major challenge. ...

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922 research outcomes, page 1 of 93