For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
448
views
28
references
 Top references
cited by
372
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      144
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: not found

      Metagenomic microbial community profiling using unique clade-specific marker genes

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large datasets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches. We validated MetaPhlAn on terabases of short reads and provide the largest metagenomic profiling to date of the human gut

          Related collections

          Most cited references28

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Rapid planetesimal formation in turbulent circumstellar discs

          Anders Johansen, Jeffrey S. Oishi, Mordecai-Mark Mac Low … (2007)
          The initial stages of planet formation in circumstellar gas discs proceed via dust grains that collide and build up larger and larger bodies (Safronov 1969). How this process continues from metre-sized boulders to kilometre-scale planetesimals is a major unsolved problem (Dominik et al. 2007): boulders stick together poorly (Benz 2000), and spiral into the protostar in a few hundred orbits due to a head wind from the slower rotating gas (Weidenschilling 1977). Gravitational collapse of the solid component has been suggested to overcome this barrier (Safronov 1969, Goldreich & Ward 1973, Youdin & Shu 2002). Even low levels of turbulence, however, inhibit sedimentation of solids to a sufficiently dense midplane layer (Weidenschilling & Cuzzi 1993, Dominik et al. 2007), but turbulence must be present to explain observed gas accretion in protostellar discs (Hartmann 1998). Here we report the discovery of efficient gravitational collapse of boulders in locally overdense regions in the midplane. The boulders concentrate initially in transient high pressures in the turbulent gas (Johansen, Klahr, & Henning 2006), and these concentrations are augmented a further order of magnitude by a streaming instability (Youdin & Goodman 2005, Johansen, Henning, & Klahr 2006, Johansen & Youdin 2007) driven by the relative flow of gas and solids. We find that gravitationally bound clusters form with masses comparable to dwarf planets and containing a distribution of boulder sizes. Gravitational collapse happens much faster than radial drift, offering a possible path to planetesimal formation in accreting circumstellar discs.
          Article 0 comments Cited 2503 times – based on 0 reviews
          Preprint
               Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            NCBI Reference Sequences: current status, policy and new initiatives

            Kim D. Pruitt, Tatiana Tatusova, William Klimke … (2009)
            NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features. The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 × 106 proteins (RefSeq release 30). Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation. We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome annotation. In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system.
            Article 0 comments Cited 328 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov Models

              Arthur Brady, Steven Salzberg (2009)
              Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made metagenomics easier, by making sequencing faster, and more difficult, by producing shorter reads than previous technologies. Classifying sequences from reads as short as 100 base pairs has until now been relatively inaccurate, requiring researchers to use older, long-read technologies. We present Phymm, a classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 bp, representing a substantial leap forward over previous composition-based classification methods. We also describe how combining Phymm with sequence alignment algorithms, further improves accuracy.
              Article 0 comments Cited 206 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101215604
                Journal ID (pubmed-jr-id): 32338
                Journal ID (nlm-ta): Nat Methods
                Journal ID (iso-abbrev): Nat. Methods
                Title: Nature methods
                ISSN (Print): 1548-7091
                ISSN (Electronic): 1548-7105
                Publication date Nihms-submitted: 22 August 2012
                Publication date (Electronic): 10 June 2012
                Publication date PMC-release: 01 February 2013
                Volume: 9
                Issue: 8
                Pages: 811-814
                Affiliations
                [1 ]Department of Biostatistics, Harvard School of Public Health, Boston (MA), USA
                [2 ]Centre for Integrative Biology, University of Trento, Trento, Italy
                Author notes
                Corresponding author: Curtis Huttenhower ( chuttenh@ 123456hsph.harvard.edu )
                Article
                Manuscript ID: NIHMS397911
                DOI: 10.1038/nmeth.2066
                PMC ID: 3443552
                PubMed ID: 22688413
                SO-VID: ee0f89e8-3c29-401f-b620-85c0bb09585d
                History
                Funding
                Funded by: National Human Genome Research Institute : NHGRI
                Award ID: R01 HG005969 || HG
                Categories
                Subject: Article

                ScienceOpen disciplines: Life sciences
                Data availability:
                ScienceOpen disciplines: Life sciences

                Comments

                Comment on this article

                scite_

                Similar content144

                See all similar

                Cited by788

                See all cited by

                Most referenced authors1,613

                See all reference authors