The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
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{"title"=>"The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific", "type"=>"journal", "authors"=>[{"first_name"=>"Douglas B.", "last_name"=>"Rusch", "scopus_author_id"=>"7004630429"}, {"first_name"=>"Aaron L.", "last_name"=>"Halpern", "scopus_author_id"=>"7103054770"}, {"first_name"=>"Granger", "last_name"=>"Sutton", "scopus_author_id"=>"56750848100"}, {"first_name"=>"Karla B.", "last_name"=>"Heidelberg", "scopus_author_id"=>"8658484300"}, {"first_name"=>"Shannon", "last_name"=>"Williamson", "scopus_author_id"=>"7203080324"}, {"first_name"=>"Shibu", "last_name"=>"Yooseph", "scopus_author_id"=>"6602156903"}, {"first_name"=>"Dongying", "last_name"=>"Wu", "scopus_author_id"=>"34976109100"}, {"first_name"=>"Jonathan A.", "last_name"=>"Eisen", "scopus_author_id"=>"35247902700"}, {"first_name"=>"Jeff M.", "last_name"=>"Hoffman", "scopus_author_id"=>"55420112000"}, {"first_name"=>"Karin", "last_name"=>"Remington", "scopus_author_id"=>"6701483567"}, {"first_name"=>"Karen", "last_name"=>"Beeson", "scopus_author_id"=>"6701442444"}, {"first_name"=>"Bao", "last_name"=>"Tran", "scopus_author_id"=>"7006180503"}, {"first_name"=>"Hamilton", "last_name"=>"Smith", "scopus_author_id"=>"7406226290"}, {"first_name"=>"Holly", "last_name"=>"Baden-Tillson", "scopus_author_id"=>"7801441756"}, {"first_name"=>"Clare", "last_name"=>"Stewart", "scopus_author_id"=>"16043600400"}, {"first_name"=>"Joyce", "last_name"=>"Thorpe", "scopus_author_id"=>"16043516600"}, {"first_name"=>"Jason", "last_name"=>"Freeman", "scopus_author_id"=>"55472402700"}, {"first_name"=>"Cynthia", "last_name"=>"Andrews-Pfannkoch", "scopus_author_id"=>"16041645800"}, {"first_name"=>"Joseph E.", "last_name"=>"Venter", "scopus_author_id"=>"16044357400"}, {"first_name"=>"Kelvin", "last_name"=>"Li", "scopus_author_id"=>"36175030700"}, {"first_name"=>"Saul", "last_name"=>"Kravitz", "scopus_author_id"=>"7004207962"}, {"first_name"=>"John F.", "last_name"=>"Heidelberg", "scopus_author_id"=>"6603942913"}, {"first_name"=>"Terry", "last_name"=>"Utterback", "scopus_author_id"=>"6701855401"}, {"first_name"=>"Yu Hui", "last_name"=>"Rogers", "scopus_author_id"=>"57197141778"}, {"first_name"=>"Luisa I.", "last_name"=>"Falcón", "scopus_author_id"=>"7003347996"}, {"first_name"=>"Valeria", "last_name"=>"Souza", "scopus_author_id"=>"7006367707"}, {"first_name"=>"Germán", "last_name"=>"Bonilla-Rosso", "scopus_author_id"=>"16041666500"}, {"first_name"=>"Luis E.", "last_name"=>"Eguiarte", "scopus_author_id"=>"6701589295"}, {"first_name"=>"David M.", "last_name"=>"Karl", "scopus_author_id"=>"7005643917"}, {"first_name"=>"Shubha", "last_name"=>"Sathyendranath", "scopus_author_id"=>"7004793287"}, {"first_name"=>"Trevor", "last_name"=>"Platt", "scopus_author_id"=>"7102275990"}, {"first_name"=>"Eldredge", "last_name"=>"Bermingham", "scopus_author_id"=>"36938170900"}, {"first_name"=>"Victor", "last_name"=>"Gallardo", "scopus_author_id"=>"7006569288"}, {"first_name"=>"Giselle", "last_name"=>"Tamayo-Castillo", "scopus_author_id"=>"6603033458"}, {"first_name"=>"Michael R.", "last_name"=>"Ferrari", "scopus_author_id"=>"57199693135"}, {"first_name"=>"Robert L.", "last_name"=>"Strausberg", "scopus_author_id"=>"7003353433"}, {"first_name"=>"Kenneth", "last_name"=>"Nealson", "scopus_author_id"=>"7006660618"}, {"first_name"=>"Robert", "last_name"=>"Friedman", "scopus_author_id"=>"7401990376"}, {"first_name"=>"Marvin", "last_name"=>"Frazier", "scopus_author_id"=>"7004786030"}, {"first_name"=>"J. Craig", "last_name"=>"Venter", "scopus_author_id"=>"35352327000"}], "year"=>2007, "source"=>"PLoS Biology", "identifiers"=>{"scopus"=>"2-s2.0-33947238287", "doi"=>"10.1371/journal.pbio.0050077", "sgr"=>"33947238287", "isbn"=>"1545-7885 (Electronic)\\r1544-9173 (Linking)", "pmid"=>"17355176", "issn"=>"15457885", "pui"=>"46422965"}, "id"=>"0b192c99-6148-34de-969d-9f64c4b47552", "abstract"=>"The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed \"fragment recruitment,\" addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed \"extreme assembly,\" made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.", "link"=>"http://www.mendeley.com/research/sorcerer-ii-global-ocean-sampling-expedition-northwest-atlantic-through-eastern-tropical-pacific", "reader_count"=>1158, "reader_count_by_academic_status"=>{"Unspecified"=>14, "Professor > Associate Professor"=>99, "Librarian"=>3, "Researcher"=>314, "Student > Doctoral Student"=>47, "Student > Ph. D. Student"=>327, "Student > Postgraduate"=>45, "Student > Master"=>143, "Other"=>25, "Student > Bachelor"=>52, "Lecturer"=>10, "Lecturer > Senior Lecturer"=>5, "Professor"=>73}, "reader_count_by_user_role"=>{"Unspecified"=>14, "Professor > Associate Professor"=>99, "Librarian"=>3, "Researcher"=>314, "Student > Doctoral Student"=>47, "Student > Ph. D. Student"=>327, "Student > Postgraduate"=>45, "Student > Master"=>143, "Other"=>25, "Student > Bachelor"=>52, "Lecturer"=>10, "Lecturer > Senior Lecturer"=>5, "Professor"=>73}, "reader_count_by_subject_area"=>{"Unspecified"=>35, "Agricultural and Biological Sciences"=>755, "Arts and Humanities"=>3, "Business, Management and Accounting"=>3, "Chemistry"=>16, "Computer Science"=>39, "Earth and Planetary Sciences"=>43, "Engineering"=>7, "Environmental Science"=>111, "Biochemistry, Genetics and Molecular Biology"=>91, "Mathematics"=>10, "Medicine and Dentistry"=>15, "Design"=>1, "Physics and Astronomy"=>7, "Psychology"=>1, "Social Sciences"=>2, "Immunology and Microbiology"=>17, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>15}, "Social Sciences"=>{"Social Sciences"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>7}, "Psychology"=>{"Psychology"=>1}, "Mathematics"=>{"Mathematics"=>10}, "Unspecified"=>{"Unspecified"=>35}, "Environmental Science"=>{"Environmental Science"=>111}, "Arts and Humanities"=>{"Arts and Humanities"=>3}, "Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>7}, "Chemistry"=>{"Chemistry"=>16}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>43}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>17}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>755}, "Computer Science"=>{"Computer Science"=>39}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>3}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>91}}, "reader_count_by_country"=>{"Hong Kong"=>1, "United States"=>62, "Malaysia"=>1, "Portugal"=>2, "Russia"=>1, "Costa Rica"=>2, "Greece"=>1, "Netherlands"=>3, "Sweden"=>6, "South Korea"=>1, "Austria"=>1, "Luxembourg"=>1, "Ireland"=>1, "Brazil"=>12, "Poland"=>2, "Slovenia"=>1, "France"=>9, "Chile"=>5, "Ecuador"=>2, "Colombia"=>2, "Philippines"=>1, "Japan"=>3, "Uzbekistan"=>1, "United Kingdom"=>9, "Spain"=>9, "India"=>4, "New Zealand"=>1, "Canada"=>11, "Belgium"=>3, "Norway"=>3, "Denmark"=>5, "Mexico"=>15, "Italy"=>4, "South Africa"=>3, "Israel"=>1, "Australia"=>6, "Germany"=>20, "Estonia"=>1, "Indonesia"=>1}, "group_count"=>51}

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  • {"month"=>"1", "year"=>"2017", "pdf_views"=>"92", "xml_views"=>"1", "html_views"=>"247"}
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  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"61", "xml_views"=>"1", "html_views"=>"59"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/952774"], "description"=>"<div><p>(A) Fragment recruitment to an extreme assembly contig indicates the assembly is\n chimeric between two organisms, based on dramatic shifts in density of recruitment,\n level of conservation, and sample distribution.</p>\n <p>(B) Fragment recruitment to a SAR11-related extreme assembly. Changes in color,\n density, and vertical location toward the top of the figure indicate transitions among\n multiple subtypes of SAR11.</p></div>", "links"=>[], "tags"=>["chimeric"], "article_id"=>623042, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_Chimeric_Extreme_Assemblies_/623042", "title"=>"Examples of Chimeric Extreme Assemblies", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:47:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/951669"], "description"=>"<p>Microbial populations were sampled from locations in the order shown. Samples were\n collected at approximately 200 miles (320 km) intervals along the eastern North\n American coast through the Gulf of Mexico into the equatorial Pacific. Samples 00 and\n 01 identify sets of sites sampled as part of the Sargasso Sea pilot study [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-b019\" target=\"_blank\">19</a>]. Samples 27 through 36 were\n sampled off the Galapagos Islands (see inset). Sites shown in gray were not analyzed\n as part of this study.</p>", "links"=>[], "tags"=>["Computational biology", "ecology", "Evolutionary biology", "genetics and genomics", "microbiology", "Virology"], "article_id"=>621924, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_Sites_/621924", "title"=>"Sampling Sites", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-03-13 00:32:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/952396"], "description"=>"<p>The recruitment metadata distinguishes eight different general categories based on\n the relative placement of paired end sequencing reads (mated reads) when recruited to\n a reference sequence in comparison to their known orientation and separation on the\n clone from which they were derived. Assuming orientation is correct, two mated reads\n can be recruited closer together, further apart, or within expected distances given\n the size of the clone from which the sequences were derived. These sequences are\n categorized as “short,” “long,” or “good,” respectively. Alternately, the mated reads\n may be recruited in a mis-oriented fashion, which trumps issues of separation. These\n reads can be categorized as “normal,” “anti-normal,” or “outie.” In addition, there\n are two other categories. “No mate” indicates that no mated read was available for\n recruitment, possibly due to sequencing error. Perhaps most useful of any of the\n recruitment categories, “missing” mates indicate that while a mated sequence was\n available, it was not recruited to the reference. “Missing” mates identify breaks in\n synteny between the environmental data and the reference sequence.</p>", "links"=>[], "tags"=>["recruitment"], "article_id"=>622662, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g004", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Categories_of_Recruitment_Metadata_/622662", "title"=>"Categories of Recruitment Metadata", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-03-13 00:44:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/953334"], "description"=>"<p>Coloring of branches indicates that the corresponding reads align at >90%\n identity to the extreme assembly segments shown in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-g007\" target=\"_blank\">Figure 7</a>; colored labels (A–X) correspond to the\n labels in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-g007\" target=\"_blank\">Figure 7</a>, indicating the\n segment or segments to which reads aligned.</p>", "links"=>[], "tags"=>["gos", "reads", "aligning", "htcc1062", "upstream", "16s", "gene", "indicates", "assemblies", "correspond", "monophyletic"], "article_id"=>623592, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g008", "stats"=>{"downloads"=>2, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_GOS_Reads_Aligning_to_P_ubique_HTCC1062_Upstream_of_16S_Gene__Indicates_That_the_Extreme_Assemblies_in_Figure_7_Correspond_to_Monophyletic_Subtypes_/623592", "title"=>"Phylogeny of GOS Reads Aligning to P. ubique HTCC1062 Upstream of 16S Gene\n Indicates That the Extreme Assemblies in Figure 7 Correspond to Monophyletic Subtypes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:51:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/951994"], "description"=>"<div><p>The horizontal axis of each panel corresponds to a 100-kb segment of genomic sequence\n from the indicated reference microbial genome. The vertical axis indicates the\n sequence identity of an alignment between a GOS sequence and the reference genomic\n sequence. The identity ranges from 100% (top) to 50% (bottom). Individual GOS\n sequencing reads were colored to reflect the sample from which they were isolated.\n Geographically nearby samples have similar colors (see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-sd001\" target=\"_blank\">Poster S1</a> for\n key). Each organism shows a distinct pattern of recruitment reflecting its origin and\n relationship to the environmental data collected during the course of this study.</p>\n <p>(A) P.\n ubique HTCC1062 recruits the greatest density of GOS sequences of\n any genome examined to date. The GOS sequences show geographic stratification into\n bands, with sequences from temperate water samples off the North American coast having\n the highest identity (yellow to yellow-green colors). At lower identity, sequences\n from all the marine environments could be aligned to HTCC1062.</p>\n <p>(B) P.\n marinus MIT9312 recruits a large number of GOS sequences into a\n single band that zigzags between 85%–95% identity on average. These sequences are\n largely derived from warm water samples in the Gulf of Mexico and eastern Pacific\n (green to greenish-blue reads).</p>\n <p>(C) P.\n marinus MED4 recruits largely the same set of reads as MIT9312 (B)\n though the sequences that form the zigzag recruit at a substantially lower identity. A\n small number of sequences from the Sargasso Sea samples (red) are found at high\n identity.</p>\n <p>(D) P.\n marinus NATL2A recruits far fewer sequences than any of the\n preceding panels. Like MED4, a small number of high-identity sequences were recruited\n from the Sargasso samples.</p>\n <p>(E) P.\n marinus MIT9313 is a deep-water low-light–adapted strain of\n <i>Prochlorococcus.</i> GOS sequences were recruited almost exclusively at\n low identity in vertical stacks that correspond to the locations of conserved genes.\n On the left side of this panel is a very distinctive pattern of recruitment that\n corresponds to the highly conserved 16S and 23S mRNA gene operon.</p>\n <p>(F) P.\n marinus CCMP1375, another deep-water low-light–adapted strain, does\n not recruit GOS sequences at high identity. Only stacks of sequences are seen\n corresponding to the location of conserved genes.</p>\n <p>(G) <i>Synechococcus</i> WH8102 recruits a modest number of high-identity\n sequences primarily from the Sargasso Sea samples. A large number of moderate identity\n matches from the Pacific and hypersaline lagoon (GS33) samples are also visible.</p>\n <p>(H) <i>Synechococcus</i> CC9605 recruits largely the same sequences as does\n <i>Synechococcus</i> WH8102, but was isolated from Pacific waters. GOS\n sequences from some of the Pacific samples recruit at high identity, while sequences\n from the Sargasso and hypersaline lagoon (bluish-purple) were recruited at moderate\n identities.</p>\n <p>(I) <i>Synechococcus</i> CC9902 is distantly related to either of the\n preceding <i>Synechococcus</i> strains. While this strain also recruits\n largely the same sequences as the WH8102 and CC9902 strains, they recruit at\n significantly lower identity.</p>\n <p>(J–O) Fragment recruitment plots to extreme assemblies seeded with phylogenetically\n informative sequences. Using this approach it is not only possible to assemble contigs\n with strong similarities to known genomes but to identify contigs from previously\n uncultured genomes. In each case a 100-kb segment from an extreme assembly is shown.\n Each plot shows a distinct pattern of recruitment that distinguishes the panels from\n each other.</p>\n <p>(J) Seeded from a Prochlorococcus marinus-related sequence, this contig recruits a\n broad swath of GOS sequences that correspond to the GOS sequences that form the zigzag\n on P.\n marinus MIT9312 recruitment plots (see [B] or <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-sd001\" target=\"_blank\">Poster S1</a> for\n comparison).</p>\n <p>(K–L) Seeded from SAR11 clones, these contigs show significant synteny to the known\n P.\n ubique HTCC1062 genome. (K) is strikingly similar to previous\n recruitment plots to the HTCC1062 genome (see [A] or <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-sd001\" target=\"_blank\">Poster S1</a>). In\n contrast, (L) identifies a different strain that recruits high-identity GOS sequences\n primarily from the Sargasso Sea samples (red).</p>\n <p>(M–O) These three panels show recruitment plots to contigs belonging to the\n uncultured <i>Actinobacter, Roseobacter,</i> and SAR86 lineages.</p></div>", "links"=>[], "tags"=>["recruitment"], "article_id"=>622249, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g002", "stats"=>{"downloads"=>3, "page_views"=>188, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fragment_Recruitment_Plots_/622249", "title"=>"Fragment Recruitment Plots", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-03-13 00:37:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/953500"], "description"=>"<p>The relative abundance of various ribotypes (rows) in each filter (columns) is\n represented by the area of the corresponding spot (if any). The listed ribotypes each\n satisfied the following criteria in at least one filter: the ribotype was among the\n five most abundant ribotypes detected in the shotgun data, and was represented by at\n least three sequencing reads. Relative abundance is based on the total number of 16S\n sequences in a given filter. Order and grouping of filters is based on the clustering\n of genomic similarity shown in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-g011\" target=\"_blank\">Figure\n 11</a>. Ribotype order was determined based on similarity of sample distribution.\n A marked contrast between temperate and tropical groups is visible. Estuarine samples\n GS11 and GS12 contained a mix of ribotypes seen in freshwater and temperate marine\n samples, while samples from nonmarine habitats or larger filter sizes were pronounced\n outliers. The presence of large amounts of <i>Burkholderia</i> and\n <i>Shewanella</i> in one Sargasso Sea sample (GS00a) makes this sample\n look much less like other Sargasso and tropical marine samples than it otherwise\n would. Note that 16S is not a measure of cell abundance since 16S genes can be\n multicopy.</p>", "links"=>[], "tags"=>["abundance"], "article_id"=>623757, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g009", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Presence_and_Abundance_of_Dominant_Ribotypes_/623757", "title"=>"Presence and Abundance of Dominant Ribotypes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:52:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/952532"], "description"=>"<p>Environmental sequences recruited near breaks in synteny have characteristic patterns\n of recruitment metadata. Indeed, each of five basic rearrangements (i.e., insertion,\n deletion, translocation, inversion, and inverted translocation) produced a distinct\n pattern when examining the recruitment metadata. Here, example recruitment plots for\n each type of rearrangement have been artificially generated. The “good” and “no mate”\n categories have been suppressed. In each case, breaks in synteny are marked by the\n presence of stacks of “missing” mate reads. The presence or absence of other\n categories distinguishes each type of rearrangement from the others.</p>", "links"=>[], "tags"=>["recruitment", "sites"], "article_id"=>622799, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g005", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fragment_Recruitment_at_Sites_of_Rearrangements_/622799", "title"=>"Fragment Recruitment at Sites of Rearrangements", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:46:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/953121"], "description"=>"<p>Each segment is constructed of a unique set of GOS sequencing reads (i.e., no read\n was used in more than one segment). Segments are arbitrarily labeled (A–X) for\n reference in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-g008\" target=\"_blank\">Figure 8</a>.</p>", "links"=>[], "tags"=>["recruitment", "20-kb", "segments", "sar11-like", "contigs", "many", "sar11", "separated", "extreme"], "article_id"=>623379, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g007", "stats"=>{"downloads"=>1, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fragment_Recruitment_Plots_to_20_kb_Segments_of_SAR11_Like_Contigs_Show_That_Many__SAR11_Subtypes_with_Distinct_Distributions_Can_Be_Separated_by_Extreme__Assembly_/623379", "title"=>"Fragment Recruitment Plots to 20-kb Segments of SAR11-Like Contigs Show That Many\n SAR11 Subtypes, with Distinct Distributions, Can Be Separated by Extreme\n Assembly", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:49:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/953857"], "description"=>"<p>Similarity between samples in terms of shared genomic content similar to <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077#pbio-0050077-g010\" target=\"_blank\">Figure 10</a>, except that the plots were\n done using a 90% identity cutoff that has proven reasonable for separating some\n moderately diverged subtypes</p>", "links"=>[], "tags"=>["Computational biology", "ecology", "Evolutionary biology", "genetics and genomics", "microbiology", "Virology"], "article_id"=>624118, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g011", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_Similarity_at_90_Identity_/624118", "title"=>"Sample Similarity at 90% Identity", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:54:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/468515"], "description"=>"<div><p>The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the <em>Sorcerer II</em> Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene <em>PstS</em>.</p> </div>", "links"=>[], "tags"=>["sampling", "northwest", "atlantic", "pacific"], "article_id"=>152343, "categories"=>["Cancer", "Microbiology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077", "stats"=>{"downloads"=>16, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Sorcerer_II_Global_Ocean_Sampling_Expedition_Northwest__Atlantic_through_Eastern_Tropical_Pacific/152343", "title"=>"The <em>Sorcerer II</em> Global Ocean Sampling Expedition: Northwest\n Atlantic through Eastern Tropical Pacific", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-03-13 00:39:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/953665"], "description"=>"<div><p>Genomic similarity, as described in the text, is an estimate of the amount of the\n genetic material in two filters that is “the same” at a given percent identity\n cutoff—not the amount of sequence in common in a finite dataset, but rather in the\n total set of organisms present on each filter. Similarities are shown for 98%\n identity.</p>\n <p>(A) Hierarchical clustering of samples based on pairwise similarities.</p>\n <p>(B) Pairwise similarities between samples, represented as a symmetric matrix of\n grayscale intensities; a darker cell in the matrix indicates greater similarity\n between the samples corresponding to the row and column, with row and column ordering\n as in (A). Groupings of similar filters appear as subtrees in (A) and as squares\n consisting of two or more adjacent rows and columns with darker shading. Colored bars\n highlight groups of samples described in the text; labels are approximate\n characterizations rather than being strictly true of every sample in a group.</p></div>", "links"=>[], "tags"=>["samples", "genomic"], "article_id"=>623928, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g010", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similarity_between_Samples_in_Terms_of_Shared_Genomic_Content_/623928", "title"=>"Similarity between Samples in Terms of Shared Genomic Content", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:53:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/952224"], "description"=>"<div><p>Phylogenies were produced using neighbor-joining. There is significant within-clade\n variation as well as an absence of strong geographic structure to variants of SAR11\n (P.\n ubique HTCC1062) and P. marinus MIT9312. Similar reads are not\n necessarily from similar locations, and reads from similar locations are not\n necessarily similar.</p>\n <p>(A) Geographic distribution of SAR11 proteorhodopsin variants. Keys to coloration:\n blue, Pacific; pink, Atlantic.</p>\n <p>(B) Geographic distribution of <i>Prochlorococcus</i> variants. Keys to\n coloration: blue, Pacific; pink, Atlantic.</p>\n <p>(C) Origins of spectral tuning of SAR11 proteorhodopsins. Reads are colored according\n to whether they contain the L (green) or Q (blue) variant at the spectral tuning\n residue described in the text. The selection of tuning residue is lineage restricted,\n but each variant must have arisen on two separate occasions.</p></div>", "links"=>[], "tags"=>["revealed"], "article_id"=>622511, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g003", "stats"=>{"downloads"=>4, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_Structure_and_Variation_as_Revealed_by_Phylogeny_/622511", "title"=>"Population Structure and Variation as Revealed by Phylogeny", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-03-13 00:41:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/954023"], "description"=>"<p>The leucine (L) and methionine (M) variants absorb maximally in the green spectrum\n (Oded Beja, personal communication) while the glutamine (Q) variant absorbs maximally\n in the blue spectrum. The relative abundance of each variant is shown as a percentage\n (<i>x</i>-axis) per sample (<i>y</i>-axis). Total abundance for\n all variants in read equivalents normalized by the abundance of recA protein are shown\n on the right side of the <i>y</i>-axis. The L and Q variants show a\n nonrandom distribution. The L variant is abundant in temperate Atlantic waters close\n to the U.S. and Canadian coast. The Q variant is abundant in warmer waters further\n from land. The M variant is moderately abundant in a wide range of samples with no\n obvious geographic/environmental association.</p>", "links"=>[], "tags"=>["proteorhodopsin", "variants", "gos"], "article_id"=>624285, "categories"=>["Microbiology", "Virology", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Douglas B Rusch", "Aaron L Halpern", "Granger Sutton", "Karla B Heidelberg", "Shannon Williamson", "Shibu Yooseph", "Dongying Wu", "Jonathan A Eisen", "Jeff M Hoffman", "Karin Remington", "Karen Beeson", "Bao Tran", "Hamilton Smith", "Holly Baden-Tillson", "Clare Stewart", "Joyce Thorpe", "Jason Freeman", "Cynthia Andrews-Pfannkoch", "Joseph E Venter", "Kelvin Li", "Saul Kravitz", "John F Heidelberg", "Terry Utterback", "Yu-Hui Rogers", "Luisa I Falcón", "Valeria Souza", "Germán Bonilla-Rosso", "Luis E Eguiarte", "David M Karl", "Shubha Sathyendranath", "Trevor Platt", "Eldredge Bermingham", "Victor Gallardo", "Giselle Tamayo-Castillo", "Michael R Ferrari", "Robert L Strausberg", "Kenneth Nealson", "Robert Friedman", "Marvin Frazier", "J. Craig Venter"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0050077.g012", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Common_Proteorhodopsin_Variants_across_GOS_Samples_/624285", "title"=>"Distribution of Common Proteorhodopsin Variants across GOS Samples", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:55:48"}

PMC Usage Stats | Further Information

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  • {"month"=>"10", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"5", "full-text"=>"62", "year"=>"2010", "pdf"=>"33", "unique-ip"=>"72", "figure"=>"7", "scanned-summary"=>"0", "supp-data"=>"2"}
  • {"scanned-page-browse"=>"0", "month"=>"11", "cited-by"=>"0", "abstract"=>"3", "full-text"=>"84", "unique-ip"=>"83", "pdf"=>"31", "year"=>"2010", "figure"=>"14", "scanned-summary"=>"0", "supp-data"=>"0"}
  • {"month"=>"12", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"4", "full-text"=>"64", "year"=>"2010", "pdf"=>"28", "unique-ip"=>"71", "figure"=>"6", "scanned-summary"=>"0", "supp-data"=>"0"}
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Relative Metric

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