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• {"link"=>{"url"=>"http://www.citeulike.org/user/sharpton/article/5003877"}, "post_time"=>"2012-07-11 22:19:18", "tag"=>["bacteria", "gut", "metagenomics", "microbiome"], "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pone.0006074"}, "username"=>"sharpton", "article_id"=>"5003877"}
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Mendeley | Further Information

{"title"=>"More than 9,000,000 unique genes in human gut bacterial community: Estimating gene numbers inside a human body", "type"=>"journal", "authors"=>[{"first_name"=>"Xing", "last_name"=>"Yang", "scopus_author_id"=>"16644357200"}, {"first_name"=>"Lu", "last_name"=>"Xie", "scopus_author_id"=>"7402590419"}, {"first_name"=>"Yixue", "last_name"=>"Li", "scopus_author_id"=>"35227517800"}, {"first_name"=>"Chaochun", "last_name"=>"Wei", "scopus_author_id"=>"55470612000"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"354931786", "sgr"=>"67650685282", "issn"=>"19326203", "pmid"=>"19562079", "scopus"=>"2-s2.0-67650685282", "doi"=>"10.1371/journal.pone.0006074", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)"}, "id"=>"4f1c7096-f1b6-3c59-a673-37717e7b1b14", "abstract"=>"BACKGROUND: Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism.\\n\\nPRINCIPAL FINDINGS: We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged.\\n\\nCONCLUSION: By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.", "link"=>"http://www.mendeley.com/research/more-9000000-unique-genes-human-gut-bacterial-community-estimating-gene-numbers-inside-human-body", "reader_count"=>86, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>22, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>2, "Student > Master"=>10, "Other"=>1, "Student > Bachelor"=>12, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>22, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>2, "Student > Master"=>10, "Other"=>1, "Student > Bachelor"=>12, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Agricultural and Biological Sciences"=>46, "Arts and Humanities"=>1, "Philosophy"=>1, "Chemical Engineering"=>2, "Computer Science"=>1, "Earth and Planetary Sciences"=>1, "Engineering"=>3, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>8, "Medicine and Dentistry"=>9, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Physics and Astronomy"=>1, "Psychology"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>5}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>46}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Czech Republic"=>1, "Netherlands"=>1, "Hungary"=>1, "Sri Lanka"=>1, "United States"=>4, "Ireland"=>1, "France"=>2, "Spain"=>2}, "group_count"=>5}

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• http://doi.org/10.1113/jphysiol.2014.271775
• http://doi.org/10.1080/19420889.2019.1594501
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• {"month"=>"5", "year"=>"2016", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"43"}
• {"month"=>"6", "year"=>"2016", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"32"}
• {"month"=>"7", "year"=>"2016", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"36"}
• {"month"=>"8", "year"=>"2016", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"32"}
• {"month"=>"9", "year"=>"2016", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"48"}
• {"month"=>"10", "year"=>"2016", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"78"}
• {"month"=>"11", "year"=>"2016", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"36"}
• {"month"=>"12", "year"=>"2016", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"59"}
• {"month"=>"1", "year"=>"2017", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"42"}
• {"month"=>"2", "year"=>"2017", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"85"}
• {"month"=>"3", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"88"}
• {"month"=>"4", "year"=>"2017", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"60"}
• {"month"=>"5", "year"=>"2017", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"56"}
• {"month"=>"6", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"57"}
• {"month"=>"7", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"1", "html_views"=>"32"}
• {"month"=>"8", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"44"}
• {"month"=>"9", "year"=>"2017", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"66"}
• {"month"=>"10", "year"=>"2017", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"72"}
• {"month"=>"11", "year"=>"2017", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"72"}
• {"month"=>"12", "year"=>"2017", "pdf_views"=>"2", "xml_views"=>"2", "html_views"=>"48"}
• {"month"=>"1", "year"=>"2018", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"38"}
• {"month"=>"2", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"40"}
• {"month"=>"3", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"38"}
• {"month"=>"4", "year"=>"2018", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"37"}
• {"month"=>"5", "year"=>"2018", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"45"}
• {"month"=>"6", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"25"}
• {"month"=>"7", "year"=>"2018", "pdf_views"=>"33", "xml_views"=>"3", "html_views"=>"46"}
• {"month"=>"8", "year"=>"2018", "pdf_views"=>"13", "xml_views"=>"1", "html_views"=>"41"}
• {"month"=>"9", "year"=>"2018", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"30"}
• {"month"=>"10", "year"=>"2018", "pdf_views"=>"8", "xml_views"=>"1", "html_views"=>"28"}
• {"month"=>"11", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"26"}
• {"month"=>"12", "year"=>"2018", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"18"}
• {"month"=>"1", "year"=>"2019", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"28"}
• {"month"=>"2", "year"=>"2019", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"31"}
• {"month"=>"3", "year"=>"2019", "pdf_views"=>"24", "xml_views"=>"1", "html_views"=>"49"}
• {"month"=>"4", "year"=>"2019", "pdf_views"=>"19", "xml_views"=>"0", "html_views"=>"43"}
• {"month"=>"5", "year"=>"2019", "pdf_views"=>"33", "xml_views"=>"0", "html_views"=>"49"}
• {"month"=>"6", "year"=>"2019", "pdf_views"=>"20", "xml_views"=>"1", "html_views"=>"36"}
• {"month"=>"7", "year"=>"2019", "pdf_views"=>"16", "xml_views"=>"0", "html_views"=>"32"}
• {"month"=>"8", "year"=>"2019", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"43"}
• {"month"=>"9", "year"=>"2019", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"22"}
• {"month"=>"10", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"33"}
• {"month"=>"11", "year"=>"2019", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"34"}
• {"month"=>"12", "year"=>"2019", "pdf_views"=>"18", "xml_views"=>"0", "html_views"=>"25"}
• {"month"=>"1", "year"=>"2020", "pdf_views"=>"24", "xml_views"=>"1", "html_views"=>"47"}
• {"month"=>"2", "year"=>"2020", "pdf_views"=>"21", "xml_views"=>"0", "html_views"=>"40"}
• {"month"=>"3", "year"=>"2020", "pdf_views"=>"12", "xml_views"=>"1", "html_views"=>"34"}
• {"month"=>"4", "year"=>"2020", "pdf_views"=>"28", "xml_views"=>"0", "html_views"=>"52"}
• {"month"=>"5", "year"=>"2020", "pdf_views"=>"51", "xml_views"=>"1", "html_views"=>"33"}
• {"month"=>"6", "year"=>"2020", "pdf_views"=>"19", "xml_views"=>"0", "html_views"=>"28"}
• {"month"=>"7", "year"=>"2020", "pdf_views"=>"20", "xml_views"=>"0", "html_views"=>"22"}
• {"month"=>"8", "year"=>"2020", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"27"}
• {"month"=>"9", "year"=>"2020", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"27"}
• {"month"=>"10", "year"=>"2020", "pdf_views"=>"14", "xml_views"=>"1", "html_views"=>"28"}
• {"month"=>"11", "year"=>"2020", "pdf_views"=>"26", "xml_views"=>"1", "html_views"=>"42"}
• {"month"=>"12", "year"=>"2020", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"9"}

Figshare

• {"files"=>["https://ndownloader.figshare.com/files/893869"], "description"=>"<p>Each genome represents a different species. Accessions and information for the ten genomes can be found in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone.0006074.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["sizes", "10", "genomes"], "article_id"=>564328, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Core_genome_sizes_for_10_Bacteroides_genomes_at_different_similarity_cutoffs_/564328", "title"=>"Core-genome sizes for 10 <i>Bacteroides</i> genomes at different similarity cutoffs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-29 01:12:08"}
• {"files"=>["https://ndownloader.figshare.com/files/893578"], "description"=>"<p>Figure A shows the pan-genome of 39 <i>E. coli</i> strains at different similarity cutoff. Figure B shows the pan-genome of 24 different <i>Clostridium</i> species. Similarity percentage cutoff in both A and B for the circle, diamond, cross, triangle and plus sign are 0.97, 0.90, 0.80, 0.60 and 0.30, respectively. The same cutoff was used for paralogs and orthologs. Each node is the average value a number of times of sampling. Sampling times can be found in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone-0006074-t002\" target=\"_blank\">Table 2</a>. The corresponding lines are generated by least square curving fitting of the nodes with function F(n) = [a−b/(x+c)]*Avg, coefficients of which are available in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone-0006074-t001\" target=\"_blank\">Table 1</a>. Accessions and information for 39 <i>E.coli</i> and 24 <i>Clostridium</i> genomes used in the figure can be found in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone.0006074.s001\" target=\"_blank\">Table S1</a> (see the “Figure” column, lines marked as “2”).</p>", "links"=>[], "tags"=>["39", "strains", "24"], "article_id"=>564038, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pan_genome_of_39_E_coli_strains_and_24_Clostridium_species_/564038", "title"=>"Pan-genome of 39 <i>E. coli</i> strains and 24 <i>Clostridium</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-29 01:07:18"}
• {"files"=>["https://ndownloader.figshare.com/files/893754"], "description"=>"<p>The pie chart shows the distribution of gut bacteria obtained by searching RDP browser. Others are: <i>Spirochaetes</i>, <i>Fusobacteria</i>, <i>Deferribacteres</i>, <i>Cyanobacteria</i>, <i>Planctomycetes</i>, <i>Lentisphaerae</i>, <i>TM7</i> and <i>Tenericutes</i>. Of the thirteen phyla, th<i>e Firmicutes</i> and <i>Bacteroidetes</i> occupy 65% and 30% of the pie, respectively, while the rest eleven phyla take up 5%.</p>", "links"=>[], "tags"=>["Computational biology", "Gastroenterology and hepatology", "genetics and genomics", "computational biology/comparative sequence analysis", "computational biology/metagenomics", "genetics and genomics/bioinformatics", "genetics and genomics/genomics"], "article_id"=>564207, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.g004", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gut_bacteria_composition_/564207", "title"=>"Gut bacteria composition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-29 01:10:07"}
• {"files"=>["https://ndownloader.figshare.com/files/893943"], "description"=>"<p>This figure shows the distribution of 202 gut bacteria genomes' gene lengths as annotated by NCBI. The genes used in this study were annotated by NCBI as protein coding sequences. Y-axis tells the number of genes with a certain length.</p>", "links"=>[], "tags"=>["genes", "202"], "article_id"=>564400, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.g007", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_length_distribution_for_genes_of_202_gut_bacteria_genomes_/564400", "title"=>"Gene length distribution for genes of 202 gut bacteria genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-29 01:13:20"}
• {"files"=>["https://ndownloader.figshare.com/files/894022"], "description"=>"<p>The strain-to-species and species-to-genus gene counting used the same similarity at 0.97, 0.90, 0.80, 0.60 and 0.30 in the estimation. Detail of the gene counting model can be found in the gene counting model part of the Result section.</p>", "links"=>[], "tags"=>["numbers", "bacterial"], "article_id"=>564477, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimated_total_gene_numbers_for_human_gut_bacterial_community_/564477", "title"=>"Estimated total gene numbers for human gut bacterial community.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-29 01:14:37"}
• {"files"=>["https://ndownloader.figshare.com/files/442372", "https://ndownloader.figshare.com/files/442385"], "description"=>"<div><h3>Background</h3><p>Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism.</p><h3>Principal Findings</h3><p>We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged.</p><h3>Conclusion</h3><p>By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future.</p><p>The list of genomes used in this paper can be found in the supplementary table.</p></div>", "links"=>[], "tags"=>["genes", "bacterial", "estimating", "numbers"], "article_id"=>147182, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0006074.s001", "https://dx.doi.org/10.1371/journal.pone.0006074.s002"], "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/More_than_9_000_000_Unique_Genes_in_Human_Gut_Bacterial_Community_Estimating_Gene_Numbers_Inside_a_Human_Body/147182", "title"=>"More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-06-29 01:59:42"}
• {"files"=>["https://ndownloader.figshare.com/files/893820"], "description"=>"<p>16S rRNA sequences of 164 genera were downloaded from RDP browser. More than 94% of the 164 genera have less than 30 species and more than 84% of the 826 species have less than 40 strains.</p>", "links"=>[], "tags"=>["16s", "rrna"], "article_id"=>564279, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cl_uster_result_of_human_gut_bacteria_based_on_16S_rRNA_sequences_/564279", "title"=>"<i>Cl</i>uster result of human gut bacteria based on 16S rRNA sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-29 01:11:19"}
• {"files"=>["https://ndownloader.figshare.com/files/893644"], "description"=>"<p>Figure A shows how the gut bacterial community is visualized as a bamboo. B gives an example how the genus <i>Faecalibacterium</i> with 4,105 strains is clustered into. First, a tree was built from the 16S rRNA distance matrix of the 4,105 strains using UPGMA method, and then suspicious branches which consist less than 0.1% of the population were trimmed off. C shows the general pipeline of our counting model. Genes were first counted among strains within a species, and then among species within a genus. The total gene number of the community can be obtained by adding genes in every genus together.</p>", "links"=>[], "tags"=>["gene-counting", "bamboo-like-tree", "bacterial"], "article_id"=>564100, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.g003", "stats"=>{"downloads"=>2, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_gene_counting_model_a_bamboo_like_tree_structure_of_human_gut_bacterial_community_/564100", "title"=>"The gene-counting model: a bamboo-like-tree structure of human gut bacterial community.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-29 01:08:20"}
• {"files"=>["https://ndownloader.figshare.com/files/893514"], "description"=>"<p>The nodes denote the total gene number after genome combination, each of which is the average value of 30 times of sampling. Sampling size scales from ten to two hundred genomes, with a step size of ten. Thresholds for circle, triangle, diamond, cross, square and asterisk markers are 1.00, 0.97, 0.90, 0.80, 0.70 and 0.60, respectively. Paralogs and orthologs used the same thresholds in this combination. Accessions and information for the two hundred and two genomes used in the figure can be found in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone.0006074.s001\" target=\"_blank\">Table S1</a> (see lines marked as “1” in the “Figure” column).</p>", "links"=>[], "tags"=>["202"], "article_id"=>563974, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pan_genome_of_202_gut_bacteria_/563974", "title"=>"Pan-genome of 202 gut bacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-29 01:06:14"}
• {"files"=>["https://ndownloader.figshare.com/files/893987"], "description"=>"<p>This table provides information for the 39 <i>E. coli</i> and 24 <i>Clostridium</i> analyzed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone-0006074-g002\" target=\"_blank\">Figure 2</a>. The nodes in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone-0006074-g002\" target=\"_blank\">Figure 2A</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone-0006074-g002\" target=\"_blank\">Figure 2B</a> are the average value for 30 and 20 times of sampling, respectively. <b>*Avg</b> genes are the average gene numbers for all genomes after they are de-paralogged (combined with itself at certain cutoff). <b>Coefficients*</b> were obtained by least square curve fitting function F(n) = [a−b/(n+c)]*Avg. a₁, b₁ and c₁ are for 39 <i>E. coli</i> in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone-0006074-g002\" target=\"_blank\">Figure 2A</a> while a₂, b₂ and c₂ are for 24 <i>Clostridium</i> in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone-0006074-g002\" target=\"_blank\">Figure 2B</a>. Accessions and other information for the genomes can be found in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006074#pone.0006074.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["coefficients", "lines", "39", "24"], "article_id"=>564447, "categories"=>["Medicine", "Chemistry", "Genetics", "Biological Sciences"], "users"=>["Xing Yang", "Lu Xie", "Yixue Li", "Chaochun Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006074.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Function_coefficients_for_lines_in_Fig_2_for_39_E_coli_and_24_Clostridium_/564447", "title"=>"Function coefficients for lines in Fig. 2 for 39 <i>E. coli</i> and 24 <i>Clostridium</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-29 01:14:07"}

PMC Usage Stats | Further Information

• {"month"=>"1", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"2", "full-text"=>"21", "year"=>"2010", "pdf"=>"5", "unique-ip"=>"19", "figure"=>"5", "scanned-summary"=>"0", "supp-data"=>"0"}
• {"scanned-page-browse"=>"0", "month"=>"2", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"12", "unique-ip"=>"16", "pdf"=>"9", "year"=>"2010", "figure"=>"0", "scanned-summary"=>"0", "supp-data"=>"0"}
• {"month"=>"3", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"21", "year"=>"2010", "pdf"=>"8", "unique-ip"=>"17", "figure"=>"3", "scanned-summary"=>"0", "supp-data"=>"0"}
• {"scanned-page-browse"=>"0", "month"=>"4", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"9", "unique-ip"=>"10", "pdf"=>"6", "year"=>"2010", "figure"=>"0", "scanned-summary"=>"0", "supp-data"=>"0"}
• {"month"=>"5", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"12", "year"=>"2010", "pdf"=>"4", "unique-ip"=>"12", "figure"=>"0", "scanned-summary"=>"0", "supp-data"=>"0"}
• {"scanned-page-browse"=>"0", "month"=>"6", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"8", "unique-ip"=>"8", "pdf"=>"7", "year"=>"2010", "figure"=>"4", "scanned-summary"=>"0", "supp-data"=>"0"}
• {"month"=>"7", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"6", "year"=>"2010", "pdf"=>"7", "unique-ip"=>"7", "figure"=>"0", "scanned-summary"=>"0", "supp-data"=>"0"}
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Relative Metric

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F1000Prime