An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes
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{"title"=>"An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes", "type"=>"journal", "authors"=>[{"first_name"=>"Xin", "last_name"=>"Jin", "scopus_author_id"=>"26652540300"}, {"first_name"=>"Mingze", "last_name"=>"He", "scopus_author_id"=>"55324276500"}, {"first_name"=>"Betsy", "last_name"=>"Ferguson", "scopus_author_id"=>"13410798300"}, {"first_name"=>"Yuhuan", "last_name"=>"Meng", "scopus_author_id"=>"36673502300"}, {"first_name"=>"Limei", "last_name"=>"Ouyang", "scopus_author_id"=>"56350151100"}, {"first_name"=>"Jingjing", "last_name"=>"Ren", "scopus_author_id"=>"55324110100"}, {"first_name"=>"Thomas", "last_name"=>"Mailund", "scopus_author_id"=>"14619483800"}, {"first_name"=>"Fei", "last_name"=>"Sun", "scopus_author_id"=>"55323935900"}, {"first_name"=>"Liangdan", "last_name"=>"Sun", "scopus_author_id"=>"25825691500"}, {"first_name"=>"Juan", "last_name"=>"Shen", "scopus_author_id"=>"55324252900"}, {"first_name"=>"Min", "last_name"=>"Zhuo", "scopus_author_id"=>"36652156200"}, {"first_name"=>"Li", "last_name"=>"Song", "scopus_author_id"=>"55324043200"}, {"first_name"=>"Jufang", "last_name"=>"Wang", "scopus_author_id"=>"55971558600"}, {"first_name"=>"Fei", "last_name"=>"Ling", "scopus_author_id"=>"24464091300"}, {"first_name"=>"Yuqi", "last_name"=>"Zhu", "scopus_author_id"=>"55324258500"}, {"first_name"=>"Christina", "last_name"=>"Hvilsom", "scopus_author_id"=>"24777994500"}, {"first_name"=>"Hans", "last_name"=>"Siegismund", "scopus_author_id"=>"6603792367"}, {"first_name"=>"Xiaoming", "last_name"=>"Liu", "scopus_author_id"=>"55218232200"}, {"first_name"=>"Zhuolin", "last_name"=>"Gong", "scopus_author_id"=>"55063247600"}, {"first_name"=>"Fang", "last_name"=>"Ji", "scopus_author_id"=>"35208702400"}, {"first_name"=>"Xinzhong", "last_name"=>"Wang", "scopus_author_id"=>"55324344900"}, {"first_name"=>"Boqing", "last_name"=>"Liu", "scopus_author_id"=>"55324212400"}, {"first_name"=>"Yu", "last_name"=>"Zhang", "scopus_author_id"=>"57196205914"}, {"first_name"=>"Jianguo", "last_name"=>"Hou", "scopus_author_id"=>"55324034700"}, {"first_name"=>"Jing", "last_name"=>"Wang", "scopus_author_id"=>"57200023832"}, {"first_name"=>"Hua", "last_name"=>"Zhao", "scopus_author_id"=>"8936856900"}, {"first_name"=>"Yanyi", "last_name"=>"Wang", "scopus_author_id"=>"57200060191"}, {"first_name"=>"Xiaodong", "last_name"=>"Fang", "scopus_author_id"=>"37076845600"}, {"first_name"=>"Guojie", "last_name"=>"Zhang", "scopus_author_id"=>"8406672400"}, {"first_name"=>"Jian", "last_name"=>"Wang", "scopus_author_id"=>"57200023833"}, {"first_name"=>"Xuejun", "last_name"=>"Zhang", "scopus_author_id"=>"34668762500"}, {"first_name"=>"Mikkel H.", "last_name"=>"Schierup", "scopus_author_id"=>"6603704923"}, {"first_name"=>"Hongli", "last_name"=>"Du", "scopus_author_id"=>"7201901404"}, {"first_name"=>"Jun", "last_name"=>"Wang", "scopus_author_id"=>"55586914400"}, {"first_name"=>"Xiaoning", "last_name"=>"Wang", "scopus_author_id"=>"11939400000"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84864400843", "doi"=>"10.1371/journal.pone.0040637", "pui"=>"365338947", "pmid"=>"22848389", "scopus"=>"2-s2.0-84864400843", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"69c7da5f-4b5d-3604-8338-632ec7a76e10", "abstract"=>"Non-human primates have emerged as an important resource for the study of human disease and evolution. The characterization of genomic variation between and within non-human primate species could advance the development of genetically defined non-human primate disease models. However, non-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab-eating macaques and eight Japanese macaques. Over 91% of the target regions were captured in the non-human primate samples, although the specificity of the capture decreased as evolutionary divergence from humans increased. Both intra-specific and inter-specific DNA variants were identified; Sanger-based resequencing validated 85.4% of 41 randomly selected SNPs. Among the short indels identified, a majority (54.6%-77.3%) of the variants resulted in a change of 3 base pairs, consistent with expectations for a selection against frame shift mutations. Taken together, these findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.", "link"=>"http://www.mendeley.com/research/effort-humanbased-exome-capture-methods-analyze-chimpanzee-macaque-exomes", "reader_count"=>37, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Master"=>5, "Other"=>4, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Master"=>5, "Other"=>4, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Chemical Engineering"=>1, "Social Sciences"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Romania"=>1, "United States"=>4, "Germany"=>1, "Spain"=>1}, "group_count"=>5}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/601892"], "description"=>"<p>(A) Comparison of sequencing based point variants and variants between references. (B) Coding SNP summary; piN refers to X and piS refers to Y. dN indicates X and dS indicates Y.</p>", "links"=>[], "tags"=>["sequencing", "variants", "coding", "snp", "refers", "pis", "dn", "indicates", "ds"], "article_id"=>272333, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.t005", "stats"=>{"downloads"=>5, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Comparison_of_sequencing_based_point_variants_and_variants_between_references_B_Coding_SNP_summary_piN_refers_to_X_and_piS_refers_to_Y_dN_indicates_X_and_dS_indicates_Y_/272333", "title"=>"(A) Comparison of sequencing based point variants and variants between references. (B) Coding SNP summary; piN refers to X and piS refers to Y. dN indicates X and dS indicates Y.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:38:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/601079"], "description"=>"<p>Evolutionary distance in human, chimpanzee and macaque lineages, showing the inferred evolutionary relationships among 21 samples based upon similarities and differences in their genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>271526, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.g004", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_/271526", "title"=>"Phylogenetic tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:25:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/601448"], "description"=>"<p>140∼1,883 coding indels were called in each individual, and 54.61%∼77.32% of them were 3 bp in length. All indels were relative to the human reference genome.</p>", "links"=>[], "tags"=>["coding", "indels"], "article_id"=>271903, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.g006", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_length_distribution_of_coding_indels_for_each_individual_/271903", "title"=>"The length distribution of coding indels for each individual.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:31:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/314213", "https://ndownloader.figshare.com/files/314254", "https://ndownloader.figshare.com/files/314272", "https://ndownloader.figshare.com/files/314290"], "description"=>"<div><p>Non-human primates have emerged as an important resource for the study of human disease and evolution. The characterization of genomic variation between and within non-human primate species could advance the development of genetically defined non-human primate disease models. However, non-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab-eating macaques and eight Japanese macaques. Over 91% of the target regions were captured in the non-human primate samples, although the specificity of the capture decreased as evolutionary divergence from humans increased. Both intra-specific and inter-specific DNA variants were identified; Sanger-based resequencing validated 85.4% of 41 randomly selected SNPs. Among the short indels identified, a majority (54.6%–77.3%) of the variants resulted in a change of 3 base pairs, consistent with expectations for a selection against frame shift mutations. Taken together, these findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.</p> </div>", "links"=>[], "tags"=>["human-based", "exome", "methods", "chimpanzee", "macaque", "exomes"], "article_id"=>121940, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0040637.s001", "https://dx.doi.org/10.1371/journal.pone.0040637.s002", "https://dx.doi.org/10.1371/journal.pone.0040637.s003", "https://dx.doi.org/10.1371/journal.pone.0040637.s004"], "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/An_Effort_to_Use_Human_Based_Exome_Capture_Methods_to_Analyze_Chimpanzee_and_Macaque_Exomes/121940", "title"=>"An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-27 00:32:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/601592"], "description"=>"<p>Summary of captured target sequence coverage for each non-human primate exome and two human exomes. The total size of the captured target is 37,627,322 bp for CE and 45,880,359 bp for JP. Each exome was compared to the human reference genome. Listed for each exome are the details of captured data including alignment, depth and coverage of target region. The exomes of all twenty one individuals were sequenced with a mean depth ≥28 fold on array designed target region (TR). Coverage of target region ranged from 91.06% to 97.73%, and 67.59% to 81.33% of sites in the target region were covered by more than 10 reads. Non-human primates were aligned to their own or closest genomes (rheMac2 was used as reference genome for crab-eating cynomolgus and Japanese macaque) to evaluate the capture efficiency.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>272049, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.t001", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_production_/272049", "title"=>"Data production.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:34:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/600967"], "description"=>"<p>Mismatch rate of each target region was calculated by comparing human reference and rhesus macaque references respectively. (A) The X-axis identifies the mismatch rate region, and the Y-axis identifies the mean depth of target region, as calculated from CE2. As the mismatch rate increases, the mean depth decreases. (B) Average sequencing depth of captured targets versus each target GC content. Targets with extreme GC content were poorly captured; the mean depth was lower compared with moderate GC content.</p>", "links"=>[], "tags"=>["sequencing", "captured", "targets", "rhesus", "macaque"], "article_id"=>271406, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_sequencing_depth_of_captured_targets_versus_human_reference_and_rhesus_macaque_reference_mismatch_/271406", "title"=>"Average sequencing depth of captured targets versus human reference and rhesus macaque reference mismatch.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:23:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/600704"], "description"=>"<p>The distribution of coverage of 18,594 gene coding regions of human CCDS by theoretical target region, target orthologous region and sequencing data from 3 species is shown. The sequencing coverage of each gene was inferred from one individual in each species. Sequencing data showed that 80.40%–80.45% of genes were covered ≥90% for both humans and chimpanzees, and 77.76% for macaques. Coverage of macaque CCDSs was higher than target orthologous region. The coverage of human and chimpanzee genes was close when concerns target region, and higher for macaque compared to target orthologous region.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>271147, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.g001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_profile_of_gene_coverage_/271147", "title"=>"The profile of gene coverage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:19:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/601255"], "description"=>"<p>Principal components analysis plot of 9 chimpanzees, 2 crab-eating macaques, 8 Japanese macaques and 2 human samples. Chimpanzees and humans cluster well within their own group, while crab-eating and Japanese macaques spread away are in relatively close proximity to each other, indicating recent genetic divergence between them.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>271708, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.g005", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principle_Component_Analysis_/271708", "title"=>"Principle Component Analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:28:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/601959"], "description"=>"<p>Each exome from 21 individuals was aligned to the human reference genome for indel identification.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology"], "article_id"=>272409, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.t006", "stats"=>{"downloads"=>0, "page_views"=>48, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Indel_summary_/272409", "title"=>"Indel summary.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:40:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/601660"], "description"=>"<p>Summary of theoretical analysis for target region, target orthologous region and target orthologous region & depth≥10. Target orthologous region was the region we used to assess for capture efficiency and the target orthologous region & depth≥10 was used for SNP detection. 18,594 CCDS genes were used to analyze the theoretical coverage.</p>", "links"=>[], "tags"=>["scanning", "regions"], "article_id"=>272115, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.t002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_different_scanning_regions_and_theoretical_coverage_of_genes_/272115", "title"=>"Comparison of different scanning regions and theoretical coverage of genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:35:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/601808"], "description"=>"<p>We examined the following genomic features for the 165,571 (for CE) and 194,017 (for JP) human targets with best reciprocal orthologs in the Indian macaque genome: the number of nucleotide differences between human and macaque, the number of indel bases between human and macaque and the GC content. (A) A target was considered “captured” if more than half of the human targeted bases were covered by at least one sequence read. (B) Otherwise, the target was not captured.</p>", "links"=>[], "tags"=>["captured"], "article_id"=>272260, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.t004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_features_of_captured_and_not_captured_targets_/272260", "title"=>"Genomic features of captured and not captured targets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:37:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/600843"], "description"=>"<p>Sequenced CE1 exome was compared with its closest reference genome (rheMac2) to examine the influence of GC content on coverage. (A) Captured targets were defined as targets with more than 50% of bases covered at least by one read. The captured targets were mainly of moderate GC content. (B) Uncaptured targets were less than a half of the bases coverd by at least one read. The uncaptured targets were dominated by high GC content, except for a small portion with low GC content.</p>", "links"=>[], "tags"=>["captured", "un-captured", "targets"], "article_id"=>271297, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GC_distribution_of_captured_and_un_captured_targets_by_CE1_/271297", "title"=>"GC distribution of captured and un-captured targets by CE1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:21:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/601741"], "description"=>"<p>A fragment from the target region of the human reference genome was aligned to the Indian macaque reference genome. The OS was calculated for every site and classified into three possible levels: OS = 0, no alignment hit, unable to be captured theoretically; OS = 1, only one hit, high level of 1∶1 orthologous, well covered; OS = 2, multiple hits at different locations in the macaque reference, would give rise to misalignment and potentially false polymorphisms.</p>", "links"=>[], "tags"=>["orthologous"], "article_id"=>272191, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Xin Jin", "Mingze He", "Betsy Ferguson", "Yuhuan Meng", "Limei Ouyang", "Jingjing Ren", "Thomas Mailund", "Fei Sun", "Liangdan Sun", "Juan Shen", "Min Zhuo", "Li Song", "Jufang Wang", "Fei Ling", "Yuqi Zhu", "Christina Hvilsom", "Hans Siegismund", "Xiaoming Liu", "Zhuolin Gong", "Fang Ji", "Xinzhong Wang", "Boqing Liu", "Yu Zhang", "Jianguo Hou", "Jing Wang", "Hua Zhao", "Yanyi Wang", "Xiaodong Fang", "Guojie Zhang", "Jian Wang", "Xuejun Zhang", "Mikkel H. Schierup", "Hongli Du", "Jun Wang", "Xiaoning Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040637.t003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_orthologous_score_OS_for_macaques_/272191", "title"=>"Distribution of orthologous score (OS) for macaques.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:36:31"}

PMC Usage Stats | Further Information

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Relative Metric

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