Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
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{"title"=>"Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content", "type"=>"journal", "authors"=>[{"first_name"=>"Nathan M.", "last_name"=>"Springer", "scopus_author_id"=>"7004439661"}, {"first_name"=>"Kai", "last_name"=>"Ying", "scopus_author_id"=>"35263118900"}, {"first_name"=>"Yan", "last_name"=>"Fu", "scopus_author_id"=>"57199382698"}, {"first_name"=>"Tieming", "last_name"=>"Ji", "scopus_author_id"=>"35310502700"}, {"first_name"=>"Cheng Ting", "last_name"=>"Yeh", "scopus_author_id"=>"35263067900"}, {"first_name"=>"Yi", "last_name"=>"Jia", "scopus_author_id"=>"54585324100"}, {"first_name"=>"Wei", "last_name"=>"Wu", "scopus_author_id"=>"57198678668"}, {"first_name"=>"Todd", "last_name"=>"Richmond", "scopus_author_id"=>"7006137427"}, {"first_name"=>"Jacob", "last_name"=>"Kitzman", "scopus_author_id"=>"33467689800"}, {"first_name"=>"Heidi", "last_name"=>"Rosenbaum", "scopus_author_id"=>"35520124400"}, {"first_name"=>"A. Leonardo", "last_name"=>"Iniguez", "scopus_author_id"=>"7005329358"}, {"first_name"=>"W. Brad", "last_name"=>"Barbazuk", "scopus_author_id"=>"25631708000"}, {"first_name"=>"Jeffrey A.", "last_name"=>"Jeddeloh", "scopus_author_id"=>"6602870372"}, {"first_name"=>"Dan", "last_name"=>"Nettleton", "scopus_author_id"=>"7005958843"}, {"first_name"=>"Patrick S.", "last_name"=>"Schnable", "scopus_author_id"=>"7006662735"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"pmid"=>"19956538", "doi"=>"10.1371/journal.pgen.1000734", "sgr"=>"73649121258", "isbn"=>"1553-7390", "scopus"=>"2-s2.0-73649121258", "issn"=>"15537390", "pui"=>"358071981"}, "id"=>"e9e34507-a364-36b3-a7cd-626e8aff5603", "abstract"=>"Following the domestication of maize over the past approximately 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.", "link"=>"http://www.mendeley.com/research/maize-inbreds-exhibit-high-levels-copy-number-variation-cnv-presenceabsence-variation-pav-genome-con", "reader_count"=>329, "reader_count_by_academic_status"=>{"Unspecified"=>7, "Professor > Associate Professor"=>23, "Researcher"=>89, "Student > Doctoral Student"=>16, "Student > Ph. D. Student"=>103, "Student > Postgraduate"=>12, "Student > Master"=>31, "Other"=>12, "Student > Bachelor"=>14, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>20}, "reader_count_by_user_role"=>{"Unspecified"=>7, "Professor > Associate Professor"=>23, "Researcher"=>89, "Student > Doctoral Student"=>16, "Student > Ph. D. Student"=>103, "Student > Postgraduate"=>12, "Student > Master"=>31, "Other"=>12, "Student > Bachelor"=>14, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>20}, "reader_count_by_subject_area"=>{"Unspecified"=>15, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>20, "Mathematics"=>2, "Agricultural and Biological Sciences"=>278, "Medicine and Dentistry"=>5, "Physics and Astronomy"=>1, "Computer Science"=>7}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>278}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>20}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>15}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>18, "Philippines"=>1, "United Kingdom"=>1, "Paraguay"=>1, "India"=>1, "Spain"=>2, "New Zealand"=>1, "Sweden"=>2, "Netherlands"=>2, "Belgium"=>1, "China"=>3, "Brazil"=>6, "Italy"=>2, "Mexico"=>1, "France"=>2, "Nigeria"=>1, "Germany"=>1}, "group_count"=>14}

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  • {"files"=>["https://ndownloader.figshare.com/files/434205", "https://ndownloader.figshare.com/files/434279", "https://ndownloader.figshare.com/files/434445", "https://ndownloader.figshare.com/files/434502", "https://ndownloader.figshare.com/files/434542", "https://ndownloader.figshare.com/files/434586", "https://ndownloader.figshare.com/files/434642", "https://ndownloader.figshare.com/files/434701", "https://ndownloader.figshare.com/files/434770", "https://ndownloader.figshare.com/files/434826", "https://ndownloader.figshare.com/files/434895", "https://ndownloader.figshare.com/files/434981", "https://ndownloader.figshare.com/files/435066", "https://ndownloader.figshare.com/files/435167", "https://ndownloader.figshare.com/files/435186", "https://ndownloader.figshare.com/files/435203", "https://ndownloader.figshare.com/files/435220"], "description"=>"<div><p>Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.</p></div>", "links"=>[], "tags"=>["maize", "inbreds", "levels", "genome"], "article_id"=>145664, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000734.s001", "https://dx.doi.org/10.1371/journal.pgen.1000734.s002", "https://dx.doi.org/10.1371/journal.pgen.1000734.s003", "https://dx.doi.org/10.1371/journal.pgen.1000734.s004", "https://dx.doi.org/10.1371/journal.pgen.1000734.s005", "https://dx.doi.org/10.1371/journal.pgen.1000734.s006", "https://dx.doi.org/10.1371/journal.pgen.1000734.s007", "https://dx.doi.org/10.1371/journal.pgen.1000734.s008", "https://dx.doi.org/10.1371/journal.pgen.1000734.s009", "https://dx.doi.org/10.1371/journal.pgen.1000734.s010", "https://dx.doi.org/10.1371/journal.pgen.1000734.s011", "https://dx.doi.org/10.1371/journal.pgen.1000734.s012", "https://dx.doi.org/10.1371/journal.pgen.1000734.s013", "https://dx.doi.org/10.1371/journal.pgen.1000734.s014", "https://dx.doi.org/10.1371/journal.pgen.1000734.s015", "https://dx.doi.org/10.1371/journal.pgen.1000734.s016", "https://dx.doi.org/10.1371/journal.pgen.1000734.s017"], "stats"=>{"downloads"=>36, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Maize_Inbreds_Exhibit_High_Levels_of_Copy_Number_Variation_CNV_and_Presence_Absence_Variation_PAV_in_Genome_Content/145664", "title"=>"Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-11-20 01:34:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/875271"], "description"=>"a<p>The proportion of polymorphic primers that amplify a product in B73 but not in Mo17.</p>", "links"=>[], "tags"=>["polymorphic", "markers"], "article_id"=>545705, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.t004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Polymorphic_markers_within_segments_/545705", "title"=>"# Polymorphic markers within segments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:35:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/875332"], "description"=>"a<p>minimum of 10 probes, 2000 bp and 2 fold change between B73 and Mo17 for B73>Mo17 and Mo17>B73 classes.</p>", "links"=>[], "tags"=>["dna"], "article_id"=>545768, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_each_category_of_DNA_segment_/545768", "title"=>"Characteristics of each category of DNA segment.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:36:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/875206"], "description"=>"a<p>The FGS refers to the filtered gene set of high-quality annotations produced by the MGSP.</p>b<p>Number of genes on Affy platform that are expressed in B73 or Mo17 seedling tissue.</p>c<p>Percent of genes that are differentially expressed (q<0.05).</p>d<p>Percent of differentially expressed genes that are expressed at higher levels in B73 than in Mo17.</p>", "links"=>[], "tags"=>["stringent"], "article_id"=>545635, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.t005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_in_stringent_segments_/545635", "title"=>"Genes in stringent segments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:33:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/874679"], "description"=>"<p>The proportion of probes that exhibit significantly higher hybridization to B73 genomic DNA than Mo17 (q<0.0001) was determined for a sliding window of 1 Mb probes with increments of 0.33 Mb. The approximate position of each centromere (from Wolfgruber et al., <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Wolfgruber1\" target=\"_blank\">[72]</a>) is indicated by a red circle on each chromosome. The locations of the <i>tb1 </i><a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Doebley2\" target=\"_blank\">[41]</a> and <i>y1 </i><a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Palaisa1\" target=\"_blank\">[40]</a> genes, which are known to have undergone selective sweeps, are indicated. The gene density (based on the filtered gene set from the MGSP) is shown below each chromosome. The gene density was determined based on the number of genes per Mb. The dark color indicates low gene density while the yellow color indicates higher gene density.</p>", "links"=>[], "tags"=>["regions"], "article_id"=>545108, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_regions_of_low_structural_diversity_/545108", "title"=>"Identification of regions of low structural diversity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:25:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/874834"], "description"=>"<p>(A) A 10 Mb region on chromosome 6 is shown. The color-coding for each probe indicates the level of conservation of the probe sequence to the Mo17 WGS sequence. The coordinates on the x-axis refer to base pair position within chromosome 6 of the B73 Refgen_v1. The 2.6 Mb region from 42.2 to 44.8 is enriched for probes that are poorly conserved or have no match in the Mo17 sequence and the majority of these probes exhibit much higher signal in B73 than in Mo17. (B) The data from 38 primer pairs are shown. Blue indicates successful amplification for a particular inbred by primer combination while red indicates no amplification. The full set of 38 primer pairs (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734.s014\" target=\"_blank\">Table S1</a> for details) amplify products in B73 but not in Mo17.</p>", "links"=>[], "tags"=>["mb", "chromosome", "b73", "mo17"], "article_id"=>545263, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.g004", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterization_of_2_Mb_region_on_chromosome_6_that_is_present_in_B73_but_missing_in_the_Mo17_genome_/545263", "title"=>"Characterization of 2 Mb region on chromosome 6 that is present in B73 but missing in the Mo17 genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:27:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/875409"], "description"=>"*<p>Significant probes indicate a q value<0.0001 from the linear model.</p>", "links"=>[], "tags"=>["polymorphisms", "hybridization"], "article_id"=>545838, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Influence_of_polymorphisms_on_hybridization_variation_/545838", "title"=>"Influence of polymorphisms on hybridization variation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:37:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/875077"], "description"=>"<p>The position and average log<sub>2</sub>(M/B) for each Mo17>B73_CNV, B73>Mo17_CNV, B73>Mo17_I and B73>Mo17_PA segment is plotted for all 10 maize chromosomes. The color-coding indicates the type of segment. The positions of the centromeres <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Wolfgruber1\" target=\"_blank\">[72]</a> are indicated by the black boxes.</p>", "links"=>[], "tags"=>["cnv", "pav", "maize"], "article_id"=>545500, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.g006", "stats"=>{"downloads"=>1, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_CNV_and_PAV_throughout_the_maize_genome_/545500", "title"=>"Distribution of CNV and PAV throughout the maize genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:31:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/875474"], "description"=>"a<p>The repetitive nature of each probe was determined by comparing to the B73 reference genome. All probes that satisfy criteria (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#s4\" target=\"_blank\">Methods</a> for details) for cereal repeat, crosshyb or multi-copy were designated as repetitive.</p>b<p>The probes were each classified based upon the most significant similarity to the Mo17 WGS sequence from JGI. The full definition for each category can be found in the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#s4\" target=\"_blank\">Methods</a> section.</p>", "links"=>[], "tags"=>["classifications", "enrichment"], "article_id"=>545898, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Probe_classifications_and_enrichment_in_specific_categories_/545898", "title"=>"Probe classifications and enrichment in specific categories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-20 01:38:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/874389"], "description"=>"<p>(A) The B73 and Mo17 sequences for a portion of the 9,009 locus (sequenced by <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Brunner1\" target=\"_blank\">[28]</a>) were aligned using Vista <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Frazer1\" target=\"_blank\">[71]</a> which displays the percent identity as a sliding window of 100 bp (y-axis is 50% to 100% identity). The location of genes annotated by Brunner et al. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Brunner1\" target=\"_blank\">[28]</a> (indicated by light blue sequences in the alignment) and repeat elements (the color-coded track right above the alignments; pink indicates retrotransposons and orange indicates transposons) are shown above the VISTA alignment. The log<sub>2</sub>(Mo17 signal/B73 signal) is shown for each probe in this region. The red probes exhibit significantly different (q<0.0001) signal in B73 and Mo17. The blue line indicates a segment with altered hybridization that was identified using DNAcopy. There are also data tracks that display the repeat annotation and B73/Mo17 similarity for each probe. Note that these annotations are based on the genome-wide analysis, not detailed analyses of these regions. In (B) we present the annotation, alignment and CGH data for a portion of the 9008 loci (sequence and annotated by Brunner et al., <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Brunner1\" target=\"_blank\">[28]</a>).</p>", "links"=>[], "tags"=>["hybridization", "differences"], "article_id"=>544823, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significant_hybridization_differences_are_due_to_structural_variation_/544823", "title"=>"Significant hybridization differences are due to structural variation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:20:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/874970"], "description"=>"<p>The distribution of the average log<sub>2</sub>(M/B) across segments was modeled using a four-component normal mixture model <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Everitt1\" target=\"_blank\">[68]</a>. The EM algorithm <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Dempster1\" target=\"_blank\">[69]</a> was used to estimate the mixing proportion, the mean, and the variance associated with each of the four normal component densities, corresponding to four segment classes (labeled with arrows). Class membership probabilities for each segment were computed using the EM estimates.</p>", "links"=>[], "tags"=>["dna"], "article_id"=>545409, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.g005", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_average_log2_M_B_for_DNA_segments_/545409", "title"=>"Distribution of average log2(M/B) for DNA segments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:30:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/874530"], "description"=>"<p>The log<sub>2</sub>(Mo17/B73) hybridization intensities are plotted for each chromosome. Data points below the line indicate higher hybridization in B73 than in Mo17. The positions of the centromeres <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000734#pgen.1000734-Wolfgruber1\" target=\"_blank\">[72]</a> are indicated by black boxes. Note that there are chromosomal regions with high rates of variation (example near 42–44 MB on chromosome 6) and regions with low rates of variation (example from 140–160 MB on chromosome 8).</p>", "links"=>[], "tags"=>["genetics and genomics/comparative genomics", "genetics and genomics/plant genetics and gene expression", "genetics and genomics/plant genomes and evolution"], "article_id"=>544959, "categories"=>["Genetics"], "users"=>["Nathan M. Springer", "Kai Ying", "Yan Fu", "Tieming Ji", "Cheng-Ting Yeh", "Yi Jia", "Wei Wu", "Todd Richmond", "Jacob Kitzman", "Heidi Rosenbaum", "A. Leonardo Iniguez", "W. Brad Barbazuk", "Jeffrey A. Jeddeloh", "Dan Nettleton", "Patrick S. Schnable"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000734.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_distribution_of_log_2_Mo17_B73_signals_/544959", "title"=>"Genomic distribution of log<sub>2</sub>(Mo17/B73) signals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-20 01:22:39"}

PMC Usage Stats | Further Information

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Relative Metric

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