Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data
Publication Date
December 27, 2016
Authors
Simeon Carstens, Michael Nilges & Michael Habeck
Volume
12
Issue
12
Pages
e1005292
DOI
http://doi.org/10.1371/journal.pcbi.1005292
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1005292
Scopus
85007553283
Mendeley
http://www.mendeley.com/research/inferential-structure-determination-chromosomes-singlecell-hic-data-1
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data", "type"=>"journal", "authors"=>[{"first_name"=>"Simeon", "last_name"=>"Carstens", "scopus_author_id"=>"55489103700"}, {"first_name"=>"Michael", "last_name"=>"Nilges", "scopus_author_id"=>"7006940093"}, {"first_name"=>"Michael", "last_name"=>"Habeck", "scopus_author_id"=>"7005882876"}], "year"=>2016, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"85007553283", "doi"=>"10.1371/journal.pcbi.1005292", "isbn"=>"1111111111", "pmid"=>"28027298", "issn"=>"15537358", "scopus"=>"2-s2.0-85007553283", "pui"=>"613954242"}, "id"=>"c355c570-8692-33a0-b407-b2c05b6b6ff9", "abstract"=>"Author Summary Spatial interactions between distant genomic regions are of fundamental importance in gene regulation and other nuclear processes. Recent chromatin crosslinking (“Hi-C”) experiments probe the spatial organization of chromosomes on a genome-wide scale to an extent that was previously unattainable. These experiments report on contacting loci and thus provide information about the three-dimensional structure of the genome. Unfortunately, the data are noisy and do not determine the structure uniquely. There is also little quantitative prior knowledge about the large-scale organization of chromosomes. Here, we address these challenges by developing a Bayesian statistical approach that combines a minimalist polymer model with chromosome size measurements and conformation capture data. Our method generates statistical ensembles of chromosome structures from extremely sparse single-cell Hi-C data. We remove potential bias by learning modeling parameters from the experimental data and apply model comparison techniques to investigate which among a set of alternative models is most supported by the Hi-C data. Our method also allows for modeling with ambiguous contact data obtained on polyploid chromosomes, which is an important step towards three-dimensional modeling of whole genomes.", "link"=>"http://www.mendeley.com/research/inferential-structure-determination-chromosomes-singlecell-hic-data-1", "reader_count"=>36, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Researcher"=>11, "Student > Ph. D. Student"=>9, "Other"=>5, "Student > Master"=>7, "Professor"=>3}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Researcher"=>11, "Student > Ph. D. Student"=>9, "Other"=>5, "Student > Master"=>7, "Professor"=>3}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>16, "Agricultural and Biological Sciences"=>15, "Physics and Astronomy"=>2, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>1, "China"=>1, "Italy"=>1, "France"=>1}, "group_count"=>0}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85007553283"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85007553283?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85007553283&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=85007553283&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/85007553283", "dc:identifier"=>"SCOPUS_ID:85007553283", "eid"=>"2-s2.0-85007553283", "dc:title"=>"Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data", "dc:creator"=>"Carstens S.", "prism:publicationName"=>"PLoS Computational Biology", "prism:issn"=>"1553734X", "prism:eIssn"=>"15537358", "prism:volume"=>"12", "prism:issueIdentifier"=>"12", "prism:pageRange"=>nil, "prism:coverDate"=>"2016-12-01", "prism:coverDisplayDate"=>"December 2016", "prism:doi"=>"10.1371/journal.pcbi.1005292", "citedby-count"=>"5", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"Institut Pasteur, Paris", "affiliation-city"=>"Paris", "affiliation-country"=>"France"}, {"@_fa"=>"true", "affilname"=>"New York University", "affiliation-city"=>"New York", "affiliation-country"=>"United States"}], "pubmed-id"=>"28027298", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e1005292", "source-id"=>"4000151810", "openaccess"=>"1", "openaccessFlag"=>true}

Twitter

Counter

  • {"month"=>"12", "year"=>"2016", "pdf_views"=>"75", "xml_views"=>"4", "html_views"=>"379"}
  • {"month"=>"1", "year"=>"2017", "pdf_views"=>"152", "xml_views"=>"5", "html_views"=>"1299"}
  • {"month"=>"2", "year"=>"2017", "pdf_views"=>"39", "xml_views"=>"0", "html_views"=>"172"}
  • {"month"=>"3", "year"=>"2017", "pdf_views"=>"29", "xml_views"=>"1", "html_views"=>"173"}
  • {"month"=>"4", "year"=>"2017", "pdf_views"=>"21", "xml_views"=>"0", "html_views"=>"93"}
  • {"month"=>"5", "year"=>"2017", "pdf_views"=>"20", "xml_views"=>"1", "html_views"=>"114"}
  • {"month"=>"6", "year"=>"2017", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"86"}
  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"18", "xml_views"=>"0", "html_views"=>"65"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"25", "xml_views"=>"1", "html_views"=>"95"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"20", "xml_views"=>"3", "html_views"=>"76"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"18", "xml_views"=>"0", "html_views"=>"65"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"24", "xml_views"=>"0", "html_views"=>"65"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"25", "xml_views"=>"2", "html_views"=>"46"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"40"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"17"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"19", "xml_views"=>"2", "html_views"=>"30"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"35"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"43"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"5", "html_views"=>"12"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"45", "xml_views"=>"1", "html_views"=>"60"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"40", "xml_views"=>"1", "html_views"=>"46"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"28", "xml_views"=>"2", "html_views"=>"24"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"5"}

PMC Usage Stats

  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"33", "full-text"=>"40", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"20", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"19", "full-text"=>"20", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"11", "full-text"=>"14", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"18", "full-text"=>"20", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"13", "full-text"=>"17", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"34", "full-text"=>"11", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"18", "cited-by"=>"1", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"11", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}

F1000Prime | Further Information

Loading … Spinner
There are currently no alerts