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<!DOCTYPE html> <html > <head> <meta charset="utf-8"> <meta rel="search" type="application/opensearchdescription+xml" href="/open_search.xml" title="Academia.edu"> <meta content="width=device-width, initial-scale=1" name="viewport"> <meta name="google-site-verification" content="bKJMBZA7E43xhDOopFZkssMMkBRjvYERV-NaN4R6mrs"> <meta name="csrf-param" content="authenticity_token" /> <meta name="csrf-token" content="bHLCBbUwVZqS9jxkYdkuQgZRhlPMdJefsTtrjVbinsojAREo8pZan6Nn+fHg0S6ZTp/ztguRjSp87EF69ycy/w==" /> <meta name="citation_title" content="Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type" /> <meta name="citation_publication_date" content="2015" /> <meta name="citation_journal_title" content="Nature Communications" /> <meta name="citation_author" content="Angela Yen" /> <meta name="citation_author" content="Manolis Kellis" /> <meta name="citation_volume" content="6" /> <meta name="citation_issue" content="1" /> <meta name="citation_firstpage" content="7973" /> <meta name="citation_issn" content="2041-1723" /> <meta name="twitter:card" content="summary" /> <meta name="twitter:url" content="https://www.academia.edu/19869778/Systematic_chromatin_state_comparison_of_epigenomes_associated_with_diverse_properties_including_sex_and_tissue_type" /> <meta name="twitter:title" content="Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type" /> <meta name="twitter:description" content="Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here" /> <meta name="twitter:image" content="https://0.academia-photos.com/40677311/11080498/12365220/s200_angela.yen.jpg" /> <meta property="fb:app_id" content="2369844204" /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://www.academia.edu/19869778/Systematic_chromatin_state_comparison_of_epigenomes_associated_with_diverse_properties_including_sex_and_tissue_type" /> <meta property="og:title" content="Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type" /> <meta property="og:image" content="http://a.academia-assets.com/images/open-graph-icons/fb-paper.gif" /> <meta property="og:description" content="Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here" /> <meta property="article:author" content="https://mit.academia.edu/AngelaYen" /> <meta name="description" content="Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here" /> <title>(PDF) Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type | Angela Yen - Academia.edu</title> <link rel="canonical" href="https://www.academia.edu/19869778/Systematic_chromatin_state_comparison_of_epigenomes_associated_with_diverse_properties_including_sex_and_tissue_type" /> <script async src="https://www.googletagmanager.com/gtag/js?id=G-5VKX33P2DS"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-5VKX33P2DS', { cookie_domain: 'academia.edu', send_page_view: false, }); gtag('event', 'page_view', { 'controller': "single_work", 'action': "show", 'controller_action': 'single_work#show', 'logged_in': 'false', 'edge': 'unknown', // Send nil if there is no A/B test bucket, in case some records get logged // with missing data - that way we can distinguish between the two cases. // ab_test_bucket should be of the form <ab_test_name>:<bucket> 'ab_test_bucket': null, }) </script> <script> var $controller_name = 'single_work'; var $action_name = "show"; var $rails_env = 'production'; var $app_rev = '65a690de66ffd0e9f9c3f528feae2fde26a171eb'; var $domain = 'academia.edu'; var $app_host = "academia.edu"; var $asset_host = "academia-assets.com"; var $start_time = new Date().getTime(); var $recaptcha_key = "6LdxlRMTAAAAADnu_zyLhLg0YF9uACwz78shpjJB"; var $recaptcha_invisible_key = "6Lf3KHUUAAAAACggoMpmGJdQDtiyrjVlvGJ6BbAj"; var $disableClientRecordHit = false; </script> <script> window.require = { config: function() { return function() {} } } </script> <script> window.Aedu = window.Aedu || {}; window.Aedu.hit_data = null; window.Aedu.serverRenderTime = new Date(1732717789000); window.Aedu.timeDifference = new Date().getTime() - 1732717789000; </script> <script type="application/ld+json">{"@context":"https://schema.org","@type":"ScholarlyArticle","abstract":"Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale.","author":[{"@context":"https://schema.org","@type":"Person","name":"Angela Yen"}],"contributor":[],"dateCreated":"2015-12-28","dateModified":"2015-12-28","datePublished":null,"headline":"Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type","inLanguage":"en","keywords":["Bioinformatics","Genetics","Biostatistics","Genomics","Computational Biology","Gene regulation","Statistical Genetics","Chromatin Biology","Quantitative Methods","Quantitative Genetics","Functional Genomics","Computational Genomics","Computational Functional Genomics","Epigenomics","Molecular Biology: Gene expression and regulation, population genetics","Epigenetics \u0026 Chromatin Biology","Bioinformatics, Computational and Systems Biology","Gene Regulation and Epigenetics","Gene expression and regulation","Computational and Systems Biology"],"locationCreated":null,"publication":null,"publisher":{"@context":"https://schema.org","@type":"Organization","name":null},"image":null,"thumbnailUrl":null,"url":"https://www.academia.edu/19869778/Systematic_chromatin_state_comparison_of_epigenomes_associated_with_diverse_properties_including_sex_and_tissue_type","sourceOrganization":[{"@context":"https://schema.org","@type":"EducationalOrganization","name":"mit"}]}</script><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/single_work_page/loswp-102fa537001ba4d8dcd921ad9bd56c474abc201906ea4843e7e7efe9dfbf561d.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/body-8d679e925718b5e8e4b18e9a4fab37f7eaa99e43386459376559080ac8f2856a.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/button-3cea6e0ad4715ed965c49bfb15dedfc632787b32ff6d8c3a474182b231146ab7.css" /><link 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Here we present\nChromDiff, a group-wise chromatin state comparison method that generates an information theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale."},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type","broadcastable":true,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [40677311]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "control"; window.loswp.useOptimizedScribd4genScript = false; window.loswp.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":40889716,"attachmentType":"pdf"}"><img alt="First page of “Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/40889716/mini_magick20190220-29834-cfws70.png?1550673415" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/assets/single_work_splash/adobe.icon-574afd46eb6b03a77a153a647fb47e30546f9215c0ee6a25df597a779717f9ef.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="40677311" href="https://mit.academia.edu/AngelaYen"><img alt="Profile image of Angela Yen" class="ds-work-card--author-avatar" src="https://0.academia-photos.com/40677311/11080498/12365220/s65_angela.yen.jpg" />Angela Yen</a></div><div class="ds-work-card--detail"></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale.</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":40889716,"attachmentType":"pdf","workUrl":"https://www.academia.edu/19869778/Systematic_chromatin_state_comparison_of_epigenomes_associated_with_diverse_properties_including_sex_and_tissue_type"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":40889716,"attachmentType":"pdf","workUrl":"https://www.academia.edu/19869778/Systematic_chromatin_state_comparison_of_epigenomes_associated_with_diverse_properties_including_sex_and_tissue_type"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div></div><div data-auto_select="false" data-client_id="331998490334-rsn3chp12mbkiqhl6e7lu2q0mlbu0f1b" data-doc_id="40889716" data-landing_url="https://www.academia.edu/19869778/Systematic_chromatin_state_comparison_of_epigenomes_associated_with_diverse_properties_including_sex_and_tissue_type" data-login_uri="https://www.academia.edu/registrations/google_one_tap" data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="99314992" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/99314992/A_framework_for_group_wise_summarization_and_comparison_of_chromatin_state_annotations">A framework for group-wise summarization and comparison of chromatin state annotations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="263823786" href="https://independent.academia.edu/HAVU325">HA VU</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Bioinformatics</p><p class="ds-related-work--abstract ds2-5-body-sm">Motivation Genome-wide maps of epigenetic modifications are powerful resources for non-coding genome annotation. Maps of multiple epigenetics marks have been integrated into cell or tissue type-specific chromatin state annotations for many cell or tissue types. With the increasing availability of multiple chromatin state maps for biologically similar samples, there is a need for methods that can effectively summarize the information about chromatin state annotations within groups of samples and identify differences across groups of samples at a high resolution. Results We developed CSREP, which takes as input chromatin state annotations for a group of samples. CSREP then probabilistically estimates the state at each genomic position and derives a representative chromatin state map for the group. CSREP uses an ensemble of multi-class logistic regression classifiers that predict the chromatin state assignment of each sample given the state maps from all other samples. The difference i...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A framework for group-wise summarization and comparison of chromatin state annotations","attachmentId":100438390,"attachmentType":"pdf","work_url":"https://www.academia.edu/99314992/A_framework_for_group_wise_summarization_and_comparison_of_chromatin_state_annotations","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/99314992/A_framework_for_group_wise_summarization_and_comparison_of_chromatin_state_annotations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="57239277" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/57239277/EpiAlign_an_alignment_based_bioinformatic_tool_for_comparing_chromatin_state_sequences">EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="65456878" href="https://independent.academia.edu/LingjueXie">Lingjue Xie</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2019</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences","attachmentId":72234476,"attachmentType":"pdf","work_url":"https://www.academia.edu/57239277/EpiAlign_an_alignment_based_bioinformatic_tool_for_comparing_chromatin_state_sequences","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/57239277/EpiAlign_an_alignment_based_bioinformatic_tool_for_comparing_chromatin_state_sequences"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="13346418" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/13346418/Integrative_analysis_of_111_reference_human_epigenomes">Integrative analysis of 111 reference human epigenomes</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="32585353" href="https://independent.academia.edu/Michaelzhang35">Michael zhang</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Nature, 2015</p><p class="ds-related-work--abstract ds2-5-body-sm">The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic info...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Integrative analysis of 111 reference human epigenomes","attachmentId":45444147,"attachmentType":"pdf","work_url":"https://www.academia.edu/13346418/Integrative_analysis_of_111_reference_human_epigenomes","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/13346418/Integrative_analysis_of_111_reference_human_epigenomes"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="52927056" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/52927056/Integrated_epigenomic_analysis_stratifies_chromatin_remodellers_into_distinct_functional_groups">Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="48659701" href="https://independent.academia.edu/PhillippaTaberlay">Phillippa Taberlay</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Epigenetics & Chromatin</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups","attachmentId":69953004,"attachmentType":"pdf","work_url":"https://www.academia.edu/52927056/Integrated_epigenomic_analysis_stratifies_chromatin_remodellers_into_distinct_functional_groups","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/52927056/Integrated_epigenomic_analysis_stratifies_chromatin_remodellers_into_distinct_functional_groups"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="76246776" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/76246776/Annotation_of_chromatin_states_in_66_complete_mouse_epigenomes_during_development">Annotation of chromatin states in 66 complete mouse epigenomes during development</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="112267968" href="https://umassmed.academia.edu/KailiFan">Kaili Fan</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Communications Biology, 2021</p><p class="ds-related-work--abstract ds2-5-body-sm">The morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors both active marks and the repressive mark H3K27me3. Highly evolutionarily conserved, these loci are enriched in silencers bound by polycomb repressive complex proteins, and the transcription start sites of their silenced target genes. 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To address this, we constructed phased, diploid genomes for four cadaveric donors (using long-read sequencing) and systematically charted noncoding regulatory elements and transcriptional activity across more than 25 tissues from these donors. Integrative analysis revealed over a million variants with allele-specific activity, coordinated, locus-scale allelic imbalances, and structural variants impacting proximal chromatin structure. We relate the personal genome analysis to the ENCODE encyclopedia, annotating allele- and tissue-specific elements that are strongly enriched for variants impacting expression and disease phenotypes. These experimental and statistical approaches, and the corresponding EN-TEx resource, provide a framework for personalized functional genomics.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Multi-tissue integrative analysis of personal epigenomes","attachmentId":79107771,"attachmentType":"pdf","work_url":"https://www.academia.edu/68735014/Multi_tissue_integrative_analysis_of_personal_epigenomes","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/68735014/Multi_tissue_integrative_analysis_of_personal_epigenomes"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="650115" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/650115/Mapping_and_analysis_of_chromatin_state_dynamics_in_nine_human_cell_types">Mapping and analysis of chromatin state dynamics in nine human cell types</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="478242" href="https://mit.academia.edu/LukeWard">Luke Ward</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Nature, 2011</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Mapping and analysis of chromatin state dynamics in nine human cell types","attachmentId":3577127,"attachmentType":"pdf","work_url":"https://www.academia.edu/650115/Mapping_and_analysis_of_chromatin_state_dynamics_in_nine_human_cell_types","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/650115/Mapping_and_analysis_of_chromatin_state_dynamics_in_nine_human_cell_types"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="30453716" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/30453716/Bridging_epigenomics_and_complex_disease_the_basics">Bridging epigenomics and complex disease: the basics</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="58056274" href="https://independent.academia.edu/RTeperino">R. Teperino</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Cellular and Molecular Life Sciences, 2013</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Bridging epigenomics and complex disease: the basics","attachmentId":50894720,"attachmentType":"pdf","work_url":"https://www.academia.edu/30453716/Bridging_epigenomics_and_complex_disease_the_basics","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/30453716/Bridging_epigenomics_and_complex_disease_the_basics"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="13869010" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/13869010/hiHMM_Bayesian_non_parametric_joint_inference_of_chromatin_state_maps">hiHMM: Bayesian non-parametric joint inference of chromatin state maps</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="8613645" href="https://ajou.academia.edu/HyunhwanJeong">Hyun-hwan Jeong</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Bioinformatics (Oxford, England), 2015</p><p class="ds-related-work--abstract ds2-5-body-sm">Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. In order to perform a principled comparison of evolutionarily distant epigenomes, we must consider species specific biases such as differences in genome size, strength of signal enrichment, and co-occurrence patterns of histone modifications. Here, we present a new Bayesian non-parametric method called hierarchically-linked infinite hidden Markov model (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types, and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison amo...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"hiHMM: Bayesian non-parametric joint inference of chromatin state maps","attachmentId":44859515,"attachmentType":"pdf","work_url":"https://www.academia.edu/13869010/hiHMM_Bayesian_non_parametric_joint_inference_of_chromatin_state_maps","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/13869010/hiHMM_Bayesian_non_parametric_joint_inference_of_chromatin_state_maps"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="99314971" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/99314971/Universal_annotation_of_the_human_genome_through_integration_of_over_a_thousand_epigenomic_datasets">Universal annotation of the human genome through integration of over a thousand epigenomic datasets</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="263823786" href="https://independent.academia.edu/HAVU325">HA VU</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2020</p><p class="ds-related-work--abstract ds2-5-body-sm">BackgroundGenome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative ‘stacked modeling’ approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges.ResultsUsing a version of ChromHMM enhanced for large-scale applications, we applied the stacked modeling appro...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Universal annotation of the human genome through integration of over a thousand epigenomic datasets","attachmentId":100438430,"attachmentType":"pdf","work_url":"https://www.academia.edu/99314971/Universal_annotation_of_the_human_genome_through_integration_of_over_a_thousand_epigenomic_datasets","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/99314971/Universal_annotation_of_the_human_genome_through_integration_of_over_a_thousand_epigenomic_datasets"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":40889716,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":40889716,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_40889716" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="14467425" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/14467425/Tackling_the_epigenome_challenges_and_opportunities_for_collaboration">Tackling the epigenome: challenges and opportunities for collaboration</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="33410446" href="https://fmi.academia.edu/DirkSch%C3%BCbeler">Dirk Schübeler</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Nature Biotechnology, 2010</p><div 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class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="1" data-entity-id="19283538" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/19283538/Comparing_genome_wide_chromatin_profiles_using_ChIP_chip_or_ChIP_seq">Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="39536408" href="https://independent.academia.edu/Ren%C3%A9Wardenaar">René Wardenaar</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Bioinformatics, 2010</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq","attachmentId":42100427,"attachmentType":"pdf","work_url":"https://www.academia.edu/19283538/Comparing_genome_wide_chromatin_profiles_using_ChIP_chip_or_ChIP_seq","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/19283538/Comparing_genome_wide_chromatin_profiles_using_ChIP_chip_or_ChIP_seq"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="2" data-entity-id="66831175" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/66831175/RoboCOP_Multivariate_State_Space_Model_Integrating_Epigenomic_Accessibility_Data_to_Elucidate_Genome_Wide_Chromatin_Occupancy">RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="50739307" href="https://independent.academia.edu/SnehaMitra3">Sneha Mitra</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Lecture Notes in Computer Science</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin 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data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/101770441/EPITRANS_A_database_that_integrates_epigenome_and_transcriptome_data">EPITRANS: A database that integrates epigenome and transcriptome data</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="3475989" href="https://hanyang.academia.edu/JinChoulChai">Jin Choul Chai</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Molecules and Cells, 2013</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"EPITRANS: A database that integrates epigenome and transcriptome data","attachmentId":102218306,"attachmentType":"pdf","work_url":"https://www.academia.edu/101770441/EPITRANS_A_database_that_integrates_epigenome_and_transcriptome_data","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/101770441/EPITRANS_A_database_that_integrates_epigenome_and_transcriptome_data"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="4" data-entity-id="24378909" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/24378909/Chromatin_conformation_signatures_of_cellular_differentiation">Chromatin conformation signatures of cellular differentiation</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="47003744" href="https://independent.academia.edu/RousseauMathieu">Mathieu Rousseau</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Genome Biology, 2009</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Chromatin conformation signatures of cellular differentiation","attachmentId":44711486,"attachmentType":"pdf","work_url":"https://www.academia.edu/24378909/Chromatin_conformation_signatures_of_cellular_differentiation","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/24378909/Chromatin_conformation_signatures_of_cellular_differentiation"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="5" data-entity-id="65849117" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/65849117/The_International_Human_Epigenome_Consortium_A_Blueprint_for_Scientific_Collaboration_and_Discovery">The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="76455583" href="https://independent.academia.edu/InukKoh">In-uk Koh</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Cell, 2016</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery","attachmentId":77268119,"attachmentType":"pdf","work_url":"https://www.academia.edu/65849117/The_International_Human_Epigenome_Consortium_A_Blueprint_for_Scientific_Collaboration_and_Discovery","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/65849117/The_International_Human_Epigenome_Consortium_A_Blueprint_for_Scientific_Collaboration_and_Discovery"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="6" data-entity-id="57544683" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/57544683/Integrative_analysis_of_haplotype_resolved_epigenomes_across_human_tissues">Integrative analysis of haplotype-resolved epigenomes across human tissues</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="37596470" href="https://independent.academia.edu/michaelzhang42">michael zhang</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Nature, 2015</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Integrative analysis of haplotype-resolved epigenomes across human tissues","attachmentId":72395669,"attachmentType":"pdf","work_url":"https://www.academia.edu/57544683/Integrative_analysis_of_haplotype_resolved_epigenomes_across_human_tissues","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/57544683/Integrative_analysis_of_haplotype_resolved_epigenomes_across_human_tissues"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" 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