{"id":"https://openalex.org/W2011884978","doi":"https://doi.org/10.1371/journal.pcbi.1000834","title":"Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens","display_name":"Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens","publication_year":2010,"publication_date":"2010-07-08","ids":{"openalex":"https://openalex.org/W2011884978","doi":"https://doi.org/10.1371/journal.pcbi.1000834","mag":"2011884978","pmid":"https://pubmed.ncbi.nlm.nih.gov/20628623"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000834","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000834","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000834&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000834&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112869578","display_name":"Sheila M. Reynolds","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sheila M. Reynolds","raw_affiliation_strings":["Department of Electrical Engineering, University of Washington, Seattle, Washington, USA","Department of Electrical Engineering, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, University of Washington, Seattle, Washington, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Electrical Engineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113478221","display_name":"Jeff Bilmes","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeff A. Bilmes","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America","Department of Electrical Engineering, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Electrical Engineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057375933","display_name":"William Stafford Noble","orcid":"https://orcid.org/0000-0001-7283-4715"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William Stafford Noble","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America","Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5057375933"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.811,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.71054074,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"6","issue":"7","first_page":"e1000834","last_page":"e1000834"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.9211268424987793},{"id":"https://openalex.org/keywords/linker-dna","display_name":"Linker DNA","score":0.762447714805603},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.6051281094551086},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6028797030448914},{"id":"https://openalex.org/keywords/linker","display_name":"Linker","score":0.5792709589004517},{"id":"https://openalex.org/keywords/homo-sapiens","display_name":"Homo sapiens","score":0.5764060020446777},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5247780680656433},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45886796712875366},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4551614820957184},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4460690915584564},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43404287099838257},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.42613035440444946},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18759816884994507}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.9211268424987793},{"id":"https://openalex.org/C193646685","wikidata":"https://www.wikidata.org/wiki/Q1826830","display_name":"Linker DNA","level":5,"score":0.762447714805603},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.6051281094551086},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6028797030448914},{"id":"https://openalex.org/C2780557392","wikidata":"https://www.wikidata.org/wiki/Q523796","display_name":"Linker","level":2,"score":0.5792709589004517},{"id":"https://openalex.org/C2777938546","wikidata":"https://www.wikidata.org/wiki/Q5","display_name":"Homo sapiens","level":2,"score":0.5764060020446777},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5247780680656433},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45886796712875366},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4551614820957184},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4460690915584564},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43404287099838257},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.42613035440444946},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18759816884994507},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000076246","descriptor_name":"CCCTC-Binding Factor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076246","descriptor_name":"CCCTC-Binding Factor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076246","descriptor_name":"CCCTC-Binding Factor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020087","descriptor_name":"Alu Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020087","descriptor_name":"Alu Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020087","descriptor_name":"Alu Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1000834","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000834","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000834&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:20628623","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20628623","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:8693e0b0834642dc9b939d96e93e5bd4","is_oa":true,"landing_page_url":"https://doaj.org/article/8693e0b0834642dc9b939d96e93e5bd4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 6, Iss 7, p e1000834 (2010)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/142712","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Learning_a_Weighted_Sequence_Model_of_the_Nucleosome_Core_and_Linker_Yields_More_Accurate_Predictions_in_Saccharomyces_cerevisiae_and_Homo_sapiens_/142712","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2900294","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2900294","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000834","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000834","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000834&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.7799999713897705}],"awards":[{"id":"https://openalex.org/G958608162","display_name":null,"funder_award_id":"T32 HG00035","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2011884978.pdf","grobid_xml":"https://content.openalex.org/works/W2011884978.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1574795164","https://openalex.org/W1943277194","https://openalex.org/W1963540515","https://openalex.org/W1965240564","https://openalex.org/W1980971292","https://openalex.org/W1988997227","https://openalex.org/W1989373989","https://openalex.org/W1992535005","https://openalex.org/W1995808589","https://openalex.org/W1996065618","https://openalex.org/W1996852546","https://openalex.org/W2002439270","https://openalex.org/W2004206635","https://openalex.org/W2004469916","https://openalex.org/W2004993130","https://openalex.org/W2014002637","https://openalex.org/W2015416439","https://openalex.org/W2024462905","https://openalex.org/W2028189691","https://openalex.org/W2029873987","https://openalex.org/W2040048585","https://openalex.org/W2052842503","https://openalex.org/W2071501400","https://openalex.org/W2072152932","https://openalex.org/W2073240448","https://openalex.org/W2073374533","https://openalex.org/W2080748087","https://openalex.org/W2086007560","https://openalex.org/W2086038224","https://openalex.org/W2087347434","https://openalex.org/W2087573417","https://openalex.org/W2090100694","https://openalex.org/W2098028543","https://openalex.org/W2101399274","https://openalex.org/W2106448802","https://openalex.org/W2107275319","https://openalex.org/W2114752404","https://openalex.org/W2115219137","https://openalex.org/W2115297659","https://openalex.org/W2134314200","https://openalex.org/W2137184377","https://openalex.org/W2147734340","https://openalex.org/W2149917410","https://openalex.org/W2151553287","https://openalex.org/W2152406248","https://openalex.org/W2153392439","https://openalex.org/W2154109129","https://openalex.org/W2165451373","https://openalex.org/W2167764944","https://openalex.org/W3128113190","https://openalex.org/W6609701964","https://openalex.org/W6672247373","https://openalex.org/W6790425969"],"related_works":["https://openalex.org/W2738317363","https://openalex.org/W2888566912","https://openalex.org/W2049798402","https://openalex.org/W2062514148","https://openalex.org/W2414773490","https://openalex.org/W2075668056","https://openalex.org/W2413484773","https://openalex.org/W2415245471","https://openalex.org/W1532969402","https://openalex.org/W1998243227"],"abstract_inverted_index":{"DNA":[0,79],"in":[1,70,94,108,133,236,258],"eukaryotes":[2],"is":[3,15,64],"packaged":[4],"into":[5],"a":[6,49,139,163,246,261,291],"chromatin":[7],"complex,":[8],"the":[9,16,22,30,33,43,56,60,71,78,115,121,125,158,171,176,211,228,284,287],"most":[10,116],"basic":[11],"element":[12],"of":[13,21,42,77,127,175,249,267,286],"which":[14],"nucleosome.":[17],"The":[18,179],"precise":[19],"positioning":[20,38,151,293],"nucleosome":[23,51,57,92,150,223,252],"cores":[24],"allows":[25],"for":[26],"selective":[27],"access":[28],"to":[29,90,148,160,185,192,234],"DNA,":[31],"and":[32,59,63,74,81,98,112,129,188,209,215,221,239,263,271],"mechanisms":[34],"that":[35,53,84,168,257,272,283],"control":[36],"this":[37,85],"are":[39,120,182,269,275],"important":[40],"pieces":[41],"gene":[44],"expression":[45],"puzzle.":[46],"We":[47,281],"describe":[48],"large-scale":[50],"pattern":[52,86,142],"jointly":[54],"characterizes":[55],"core":[58],"adjacent":[61,199],"linkers":[62],"predominantly":[65],"characterized":[66],"by":[67],"long-range":[68],"oscillations":[69],"mono,":[72],"di-":[73,128],"tri-nucleotide":[75,130],"content":[76],"sequence,":[80],"we":[82],"show":[83],"can":[87,189],"be":[88,161,190],"used":[89,147,191],"predict":[91,149],"positions":[93,197,274],"both":[95,109,259],"Homo":[96],"sapiens":[97,111],"Saccharomyces":[99],"cerevisiae":[100,251],"more":[101],"accurately":[102,193],"than":[103,143],"previously":[104,146],"published":[105,233,243],"methods.":[106],"Surprisingly,":[107],"H.":[110,237],"S.":[113,250],"cerevisiae,":[114],"informative":[117],"individual":[118],"features":[119,131],"mono-nucleotide":[122],"patterns,":[123],"although":[124],"inclusion":[126],"results":[132,232,255],"improved":[134],"performance.":[135],"Our":[136,225,254],"approach":[137,167,226],"combines":[138],"much":[140],"longer":[141],"has":[144],"been":[145],"from":[152,173,198],"sequence-301":[153],"base":[154],"pairs,":[155],"centered":[156],"at":[157],"position":[159],"scored-with":[162],"novel":[164],"discriminative":[165],"classification":[166,231],"selectively":[169],"weights":[170],"contributions":[172],"each":[174],"input":[177],"features.":[178],"resulting":[180],"scores":[181],"relatively":[183,264],"insensitive":[184],"local":[186],"AT-content":[187],"discriminate":[194],"putative":[195],"dyad":[196],"linker":[200,218],"regions":[201],"without":[202,210],"requiring":[203],"an":[204],"additional":[205],"dynamic":[206],"programming":[207],"step":[208],"attendant":[212],"edge":[213],"effects":[214],"assumptions":[216],"about":[217],"length":[219],"modeling":[220],"overall":[222],"density.":[224],"produces":[227],"best":[229],"dyad-linker":[230],"date":[235],"sapiens,":[238],"outperforms":[240],"two":[241],"recently":[242],"models":[244],"on":[245,278],"large":[247],"set":[248],"positions.":[253],"suggest":[256],"genomes,":[260],"comparable":[262],"small":[265],"fraction":[266],"nucleosomes":[268,289],"well-positioned":[270],"these":[273],"predictable":[276],"based":[277],"sequence":[279],"alone.":[280],"believe":[282],"bulk":[285],"remaining":[288],"follow":[290],"statistical":[292],"model.":[294]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
