{"id":"https://openalex.org/W2098028543","doi":"https://doi.org/10.1371/journal.pcbi.1000134","title":"Predicting Human Nucleosome Occupancy from Primary Sequence","display_name":"Predicting Human Nucleosome Occupancy from Primary Sequence","publication_year":2008,"publication_date":"2008-08-21","ids":{"openalex":"https://openalex.org/W2098028543","doi":"https://doi.org/10.1371/journal.pcbi.1000134","mag":"2098028543","pmid":"https://pubmed.ncbi.nlm.nih.gov/18725940"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000134","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000134","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000134&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.1000134&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079662689","display_name":"Shobhit Gupta","orcid":"https://orcid.org/0000-0001-5169-3263"},"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":"Shobhit Gupta","raw_affiliation_strings":["Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102006630","display_name":"Jonathan H. Dennis","orcid":"https://orcid.org/0000-0003-0621-7019"},"institutions":[{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Dennis","raw_affiliation_strings":["Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040512461","display_name":"Robert E. Thurman","orcid":null},"institutions":[{"id":"https://openalex.org/I2801852214","display_name":"University of Washington Medical Center","ror":"https://ror.org/00wbzw723","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801852214"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert E. Thurman","raw_affiliation_strings":["Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I2801852214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014149423","display_name":"Robert E. Kingston","orcid":"https://orcid.org/0000-0003-3628-4335"},"institutions":[{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Kingston","raw_affiliation_strings":["Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006847496","display_name":"J Stamatoyannopoulos","orcid":"https://orcid.org/0000-0002-2664-5769"},"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":"John A. Stamatoyannopoulos","raw_affiliation_strings":["Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, 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":6,"corresponding_author_ids":["https://openalex.org/A5006847496","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":5.6706,"has_fulltext":true,"cited_by_count":137,"citation_normalized_percentile":{"value":0.96801086,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"4","issue":"8","first_page":"e1000134","last_page":"e1000134"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"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":0.9689629673957825},{"id":"https://openalex.org/keywords/micrococcal-nuclease","display_name":"Micrococcal nuclease","score":0.7185006141662598},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6537747979164124},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5783277153968811},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5463285446166992},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5041400194168091},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.5017898082733154},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5006258487701416},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2899376153945923},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15144342184066772}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.9689629673957825},{"id":"https://openalex.org/C139024627","wikidata":"https://www.wikidata.org/wiki/Q4293132","display_name":"Micrococcal nuclease","level":5,"score":0.7185006141662598},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6537747979164124},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5783277153968811},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5463285446166992},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5041400194168091},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.5017898082733154},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5006258487701416},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2899376153945923},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15144342184066772}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1000134","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000134","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000134&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:18725940","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18725940","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:9838eb94549f481d8318761735d312f9","is_oa":true,"landing_page_url":"https://doaj.org/article/9838eb94549f481d8318761735d312f9","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 4, Iss 8, p e1000134 (2008)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/149734","is_oa":true,"landing_page_url":"https://figshare.com/articles/Predicting_Human_Nucleosome_Occupancy_from_Primary_Sequence/149734","pdf_url":null,"source":{"id":"https://openalex.org/S4306400572","display_name":"OPAL (Open@LaTrobe) (La Trobe University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I196829312","host_organization_name":"La Trobe University","host_organization_lineage":["https://openalex.org/I196829312"],"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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2515632","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2515632","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.1000134","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000134","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000134&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/15","display_name":"Life in Land","score":0.47999998927116394}],"awards":[],"funders":[{"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/W2098028543.pdf","grobid_xml":"https://content.openalex.org/works/W2098028543.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W160239957","https://openalex.org/W1498828547","https://openalex.org/W1542652324","https://openalex.org/W1577271338","https://openalex.org/W1582484699","https://openalex.org/W1605106831","https://openalex.org/W1963692635","https://openalex.org/W1968754848","https://openalex.org/W1978893041","https://openalex.org/W1979204453","https://openalex.org/W1983685543","https://openalex.org/W1987020026","https://openalex.org/W1996234697","https://openalex.org/W1996270170","https://openalex.org/W1996852546","https://openalex.org/W1999327905","https://openalex.org/W2004469916","https://openalex.org/W2012055868","https://openalex.org/W2021794665","https://openalex.org/W2023863464","https://openalex.org/W2024447590","https://openalex.org/W2029873987","https://openalex.org/W2030369966","https://openalex.org/W2041195887","https://openalex.org/W2043938026","https://openalex.org/W2047422719","https://openalex.org/W2050298575","https://openalex.org/W2053876385","https://openalex.org/W2061773171","https://openalex.org/W2062917424","https://openalex.org/W2064065176","https://openalex.org/W2067214511","https://openalex.org/W2069281865","https://openalex.org/W2072152932","https://openalex.org/W2076446466","https://openalex.org/W2076950513","https://openalex.org/W2077827909","https://openalex.org/W2080748087","https://openalex.org/W2085209572","https://openalex.org/W2086534074","https://openalex.org/W2087347434","https://openalex.org/W2090098862","https://openalex.org/W2098490793","https://openalex.org/W2101351978","https://openalex.org/W2109866944","https://openalex.org/W2110312780","https://openalex.org/W2114803986","https://openalex.org/W2126888219","https://openalex.org/W2129020471","https://openalex.org/W2132440338","https://openalex.org/W2133958955","https://openalex.org/W2134314200","https://openalex.org/W2143142222","https://openalex.org/W2144792857","https://openalex.org/W2151029800","https://openalex.org/W2157825442","https://openalex.org/W2163585426","https://openalex.org/W2165503425","https://openalex.org/W2169674658","https://openalex.org/W2177510297","https://openalex.org/W2544883878","https://openalex.org/W4232420716","https://openalex.org/W4239324665","https://openalex.org/W6634414245","https://openalex.org/W6672247373","https://openalex.org/W6790425969"],"related_works":["https://openalex.org/W2051621781","https://openalex.org/W2171605297","https://openalex.org/W2017912870","https://openalex.org/W2904555596","https://openalex.org/W2332545061","https://openalex.org/W2184399832","https://openalex.org/W2471002338","https://openalex.org/W2038203462","https://openalex.org/W1482706825","https://openalex.org/W1979616193"],"abstract_inverted_index":{"Nucleosomes":[0],"are":[1,88,145],"the":[2,10,15,83,121,124,132,134,167,171,225,237],"fundamental":[3],"repeating":[4],"unit":[5],"of":[6,14,42,53,98,151,180,187,194,204,228,242],"chromatin":[7,36],"and":[8,85,153,177,182,235],"comprise":[9],"structural":[11],"building":[12],"blocks":[13],"living":[16],"eukaryotic":[17],"genome.":[18],"Micrococcal":[19],"nuclease":[20],"(MNase)":[21],"has":[22],"long":[23],"been":[24,47],"used":[25,48],"to":[26,49,72,147],"delineate":[27],"nucleosomal":[28],"organization.":[29,244],"Microarray-based":[30],"nucleosome":[31,63,73,99,212,229,243],"mapping":[32],"experiments":[33,75],"in":[34,131,231],"yeast":[35],"have":[37,46,58],"revealed":[38],"regularly-spaced":[39],"translational":[40],"phasing":[41,213],"nucleosomes.":[43],"These":[44],"data":[45,112],"train":[50],"computational":[51],"models":[52,87],"sequence-directed":[54],"nuclesosome":[55],"positioning,":[56],"which":[57],"identified":[59],"ubiquitous":[60],"strong":[61],"intrinsic":[62],"positioning":[64,74,230,240],"signals.":[65],"Here,":[66],"we":[67,103,144,209],"successfully":[68],"apply":[69],"this":[70,142],"approach":[71],"from":[76,113,160],"human":[77,168],"chromatin.":[78],"The":[79,221],"predictions":[80],"made":[81],"by":[82,157],"human-trained":[84],"yeast-trained":[86],"strongly":[89],"correlated,":[90],"suggesting":[91],"a":[92,192],"shared":[93],"mechanism":[94,227],"for":[95],"sequence-based":[96],"determination":[97],"occupancy.":[100],"In":[101,120],"addition,":[102],"observed":[104],"striking":[105],"complementarity":[106],"between":[107],"classifiers":[108],"trained":[109],"on":[110],"experimental":[111],"weakly":[114],"versus":[115],"heavily":[116],"digested":[117],"MNase":[118],"samples.":[119],"former":[122],"case,":[123],"resulting":[125],"model":[126,143],"accurately":[127],"identifies":[128],"nucleosome-forming":[129,152,181,198],"sequences;":[130],"latter,":[133],"classifier":[135,162,172],"excels":[136],"at":[137],"identifying":[138],"nucleosome-free":[139,219],"regions.":[140,220],"Using":[141],"able":[146],"identify":[148],"several":[149],"characteristics":[150],"nucleosome-disfavoring":[154,183,195],"sequences.":[155,184],"First,":[156],"combining":[158],"results":[159,222],"each":[161],"applied":[163],"de":[164],"novo":[165],"across":[166],"ENCODE":[169],"regions,":[170],"reveals":[173],"distinct":[174],"sequence":[175],"composition":[176],"periodicity":[178],"features":[179],"Short":[185],"runs":[186,203],"dinucleotide":[188],"repeat":[189],"appear":[190],"as":[191],"hallmark":[193],"sequences,":[196],"while":[197],"sequences":[199],"contain":[200],"short":[201],"periodic":[202],"GC":[205],"base":[206],"pairs.":[207],"Second,":[208],"show":[210],"that":[211,224],"is":[214,233],"most":[215],"frequently":[216],"predicted":[217],"flanking":[218],"suggest":[223],"major":[226],"vivo":[232],"boundary-event-driven":[234],"affirm":[236],"classical":[238],"statistical":[239],"theory":[241]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":16}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
