{"id":"https://openalex.org/W2101399274","doi":"https://doi.org/10.1093/bioinformatics/btp216","title":"Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy","display_name":"Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy","publication_year":2009,"publication_date":"2009-05-27","ids":{"openalex":"https://openalex.org/W2101399274","doi":"https://doi.org/10.1093/bioinformatics/btp216","mag":"2101399274","pmid":"https://pubmed.ncbi.nlm.nih.gov/19478009"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp216","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i348/48993422/bioinformatics_25_12_i348.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i348/48993422/bioinformatics_25_12_i348.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042719322","display_name":"Shai Lubliner","orcid":null},"institutions":[{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Shai Lubliner","raw_affiliation_strings":["1 Department of Computer Science and Applied Mathematics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Applied Mathematics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel","institution_ids":["https://openalex.org/I53964585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012450539","display_name":"Eran Segal","orcid":"https://orcid.org/0000-0002-6859-1164"},"institutions":[{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Eran Segal","raw_affiliation_strings":["1 Department of Computer Science and Applied Mathematics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Applied Mathematics and 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel","institution_ids":["https://openalex.org/I53964585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5042719322"],"corresponding_institution_ids":["https://openalex.org/I53964585"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.3438,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.80038852,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"25","issue":"12","first_page":"i348","last_page":"i355"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":1.0,"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":1.0,"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":0.9945999979972839,"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/T10604","display_name":"RNA Research and Splicing","score":0.9937000274658203,"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":0.9653562307357788},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7451437711715698},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6552261114120483},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5834298133850098},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.5824490785598755},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5388924479484558},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4626307189464569},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4619140625},{"id":"https://openalex.org/keywords/linker-dna","display_name":"Linker DNA","score":0.45675429701805115},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3451242446899414},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20250585675239563}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.9653562307357788},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7451437711715698},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6552261114120483},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5834298133850098},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.5824490785598755},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5388924479484558},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4626307189464569},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4619140625},{"id":"https://openalex.org/C193646685","wikidata":"https://www.wikidata.org/wiki/Q1826830","display_name":"Linker DNA","level":5,"score":0.45675429701805115},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3451242446899414},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20250585675239563}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btp216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp216","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i348/48993422/bioinformatics_25_12_i348.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19478009","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19478009","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:1458991","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC2687970","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2687970","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2687970","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp216","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i348/48993422/bioinformatics_25_12_i348.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101399274.pdf","grobid_xml":"https://content.openalex.org/works/W2101399274.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1973729666","https://openalex.org/W1980971292","https://openalex.org/W1996852546","https://openalex.org/W2011779452","https://openalex.org/W2029873987","https://openalex.org/W2030023744","https://openalex.org/W2052842503","https://openalex.org/W2076446466","https://openalex.org/W2077187993","https://openalex.org/W2080748087","https://openalex.org/W2081119693","https://openalex.org/W2081127803","https://openalex.org/W2087814426","https://openalex.org/W2114752404","https://openalex.org/W2115219137","https://openalex.org/W2125838338","https://openalex.org/W2134314200","https://openalex.org/W2144123178","https://openalex.org/W2144792857","https://openalex.org/W2147734340","https://openalex.org/W2149917410","https://openalex.org/W2154109129","https://openalex.org/W2167764944","https://openalex.org/W2290630051"],"related_works":["https://openalex.org/W2062514148","https://openalex.org/W2063259914","https://openalex.org/W2104603433","https://openalex.org/W2024605487","https://openalex.org/W3118167814","https://openalex.org/W2004767437","https://openalex.org/W2062722074","https://openalex.org/W2092186136","https://openalex.org/W2910580209","https://openalex.org/W2509901635"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
