{"id":"https://openalex.org/W2044095773","doi":"https://doi.org/10.1145/1854776.1854860","title":"A computational exploration of gene regulation by nucleosome position","display_name":"A computational exploration of gene regulation by nucleosome position","publication_year":2010,"publication_date":"2010-08-02","ids":{"openalex":"https://openalex.org/W2044095773","doi":"https://doi.org/10.1145/1854776.1854860","mag":"2044095773"},"language":"en","primary_location":{"id":"doi:10.1145/1854776.1854860","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854860","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040441412","display_name":"Justin A. Fincher","orcid":null},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin A. Fincher","raw_affiliation_strings":["Florida State University, Tallahassee, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida State University, Tallahassee, FL","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004937273","display_name":"Gary Tyson","orcid":"https://orcid.org/0009-0002-5081-2843"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gary Tyson","raw_affiliation_strings":["Florida State University, Tallahassee, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida State University, Tallahassee, FL","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102006630","display_name":"Jonathan H. Dennis","orcid":"https://orcid.org/0000-0003-0621-7019"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan H. Dennis","raw_affiliation_strings":["Florida State University, Tallahassee, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida State University, Tallahassee, FL","institution_ids":["https://openalex.org/I103163165"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I103163165"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14524158,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"469","last_page":"471"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9997000098228455,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9958000183105469,"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":0.9327949285507202},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.6445845365524292},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.583836555480957},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5632808208465576},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5256289839744568},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5128265023231506},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4654320776462555},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4650470018386841},{"id":"https://openalex.org/keywords/linker-dna","display_name":"Linker DNA","score":0.4343516230583191},{"id":"https://openalex.org/keywords/genomic-dna","display_name":"genomic DNA","score":0.4237905442714691}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.9327949285507202},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.6445845365524292},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.583836555480957},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5632808208465576},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5256289839744568},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5128265023231506},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4654320776462555},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4650470018386841},{"id":"https://openalex.org/C193646685","wikidata":"https://www.wikidata.org/wiki/Q1826830","display_name":"Linker DNA","level":5,"score":0.4343516230583191},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.4237905442714691}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1854776.1854860","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854860","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1974813112","https://openalex.org/W1994288562","https://openalex.org/W2038963685","https://openalex.org/W2076446466","https://openalex.org/W2098028543","https://openalex.org/W2110776599","https://openalex.org/W2155453721"],"related_works":["https://openalex.org/W2062514148","https://openalex.org/W2063259914","https://openalex.org/W2024605487","https://openalex.org/W4213216609","https://openalex.org/W3118167814","https://openalex.org/W2062722074","https://openalex.org/W2092186136","https://openalex.org/W2004767437","https://openalex.org/W2509901635","https://openalex.org/W2036280079"],"abstract_inverted_index":{"More":[0],"than":[1,43],"two":[2],"meters":[3],"of":[4,13,23,60,158,184,193],"DNA":[5,24,33,87,98,147,194],"is":[6,18],"organized":[7,40],"inside":[8],"a":[9,75,134,146,156],"five":[10],"micrometer":[11],"nucleus":[12],"every":[14],"human":[15,108],"cell.":[16],"This":[17,89],"accomplished":[19],"by":[20,166,174],"the":[21,51,56,106,112,167],"wrapping":[22],"around":[25,126],"protein":[26,127,159],"\"spools\"":[27],"(histones)":[28],"to":[29,38,80,96,115,154,189],"form":[30],"nucleosomes.":[31],"Some":[32],"sequences":[34],"are":[35,50,170],"more":[36],"likely":[37],"be":[39],"into":[41],"nucleosomes":[42,61],"others.":[44],"Because":[45],"nucleosomes,":[46],"not":[47,171],"bare":[48],"DNA,":[49],"substrate":[52],"for":[53,105],"DNA-templated":[54],"reactions,":[55],"position":[57],"and":[58,100,150],"density":[59],"play":[62],"an":[63],"important":[64],"role":[65],"in":[66],"these":[67,140],"processes":[68],"(e.g.,":[69],"affecting":[70],"gene":[71],"regulation).":[72],"We":[73,110,179],"used":[74,95,111],"machine":[76],"learning":[77],"tool":[78],"trained":[79],"distinguish":[81],"nucleosome":[82,85,102,118,136],"forming":[83],"from":[84],"inhibitory":[86],"sequences.":[88],"Support":[90],"Vector":[91],"Machine":[92],"(SVM)":[93],"was":[94],"evaluate":[97],"sequence":[99,163,176],"generate":[101],"occupancy":[103],"predictions":[104],"entire":[107],"genome.":[109],"resulting":[113],"scores":[114],"characterize":[116],"DNA-encoded":[117],"positioning":[119,137],"signals":[120],"at":[121],"specific":[122],"genomic":[123],"regions.":[124],"Scores":[125],"coding":[128],"regions,":[129],"specifically":[130],"intron-exon":[131],"boundaries,":[132],"showed":[133],"characteristic":[135],"pattern.":[138],"Previously":[139],"boundaries":[141],"had":[142],"been":[143],"identified":[144],"using":[145],"consensus":[148],"sequence,":[149],"we":[151],"were":[152],"able":[153],"identify":[155],"subset":[157],"genes":[160],"based":[161],"on":[162],"features":[164],"recognized":[165],"SVM":[168],"that":[169,181],"readily":[172],"identifiable":[173],"traditional":[175],"evaluation":[177],"techniques.":[178],"anticipate":[180],"this":[182],"type":[183],"analysis":[185],"will":[186],"allow":[187],"us":[188],"refine":[190],"our":[191],"understanding":[192],"regulatory":[195],"processes.":[196]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}