{"id":"https://openalex.org/W4231911399","doi":"https://doi.org/10.1109/csb.2004.1332542","title":"Using enhancing signals to improve specificity of ab initio splice site sensors","display_name":"Using enhancing signals to improve specificity of ab initio splice site sensors","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W4231911399","doi":"https://doi.org/10.1109/csb.2004.1332542"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332542","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332542","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"type":"article","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/A5061060636","display_name":"A. Tchourbanov","orcid":null},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]},{"id":"https://openalex.org/I2802450327","display_name":"University of Nebraska System","ror":"https://ror.org/0238rvs44","country_code":"US","type":"education","lineage":["https://openalex.org/I2802450327"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. Tchourbanov","raw_affiliation_strings":["Department of Computer Science, University of Nebraska at Omaha, Omaha, NE, USA","University of Nebraska System, Lincoln, NE, US"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]},{"raw_affiliation_string":"University of Nebraska System, Lincoln, NE, US","institution_ids":["https://openalex.org/I2802450327"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015948340","display_name":"H.H. Ali","orcid":null},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"H.H. Ali","raw_affiliation_strings":["Dept. of Comput. Sci., Nebraska Univ., Omaha, NE, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Comput. Sci., Nebraska Univ., Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085465318","display_name":"J. Deogun","orcid":null},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Deogun","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA","institution_ids":["https://openalex.org/I114395901"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5061060636"],"corresponding_institution_ids":["https://openalex.org/I122266389","https://openalex.org/I2802450327"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.39179954,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"8","issue":null,"first_page":"641","last_page":"642"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","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/T10604","display_name":"RNA Research and Splicing","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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/splice","display_name":"splice","score":0.9250192642211914},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.7916262149810791},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6547368764877319},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5367269515991211},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5186954736709595},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.4865240454673767},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.45966681838035583},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4342794716358185},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.43184250593185425},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4098990559577942},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36916404962539673},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.345296710729599},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.33741652965545654},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3281140923500061},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10623079538345337},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.07258975505828857}],"concepts":[{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.9250192642211914},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.7916262149810791},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6547368764877319},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5367269515991211},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5186954736709595},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.4865240454673767},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.45966681838035583},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4342794716358185},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.43184250593185425},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4098990559577942},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36916404962539673},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.345296710729599},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.33741652965545654},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3281140923500061},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10623079538345337},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.07258975505828857},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2004.1332542","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332542","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W2088440342","https://openalex.org/W2110400205","https://openalex.org/W2128195632","https://openalex.org/W2150298398","https://openalex.org/W2162396524"],"related_works":["https://openalex.org/W2029220916","https://openalex.org/W2274928342","https://openalex.org/W1943031701","https://openalex.org/W3129862691","https://openalex.org/W2095502359","https://openalex.org/W1993348797","https://openalex.org/W2887346131","https://openalex.org/W2023018590","https://openalex.org/W2008832338","https://openalex.org/W2014791263"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3],"describe":[4],"a":[5,44,69],"new":[6],"approach":[7],"to":[8,23,59,81,94],"improve":[9,82],"the":[10,28,66,83,114],"precision":[11],"of":[12,68,85,97,121],"splice":[13,30,78,86],"site":[14,87],"annotation":[15],"in":[16],"human":[17,29],"genes.":[18],"The":[19,89,117],"problem":[20],"is":[21,43,92,106,120],"known":[22],"be":[24],"extremely":[25],"challenging":[26],"since":[27],"signals":[31,103],"are":[32],"highly":[33],"indistinct":[34],"and":[35,52,111],"frequent":[36],"cryptic":[37],"sites":[38,79],"confuse":[39],"signal":[40],"sensors.":[41],"There":[42],"strong":[45],"evidence":[46],"that":[47],"exonic":[48,53],"splicing":[49,54,60],"enhancers":[50],"(ESE)":[51],"silencers":[55],"(ESS)":[56],"influence":[57],"commitment":[58],"at":[61],"early":[62],"stages.":[63],"We":[64],"propose":[65],"use":[67],"naive":[70],"Bayesian":[71],"network":[72],"(BN)":[73],"combined":[74],"with":[75],"Boltzmann":[76],"machine":[77],"sensor,":[80],"specificity":[84,98],"prediction.":[88],"SpIiceScan":[90],"program":[91],"implemented":[93],"demonstrate":[95],"feasibility":[96],"enhancement":[99],"based":[100],"on":[101],"ESE/ESS":[102],"interactions.":[104],"SpliceScan":[105],"more":[107],"sensitive":[108],"than":[109],"GeneSplicer":[110],"NNSplice":[112],"for":[113,124],"same":[115],"specificity.":[116],"designed":[118],"method":[119],"particular":[122],"value":[123],"ab":[125],"initio":[126],"gene":[127],"annotation.":[128]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
