{"id":"https://openalex.org/W2046673993","doi":"https://doi.org/10.1186/1471-2105-14-s1-s3","title":"A negative selection heuristic to predict new transcriptional targets","display_name":"A negative selection heuristic to predict new transcriptional targets","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2046673993","doi":"https://doi.org/10.1186/1471-2105-14-s1-s3","mag":"2046673993","pmid":"https://pubmed.ncbi.nlm.nih.gov/23368951"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s1-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S1-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S1-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025973233","display_name":"Luigi Cerulo","orcid":"https://orcid.org/0000-0001-8342-3487"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Luigi Cerulo","raw_affiliation_strings":["Department of Science, University of Sannio, Benevento, Italy. lcerulo@unisannio.it","Department of Science, University of Sannio, Benevento, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Science, University of Sannio, Benevento, Italy. lcerulo@unisannio.it","institution_ids":["https://openalex.org/I16337185"]},{"raw_affiliation_string":"Department of Science, University of Sannio, Benevento, Italy","institution_ids":["https://openalex.org/I16337185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068855074","display_name":"Vincenzo Paduano","orcid":null},"institutions":[{"id":"https://openalex.org/I4210115745","display_name":"Biogem","ror":"https://ror.org/01ymr5447","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I2801626668","https://openalex.org/I4210115745"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Vincenzo Paduano","raw_affiliation_strings":["BioGeM s.c.a r.l., Institute of Genetic Research \"Gaetano Salvatore\", Ariano Irpino, (AV), Italy"],"affiliations":[{"raw_affiliation_string":"BioGeM s.c.a r.l., Institute of Genetic Research \"Gaetano Salvatore\", Ariano Irpino, (AV), Italy","institution_ids":["https://openalex.org/I4210115745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009018743","display_name":"Pietro Zoppoli","orcid":"https://orcid.org/0000-0002-7860-9655"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]},{"id":"https://openalex.org/I4210145812","display_name":"Cancer Genetics (United States)","ror":"https://ror.org/05feyya22","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145812"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pietro Zoppoli","raw_affiliation_strings":["Institute for Cancer Genetics, Columbia University, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Cancer Genetics, Columbia University, New York, NY, USA","institution_ids":["https://openalex.org/I4210145812","https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085527072","display_name":"Michele Ceccarelli","orcid":"https://orcid.org/0000-0002-4702-6617"},"institutions":[{"id":"https://openalex.org/I16337185","display_name":"University of Sannio","ror":"https://ror.org/04vc81p87","country_code":"IT","type":"education","lineage":["https://openalex.org/I16337185"]},{"id":"https://openalex.org/I4210115745","display_name":"Biogem","ror":"https://ror.org/01ymr5447","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I2801626668","https://openalex.org/I4210115745"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Michele Ceccarelli","raw_affiliation_strings":["BioGeM s.c.a r.l., Institute of Genetic Research \"Gaetano Salvatore\", Ariano Irpino, (AV), Italy","Department of Science, University of Sannio, Benevento, Italy"],"affiliations":[{"raw_affiliation_string":"BioGeM s.c.a r.l., Institute of Genetic Research \"Gaetano Salvatore\", Ariano Irpino, (AV), Italy","institution_ids":["https://openalex.org/I4210115745"]},{"raw_affiliation_string":"Department of Science, University of Sannio, Benevento, Italy","institution_ids":["https://openalex.org/I16337185"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025973233"],"corresponding_institution_ids":["https://openalex.org/I16337185"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7453,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.71391938,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"14","issue":"S1","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"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/T10885","display_name":"Gene expression and cancer classification","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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9970999956130981,"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/computer-science","display_name":"Computer science","score":0.7035343647003174},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.6709850430488586},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6609240174293518},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6474704742431641},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5796120762825012},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.49706700444221497},{"id":"https://openalex.org/keywords/supervised-learning","display_name":"Supervised learning","score":0.4622404873371124},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3385326862335205},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.2846851348876953}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7035343647003174},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.6709850430488586},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6609240174293518},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6474704742431641},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5796120762825012},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.49706700444221497},{"id":"https://openalex.org/C136389625","wikidata":"https://www.wikidata.org/wiki/Q334384","display_name":"Supervised learning","level":3,"score":0.4622404873371124},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3385326862335205},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2846851348876953}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-14-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s1-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S1-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23368951","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23368951","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2563942","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3548675","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3548675","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3548675","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s1-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S1-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.49000000953674316}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2046673993.pdf","grobid_xml":"https://content.openalex.org/works/W2046673993.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W10719664","https://openalex.org/W22461475","https://openalex.org/W23149702","https://openalex.org/W130536385","https://openalex.org/W154167777","https://openalex.org/W587005977","https://openalex.org/W1481919380","https://openalex.org/W1536636010","https://openalex.org/W1568244992","https://openalex.org/W1570448133","https://openalex.org/W1575352736","https://openalex.org/W1575713778","https://openalex.org/W1581299182","https://openalex.org/W1594223874","https://openalex.org/W1668147540","https://openalex.org/W1861993554","https://openalex.org/W2007471837","https://openalex.org/W2025803032","https://openalex.org/W2044525257","https://openalex.org/W2046635524","https://openalex.org/W2050871273","https://openalex.org/W2053707267","https://openalex.org/W2054286320","https://openalex.org/W2056939983","https://openalex.org/W2056983531","https://openalex.org/W2061425021","https://openalex.org/W2084018951","https://openalex.org/W2098664089","https://openalex.org/W2101029276","https://openalex.org/W2107340752","https://openalex.org/W2108421561","https://openalex.org/W2108740562","https://openalex.org/W2109943925","https://openalex.org/W2109972881","https://openalex.org/W2115108153","https://openalex.org/W2119531440","https://openalex.org/W2123958887","https://openalex.org/W2134510195","https://openalex.org/W2135030836","https://openalex.org/W2136362180","https://openalex.org/W2146856779","https://openalex.org/W2156772624","https://openalex.org/W2157963336","https://openalex.org/W2160095931","https://openalex.org/W2162422091","https://openalex.org/W2163296115","https://openalex.org/W2165604360","https://openalex.org/W2531563875","https://openalex.org/W2911834049","https://openalex.org/W3099289621","https://openalex.org/W4248050719"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W4321636575","https://openalex.org/W2357796999","https://openalex.org/W2045526782","https://openalex.org/W2741131631","https://openalex.org/W1986418932","https://openalex.org/W1984019423","https://openalex.org/W2996519767","https://openalex.org/W4389256085","https://openalex.org/W4285328440"],"abstract_inverted_index":{"The":[0],"availability":[1],"of":[2,14,22,36,45],"only":[3],"positive":[4],"examples":[5],"in":[6,29,42],"learning":[7],"transcriptional":[8,47],"relationships":[9],"negatively":[10],"affects":[11],"the":[12,20,34,43],"performance":[13,35],"supervised":[15],"classifiers.":[16],"We":[17],"show":[18],"that":[19],"selection":[21],"reliable":[23],"negative":[24],"examples,":[25],"a":[26],"practice":[27],"adopted":[28],"text":[30],"mining":[31],"approaches,":[32],"improves":[33],"such":[37],"classifiers":[38],"opening":[39],"new":[40,46],"perspectives":[41],"identification":[44],"targets.":[48]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-03-17T17:19:04.345684","created_date":"2025-10-10T00:00:00"}
