{"id":"https://openalex.org/W4200328078","doi":"https://doi.org/10.1093/bioinformatics/btab815","title":"Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions","display_name":"Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions","publication_year":2021,"publication_date":"2021-11-30","ids":{"openalex":"https://openalex.org/W4200328078","doi":"https://doi.org/10.1093/bioinformatics/btab815","pmid":"https://pubmed.ncbi.nlm.nih.gov/34864898"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab815","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab815","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087844608","display_name":"Michele Leone","orcid":"https://orcid.org/0000-0002-2618-5985"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Michele Leone","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano , 20133 Milan, Italy"],"raw_orcid":"https://orcid.org/0000-0002-2618-5985","affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano , 20133 Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007401420","display_name":"Eugenia Galeota","orcid":"https://orcid.org/0000-0002-4413-7389"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Eugenia Galeota","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , 20139 Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , 20139 Milan, Italy","institution_ids":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085346183","display_name":"Marco Masseroli","orcid":"https://orcid.org/0000-0003-2574-1174"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Masseroli","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano , 20133 Milan, Italy"],"raw_orcid":"https://orcid.org/0000-0003-2574-1174","affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano , 20133 Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012974572","display_name":"Mattia Pelizzola","orcid":"https://orcid.org/0000-0001-6672-9636"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mattia Pelizzola","raw_affiliation_strings":["Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , 20139 Milan, Italy"],"raw_orcid":"https://orcid.org/0000-0001-6672-9636","affiliations":[{"raw_affiliation_string":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , 20139 Milan, Italy","institution_ids":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5087844608"],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":null,"fwci":0.0746,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.42047222,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"38","issue":"5","first_page":"1183","last_page":"1190"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5188999772071838,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5188999772071838,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.18029999732971191,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.10980000346899033,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.7712541818618774},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.617362380027771},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5523194670677185},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5476244688034058},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5175237655639648},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4811647832393646},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39280349016189575},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3546794652938843},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33744168281555176},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24397894740104675},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16486859321594238}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7712541818618774},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.617362380027771},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5523194670677185},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5476244688034058},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5175237655639648},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4811647832393646},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39280349016189575},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3546794652938843},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33744168281555176},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24397894740104675},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16486859321594238},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab815","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab815","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34864898","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34864898","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":"Journal Article"},{"id":"pmh:oai:boa.unimib.it:10281/446759","is_oa":false,"landing_page_url":"https://hdl.handle.net/10281/446759","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:re.public.polimi.it:11311/1203856","is_oa":false,"landing_page_url":"http://hdl.handle.net/11311/1203856","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W151377110","https://openalex.org/W1506343731","https://openalex.org/W1730959447","https://openalex.org/W1974604287","https://openalex.org/W1974673798","https://openalex.org/W1979594866","https://openalex.org/W1981030303","https://openalex.org/W1986711353","https://openalex.org/W2001502812","https://openalex.org/W2022936129","https://openalex.org/W2084160423","https://openalex.org/W2100471807","https://openalex.org/W2101696428","https://openalex.org/W2113142309","https://openalex.org/W2116041602","https://openalex.org/W2118258530","https://openalex.org/W2120358246","https://openalex.org/W2121784992","https://openalex.org/W2124045889","https://openalex.org/W2128016314","https://openalex.org/W2133452708","https://openalex.org/W2142680014","https://openalex.org/W2146339031","https://openalex.org/W2147763010","https://openalex.org/W2153110406","https://openalex.org/W2163353298","https://openalex.org/W2349918789","https://openalex.org/W2409168136","https://openalex.org/W2462007197","https://openalex.org/W2544405043","https://openalex.org/W2584394140","https://openalex.org/W2604812607","https://openalex.org/W2767826728","https://openalex.org/W2768013244","https://openalex.org/W2776802713","https://openalex.org/W2796142446","https://openalex.org/W2901027836","https://openalex.org/W2923931114","https://openalex.org/W2941930792","https://openalex.org/W2950691269","https://openalex.org/W2962172119","https://openalex.org/W2982420272","https://openalex.org/W2984636935","https://openalex.org/W3000297876","https://openalex.org/W3003192283","https://openalex.org/W3003289036","https://openalex.org/W3009888830","https://openalex.org/W3088585127","https://openalex.org/W3090120032","https://openalex.org/W3124680305","https://openalex.org/W4233036449","https://openalex.org/W4245561281","https://openalex.org/W6606062967","https://openalex.org/W6714339427","https://openalex.org/W6806115372"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2341492732","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W4287027380","https://openalex.org/W1699080303"],"abstract_inverted_index":{"MOTIVATION:":[0],"Approaches":[1],"such":[2],"as":[3],"chromatin":[4],"immunoprecipitation":[5],"followed":[6],"by":[7,135,183],"sequencing":[8],"(ChIP-seq)":[9],"represent":[10],"the":[11,14,57,77,123,126,132,173,201],"standard":[12],"for":[13,125,207],"identification":[15],"of":[16,19,30,37,62,76,116,138,162,187,200],"binding":[17],"sites":[18],"DNA-associated":[20],"proteins,":[21],"including":[22],"transcription":[23],"factors":[24],"and":[25,44,59,73,79,118,144],"histone":[26],"marks.":[27],"Public":[28],"repositories":[29],"omics":[31,98],"data":[32,84,89,99,215],"contain":[33],"a":[34,51,163],"huge":[35],"number":[36],"experimental":[38],"ChIP-seq":[39,83],"data,":[40],"but":[41,81],"their":[42,169],"reuse":[43],"integrative":[45],"analysis":[46],"across":[47],"multiple":[48],"conditions":[49],"remain":[50],"daunting":[52],"task.":[53],"RESULTS:":[54],"We":[55],"present":[56],"Combinatorial":[58],"Semantic":[60],"Analysis":[61],"Functional":[63],"Elements":[64],"(CombSAFE),":[65],"an":[66],"efficient":[67],"computational":[68],"method":[69],"able":[70],"to":[71,148,167],"integrate":[72],"take":[74],"advantage":[75],"valuable":[78],"numerous,":[80],"heterogeneous,":[82],"publicly":[85],"available":[86,206,217],"in":[87,190],"big":[88],"repositories.":[90],"Leveraging":[91],"natural":[92],"language":[93],"processing":[94],"techniques,":[95],"it":[96,113,157],"integrates":[97],"samples":[100],"with":[101,140,154],"semantic":[102,175],"annotations":[103],"from":[104],"selected":[105],"biomedical":[106],"ontologies;":[107],"then,":[108],"using":[109],"hidden":[110],"Markov":[111],"models,":[112],"identifies":[114],"combinations":[115,186],"static":[117],"dynamic":[119],"functional":[120,142,160,188],"elements":[121,143,189],"throughout":[122,172],"genome":[124],"corresponding":[127],"samples.":[128],"CombSAFE":[129,202],"allows":[130,158],"analyzing":[131],"whole":[133],"genome,":[134],"clustering":[136],"patterns":[137],"regions":[139],"similar":[141],"through":[145],"enrichment":[146],"analyses":[147],"discover":[149],"ontological":[150],"terms":[151],"significantly":[152],"associated":[153],"them.":[155],"Moreover,":[156],"comparing":[159],"states":[161],"specific":[164],"genomic":[165],"region":[166],"analyze":[168],"different":[170,191],"behavior":[171],"various":[174],"annotations.":[176],"Such":[177],"findings":[178],"can":[179],"provide":[180],"novel":[181],"insights":[182],"identifying":[184],"unexpected":[185],"biological":[192],"conditions.":[193],"AVAILABILITY":[194],"AND":[195],"IMPLEMENTATION:":[196],"The":[197],"Python":[198],"implementation":[199],"pipeline":[203],"is":[204],"freely":[205],"non-commercial":[208],"use":[209],"at:":[210],"https://github.com/DEIB-GECO/CombSAFE.":[211],"SUPPLEMENTARY":[212],"INFORMATION:":[213],"Supplementary":[214],"are":[216],"at":[218],"Bioinformatics":[219],"online.":[220]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}