{"id":"https://openalex.org/W2906979530","doi":"https://doi.org/10.1142/s0129054118430074","title":"Identifying Potential Regulatory Elements by Transcription Factor Binding Site Alignment Using Partial Order Graphs","display_name":"Identifying Potential Regulatory Elements by Transcription Factor Binding Site Alignment Using Partial Order Graphs","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2906979530","doi":"https://doi.org/10.1142/s0129054118430074","mag":"2906979530"},"language":"en","primary_location":{"id":"doi:10.1142/s0129054118430074","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0129054118430074","pdf_url":null,"source":{"id":"https://openalex.org/S68047077","display_name":"International Journal of Foundations of Computer Science","issn_l":"0129-0541","issn":["0129-0541","1793-6373"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Foundations of Computer Science","raw_type":"journal-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/A5031586485","display_name":"Maryam Abdollahyan","orcid":"https://orcid.org/0000-0001-9858-5059"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Maryam Abdollahyan","raw_affiliation_strings":["School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom","institution_ids":["https://openalex.org/I166337079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031649400","display_name":"Greg Elgar","orcid":"https://orcid.org/0000-0001-7323-1596"},"institutions":[{"id":"https://openalex.org/I2801081054","display_name":"The Francis Crick Institute","ror":"https://ror.org/04tnbqb63","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801081054"]},{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Greg Elgar","raw_affiliation_strings":["Regulatory Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Regulatory Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom","institution_ids":["https://openalex.org/I2801081054","https://openalex.org/I4210151791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091487258","display_name":"Fabrizio Smeraldi","orcid":"https://orcid.org/0000-0002-0057-8940"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fabrizio Smeraldi","raw_affiliation_strings":["School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom","institution_ids":["https://openalex.org/I166337079"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5031586485"],"corresponding_institution_ids":["https://openalex.org/I166337079"],"apc_list":null,"apc_paid":null,"fwci":0.0928,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.49891961,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"29","issue":"08","first_page":"1345","last_page":"1354"},"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":0.9980000257492065,"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":0.9965999722480774,"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/dna-binding-site","display_name":"DNA binding site","score":0.7231072783470154},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.5518833994865417},{"id":"https://openalex.org/keywords/hox-gene","display_name":"Hox gene","score":0.5219333171844482},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5197957754135132},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.5110474824905396},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.49039649963378906},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4819364547729492},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47678637504577637},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4316246509552002},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3375546932220459},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31110262870788574},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28168684244155884},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.23264864087104797}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.7231072783470154},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.5518833994865417},{"id":"https://openalex.org/C111039654","wikidata":"https://www.wikidata.org/wiki/Q253149","display_name":"Hox gene","level":4,"score":0.5219333171844482},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5197957754135132},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.5110474824905396},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.49039649963378906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4819364547729492},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47678637504577637},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4316246509552002},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3375546932220459},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31110262870788574},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28168684244155884},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.23264864087104797},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1142/s0129054118430074","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0129054118430074","pdf_url":null,"source":{"id":"https://openalex.org/S68047077","display_name":"International Journal of Foundations of Computer Science","issn_l":"0129-0541","issn":["0129-0541","1793-6373"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Foundations of Computer Science","raw_type":"journal-article"},{"id":"pmh:oai:qmro.qmul.ac.uk:123456789/54943","is_oa":false,"landing_page_url":"https://qmro.qmul.ac.uk/handle/123456789/54943","pdf_url":null,"source":{"id":"https://openalex.org/S4306400530","display_name":"Queen Mary Research Online (Queen Mary University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I166337079","host_organization_name":"Queen Mary University of London","host_organization_lineage":["https://openalex.org/I166337079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1554931738","https://openalex.org/W1964733653","https://openalex.org/W1999928217","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2088980001","https://openalex.org/W2089968837","https://openalex.org/W2109533092","https://openalex.org/W2117549173","https://openalex.org/W2140952049","https://openalex.org/W2142113273","https://openalex.org/W2143228020","https://openalex.org/W2150612336","https://openalex.org/W2151845703","https://openalex.org/W2157679927","https://openalex.org/W2162923930","https://openalex.org/W2165228646","https://openalex.org/W2165735666","https://openalex.org/W2169056802","https://openalex.org/W2287824100","https://openalex.org/W4240861547"],"related_works":["https://openalex.org/W4221130891","https://openalex.org/W2131240292","https://openalex.org/W2070964166","https://openalex.org/W2167063030","https://openalex.org/W2615895636","https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2134434282","https://openalex.org/W3048510984","https://openalex.org/W3037778845"],"abstract_inverted_index":{"Identification":[0],"and":[1,87,121],"functional":[2],"characterization":[3],"of":[4,27,60,63,92,95,107,118],"regulatory":[5,22,34,115],"elements":[6,53],"in":[7,33,49,66,97],"the":[8,25,61,89,98],"human":[9],"genome":[10],"is":[11,24],"a":[12,41,57,67,79,105,114],"challenging":[13],"task.":[14],"A":[15],"sequence":[16,62],"feature":[17],"commonly":[18],"used":[19],"to":[20,44,72,83],"predict":[21],"activity":[23],"co-occurrence":[26],"transcription":[28],"factor":[29],"binding":[30,75,123],"sites":[31],"(TFBSs)":[32],"regions.":[35],"In":[36],"this":[37],"work,":[38],"we":[39],"present":[40],"graph-based":[42],"approach":[43,103],"detect":[45],"frequently":[46],"co-occurring":[47,119],"TFBSs":[48,64,96],"evolutionarily":[50],"conserved":[51],"non-coding":[52],"(CNEs).":[54],"We":[55,77,100],"introduce":[56],"graph":[58],"representation":[59],"identified":[65],"CNE":[68],"that":[69],"allows":[70],"us":[71],"handle":[73],"overlapping":[74],"sites.":[76],"use":[78],"dynamic":[80],"programming":[81],"algorithm":[82],"align":[84],"such":[85],"graphs":[86],"determine":[88],"relative":[90],"enrichment":[91],"short":[93],"sequences":[94],"alignments.":[99],"evaluate":[101],"our":[102],"on":[104],"set":[106],"functionally":[108],"validated":[109],"CNEs.":[110],"Our":[111],"findings":[112],"include":[113],"signature":[116],"composed":[117],"Pbx-Hox":[120],"Meis":[122],"motifs":[124],"associated":[125],"with":[126],"hindbrain":[127],"enhancer":[128],"activity.":[129]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
