{"id":"https://openalex.org/W2903713057","doi":"https://doi.org/10.1016/j.gpb.2018.05.003","title":"TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers","display_name":"TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers","publication_year":2018,"publication_date":"2018-10-01","ids":{"openalex":"https://openalex.org/W2903713057","doi":"https://doi.org/10.1016/j.gpb.2018.05.003","mag":"2903713057","pmid":"https://pubmed.ncbi.nlm.nih.gov/30578915"},"language":"en","primary_location":{"id":"doi:10.1016/j.gpb.2018.05.003","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2018.05.003","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.gpb.2018.05.003","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064001499","display_name":"Dimitrios Kleftogiannis","orcid":"https://orcid.org/0000-0003-1086-821X"},"institutions":[{"id":"https://openalex.org/I142947616","display_name":"Institute of Cancer Research","ror":"https://ror.org/043jzw605","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I142947616"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Dimitrios Kleftogiannis","raw_affiliation_strings":["Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research (ICR) , London, SM2 5NG , United Kingdom"],"affiliations":[{"raw_affiliation_string":"Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research (ICR) , London, SM2 5NG , United Kingdom","institution_ids":["https://openalex.org/I142947616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036736055","display_name":"Haitham Ashoor","orcid":"https://orcid.org/0000-0003-2527-0317"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haitham Ashoor","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine , Farmington, CT, 06032 , USA"],"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine , Farmington, CT, 06032 , USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055569646","display_name":"Vladimir B. Baji\u0107","orcid":"https://orcid.org/0000-0001-5435-4750"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Vladimir B. Bajic","raw_affiliation_strings":["Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal, 23955-6900 , Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST) , Thuwal, 23955-6900 , Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5055569646"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":0.1838,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.53944808,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"16","issue":"5","first_page":"332","last_page":"341"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9979000091552734,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9979000091552734,"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":0.9965999722480774,"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"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9872999787330627,"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/motif","display_name":"Motif (music)","score":0.7535098791122437},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.7507225275039673},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6617941856384277},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4630705416202545},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.42474937438964844},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3919890224933624},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17787763476371765},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09492117166519165},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.05347058176994324}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7535098791122437},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.7507225275039673},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6617941856384277},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4630705416202545},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.42474937438964844},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3919890224933624},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17787763476371765},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09492117166519165},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.05347058176994324},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1016/j.gpb.2018.05.003","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2018.05.003","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30578915","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30578915","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:a085184233854093b739c01d3764615f","is_oa":true,"landing_page_url":"https://doaj.org/article/a085184233854093b739c01d3764615f","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Genomics, Proteomics & Bioinformatics, Vol 16, Iss 5, Pp 332-341 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5362673","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6364045","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:6364045","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6364045","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":"Genomics Proteomics Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/630363","is_oa":true,"landing_page_url":"http://hdl.handle.net/10754/630363","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"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":"Article"}],"best_oa_location":{"id":"doi:10.1016/j.gpb.2018.05.003","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2018.05.003","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G1615897265","display_name":null,"funder_award_id":"BAS/1/1606-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1965335252","https://openalex.org/W1987523347","https://openalex.org/W1991740019","https://openalex.org/W1995837988","https://openalex.org/W2007694108","https://openalex.org/W2015845481","https://openalex.org/W2016015848","https://openalex.org/W2020046094","https://openalex.org/W2046240326","https://openalex.org/W2046842005","https://openalex.org/W2067831935","https://openalex.org/W2073700708","https://openalex.org/W2077038036","https://openalex.org/W2094468530","https://openalex.org/W2098740506","https://openalex.org/W2105081948","https://openalex.org/W2118646732","https://openalex.org/W2119387367","https://openalex.org/W2119419044","https://openalex.org/W2120515362","https://openalex.org/W2128817132","https://openalex.org/W2135993011","https://openalex.org/W2137704220","https://openalex.org/W2140240158","https://openalex.org/W2146543014","https://openalex.org/W2150360013","https://openalex.org/W2154053567","https://openalex.org/W2154854793","https://openalex.org/W2167331352","https://openalex.org/W2169819154","https://openalex.org/W2183523328","https://openalex.org/W2212528563","https://openalex.org/W2281170636","https://openalex.org/W2512588567","https://openalex.org/W2535173298","https://openalex.org/W2545093874","https://openalex.org/W2593488635","https://openalex.org/W2951461859","https://openalex.org/W4251988601","https://openalex.org/W6729220679","https://openalex.org/W6833780757"],"related_works":["https://openalex.org/W2152841149","https://openalex.org/W2586783543","https://openalex.org/W2073661767","https://openalex.org/W4387598842","https://openalex.org/W2143211236","https://openalex.org/W2973036402","https://openalex.org/W3204573466","https://openalex.org/W4294190570","https://openalex.org/W4327913206","https://openalex.org/W4280563114"],"abstract_inverted_index":{"In":[0],"mammalian":[1],"cells,":[2],"transcribed":[3,158,166],"enhancers":[4,37],"(TrEns)":[5],"play":[6],"important":[7],"roles":[8],"in":[9,21,63,134,159,167],"the":[10,27,33,59,114,144],"initiation":[11],"of":[12,17,26,36,48,91,105,129,149,155,179],"gene":[13,18],"expression":[14,19],"and":[15,122,185],"maintenance":[16],"levels":[20],"a":[22,45,64,74,94,102],"spatiotemporal":[23],"manner.":[24],"One":[25],"most":[28],"challenging":[29],"questions":[30],"is":[31,143],"how":[32],"genomic":[34],"characteristics":[35,51],"relate":[38],"to":[39,100,146],"enhancer":[40,49],"activities.":[41],"To":[42,68],"date,":[43],"only":[44],"limited":[46],"number":[47],"sequence":[50],"have":[52],"been":[53],"investigated,":[54],"leaving":[55],"space":[56],"for":[57,108],"exploring":[58],"enhancers'":[60,180],"DNA":[61],"code":[62],"more":[65],"systematic":[66],"way.":[67],"address":[69],"this":[70],"problem,":[71],"we":[72,97,172],"developed":[73],"novel":[75],"computational":[76],"framework,":[77],"Transcribed":[78],"Enhancer":[79],"Landscape":[80],"Search":[81],"(TELS),":[82],"aimed":[83],"at":[84,190],"identifying":[85],"predictive":[86,178],"cell":[87,138,161,169],"type/tissue-specific":[88,139],"motif":[89,106,176],"signatures":[90,107,177],"TrEns.":[92,140],"As":[93],"case":[95],"study,":[96],"used":[98],"TELS":[99,183],"compile":[101],"comprehensive":[103],"catalog":[104],"all":[109],"known":[110],"TrEns":[111,156,164],"identified":[112],"by":[113],"FANTOM5":[115],"consortium":[116],"across":[117],"112":[118],"human":[119],"primary":[120],"cells":[121],"tissues.":[123],"Our":[124,141],"results":[125],"confirm":[126],"that":[127,151],"combinations":[128,148],"different":[130,168],"short":[131],"motifs":[132,150],"characterize":[133],"an":[135],"optimized":[136],"manner":[137],"study":[142],"first":[145],"report":[147,174],"maximize":[152],"classification":[153],"performance":[154],"exclusively":[157,165],"one":[160],"type/tissue":[162],"from":[163],"types/tissues.":[170],"Moreover,":[171],"also":[173],"31":[175],"broad":[181],"activity.":[182],"codes":[184],"material":[186],"are":[187],"publicly":[188],"available":[189],"http://www.cbrc.kaust.edu.sa/TELS.":[191]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-20T23:13:51.555489","created_date":"2025-10-10T00:00:00"}