{"id":"https://openalex.org/W7225635381","doi":"https://doi.org/10.1002/imo2.70154","title":"A two\u2010stage framework for generalized eukaryotic promoter prediction and activity classification","display_name":"A two\u2010stage framework for generalized eukaryotic promoter prediction and activity classification","publication_year":2026,"publication_date":"2026-11-08","ids":{"openalex":"https://openalex.org/W7225635381","doi":"https://doi.org/10.1002/imo2.70154"},"language":"en","primary_location":{"id":"doi:10.1002/imo2.70154","doi":"https://doi.org/10.1002/imo2.70154","is_oa":true,"landing_page_url":"https://doi.org/10.1002/imo2.70154","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/imo2.70154","source":{"id":"https://openalex.org/S4404660751","display_name":"iMetaOmics.","issn_l":"2996-9506","issn":["2996-9506","2996-9514"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"iMetaOmics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/imo2.70154","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015921948","display_name":"Muhammad Shujaat","orcid":"https://orcid.org/0000-0003-1752-3927","observed_orcids":["https://orcid.org/0000-0003-1752-3927"]},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Muhammad Shujaat","raw_affiliation_strings":["College of Civil and Transportation Engineering Shenzhen University Shenzhen China","Institute for Advanced Study Shenzhen University Shenzhen China"],"raw_orcid":"https://orcid.org/0000-0003-1752-3927","affiliations":[{"raw_affiliation_string":"College of Civil and Transportation Engineering Shenzhen University Shenzhen China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"Institute for Advanced Study Shenzhen University Shenzhen China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053610759","display_name":"Shi-Qing Mao","orcid":"https://orcid.org/0000-0001-9902-0199","observed_orcids":["https://orcid.org/0000-0001-9902-0199"]},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shi\u2010Qing Mao","raw_affiliation_strings":["Institute for Advanced Study Shenzhen University Shenzhen China"],"raw_orcid":"https://orcid.org/0000-0001-9902-0199","affiliations":[{"raw_affiliation_string":"Institute for Advanced Study Shenzhen University Shenzhen China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053610759"],"corresponding_institution_ids":["https://openalex.org/I180726961"],"apc_list":{"value":0,"currency":"USD","value_usd":0},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9667999744415283,"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":0.9667999744415283,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.02250000089406967,"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":0.002899999963119626,"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/cage","display_name":"CAGE","score":0.7350000143051147},{"id":"https://openalex.org/keywords/fantom5","display_name":"FANTOM5","score":0.9779999852180481},{"id":"https://openalex.org/keywords/sequence-patterns","display_name":"sequence patterns","score":0.4320000112056732},{"id":"https://openalex.org/keywords/cross-species-transmission","display_name":"interspecies transmission","score":0.5350000262260437},{"id":"https://openalex.org/keywords/vertebrates","display_name":"vertebrates","score":0.5770000219345093},{"id":"https://openalex.org/keywords/shap","display_name":"SHAP","score":0.7229999899864197},{"id":"https://openalex.org/keywords/convolutional-neural-networks","display_name":"convolutional neural networks","score":0.6890000104904175},{"id":"https://openalex.org/keywords/web-server","display_name":"web server","score":0.7260000109672546}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6287000179290771},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6189000010490417},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5730999708175659},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.5648999810218811},{"id":"https://openalex.org/C2775871807","wikidata":"https://www.wikidata.org/wiki/Q24963883","display_name":"Promoter activity","level":5,"score":0.5537999868392944},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.492000013589859},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.48899999260902405},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4546000063419342},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4544000029563904},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4302000105381012},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4262999892234802},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3950999975204468},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3831999897956848},{"id":"https://openalex.org/C2992339755","wikidata":"https://www.wikidata.org/wiki/Q3817769","display_name":"Transcriptional activity","level":4,"score":0.3594000041484833},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.34310001134872437},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3407000005245209},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.33739998936653137},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.33480000495910645},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.3043000102043152},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.29600000381469727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2957000136375427},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.28790000081062317},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2865999937057495},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.28040000796318054},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2759000062942505},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.27219998836517334},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2712000012397766},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2709999978542328},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.2648000121116638},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.2621999979019165},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.26089999079704285},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.25529998540878296},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.2547000050544739}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/imo2.70154","doi":"https://doi.org/10.1002/imo2.70154","is_oa":true,"landing_page_url":"https://doi.org/10.1002/imo2.70154","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/imo2.70154","source":{"id":"https://openalex.org/S4404660751","display_name":"iMetaOmics.","issn_l":"2996-9506","issn":["2996-9506","2996-9514"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"iMetaOmics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1002/imo2.70154","doi":"https://doi.org/10.1002/imo2.70154","is_oa":true,"landing_page_url":"https://doi.org/10.1002/imo2.70154","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/imo2.70154","source":{"id":"https://openalex.org/S4404660751","display_name":"iMetaOmics.","issn_l":"2996-9506","issn":["2996-9506","2996-9514"],"is_oa":true,"is_in_doaj":true,"is_core":false,"listed_in":["doaj"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"iMetaOmics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225635381.pdf","grobid_xml":"https://content.openalex.org/works/W7225635381.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1570336400","https://openalex.org/W2148114118","https://openalex.org/W2170747616","https://openalex.org/W2460139914","https://openalex.org/W2754289562","https://openalex.org/W2905321002","https://openalex.org/W2932524182","https://openalex.org/W2963739921","https://openalex.org/W3117695338","https://openalex.org/W3190940513","https://openalex.org/W4285405240","https://openalex.org/W4297257598","https://openalex.org/W4308336505","https://openalex.org/W4399153512","https://openalex.org/W4403845965"],"related_works":["https://openalex.org/W4323664198","https://openalex.org/W1981800986","https://openalex.org/W1976882280","https://openalex.org/W2387088330","https://openalex.org/W4384299481","https://openalex.org/W4221138063","https://openalex.org/W2949453554","https://openalex.org/W2047902224","https://openalex.org/W4229041858","https://openalex.org/W4200176031"],"abstract_inverted_index":{"Promoter-Net":[0],"performs":[1],"generalized":[2],"eukaryotic":[3,19],"promoter":[4,8,92],"recognition":[5],"and":[6,21,50,65,82,93],"species-contextual":[7],"activity":[9,46,94],"classification.":[10],"Stage":[11,29],"1":[12],"learns":[13],"promoter-associated":[14],"sequence":[15,89],"patterns":[16],"across":[17],"multiple":[18],"species":[20],"is":[22,99],"evaluated":[23],"on":[24],"an":[25],"entirely":[26],"withheld":[27],"species.":[28],"2":[30],"uses":[31],"Functional":[32],"Annotation":[33],"of":[34,42],"the":[35],"Mammalian":[36],"Genome":[37],"5":[38],"(FANTOM5)":[39],"Cap":[40],"Analysis":[41],"Gene":[43],"Expression":[44],"(CAGE)":[45],"to":[47,91],"distinguish":[48],"high-":[49],"low-activity":[51],"promoters":[52],"within":[53],"six":[54],"vertebrates.":[55],"Cross-validation,":[56],"pooled":[57],"versus":[58],"species-specific":[59],"testing,":[60],"sequence-diversity":[61],"analyses,":[62],"motif":[63],"enrichment,":[64],"surrogate-convolutional":[66],"neural":[67],"network":[68],"(CNN)":[69],"SHapley":[70],"Additive":[71],"exPlanations":[72],"(SHAP)":[73],"interpretation":[74],"support":[75],"model":[76],"evaluation.":[77],"The":[78,96],"public":[79],"web":[80,97],"server":[81,98],"repository":[83],"provide":[84],"a":[85],"reproducible":[86],"workflow":[87],"from":[88],"input":[90],"prediction.":[95],"available":[100],"at":[101],"https://promoter-prediction-app.onrender.com/":[102]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-10T00:00:00"}