{"id":"https://openalex.org/W4200363822","doi":"https://doi.org/10.1093/bib/bbab525","title":"A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape","display_name":"A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape","publication_year":2021,"publication_date":"2021-11-15","ids":{"openalex":"https://openalex.org/W4200363822","doi":"https://doi.org/10.1093/bib/bbab525","pmid":"https://pubmed.ncbi.nlm.nih.gov/34929739"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab525","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab525","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5100741917","display_name":"Yongqing Zhang","orcid":"https://orcid.org/0000-0003-3422-8305"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]},{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongqing Zhang","raw_affiliation_strings":["School of Computer Science and Engineering, University of Electronic Science and Technology of China, 611731, Chengdu, China","School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, University of Electronic Science and Technology of China, 611731, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]},{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115602493","display_name":"Zixuan Wang","orcid":"https://orcid.org/0009-0007-6723-1822"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixuan Wang","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050258340","display_name":"Yuanqi Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanqi Zeng","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100420960","display_name":"Yuhang Liu","orcid":"https://orcid.org/0000-0002-3445-0304"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhang Liu","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017707130","display_name":"Shuwen Xiong","orcid":"https://orcid.org/0000-0002-0935-9787"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuwen Xiong","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045796220","display_name":"Maocheng Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Maocheng Wang","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110286429","display_name":"Jiliu Zhou","orcid":"https://orcid.org/0000-0002-4052-7638"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiliu Zhou","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017426085","display_name":"Quan Zou","orcid":"https://orcid.org/0000-0001-6406-1142"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Quan Zou","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 610054, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 610054, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017426085"],"corresponding_institution_ids":["https://openalex.org/I150229711"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.0927,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.93053639,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"23","issue":"1","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9941999912261963,"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":0.9937999844551086,"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/interpretability","display_name":"Interpretability","score":0.7084482312202454},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.705898642539978},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6621758937835693},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6615310907363892},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5361153483390808},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4661020040512085},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4554665684700012},{"id":"https://openalex.org/keywords/convolution","display_name":"Convolution (computer science)","score":0.4521869719028473},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.42942702770233154},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.40500926971435547},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3940108120441437},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39330220222473145},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39288127422332764},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23352009057998657},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21987849473953247},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.19731441140174866},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1834060251712799},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.15325278043746948},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07687890529632568}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7084482312202454},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.705898642539978},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6621758937835693},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6615310907363892},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5361153483390808},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4661020040512085},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4554665684700012},{"id":"https://openalex.org/C45347329","wikidata":"https://www.wikidata.org/wiki/Q5166604","display_name":"Convolution (computer science)","level":3,"score":0.4521869719028473},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.42942702770233154},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.40500926971435547},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3940108120441437},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39330220222473145},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39288127422332764},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23352009057998657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21987849473953247},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.19731441140174866},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1834060251712799},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.15325278043746948},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07687890529632568}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab525","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab525","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34929739","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34929739","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1674180717","display_name":null,"funder_award_id":"61922020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5418740185","display_name":null,"funder_award_id":"2017M612948","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G8147465199","display_name":null,"funder_award_id":"61702058","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1990893875","https://openalex.org/W2008041603","https://openalex.org/W2022736304","https://openalex.org/W2060075610","https://openalex.org/W2078034709","https://openalex.org/W2082500271","https://openalex.org/W2129795133","https://openalex.org/W2167672183","https://openalex.org/W2198606573","https://openalex.org/W2330303612","https://openalex.org/W2336509392","https://openalex.org/W2509668036","https://openalex.org/W2602000457","https://openalex.org/W2737959952","https://openalex.org/W2739636023","https://openalex.org/W2783734371","https://openalex.org/W2785792383","https://openalex.org/W2789652838","https://openalex.org/W2795716241","https://openalex.org/W2885815722","https://openalex.org/W2896262061","https://openalex.org/W2901303766","https://openalex.org/W2909622349","https://openalex.org/W2910211803","https://openalex.org/W2943386850","https://openalex.org/W2966164316","https://openalex.org/W2966369432","https://openalex.org/W2980975636","https://openalex.org/W3041434156","https://openalex.org/W3090491025","https://openalex.org/W3102474308","https://openalex.org/W3104774463","https://openalex.org/W3113034426","https://openalex.org/W3121554924","https://openalex.org/W3122486793","https://openalex.org/W3130819465","https://openalex.org/W3130970563","https://openalex.org/W3149911829","https://openalex.org/W6631190155","https://openalex.org/W6786075446","https://openalex.org/W7029276679"],"related_works":["https://openalex.org/W2162836426","https://openalex.org/W2734802753","https://openalex.org/W2149312834","https://openalex.org/W3089376739","https://openalex.org/W1534925089","https://openalex.org/W4200283209","https://openalex.org/W2143172590","https://openalex.org/W2294175390","https://openalex.org/W311334411","https://openalex.org/W3121554924"],"abstract_inverted_index":{"The":[0,168],"discovery":[1],"of":[2,109,123,150,155,171],"putative":[3,85],"transcription":[4,139],"factor":[5],"binding":[6,15],"sites":[7],"(TFBSs)":[8],"is":[9],"important":[10],"for":[11,30,82,113,138],"understanding":[12],"the":[13,46,107,117,121,135,146,153],"underlying":[14],"mechanism":[16],"and":[17,33,53,56,61,77,105,162],"cellular":[18],"functions.":[19],"Recently,":[20],"many":[21],"computational":[22],"methods":[23,41,101],"have":[24,57],"been":[25],"proposed":[26],"to":[27,43,126],"jointly":[28],"account":[29],"DNA":[31],"sequence":[32,52,161],"shape":[34,54,131,163],"properties":[35],"in":[36,59,102],"TFBSs":[37,127],"prediction.":[38],"However,":[39],"these":[40],"fail":[42],"fully":[44],"utilize":[45],"latent":[47],"features":[48,132],"derived":[49],"from":[50],"both":[51,160],"profiles":[55],"limitation":[58],"interpretability":[60],"knowledge":[62],"discovery.":[63],"To":[64],"this":[65],"end,":[66],"we":[67],"present":[68],"a":[69],"novel":[70],"Deep":[71],"Convolution":[72],"Attention":[73],"network":[74],"combining":[75],"Sequence":[76],"Shape,":[78],"dubbed":[79],"as":[80],"D-SSCA,":[81],"precisely":[83],"predicting":[84,103],"TFBSs.":[86],"Experiments":[87],"conducted":[88],"on":[89],"165":[90],"ENCODE":[91],"ChIP-seq":[92],"datasets":[93],"reveal":[94],"that":[95,130],"D-SSCA":[96,143,172],"significantly":[97],"outperforms":[98],"several":[99],"state-of-the-art":[100],"TFBSs,":[104,151],"justify":[106],"utility":[108],"channel":[110],"attention":[111],"module":[112],"feature":[114],"refinements.":[115],"Besides,":[116],"thorough":[118],"analysis":[119],"about":[120],"contribution":[122],"five":[124],"shapes":[125],"prediction":[128,149],"demonstrates":[129],"can":[133,144,173],"improve":[134],"predictive":[136],"power":[137],"factors-DNA":[140],"binding.":[141],"Furthermore,":[142],"realize":[145],"cross-cell":[147],"line":[148],"indicating":[152],"occupancy":[154],"common":[156],"interplay":[157],"patterns":[158],"concerning":[159],"across":[164],"various":[165],"cell":[166],"lines.":[167],"source":[169],"code":[170],"be":[174],"found":[175],"at":[176],"https://github.com/MoonLord0525/.":[177]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":8}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
