{"id":"https://openalex.org/W4396627750","doi":"https://doi.org/10.1093/bib/bbae193","title":"Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation","display_name":"Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation","publication_year":2024,"publication_date":"2024-03-27","ids":{"openalex":"https://openalex.org/W4396627750","doi":"https://doi.org/10.1093/bib/bbae193","pmid":"https://pubmed.ncbi.nlm.nih.gov/38701419"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae193","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae193/57390467/bbae193.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae193/57390467/bbae193.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100616298","display_name":"Guang Yang","orcid":"https://orcid.org/0009-0005-7409-3435"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guang Yang","raw_affiliation_strings":["School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"],"raw_orcid":"https://orcid.org/0009-0005-7409-3435","affiliations":[{"raw_affiliation_string":"School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100402808","display_name":"Jianing Li","orcid":"https://orcid.org/0009-0006-2298-8074"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianing Li","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"],"raw_orcid":"https://orcid.org/0009-0006-2298-8074","affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060611973","display_name":"Jinlu Hu","orcid":"https://orcid.org/0000-0001-6125-0888"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jinlu Hu","raw_affiliation_strings":["School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000609872","display_name":"Jian\u2010Yu Shi","orcid":"https://orcid.org/0000-0002-2303-273X"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jian-Yu Shi","raw_affiliation_strings":["School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China"],"raw_orcid":"https://orcid.org/0000-0002-2303-273X","affiliations":[{"raw_affiliation_string":"School of Life Sciences, Northwestern Polytechnical University , Xi\u2019an, Shaanxi, 710072 , China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000609872","https://openalex.org/A5060611973"],"corresponding_institution_ids":["https://openalex.org/I17145004"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.6795,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.83457665,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"25","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9969000220298767,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9969000220298767,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9948999881744385,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9930999875068665,"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/promoter","display_name":"Promoter","score":0.9391254186630249},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.532968282699585},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41412466764450073},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3528924882411957},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34620600938796997},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3309544026851654},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.30708277225494385},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07257997989654541}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.9391254186630249},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.532968282699585},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41412466764450073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3528924882411957},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34620600938796997},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3309544026851654},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.30708277225494385},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07257997989654541}],"mesh":[{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000458","descriptor_name":"Cyanobacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"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":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"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":3,"locations":[{"id":"doi:10.1093/bib/bbae193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae193","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae193/57390467/bbae193.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38701419","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38701419","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11066903","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11066903","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11066903/pdf/bbae193.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae193","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae193/57390467/bbae193.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3876617407","display_name":null,"funder_award_id":"32270128","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4276050119","display_name":null,"funder_award_id":"62372375","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"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396627750.pdf"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1577822803","https://openalex.org/W1579020777","https://openalex.org/W1712429651","https://openalex.org/W1971456303","https://openalex.org/W1989825955","https://openalex.org/W1993857606","https://openalex.org/W2009659265","https://openalex.org/W2062569898","https://openalex.org/W2081621224","https://openalex.org/W2083122216","https://openalex.org/W2099553504","https://openalex.org/W2156125289","https://openalex.org/W2158266834","https://openalex.org/W2187089797","https://openalex.org/W2526784604","https://openalex.org/W2587688848","https://openalex.org/W2768552973","https://openalex.org/W2781528640","https://openalex.org/W2787044201","https://openalex.org/W2807841289","https://openalex.org/W2892013535","https://openalex.org/W2932524182","https://openalex.org/W2996875961","https://openalex.org/W3002050175","https://openalex.org/W3021404320","https://openalex.org/W3039032764","https://openalex.org/W3103787556","https://openalex.org/W3109860017","https://openalex.org/W3126259666","https://openalex.org/W4205773768","https://openalex.org/W4220853921","https://openalex.org/W4292722723","https://openalex.org/W4297257598","https://openalex.org/W4310208579","https://openalex.org/W4322772387","https://openalex.org/W4323568641","https://openalex.org/W4379984736","https://openalex.org/W4383113554","https://openalex.org/W4387682146","https://openalex.org/W6634533046","https://openalex.org/W6647921801","https://openalex.org/W6652647719","https://openalex.org/W6850370708"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W1969771092","https://openalex.org/W2795723184","https://openalex.org/W2025529750","https://openalex.org/W2891858816","https://openalex.org/W184057646","https://openalex.org/W2042874675","https://openalex.org/W129398428","https://openalex.org/W3212414177","https://openalex.org/W1975811142"],"abstract_inverted_index":{"It":[0],"is":[1,187],"a":[2,10,79,101,123,180],"vital":[3],"step":[4],"to":[5,17,33],"recognize":[6],"cyanobacteria":[7],"promoters":[8,47,94,119],"on":[9,30,107],"genome-wide":[11],"scale.":[12],"Computational":[13],"methods":[14,28,62,143],"are":[15],"promising":[16],"assist":[18],"in":[19],"difficult":[20],"biological":[21],"identification.":[22],"When":[23],"building":[24],"recognition":[25],"models,":[26],"these":[27,73],"rely":[29],"non-promoter":[31,81],"generation":[32,82],"cope":[34],"with":[35,141],"the":[36,42,90,108,115,145,163,166],"lack":[37],"of":[38,126,147,165],"real":[39],"non-promoters.":[40,97],"Nevertheless,":[41],"factitious":[43,91],"significant":[44],"difference":[45,92,117],"between":[46,93,118],"and":[48,95,120,130,133,151,157,169],"non-promoters":[49,121],"causes":[50],"over-optimistic":[51],"prediction.":[52],"Moreover,":[53],"designed":[54],"for":[55],"E.":[56],"coli":[57],"or":[58],"B.":[59],"subtilis,":[60],"existing":[61],"cannot":[63],"uncover":[64],"novel,":[65],"distinct":[66],"motifs":[67],"among":[68],"cyanobacterial":[69,182],"promoters.":[70],"To":[71],"address":[72],"issues,":[74],"this":[75],"work":[76],"first":[77],"proposes":[78],"novel":[80,102,181],"strategy":[83],"called":[84],"phantom":[85,149,177],"sampling,":[86,178],"which":[87,112,186],"can":[88,113],"eliminate":[89],"generated":[96],"Furthermore,":[98],"it":[99],"elaborates":[100],"promoter":[103,183],"prediction":[104],"model":[105],"based":[106],"Siamese":[109,167],"network":[110,168],"(SiamProm),":[111],"amplify":[114],"hidden":[116],"through":[122],"joint":[124],"characterization":[125],"global":[127],"associations,":[128],"upstream":[129],"downstream":[131],"contexts,":[132],"neighboring":[134],"associations":[135],"w.r.t.":[136],"k-mer":[137],"tokens.":[138],"The":[139],"comparison":[140],"state-of-the-art":[142],"demonstrates":[144],"superiority":[146],"our":[148,176],"sampling":[150],"SiamProm.":[152],"Both":[153],"comprehensive":[154],"ablation":[155],"studies":[156],"feature":[158],"space":[159],"illustrations":[160],"also":[161],"validate":[162],"effectiveness":[164],"its":[170],"components.":[171],"More":[172],"importantly,":[173],"SiamProm,":[174],"upon":[175],"finds":[179],"motif":[184],"('GCGATCGC'),":[185],"palindrome-patterned,":[188],"content-conserved,":[189],"but":[190],"position-shifted.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
