{"id":"https://openalex.org/W2142784993","doi":"https://doi.org/10.1093/bioinformatics/btp359","title":"A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles","display_name":"A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles","publication_year":2009,"publication_date":"2009-06-10","ids":{"openalex":"https://openalex.org/W2142784993","doi":"https://doi.org/10.1093/bioinformatics/btp359","mag":"2142784993","pmid":"https://pubmed.ncbi.nlm.nih.gov/19515962"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp359","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp359","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2006/48994606/bioinformatics_25_16_2006.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2006/48994606/bioinformatics_25_16_2006.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076453110","display_name":"Yanglan Gan","orcid":"https://orcid.org/0000-0001-5931-9006"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yanglan Gan","raw_affiliation_strings":["1 Department of Computer Science and Technology, Tongji University, Shanghai 201804, 2School of Computer Science and 3Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Technology, Tongji University, Shanghai 201804, 2School of Computer Science and 3Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China","institution_ids":["https://openalex.org/I116953780","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086316879","display_name":"Jihong Guan","orcid":"https://orcid.org/0000-0003-2313-7635"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jihong Guan","raw_affiliation_strings":["1 Department of Computer Science and Technology, Tongji University, Shanghai 201804, 2School of Computer Science and 3Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Technology, Tongji University, Shanghai 201804, 2School of Computer Science and 3Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China","institution_ids":["https://openalex.org/I116953780","https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017862559","display_name":"Shuigeng Zhou","orcid":"https://orcid.org/0000-0002-1949-2768"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuigeng Zhou","raw_affiliation_strings":["1 Department of Computer Science and Technology, Tongji University, Shanghai 201804, 2School of Computer Science and 3Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Technology, Tongji University, Shanghai 201804, 2School of Computer Science and 3Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China","institution_ids":["https://openalex.org/I116953780","https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076453110"],"corresponding_institution_ids":["https://openalex.org/I116953780","https://openalex.org/I24943067"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3429,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.80291815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"25","issue":"16","first_page":"2006","last_page":"2012"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9976000189781189,"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":0.9976000189781189,"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":0.9944000244140625,"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":0.9937999844551086,"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/promoter","display_name":"Promoter","score":0.9498296976089478},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5038275122642517},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.48461470007896423},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.42617419362068176},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40412548184394836},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3919888138771057},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36222025752067566},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3224978446960449},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15886041522026062}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.9498296976089478},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5038275122642517},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.48461470007896423},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.42617419362068176},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40412548184394836},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3919888138771057},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36222025752067566},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3224978446960449},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15886041522026062},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","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/bioinformatics/btp359","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp359","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2006/48994606/bioinformatics_25_16_2006.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19515962","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19515962","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp359","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp359","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2006/48994606/bioinformatics_25_16_2006.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2687046332","display_name":null,"funder_award_id":"NCET-06","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G269071601","display_name":null,"funder_award_id":"60873070","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4020255992","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7608752429","display_name":null,"funder_award_id":"Talent","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7956262130","display_name":null,"funder_award_id":"NCET-06-0376","funder_id":"https://openalex.org/F4320334924","funder_display_name":"Program for New Century Excellent Talents in University"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320334924","display_name":"Program for New Century Excellent Talents in University","ror":"https://ror.org/01mv9t934"},{"id":"https://openalex.org/F4320335766","display_name":"Shanghai Leading Academic Discipline Project","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2142784993.pdf","grobid_xml":"https://content.openalex.org/works/W2142784993.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W70421016","https://openalex.org/W1970019286","https://openalex.org/W1972875048","https://openalex.org/W1983524036","https://openalex.org/W1996852546","https://openalex.org/W1997481046","https://openalex.org/W2003463914","https://openalex.org/W2009095852","https://openalex.org/W2027349221","https://openalex.org/W2031123552","https://openalex.org/W2040960612","https://openalex.org/W2041804048","https://openalex.org/W2057692691","https://openalex.org/W2083479872","https://openalex.org/W2088306370","https://openalex.org/W2095994064","https://openalex.org/W2097353028","https://openalex.org/W2104730528","https://openalex.org/W2106756765","https://openalex.org/W2107107622","https://openalex.org/W2107578440","https://openalex.org/W2111400482","https://openalex.org/W2113197426","https://openalex.org/W2117179531","https://openalex.org/W2130919037","https://openalex.org/W2137458297","https://openalex.org/W2140948028","https://openalex.org/W2146135000","https://openalex.org/W2147372875","https://openalex.org/W2151029800","https://openalex.org/W2153432157","https://openalex.org/W2164604555","https://openalex.org/W2168783124","https://openalex.org/W2410722745","https://openalex.org/W2740984310","https://openalex.org/W4213167074","https://openalex.org/W6602876734","https://openalex.org/W6664948953"],"related_works":["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/W1975811142","https://openalex.org/W2987420353","https://openalex.org/W1491897707"],"abstract_inverted_index":{"The":[0],"implementation":[1],"of":[2],"the":[3],"program":[4],"PNNP":[5],"is":[6],"available":[7],"at":[8],"http://admis.tongji.edu.cn/Projects/pnnp.aspx.":[9]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
