{"id":"https://openalex.org/W2799487719","doi":"https://doi.org/10.1093/bioinformatics/bty364","title":"Predicting RNA\u2013protein binding sites and motifs through combining local and global deep convolutional neural networks","display_name":"Predicting RNA\u2013protein binding sites and motifs through combining local and global deep convolutional neural networks","publication_year":2018,"publication_date":"2018-05-01","ids":{"openalex":"https://openalex.org/W2799487719","doi":"https://doi.org/10.1093/bioinformatics/bty364","mag":"2799487719","pmid":"https://pubmed.ncbi.nlm.nih.gov/29722865"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty364","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty364","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/20/3427/26024370/bty364.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/34/20/3427/26024370/bty364.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091365447","display_name":"Xiaoyong Pan","orcid":"https://orcid.org/0000-0001-5010-464X"},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Xiaoyong Pan","raw_affiliation_strings":["Department of Medical informatics, Erasmus Medical Center, CE Rotterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Medical informatics, Erasmus Medical Center, CE Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076024045","display_name":"Hong\u2010Bin Shen","orcid":"https://orcid.org/0000-0002-4029-3325"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hong-Bin Shen","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5076024045","https://openalex.org/A5091365447"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I2801952686"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":10.7054,"has_fulltext":true,"cited_by_count":199,"citation_normalized_percentile":{"value":0.98997329,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"34","issue":"20","first_page":"3427","last_page":"3436"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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/T10604","display_name":"RNA Research and Splicing","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","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"}}],"keywords":[{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7614070177078247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5971330404281616},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5521419048309326},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.5436567068099976},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4905704855918884},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.47170424461364746},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3491809368133545},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23482707142829895},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1809883713722229},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11362269520759583}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7614070177078247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5971330404281616},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5521419048309326},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.5436567068099976},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4905704855918884},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.47170424461364746},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3491809368133545},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23482707142829895},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1809883713722229},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11362269520759583}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty364","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty364","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/20/3427/26024370/bty364.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:29722865","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29722865","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},{"id":"pmh:oai:pure.eur.nl:openaire_cris_publications/44819bef-7a28-4669-b1e9-2037e58f86e4","is_oa":false,"landing_page_url":"https://pure.eur.nl/en/publications/44819bef-7a28-4669-b1e9-2037e58f86e4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401266","display_name":"EUR Research Repository (Erasmus University Rotterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I913958620","host_organization_name":"Erasmus University Rotterdam","host_organization_lineage":["https://openalex.org/I913958620"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Pan, X & Shen, HB 2018, 'Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks', Bioinformatics, vol. 34, no. 20, pp. 3427-3436. https://doi.org/10.1093/bioinformatics/bty364","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty364","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty364","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/20/3427/26024370/bty364.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":[],"awards":[{"id":"https://openalex.org/G1893126133","display_name":null,"funder_award_id":"6167128","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/G3067877348","display_name":null,"funder_award_id":"61671288","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/G3549782018","display_name":null,"funder_award_id":"61671288, 91530321, 61603161","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4624300543","display_name":null,"funder_award_id":"61462018","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4864808734","display_name":null,"funder_award_id":"17JC1403500)","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G5167091242","display_name":null,"funder_award_id":"No. 1","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G58300775","display_name":null,"funder_award_id":"61762026","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","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/G6154466079","display_name":null,"funder_award_id":"61725302","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6436593650","display_name":null,"funder_award_id":"17JC1403500","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G6511264965","display_name":null,"funder_award_id":"16JC1404300","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7272398329","display_name":null,"funder_award_id":"616712","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7561120402","display_name":null,"funder_award_id":"17JC1403500","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7706902215","display_name":null,"funder_award_id":"16JC1404300, 17JC1403500","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G7829283020","display_name":null,"funder_award_id":"16JC1404300","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G8179239958","display_name":null,"funder_award_id":"91530321","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8291303907","display_name":null,"funder_award_id":"61725302, 61671288, 91530321, 61603161, 61462018","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8348872005","display_name":null,"funder_award_id":"91530321, 61603161","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8377926864","display_name":null,"funder_award_id":"61603161","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8589789725","display_name":null,"funder_award_id":"No. 16JC1404300","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2799487719.pdf","grobid_xml":"https://content.openalex.org/works/W2799487719.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1494484168","https://openalex.org/W1951403192","https://openalex.org/W1965557392","https://openalex.org/W1980913885","https://openalex.org/W1984574291","https://openalex.org/W1997535872","https://openalex.org/W2038438413","https://openalex.org/W2041440237","https://openalex.org/W2053003053","https://openalex.org/W2063798177","https://openalex.org/W2064675550","https://openalex.org/W2068205681","https://openalex.org/W2073733397","https://openalex.org/W2073858449","https://openalex.org/W2094589433","https://openalex.org/W2095705004","https://openalex.org/W2097117768","https://openalex.org/W2097606916","https://openalex.org/W2100049434","https://openalex.org/W2100495367","https://openalex.org/W2101234009","https://openalex.org/W2101289642","https://openalex.org/W2103375140","https://openalex.org/W2103777723","https://openalex.org/W2105694586","https://openalex.org/W2108191354","https://openalex.org/W2112796928","https://openalex.org/W2114532236","https://openalex.org/W2117660195","https://openalex.org/W2118239316","https://openalex.org/W2119493141","https://openalex.org/W2123525093","https://openalex.org/W2128220972","https://openalex.org/W2132863465","https://openalex.org/W2152941241","https://openalex.org/W2157009395","https://openalex.org/W2158266834","https://openalex.org/W2159249646","https://openalex.org/W2198606573","https://openalex.org/W2245239316","https://openalex.org/W2285139619","https://openalex.org/W2302255633","https://openalex.org/W2307041907","https://openalex.org/W2323943568","https://openalex.org/W2336509392","https://openalex.org/W2345512687","https://openalex.org/W2481737556","https://openalex.org/W2507804718","https://openalex.org/W2567167447","https://openalex.org/W2574018027","https://openalex.org/W2600989574","https://openalex.org/W2627065724","https://openalex.org/W2789926271","https://openalex.org/W2919115771","https://openalex.org/W2950463913","https://openalex.org/W6674330103","https://openalex.org/W6674914833","https://openalex.org/W6675354045","https://openalex.org/W6682234737","https://openalex.org/W6698183232","https://openalex.org/W7073647534"],"related_works":["https://openalex.org/W4391621807","https://openalex.org/W4321487865","https://openalex.org/W4313906399","https://openalex.org/W4391621790","https://openalex.org/W4239306820","https://openalex.org/W4391266461","https://openalex.org/W4379233576","https://openalex.org/W2753172052","https://openalex.org/W3080365360","https://openalex.org/W1935063092"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":28},{"year":2021,"cited_by_count":42},{"year":2020,"cited_by_count":32},{"year":2019,"cited_by_count":32},{"year":2018,"cited_by_count":9}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
