{"id":"https://openalex.org/W4291618428","doi":"https://doi.org/10.1371/journal.pcbi.1010404","title":"iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank","display_name":"iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank","publication_year":2022,"publication_date":"2022-08-15","ids":{"openalex":"https://openalex.org/W4291618428","doi":"https://doi.org/10.1371/journal.pcbi.1010404","pmid":"https://pubmed.ncbi.nlm.nih.gov/35969645"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010404","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010404","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010404&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010404&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100728432","display_name":"Wenxiang Zhang","orcid":"https://orcid.org/0009-0000-3429-1297"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenxiang Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027112671","display_name":"Jialu Hou","orcid":"https://orcid.org/0000-0003-4737-7721"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jialu Hou","raw_affiliation_strings":["School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040486509","display_name":"Bin Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin Liu","raw_affiliation_strings":["Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China","School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China","institution_ids":["https://openalex.org/I125839683"]},{"raw_affiliation_string":"School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China","institution_ids":["https://openalex.org/I125839683"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5040486509"],"corresponding_institution_ids":["https://openalex.org/I125839683"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.5755,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.9215741,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"18","issue":"8","first_page":"e1010404","last_page":"e1010404"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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":0.9961000084877014,"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/piwi-interacting-rna","display_name":"Piwi-interacting RNA","score":0.9427778720855713},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6476158499717712},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5401010513305664},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5374302268028259},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48483145236968994},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.4192246198654175},{"id":"https://openalex.org/keywords/complex-disease","display_name":"Complex disease","score":0.4112371802330017},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3910498023033142},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3436114192008972},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3387518525123596},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.25464558601379395},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.21949270367622375},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15586507320404053},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.08993801474571228},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07438835501670837}],"concepts":[{"id":"https://openalex.org/C147724379","wikidata":"https://www.wikidata.org/wiki/Q2367421","display_name":"Piwi-interacting RNA","level":5,"score":0.9427778720855713},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6476158499717712},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5401010513305664},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5374302268028259},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48483145236968994},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.4192246198654175},{"id":"https://openalex.org/C3018605307","wikidata":"https://www.wikidata.org/wiki/Q200779","display_name":"Complex disease","level":3,"score":0.4112371802330017},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3910498023033142},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3436114192008972},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3387518525123596},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.25464558601379395},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.21949270367622375},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15586507320404053},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.08993801474571228},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07438835501670837},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1010404","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010404","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010404&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35969645","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35969645","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1010404","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010404","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:f68f5601048e4481852f90021e4b04fb","is_oa":true,"landing_page_url":"https://doaj.org/article/f68f5601048e4481852f90021e4b04fb","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 8, p e1010404 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9410559","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9410559","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010404","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010404","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010404&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G3425444037","display_name":null,"funder_award_id":"2018AAA0100100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4291618428.pdf","grobid_xml":"https://content.openalex.org/works/W4291618428.grobid-xml"},"referenced_works_count":78,"referenced_works":["https://openalex.org/W1970769181","https://openalex.org/W1976342457","https://openalex.org/W1981039744","https://openalex.org/W1985863431","https://openalex.org/W2003663539","https://openalex.org/W2008056655","https://openalex.org/W2009644747","https://openalex.org/W2013210832","https://openalex.org/W2022732522","https://openalex.org/W2035930185","https://openalex.org/W2047988520","https://openalex.org/W2048218599","https://openalex.org/W2050385516","https://openalex.org/W2087064593","https://openalex.org/W2089487356","https://openalex.org/W2101234009","https://openalex.org/W2101626488","https://openalex.org/W2115584760","https://openalex.org/W2128049108","https://openalex.org/W2129245267","https://openalex.org/W2130765911","https://openalex.org/W2147660582","https://openalex.org/W2162871848","https://openalex.org/W2264143181","https://openalex.org/W2294661159","https://openalex.org/W2313125707","https://openalex.org/W2389683878","https://openalex.org/W2419892062","https://openalex.org/W2574217686","https://openalex.org/W2579869402","https://openalex.org/W2620580060","https://openalex.org/W2771019114","https://openalex.org/W2771972353","https://openalex.org/W2809363952","https://openalex.org/W2811444387","https://openalex.org/W2898073868","https://openalex.org/W2898731714","https://openalex.org/W2899915536","https://openalex.org/W2911964244","https://openalex.org/W2912419357","https://openalex.org/W2950954328","https://openalex.org/W2955033696","https://openalex.org/W2968344903","https://openalex.org/W2972223935","https://openalex.org/W2981242070","https://openalex.org/W3000503908","https://openalex.org/W3003038853","https://openalex.org/W3008666266","https://openalex.org/W3010916046","https://openalex.org/W3022179362","https://openalex.org/W3022704604","https://openalex.org/W3025373576","https://openalex.org/W3037078148","https://openalex.org/W3041467169","https://openalex.org/W3042997124","https://openalex.org/W3043480632","https://openalex.org/W3082883165","https://openalex.org/W3084310327","https://openalex.org/W3112172360","https://openalex.org/W3119632172","https://openalex.org/W3127064341","https://openalex.org/W3131013500","https://openalex.org/W3138710788","https://openalex.org/W3143063265","https://openalex.org/W3155148776","https://openalex.org/W3159197832","https://openalex.org/W3176004707","https://openalex.org/W3179235883","https://openalex.org/W3186054896","https://openalex.org/W3191637674","https://openalex.org/W3195161349","https://openalex.org/W3203741962","https://openalex.org/W3207365242","https://openalex.org/W3217082130","https://openalex.org/W4282945893","https://openalex.org/W4289883804","https://openalex.org/W6675354045","https://openalex.org/W6677385034"],"related_works":["https://openalex.org/W2158912913","https://openalex.org/W4221011377","https://openalex.org/W2027956742","https://openalex.org/W2924035798","https://openalex.org/W3192072282","https://openalex.org/W3025373576","https://openalex.org/W2789736974","https://openalex.org/W2271855253","https://openalex.org/W2987802490","https://openalex.org/W4294707127"],"abstract_inverted_index":{"Piwi-interacting":[0],"RNAs":[1],"(piRNAs)":[2],"are":[3,52],"regarded":[4],"as":[5],"drug":[6],"targets":[7],"and":[8,13,23,25,39,49,68,88,107],"biomarkers":[9],"for":[10],"the":[11,26,42,55,78,101,128],"diagnosis":[12],"therapy":[14],"of":[15,45,57,60,73],"diseases.":[16,40,74],"However,":[17],"biological":[18,46],"experiments":[19],"cost":[20],"substantial":[21],"time":[22],"resources,":[24],"existing":[27],"computational":[28],"methods":[29],"only":[30,99],"focus":[31],"on":[32,71,91],"identifying":[33],"missing":[34,102],"associations":[35,59,85,103,126],"between":[36,86,104],"known":[37,105],"piRNAs":[38,51,63,87,106],"With":[41],"fast":[43],"development":[44],"experiments,":[47],"more":[48,50],"detected.":[53],"Therefore,":[54],"identification":[56],"piRNA-disease":[58,125],"newly":[61,115],"detected":[62,116],"has":[64],"significant":[65],"theoretical":[66],"value":[67],"practical":[69],"significance":[70],"pathogenesis":[72],"In":[75],"this":[76],"study,":[77],"iPiDA-LTR":[79,96,122],"predictor":[80,97],"is":[81],"proposed":[82],"to":[83,93],"identify":[84],"diseases":[89,112],"based":[90],"Learning":[92],"Rank.":[94],"The":[95],"not":[98],"identifies":[100],"diseases,":[108],"but":[109],"also":[110],"detects":[111],"associated":[113],"with":[114],"piRNAs.":[117],"Experimental":[118],"results":[119],"demonstrate":[120],"that":[121],"effectively":[123],"predicts":[124],"outperforming":[127],"other":[129],"related":[130],"methods.":[131]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
