{"id":"https://openalex.org/W3025373576","doi":"https://doi.org/10.1093/bib/bbaa058","title":"iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning","display_name":"iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning","publication_year":2020,"publication_date":"2020-03-24","ids":{"openalex":"https://openalex.org/W3025373576","doi":"https://doi.org/10.1093/bib/bbaa058","mag":"3025373576","pmid":"https://pubmed.ncbi.nlm.nih.gov/32393982"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa058","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa058","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/A5081941068","display_name":"Hang Wei","orcid":"https://orcid.org/0000-0002-0579-1716"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hang Wei","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108152822","display_name":"Yong Xu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yong Xu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5100395591","display_name":"Bin Liu","orcid":"https://orcid.org/0000-0003-3685-9469"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bin Liu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081941068"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.3198,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.89138678,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"22","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983999729156494,"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":0.9983999729156494,"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":0.9976999759674072,"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":0.9965000152587891,"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":0.9639594554901123},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.6570664644241333},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5583857893943787},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47646522521972656},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.4696368873119354},{"id":"https://openalex.org/keywords/complex-disease","display_name":"Complex disease","score":0.4649891257286072},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3790598213672638},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3702607750892639},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.360276460647583},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28743213415145874},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.21799635887145996},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13948550820350647},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.10149821639060974},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.09330111742019653},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.05832403898239136}],"concepts":[{"id":"https://openalex.org/C147724379","wikidata":"https://www.wikidata.org/wiki/Q2367421","display_name":"Piwi-interacting RNA","level":5,"score":0.9639594554901123},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6570664644241333},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5583857893943787},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47646522521972656},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.4696368873119354},{"id":"https://openalex.org/C3018605307","wikidata":"https://www.wikidata.org/wiki/Q200779","display_name":"Complex disease","level":3,"score":0.4649891257286072},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3790598213672638},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3702607750892639},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.360276460647583},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28743213415145874},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.21799635887145996},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13948550820350647},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.10149821639060974},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.09330111742019653},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.05832403898239136},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa058","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa058","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:32393982","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32393982","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/G4864480503","display_name":null,"funder_award_id":"61822306","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6876496325","display_name":null,"funder_award_id":"JQ19019","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"},{"id":"https://openalex.org/G75457812","display_name":null,"funder_award_id":"61672184","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/F4320322919","display_name":"Natural Science Foundation of Beijing Municipality","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1763867024","https://openalex.org/W1893639437","https://openalex.org/W1970698209","https://openalex.org/W1977733607","https://openalex.org/W2013210832","https://openalex.org/W2027461913","https://openalex.org/W2047988520","https://openalex.org/W2048218599","https://openalex.org/W2050871273","https://openalex.org/W2076931586","https://openalex.org/W2077373870","https://openalex.org/W2087064593","https://openalex.org/W2101234009","https://openalex.org/W2106029302","https://openalex.org/W2118980569","https://openalex.org/W2124045889","https://openalex.org/W2125283600","https://openalex.org/W2128049108","https://openalex.org/W2141222510","https://openalex.org/W2152970345","https://openalex.org/W2153330772","https://openalex.org/W2157825442","https://openalex.org/W2158698691","https://openalex.org/W2264143181","https://openalex.org/W2281614104","https://openalex.org/W2389683878","https://openalex.org/W2531500048","https://openalex.org/W2544883878","https://openalex.org/W2563376882","https://openalex.org/W2579869402","https://openalex.org/W2601934706","https://openalex.org/W2605763657","https://openalex.org/W2607159126","https://openalex.org/W2620580060","https://openalex.org/W2765541862","https://openalex.org/W2770191688","https://openalex.org/W2771972353","https://openalex.org/W2780584018","https://openalex.org/W2780936345","https://openalex.org/W2788536989","https://openalex.org/W2789316776","https://openalex.org/W2799603881","https://openalex.org/W2898731714","https://openalex.org/W2903914925","https://openalex.org/W2907590003","https://openalex.org/W2911964244","https://openalex.org/W2923922207","https://openalex.org/W2936144882","https://openalex.org/W2939164430","https://openalex.org/W2942820662","https://openalex.org/W2947612926","https://openalex.org/W2955033696","https://openalex.org/W2962928958","https://openalex.org/W2969993699","https://openalex.org/W2972223935","https://openalex.org/W2975802621","https://openalex.org/W2980767508","https://openalex.org/W2984339599","https://openalex.org/W3000503908","https://openalex.org/W4256413664","https://openalex.org/W6638057232","https://openalex.org/W6675354045","https://openalex.org/W6757816279"],"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/W4310456519","https://openalex.org/W2789736974","https://openalex.org/W2271855253","https://openalex.org/W2987802490","https://openalex.org/W4294707127"],"abstract_inverted_index":{"Accumulated":[0],"researches":[1],"have":[2],"revealed":[3],"that":[4],"Piwi-interacting":[5],"RNAs":[6],"(piRNAs)":[7],"are":[8,19],"regulating":[9],"the":[10,23,29,32,70,75,94,99,117,134,148,153,170,179,190,194],"development":[11],"of":[12,25,31,78,101,182],"germ":[13],"and":[14,17,50,74,116,147],"stem":[15],"cells,":[16],"they":[18],"closely":[20],"associated":[21,195],"with":[22,47,161],"progression":[24],"many":[26],"diseases.":[27],"As":[28],"number":[30],"detected":[33],"piRNAs":[34],"is":[35,39,60],"increasing":[36],"rapidly,":[37],"it":[38,59],"important":[40],"to":[41,64,92,132,168,188,192],"computationally":[42],"identify":[43,93],"new":[44],"piRNA-disease":[45,72,80,95,102,119],"associations":[46,73,103,146,150],"low":[48],"cost":[49],"provide":[51],"candidate":[52],"piRNA":[53,110],"targets":[54],"for":[55,197],"disease":[56,113],"treatment.":[57],"However,":[58],"a":[61,87],"challenging":[62],"problem":[63],"learn":[65],"effective":[66],"association":[67,120],"patterns":[68],"from":[69,104,152],"positive":[71,145],"large":[76],"amount":[77],"unknown":[79,154],"pairs.":[81,155],"In":[82],"this":[83],"study,":[84],"we":[85],"proposed":[86],"computational":[88],"predictor":[89],"called":[90],"iPiDi-PUL":[91,97,183],"associations.":[96],"extracted":[98],"features":[100,131],"three":[105],"biological":[106],"data":[107],"sources,":[108],"including":[109],"sequence":[111],"information,":[112],"semantic":[114],"terms":[115],"available":[118],"network.":[121],"Principal":[122],"component":[123],"analysis":[124],"(PCA)":[125],"was":[126,184],"then":[127],"performed":[128],"on":[129,143],"these":[130,162],"extract":[133],"key":[135],"features.":[136],"The":[137],"training":[138,164],"datasets":[139],"were":[140,166],"constructed":[141],"based":[142],"known":[144],"negative":[149],"selected":[151],"Various":[156],"random":[157],"forest":[158],"classifiers":[159],"trained":[160],"different":[163],"sets":[165],"merged":[167],"give":[169],"predictive":[171],"results":[172],"via":[173],"an":[174],"ensemble":[175],"learning":[176],"approach.":[177],"Finally,":[178],"web":[180],"server":[181],"established":[185],"at":[186],"http://bliulab.net/iPiDi-PUL":[187],"help":[189],"researchers":[191],"explore":[193],"diseases":[196],"newly":[198],"discovered":[199],"piRNAs.":[200]},"counts_by_year":[{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
