{"id":"https://openalex.org/W3037253559","doi":"https://doi.org/10.1093/bioinformatics/btaa580","title":"ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins","display_name":"ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins","publication_year":2020,"publication_date":"2020-06-14","ids":{"openalex":"https://openalex.org/W3037253559","doi":"https://doi.org/10.1093/bioinformatics/btaa580","mag":"3037253559","pmid":"https://pubmed.ncbi.nlm.nih.gov/32573679"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa580","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4797/34560247/btaa580.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4797/34560247/btaa580.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005417395","display_name":"Shu Yang","orcid":"https://orcid.org/0000-0002-8507-7191"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Shu Yang","raw_affiliation_strings":["University of British Columbia Department of Computer Science, , Vancouver, BC V6T1Z4, Canada"],"raw_orcid":"https://orcid.org/0000-0002-8507-7191","affiliations":[{"raw_affiliation_string":"University of British Columbia Department of Computer Science, , Vancouver, BC V6T1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100450538","display_name":"Xiaoxi Liu","orcid":"https://orcid.org/0000-0002-1933-8613"},"institutions":[{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Xiaoxi Liu","raw_affiliation_strings":["RIKEN Center for Integrative Medical Sciences (IMS) , Yokohama 230-0045, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RIKEN Center for Integrative Medical Sciences (IMS) , Yokohama 230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113567130","display_name":"Raymond T. Ng","orcid":"https://orcid.org/0000-0003-3692-8524"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Raymond T Ng","raw_affiliation_strings":["University of British Columbia Department of Computer Science, , Vancouver, BC V6T1Z4, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of British Columbia Department of Computer Science, , Vancouver, BC V6T1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005417395","https://openalex.org/A5113567130"],"corresponding_institution_ids":["https://openalex.org/I141945490"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5835,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.65031099,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"36","issue":"18","first_page":"4797","last_page":"4804"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.2854999899864197,"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/T10604","display_name":"RNA Research and Splicing","score":0.2854999899864197,"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":0.21279999613761902,"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":0.08250000327825546,"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/nucleic-acid","display_name":"Nucleic acid","score":0.7538046836853027},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6191344261169434},{"id":"https://openalex.org/keywords/recommender-system","display_name":"Recommender system","score":0.6129875183105469},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4433860182762146},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.41549813747406006},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3424355983734131},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2811339497566223},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.24827316403388977},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18429893255233765},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.06712493300437927},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.061392635107040405}],"concepts":[{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.7538046836853027},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6191344261169434},{"id":"https://openalex.org/C557471498","wikidata":"https://www.wikidata.org/wiki/Q554950","display_name":"Recommender system","level":2,"score":0.6129875183105469},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4433860182762146},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.41549813747406006},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3424355983734131},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2811339497566223},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.24827316403388977},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18429893255233765},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.06712493300437927},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.061392635107040405}],"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":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa580","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4797/34560247/btaa580.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32573679","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32573679","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:pubmedcentral.nih.gov:7750938","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7750938","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa580","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/18/4797/34560247/btaa580.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.550000011920929,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3037253559.pdf","grobid_xml":"https://content.openalex.org/works/W3037253559.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1501531009","https://openalex.org/W1528632786","https://openalex.org/W1584707462","https://openalex.org/W1690919088","https://openalex.org/W1731645091","https://openalex.org/W1901968134","https://openalex.org/W1969156759","https://openalex.org/W1978883675","https://openalex.org/W1988581590","https://openalex.org/W1994122295","https://openalex.org/W2019381697","https://openalex.org/W2033169664","https://openalex.org/W2055431298","https://openalex.org/W2080152736","https://openalex.org/W2103375140","https://openalex.org/W2105694586","https://openalex.org/W2119501676","https://openalex.org/W2127982146","https://openalex.org/W2130479394","https://openalex.org/W2132863465","https://openalex.org/W2149769193","https://openalex.org/W2155439547","https://openalex.org/W2157009395","https://openalex.org/W2165698076","https://openalex.org/W2170386697","https://openalex.org/W2171111703","https://openalex.org/W2174181728","https://openalex.org/W2182456467","https://openalex.org/W2198153867","https://openalex.org/W2284413061","https://openalex.org/W2309916540","https://openalex.org/W2419834209","https://openalex.org/W2433743436","https://openalex.org/W2481737556","https://openalex.org/W2493916176","https://openalex.org/W2544791529","https://openalex.org/W2585261240","https://openalex.org/W2772865572","https://openalex.org/W2785792383","https://openalex.org/W2793344725","https://openalex.org/W2795167067","https://openalex.org/W2799487719","https://openalex.org/W2801121099","https://openalex.org/W2810268516","https://openalex.org/W2903628238","https://openalex.org/W2904570115","https://openalex.org/W2944704300","https://openalex.org/W2950856588","https://openalex.org/W3003684254"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,101,210,239],"interaction":[2,43],"between":[3],"proteins":[4,25,29],"and":[5,15,31,93,127,196,234],"nucleic":[6,23,117],"acids":[7,42],"plays":[8],"a":[9,62,88,116,178,201,217],"crucial":[10],"role":[11],"in":[12,51,54,91],"gene":[13],"regulation":[14],"cell":[16],"function.":[17],"Determining":[18],"the":[19,36,40,74,84,185,222,226],"binding":[20,48,76,102,139,156,223],"preferences":[21,77,103],"of":[22,65,104,130,187],"acid-binding":[24],"(NBPs),":[26],"namely":[27],"RNA-binding":[28],"(RBPs)":[30],"transcription":[32],"factors":[33],"(TFs),":[34],"is":[35,135,242],"key":[37],"to":[38,137,171,220],"decipher":[39],"protein-nucleic":[41],"code.":[44],"Today,":[45],"available":[46,155,244,252],"NBP":[47,75],"data":[49,86,250],"from":[50,124,167],"vivo":[52],"or":[53,143],"vitro":[55],"experiments":[56],"are":[57,78,251],"still":[58],"limited,":[59],"which":[60,152],"leaves":[61],"large":[63],"portion":[64],"NBPs":[66,107,146,151,228],"uncovered.":[67],"Unfortunately,":[68],"existing":[69],"computational":[70],"methods":[71,206],"that":[72,121,213,229],"model":[73],"mostly":[79],"protein":[80,90],"specific:":[81],"they":[82],"need":[83],"experimental":[85,232],"for":[87,141,194,198,225],"specific":[89],"interest,":[92],"thus":[94],"only":[95,159],"focus":[96],"on":[97,189,207],"experimentally":[98,105],"characterized":[99],"NBPs.":[100],"unexplored":[106,142],"remain":[108],"largely":[109],"unknown.":[110],"RESULTS:":[111],"Here,":[112],"we":[113],"introduce":[114],"ProbeRating,":[115],"acid":[118],"recommender":[119,181],"system":[120],"utilizes":[122],"techniques":[123],"deep":[125],"learning":[126],"word":[128],"embeddings":[129],"natural":[131],"language":[132],"processing.":[133],"ProbeRating":[134,164,188,203,214],"developed":[136],"predict":[138],"profiles":[140],"poorly":[144],"studied":[145],"by":[147],"exploiting":[148],"their":[149],"homologs":[150],"currently":[153],"have":[154],"data.":[157],"Requiring":[158],"sequence":[160],"information":[161],"as":[162],"input,":[163],"adapts":[165],"FastText":[166],"Facebook":[168],"AI":[169],"Research":[170],"extract":[172],"biological":[173],"features.":[174],"It":[175],"then":[176],"builds":[177],"neural":[179],"network-based":[180],"system.":[182],"We":[183],"evaluate":[184],"performance":[186],"two":[190],"different":[191],"tasks:":[192],"one":[193,197],"RBP":[195],"TF.":[199],"As":[200],"result,":[202],"outperforms":[204],"previous":[205],"both":[208],"tasks.":[209],"results":[211],"show":[212],"can":[215],"be":[216],"useful":[218],"tool":[219],"study":[221],"mechanism":[224],"many":[227],"lack":[230],"direct":[231],"evidence.":[233],"implementation.":[235],"AVAILABILITY":[236],"AND":[237],"IMPLEMENTATION:":[238],"source":[240],"code":[241],"freely":[243],"at":[245,253],"<https://github.com/syang11/ProbeRating>.":[246],"SUPPLEMENTARY":[247],"INFORMATION:":[248],"Supplementary":[249],"Bioinformatics":[254],"online.":[255]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}