{"id":"https://openalex.org/W2969891778","doi":"https://doi.org/10.1371/journal.pcbi.1007227","title":"PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks","display_name":"PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks","publication_year":2019,"publication_date":"2019-08-19","ids":{"openalex":"https://openalex.org/W2969891778","doi":"https://doi.org/10.1371/journal.pcbi.1007227","mag":"2969891778","pmid":"https://pubmed.ncbi.nlm.nih.gov/31425505"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007227","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007227","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007227&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.1007227&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091758959","display_name":"Jianan Lin","orcid":"https://orcid.org/0000-0003-3894-6902"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]},{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianan Lin","raw_affiliation_strings":["Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America","The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-3894-6902","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100458681","display_name":"Yuping Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuping Zhang","raw_affiliation_strings":["Center for Quantitative Medicine, University of Connecticut, Farmington, Connecticut, United States of America","Department of Statistics, University of Connecticut, Storrs, Connecticut, United States of America","Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-8986-0354","affiliations":[{"raw_affiliation_string":"Center for Quantitative Medicine, University of Connecticut, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Department of Statistics, University of Connecticut, Storrs, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068836840","display_name":"Wayne N. Frankel","orcid":"https://orcid.org/0000-0003-2241-5314"},"institutions":[{"id":"https://openalex.org/I2799503643","display_name":"Columbia University Irving Medical Center","ror":"https://ror.org/01esghr10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799503643"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wayne N. Frankel","raw_affiliation_strings":["Department of Genetics and Development and Institute for Genomic Medicine, Columbia University Medical Center, New York City, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Development and Institute for Genomic Medicine, Columbia University Medical Center, New York City, New York, United States of America","institution_ids":["https://openalex.org/I2799503643"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054640838","display_name":"Zhengqing Ouyang","orcid":"https://orcid.org/0000-0003-2842-8503"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]},{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhengqing Ouyang","raw_affiliation_strings":["Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America","Department of Genetics and Genome Sciences, University of Connecticut, Farmington, Connecticut, United States of America","Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America","The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2842-8503","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Department of Genetics and Genome Sciences, University of Connecticut, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5054640838"],"corresponding_institution_ids":["https://openalex.org/I140172145","https://openalex.org/I4210115256"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6838,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.69286424,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"15","issue":"8","first_page":"e1007227","last_page":"e1007227"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":1.0,"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":1.0,"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":0.9998999834060669,"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":0.9998000264167786,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.7842693328857422},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6217668056488037},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5970383286476135},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5871561765670776},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47457316517829895},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.4678274989128113},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.4116050601005554},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.37897789478302},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.34629321098327637},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2666732668876648},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2191314995288849}],"concepts":[{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.7842693328857422},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6217668056488037},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5970383286476135},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5871561765670776},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47457316517829895},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4678274989128113},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4116050601005554},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.37897789478302},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.34629321098327637},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2666732668876648},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2191314995288849}],"mesh":[{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000067878","descriptor_name":"CELF Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007227","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007227","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007227&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:31425505","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31425505","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:doaj.org/article:8b33b6af470e40fa99dc81b1cafd0c83","is_oa":true,"landing_page_url":"https://doaj.org/article/8b33b6af470e40fa99dc81b1cafd0c83","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 8, p e1007227 (2019)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/9684182","is_oa":true,"landing_page_url":"https://figshare.com/articles/PRAS_Predicting_functional_targets_of_RNA_binding_proteins_based_on_CLIP-seq_peaks/9684182","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:mouseion.jax.org:stfb2019-1181","is_oa":true,"landing_page_url":"https://mouseion.jax.org/stfb2019/180","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"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":"Faculty Research 2019","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6716675","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6716675","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":"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.1007227","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007227","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007227&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":[],"awards":[{"id":"https://openalex.org/G8167054483","display_name":null,"funder_award_id":"R35GM124998","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306799","display_name":"Pharmaceutical Research and Manufacturers of America Foundation","ror":"https://ror.org/01z88k350"},{"id":"https://openalex.org/F4320310017","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2969891778.pdf","grobid_xml":"https://content.openalex.org/works/W2969891778.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1534812231","https://openalex.org/W1974377677","https://openalex.org/W1975392407","https://openalex.org/W1981531168","https://openalex.org/W1985217779","https://openalex.org/W1992481904","https://openalex.org/W1998831398","https://openalex.org/W2000031546","https://openalex.org/W2002003942","https://openalex.org/W2015034754","https://openalex.org/W2021699617","https://openalex.org/W2022425730","https://openalex.org/W2022543706","https://openalex.org/W2036583346","https://openalex.org/W2037175112","https://openalex.org/W2039641169","https://openalex.org/W2044117548","https://openalex.org/W2044384139","https://openalex.org/W2050108172","https://openalex.org/W2053003053","https://openalex.org/W2059339710","https://openalex.org/W2059646461","https://openalex.org/W2073424121","https://openalex.org/W2079136832","https://openalex.org/W2081223805","https://openalex.org/W2086132527","https://openalex.org/W2091934163","https://openalex.org/W2102619694","https://openalex.org/W2102900988","https://openalex.org/W2105924780","https://openalex.org/W2112194054","https://openalex.org/W2114532236","https://openalex.org/W2116486533","https://openalex.org/W2127982146","https://openalex.org/W2128016314","https://openalex.org/W2129216514","https://openalex.org/W2133678000","https://openalex.org/W2138963732","https://openalex.org/W2141343226","https://openalex.org/W2149366901","https://openalex.org/W2167866392","https://openalex.org/W2171967549","https://openalex.org/W2179438025","https://openalex.org/W2259938310","https://openalex.org/W2307041907","https://openalex.org/W2537007468","https://openalex.org/W2607074636","https://openalex.org/W2611449604","https://openalex.org/W2750472843","https://openalex.org/W2913790533","https://openalex.org/W3046003662"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W3150324899","https://openalex.org/W4392059188","https://openalex.org/W4388725868","https://openalex.org/W2104762330","https://openalex.org/W4379374180","https://openalex.org/W2523545060"],"abstract_inverted_index":{"RNA-protein":[0],"interaction":[1],"plays":[2],"important":[3],"roles":[4],"in":[5,10,102,132],"post-transcriptional":[6],"regulation.":[7],"Recent":[8],"advancements":[9],"cross-linking":[11],"and":[12,65,105],"immunoprecipitation":[13],"followed":[14],"by":[15,117],"sequencing":[16],"(CLIP-seq)":[17],"technologies":[18],"make":[19],"it":[20,38,119],"possible":[21],"to":[22,42,120,141],"detect":[23],"the":[24,44,56,63,68,80,89,110,121],"binding":[25,31,49,69],"peaks":[26,70],"of":[27,47,67,71,82,92,112,126],"a":[28],"given":[29],"RNA":[30,128],"protein":[32],"(RBP)":[33],"at":[34,153],"transcriptome":[35],"scale.":[36],"However,":[37],"is":[39,150],"still":[40],"challenging":[41],"predict":[43],"functional":[45,74,90],"consequences":[46],"RBP":[48],"peaks.":[50,148],"In":[51],"this":[52],"study,":[53],"we":[54],"propose":[55],"Protein-RNA":[57],"Association":[58],"Strength":[59],"(PRAS),":[60],"which":[61],"integrates":[62],"intensities":[64],"positions":[66],"RBPs":[72,101,131,144],"for":[73,114],"mRNA":[75],"targets":[76,91],"prediction.":[77],"We":[78,107],"illustrate":[79],"superiority":[81],"PRAS":[83,113,137,149],"over":[84],"existing":[85],"approaches":[86],"on":[87],"predicting":[88],"two":[93,133],"related":[94,130],"but":[95],"divergent":[96],"CELF":[97],"(CUGBP,":[98],"ELAV-like":[99],"factor)":[100],"mouse":[103],"brain":[104],"muscle.":[106],"also":[108],"demonstrate":[109],"potential":[111],"wide":[115],"adoption":[116],"applying":[118],"enhanced":[122],"CLIP-seq":[123,147],"(eCLIP)":[124],"datasets":[125],"37":[127],"decay":[129],"human":[134],"cell":[135],"lines.":[136],"can":[138],"be":[139],"utilized":[140],"investigate":[142],"any":[143],"with":[145],"available":[146,152],"freely":[151],"http://ouyanglab.jax.org/pras/.":[154]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}