{"id":"https://openalex.org/W2594622866","doi":"https://doi.org/10.1093/bioinformatics/btx087","title":"MotifMap-RNA: a genome-wide map of RBP binding sites","display_name":"MotifMap-RNA: a genome-wide map of RBP binding sites","publication_year":2017,"publication_date":"2017-02-15","ids":{"openalex":"https://openalex.org/W2594622866","doi":"https://doi.org/10.1093/bioinformatics/btx087","mag":"2594622866","pmid":"https://pubmed.ncbi.nlm.nih.gov/28334276"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2029/25155829/btx087.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2029/25155829/btx087.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100345600","display_name":"Yu Liu","orcid":"https://orcid.org/0000-0001-5563-6397"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Liu","raw_affiliation_strings":["Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086505023","display_name":"Sha Sun","orcid":"https://orcid.org/0000-0002-0044-6403"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sha Sun","raw_affiliation_strings":["Department of Developmental and Cell Biology, University of California, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030305869","display_name":"Timothy W. Bredy","orcid":"https://orcid.org/0000-0003-3280-126X"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy Bredy","raw_affiliation_strings":["Department of Neurobiology and Behavior, University of California, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurobiology and Behavior, University of California, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021955687","display_name":"Marcelo A. Wood","orcid":"https://orcid.org/0000-0003-2029-4176"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcelo Wood","raw_affiliation_strings":["Department of Neurobiology and Behavior, University of California, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurobiology and Behavior, University of California, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070785063","display_name":"Robert C. Spitale","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert C Spitale","raw_affiliation_strings":["Department of Pharmaceutical Sciences and the Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences and the Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088813478","display_name":"Pierre Baldi","orcid":"https://orcid.org/0000-0001-8752-4664"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pierre Baldi","raw_affiliation_strings":["Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5070785063","https://openalex.org/A5088813478"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6082,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.64887771,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"13","first_page":"2029","last_page":"2031"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9569000005722046,"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":0.9569000005722046,"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":0.010300000198185444,"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":0.009700000286102295,"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","display_name":"RNA","score":0.7177993655204773},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.7004855871200562},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6346961259841919},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.6154147386550903},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5487032532691956},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5360690951347351},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42699068784713745},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41540294885635376}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7177993655204773},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.7004855871200562},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6346961259841919},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.6154147386550903},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5487032532691956},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5360690951347351},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42699068784713745},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41540294885635376}],"mesh":[{"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":"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"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":"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2029/25155829/btx087.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28334276","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28334276","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:espace.library.uq.edu.au:UQ:682235","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2029/25155829/btx087.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2594622866.pdf","grobid_xml":"https://content.openalex.org/works/W2594622866.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1984574291","https://openalex.org/W1995224771","https://openalex.org/W2015175027","https://openalex.org/W2026671856","https://openalex.org/W2058615001","https://openalex.org/W2076875970","https://openalex.org/W2087377443","https://openalex.org/W2098412979","https://openalex.org/W2105694586","https://openalex.org/W2118750355","https://openalex.org/W2122358139","https://openalex.org/W2136949432","https://openalex.org/W2138590306","https://openalex.org/W2146042781","https://openalex.org/W2150198686","https://openalex.org/W2212393023","https://openalex.org/W2307041907","https://openalex.org/W2941567788"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W2147993839","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W3178279768","https://openalex.org/W4379233576","https://openalex.org/W2753172052","https://openalex.org/W1935063092","https://openalex.org/W3080365360"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA":[1,12],"plays":[2],"a":[3],"critical":[4],"role":[5],"in":[6,16,36,41],"gene":[7],"expression":[8],"and":[9,35,78,81,95],"its":[10],"regulation.":[11],"binding":[13,33,38,55,71,88],"proteins":[14],"(RBPs),":[15],"turn,":[17],"are":[18,99,118],"important":[19],"regulators":[20],"of":[21,27,44,67,86,105],"RNA.":[22],"Thanks":[23],"to":[24,51],"the":[25,42,58,106],"availability":[26],"large":[28,83],"scale":[29,84],"data":[30,94,117],"for":[31,73],"RBP":[32,54,74],"motifs":[34,75],"vivo":[37],"sites":[39,56,72],"results":[40],"form":[43],"eCLIP":[45],"experiments,":[46],"it":[47],"is":[48],"now":[49],"possible":[50],"computationally":[52],"predict":[53],"across":[57,76],"whole":[59],"genome.":[60],"RESULTS:":[61],"We":[62],"describe":[63],"MotifMap-RNA,":[64],"an":[65],"extension":[66],"MotifMap":[68,107],"which":[69],"predicts":[70],"human":[77],"mouse":[79],"genomes":[80],"allows":[82],"querying":[85],"predicted":[87],"sites.":[89],"AVAILABILITY":[90],"AND":[91],"IMPLEMENTATION:":[92],"The":[93],"corresponding":[96],"web":[97,108],"server":[98],"available":[100,119],"from:":[101],"http://motifmap-rna.ics.uci.edu/":[102],"as":[103],"part":[104],"portal.":[109],"CONTACT:":[110],"rspitale@uci.edu":[111],"or":[112],"pfbaldi@uci.edu.":[113],"SUPPLEMENTARY":[114],"INFORMATION:":[115],"Supplementary":[116],"at":[120],"Bioinformatics":[121],"online.":[122]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
