{"id":"https://openalex.org/W2590432065","doi":"https://doi.org/10.1007/978-1-4939-6753-7_13","title":"Finding RNA\u2013Protein Interaction Sites Using HMMs","display_name":"Finding RNA\u2013Protein Interaction Sites Using HMMs","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2590432065","doi":"https://doi.org/10.1007/978-1-4939-6753-7_13","mag":"2590432065","pmid":"https://pubmed.ncbi.nlm.nih.gov/28224499","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5568642"},"language":"en","primary_location":{"id":"doi:10.1007/978-1-4939-6753-7_13","doi":"https://doi.org/10.1007/978-1-4939-6753-7_13","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-4939-6753-7_13","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W3139982614","display_name":"Hidden Markov Models"},"type":"book-chapter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5568642","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100453525","display_name":"Tao Wang","orcid":"https://orcid.org/0000-0002-4355-149X","observed_orcids":["https://orcid.org/0000-0002-4355-149X"]},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tao Wang","raw_affiliation_strings":["Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009725588","display_name":"Jonghyun Yun","orcid":"https://orcid.org/0000-0002-9599-4356","observed_orcids":["https://orcid.org/0000-0002-9599-4356"]},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonghyun Yun","raw_affiliation_strings":["Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA","institution_ids":["https://openalex.org/I189196454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107174144","display_name":"Yang Xie","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Xie","raw_affiliation_strings":["Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Quantitative Biomedical Research Center, Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, TX, 75290, USA","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009964025","display_name":"Guanghua Xiao","orcid":"https://orcid.org/0000-0001-9387-9883","observed_orcids":["https://orcid.org/0000-0001-9387-9883","https://orcid.org/0009-0000-9631-743X"]},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Guanghua Xiao","raw_affiliation_strings":["Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA. Guanghua.Xiao@UTSouthwestern.edu","Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA. Guanghua.Xiao@UTSouthwestern.edu","institution_ids":["https://openalex.org/I189196454"]},{"raw_affiliation_string":"Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA","institution_ids":["https://openalex.org/I189196454"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5009964025"],"corresponding_institution_ids":["https://openalex.org/I189196454"],"apc_list":null,"apc_paid":null,"fwci":1.3603,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.78715685,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"1552","issue":null,"first_page":"177","last_page":"184"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9672999978065491,"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":0.9672999978065491,"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":0.015399999916553497,"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":0.00419999985024333,"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/protein-rna-interactions","display_name":"RNA-protein interactions","score":0.777999997138977},{"id":"https://openalex.org/keywords/rna-binding-proteins","display_name":"RNA-binding proteins","score":0.9070000052452087},{"id":"https://openalex.org/keywords/clip-seq","display_name":"CLIP-seq","score":0.796999990940094},{"id":"https://openalex.org/keywords/hidden-markov-models","display_name":"hidden Markov models","score":0.9390000104904175},{"id":"https://openalex.org/keywords/peak-calling","display_name":"peak calling","score":0.8939999938011169},{"id":"https://openalex.org/keywords/rna-processing","display_name":"RNA processing","score":0.6669999957084656}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.7554129362106323},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7166088223457336},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.628993570804596},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.5168864727020264},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47685325145721436},{"id":"https://openalex.org/C71829478","wikidata":"https://www.wikidata.org/wiki/Q901305","display_name":"Immunoprecipitation","level":3,"score":0.45173487067222595},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.4454781711101532},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3485856056213379},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31129950284957886},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2879346013069153},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2041337490081787}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1007/978-1-4939-6753-7_13","doi":"https://doi.org/10.1007/978-1-4939-6753-7_13","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-4939-6753-7_13","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},{"id":"pmid:28224499","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28224499","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,"listed_in":[],"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":"Methods in molecular biology (Clifton, N.J.)","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:4461810","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5568642","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5568642","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5568642","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,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Methods Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:4461810","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5568642","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G419846323","display_name":"Integrative Analysis to Identify Regulation Targets of RNA-Binding Proteins","funder_award_id":"R01GM115473","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6471015985","display_name":"Integrative Analysis to Identify Therapeutic Targets for Lung Cancer","funder_award_id":"R01CA172211","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1965173359","https://openalex.org/W1981898947","https://openalex.org/W1991133427","https://openalex.org/W2012468371","https://openalex.org/W2019522436","https://openalex.org/W2044117548","https://openalex.org/W2053003053","https://openalex.org/W2053998703","https://openalex.org/W2073424121","https://openalex.org/W2086474057","https://openalex.org/W2104806799","https://openalex.org/W2114532236","https://openalex.org/W2125741255","https://openalex.org/W2129216514","https://openalex.org/W2149366901","https://openalex.org/W2153410912","https://openalex.org/W2163731275"],"related_works":["https://openalex.org/W7101003092","https://openalex.org/W3000598743","https://openalex.org/W2000031546","https://openalex.org/W2110428330","https://openalex.org/W2622798100","https://openalex.org/W7096626094","https://openalex.org/W2904460723","https://openalex.org/W6945854373","https://openalex.org/W2530260869","https://openalex.org/W2905063004"],"abstract_inverted_index":null,"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2017-03-03T00:00:00"}