{"id":"https://openalex.org/W2042364203","doi":"https://doi.org/10.1109/isb.2012.6314128","title":"Predicting protein-RNA residue-base contacts using two-dimensional conditional random field","display_name":"Predicting protein-RNA residue-base contacts using two-dimensional conditional random field","publication_year":2012,"publication_date":"2012-08-01","ids":{"openalex":"https://openalex.org/W2042364203","doi":"https://doi.org/10.1109/isb.2012.6314128","mag":"2042364203"},"language":"en","primary_location":{"id":"doi:10.1109/isb.2012.6314128","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isb.2012.6314128","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 6th International Conference on Systems Biology (ISB)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039138118","display_name":"Morihiro Hayashida","orcid":"https://orcid.org/0000-0001-7961-0175"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Morihiro Hayashida","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101992610","display_name":"Mayumi Kamada","orcid":"https://orcid.org/0000-0002-2555-7345"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Mayumi Kamada","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012709797","display_name":"Jiangning Song","orcid":"https://orcid.org/0000-0001-8031-9086"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210139473","display_name":"Tianjin Institute of Industrial Biotechnology","ror":"https://ror.org/042pyga86","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210139473"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Jiangning Song","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia","Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China","institution_ids":["https://openalex.org/I4210139473","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":"https://orcid.org/0000-0001-9763-797X"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuya Akutsu","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039138118"],"corresponding_institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"],"apc_list":null,"apc_paid":null,"fwci":0.1345,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.52203469,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"b 48","issue":"3","first_page":"152","last_page":"157"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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/T10604","display_name":"RNA Research and Splicing","score":0.9987000226974487,"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/conditional-random-field","display_name":"Conditional random field","score":0.795274019241333},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.6734805107116699},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6571341753005981},{"id":"https://openalex.org/keywords/crfs","display_name":"CRFS","score":0.5655304789543152},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5394770503044128},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5209154486656189},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.473435640335083},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3391984701156616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3003751039505005},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2991766035556793},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.19375941157341003}],"concepts":[{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.795274019241333},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6734805107116699},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6571341753005981},{"id":"https://openalex.org/C2775953691","wikidata":"https://www.wikidata.org/wiki/Q5013874","display_name":"CRFS","level":3,"score":0.5655304789543152},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5394770503044128},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5209154486656189},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.473435640335083},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3391984701156616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3003751039505005},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2991766035556793},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19375941157341003},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/isb.2012.6314128","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isb.2012.6314128","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 6th International Conference on Systems Biology (ISB)","raw_type":"proceedings-article"},{"id":"mag:2895456254","is_oa":false,"landing_page_url":"http://ci.nii.ac.jp/naid/110009432492","pdf_url":null,"source":{"id":"https://openalex.org/S52256385","display_name":"BIOSILICO","issn_l":"1478-5382","issn":["1478-5382","1878-1209"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"BIOSILICO","raw_type":null},{"id":"mag:3176114347","is_oa":false,"landing_page_url":"https://jglobal.jst.go.jp/en/detail?JGLOBAL_ID=201202206935280847","pdf_url":null,"source":{"id":"https://openalex.org/S4306549042","display_name":"\u60c5\u5831\u51e6\u7406\u5b66\u4f1a\u7814\u7a76\u5831\u544a(CD-ROM)","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":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"\u60c5\u5831\u51e6\u7406\u5b66\u4f1a\u7814\u7a76\u5831\u544a(CD-ROM)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.7099999785423279,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"},{"id":"https://openalex.org/F4320334737","display_name":"National Medical Research Council","ror":"https://ror.org/04x3cxs03"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1554544485","https://openalex.org/W1688901160","https://openalex.org/W1964803612","https://openalex.org/W1979762151","https://openalex.org/W1989517036","https://openalex.org/W2007922755","https://openalex.org/W2046788335","https://openalex.org/W2051669046","https://openalex.org/W2079873244","https://openalex.org/W2097282516","https://openalex.org/W2097892623","https://openalex.org/W2105134671","https://openalex.org/W2107884096","https://openalex.org/W2108619558","https://openalex.org/W2119493141","https://openalex.org/W2128330762","https://openalex.org/W2130682154","https://openalex.org/W2138551420","https://openalex.org/W2141885858","https://openalex.org/W2147880316","https://openalex.org/W2151457629","https://openalex.org/W2161062388","https://openalex.org/W2162365094","https://openalex.org/W2164918853","https://openalex.org/W2167884443","https://openalex.org/W2170441710","https://openalex.org/W2772934464","https://openalex.org/W2798766386","https://openalex.org/W3199143553","https://openalex.org/W4230606671","https://openalex.org/W4236796448","https://openalex.org/W4242209908","https://openalex.org/W4320301318","https://openalex.org/W6682082992"],"related_works":["https://openalex.org/W2055466819","https://openalex.org/W50079190","https://openalex.org/W2356597680","https://openalex.org/W182104056","https://openalex.org/W2111726165","https://openalex.org/W2011251309","https://openalex.org/W2796133761","https://openalex.org/W3088215229","https://openalex.org/W2511246383","https://openalex.org/W2163278254"],"abstract_inverted_index":{"Understanding":[0],"of":[1,14,72,86,93,121,129,144,160,167,173],"interactions":[2,28,36,61,149,185],"between":[3,29,37,62,80,150,186],"proteins":[4,88],"and":[5,12,26,32,98,124,153,163,189,201],"RNAs":[6],"is":[7,41,108,125,203],"essential":[8],"to":[9,58,110],"reveal":[10],"networks":[11],"functions":[13],"molecules":[15],"in":[16,54,95,118,138],"cellular":[17],"systems.":[18],"Many":[19],"studies":[20],"have":[21,48],"been":[22],"done":[23],"for":[24,89,147,183],"analyzing":[25],"investigating":[27],"protein":[30,38,57,151],"residues":[31,44,53,81,94,152],"RNA":[33,154],"bases.":[34,155],"For":[35],"residues,":[39],"it":[40,100],"supported":[42],"that":[43,195],"at":[45],"interacting":[46,91,96],"sites":[47],"co-evolved":[49],"with":[50,101,199,210],"the":[51,55,60,63,70,102,119,196,207],"corresponding":[52],"partner":[56],"keep":[59],"proteins.":[64],"In":[65,134],"our":[66,177],"previous":[67],"work,":[68],"on":[69],"basis":[71],"this":[73,139],"idea,":[74],"we":[75,141,157,179],"calculated":[76],"mutual":[77,145],"information":[78,146],"(MI)":[79],"from":[82,115],"multiple":[83],"sequence":[84],"alignments":[85],"homologous":[87],"identifying":[90],"pairs":[92],"proteins,":[97],"combined":[99],"discriminative":[103],"random":[104,131],"field":[105,120],"(DRF),":[106],"which":[107],"useful":[109,205],"extract":[111],"some":[112],"characteristic":[113],"regions":[114],"an":[116],"image":[117,122],"processing,":[123],"a":[126,135,168],"special":[127],"type":[128],"conditional":[130],"fields":[132],"(CRFs).":[133],"similar":[136],"way,":[137],"paper,":[140],"make":[142],"use":[143],"predicting":[148],"Furthermore,":[156],"introduce":[158],"labels":[159,202],"amino":[161],"acids":[162],"bases":[164],"as":[165],"features":[166],"simple":[169],"two-dimensional":[170],"CRF":[171,197,208],"instead":[172],"DRF.":[174],"To":[175],"evaluate":[176],"method,":[178],"perform":[180],"computational":[181],"experiments":[182],"several":[184],"Pfam":[187],"domains":[188],"Rfam":[190],"entries.":[191],"The":[192],"results":[193],"suggest":[194],"model":[198,209],"MI":[200],"more":[204],"than":[206],"only":[211],"MI.":[212]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}