{"id":"https://openalex.org/W2766137885","doi":"https://doi.org/10.1142/s0219720017500238","title":"Evaluating the quality of SHAPE data simulated by <i>k-mers</i> for RNA structure prediction","display_name":"Evaluating the quality of SHAPE data simulated by <i>k-mers</i> for RNA structure prediction","publication_year":2017,"publication_date":"2017-10-19","ids":{"openalex":"https://openalex.org/W2766137885","doi":"https://doi.org/10.1142/s0219720017500238","mag":"2766137885","pmid":"https://pubmed.ncbi.nlm.nih.gov/29113564"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720017500238","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720017500238","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5044280010","display_name":"Soheila Montaseri","orcid":null},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Soheila Montaseri","raw_affiliation_strings":["Department of Computer Science, School of Mathematics Statistics, and Computer Science, University of Tehran, Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematics Statistics, and Computer Science, University of Tehran, Tehran, Iran","institution_ids":["https://openalex.org/I23946033"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067478126","display_name":"Fatemeh Zare\u2010Mirakabad","orcid":"https://orcid.org/0000-0003-2849-3778"},"institutions":[{"id":"https://openalex.org/I158248296","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43","country_code":"IR","type":"education","lineage":["https://openalex.org/I158248296"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Fatemeh Zare-Mirakabad","raw_affiliation_strings":["Department of Computer Science, Faculty of Mathematics and Computer Science, Amirkabir, University of Technology, Tehran, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Mathematics and Computer Science, Amirkabir, University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I158248296"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052221301","display_name":"\u200eMohammad Ganjtabesh","orcid":"https://orcid.org/0000-0001-8062-8794"},"institutions":[{"id":"https://openalex.org/I4210146419","display_name":"Institute for Research in Fundamental Sciences","ror":"https://ror.org/04xreqs31","country_code":"IR","type":"facility","lineage":["https://openalex.org/I4210146419"]},{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Mohammad Ganjtabesh","raw_affiliation_strings":["Department of Computer Science, School of Mathematics Statistics, and Computer Science, University of Tehran, Tehran, Iran","School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, P.O. Box: 19395-5746, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematics Statistics, and Computer Science, University of Tehran, Tehran, Iran","institution_ids":["https://openalex.org/I23946033"]},{"raw_affiliation_string":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, P.O. Box: 19395-5746, Iran","institution_ids":["https://openalex.org/I4210146419"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052221301"],"corresponding_institution_ids":["https://openalex.org/I23946033","https://openalex.org/I4210146419"],"apc_list":null,"apc_paid":null,"fwci":0.319,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.58781455,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"15","issue":"06","first_page":"1750023","last_page":"1750023"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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":0.9987000226974487,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9904000163078308,"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":0.7039667367935181},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.6024933457374573},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5311012864112854},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5172889232635498},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5119487047195435},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.48033323884010315},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4584265947341919},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4493213891983032},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.4473405182361603},{"id":"https://openalex.org/keywords/helix","display_name":"Helix (gastropod)","score":0.4349808692932129},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.39473265409469604},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32171761989593506},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30001747608184814},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.22082844376564026},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2015644609928131},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13050061464309692}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7039667367935181},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.6024933457374573},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5311012864112854},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5172889232635498},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5119487047195435},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.48033323884010315},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4584265947341919},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4493213891983032},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.4473405182361603},{"id":"https://openalex.org/C2778530040","wikidata":"https://www.wikidata.org/wiki/Q1937315","display_name":"Helix (gastropod)","level":3,"score":0.4349808692932129},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.39473265409469604},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32171761989593506},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30001747608184814},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.22082844376564026},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2015644609928131},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13050061464309692},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C2779965526","wikidata":"https://www.wikidata.org/wiki/Q308841","display_name":"Snail","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000215","descriptor_name":"Acylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000215","descriptor_name":"Acylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000215","descriptor_name":"Acylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720017500238","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720017500238","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:29113564","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29113564","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1026654479","display_name":null,"funder_award_id":"BS-1394-01-09","funder_id":"https://openalex.org/F4320323645","funder_display_name":"Institute for Research in Fundamental Sciences"}],"funders":[{"id":"https://openalex.org/F4320323645","display_name":"Institute for Research in Fundamental Sciences","ror":"https://ror.org/04xreqs31"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W611505772","https://openalex.org/W1543796220","https://openalex.org/W2020077467","https://openalex.org/W2025763720","https://openalex.org/W2031621142","https://openalex.org/W2036412199","https://openalex.org/W2054931730","https://openalex.org/W2098571862","https://openalex.org/W2100321825","https://openalex.org/W2101690699","https://openalex.org/W2118688581","https://openalex.org/W2141157874","https://openalex.org/W2148725278","https://openalex.org/W2159117141","https://openalex.org/W2162010981","https://openalex.org/W2162224067","https://openalex.org/W2558432341"],"related_works":["https://openalex.org/W4386361828","https://openalex.org/W4318218930","https://openalex.org/W2061103938","https://openalex.org/W2029624882","https://openalex.org/W2607456967","https://openalex.org/W2158031555","https://openalex.org/W2954092143","https://openalex.org/W2347162849","https://openalex.org/W1540181017","https://openalex.org/W140615050"],"abstract_inverted_index":{"Finding":[0],"an":[1,20,51,101],"effective":[2],"measure":[3,38],"to":[4,37,60,69,79,168,202],"predict":[5],"a":[6,13,43,70,86],"more":[7],"accurate":[8],"RNA":[9,52,65,102,175],"secondary":[10],"structure":[11,66],"is":[12,105,135],"challenging":[14],"problem.":[15],"In":[16],"the":[17,39,62,81,94,109,127,139,144,170,174,182,188,203],"last":[18],"decade,":[19],"experimental":[21,82,204],"method,":[22],"known":[23],"as":[24],"selective":[25],"[Formula:":[26,196],"see":[27,148,197],"text]-hydroxyl":[28],"acylation":[29],"analyzed":[30],"by":[31,107,143,192],"primer":[32],"extension":[33],"(SHAPE),":[34],"was":[35],"proposed":[36],"tendency":[40],"of":[41,64,73,115,129,154,185],"forming":[42],"base":[44],"pair":[45],"for":[46,97,112,151,173],"almost":[47],"all":[48,113],"nucleotides":[49],"in":[50,77,100,120],"sequence.":[53,103],"These":[54],"SHAPE":[55,74,95,110,131,140,156,171,189,205],"reactivities":[56,111],"are":[57,161,199],"then":[58],"utilized":[59],"improve":[61],"accuracy":[63],"prediction.":[67],"Due":[68],"significant":[71],"impact":[72],"reactivity":[75,96],"and":[76,122],"order":[78],"reduce":[80],"costs,":[83],"we":[84],"propose":[85],"new":[87],"model":[88,92,146,167],"called":[89],"HL-k-mer.":[90],"This":[91,104],"simulates":[93],"each":[98],"nucleotide":[99],"done":[106],"fetching":[108],"sub-sequences":[114],"length":[116],"k":[117],"(k-mers)":[118],"appearing":[119],"helix":[121],"loop":[123],"regions.":[124],"For":[125],"evaluating":[126],"quality":[128],"simulated":[130,142,155,191],"data,":[132,157],"ESD-Fold":[133],"method":[134],"used":[136],"based":[137],"on":[138],"data":[141,172,190],"HL-k-mer":[145],"([Formula:":[147],"text]).":[149],"Also,":[150],"further":[152],"evaluation":[153],"three":[158],"different":[159],"methods":[160],"employed.":[162],"We":[163],"also":[164],"extend":[165],"this":[166],"simulate":[169],"pseudoknotted":[176],"structure.":[177],"The":[178],"results":[179],"indicate":[180],"that":[181],"average":[183],"accuracies":[184],"prediction":[186],"using":[187],"our":[193],"models":[194],"(for":[195],"text])":[198],"higher":[200],"compared":[201],"data.":[206]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2017-11-10T00:00:00"}
