{"id":"https://openalex.org/W2004368241","doi":"https://doi.org/10.1109/bibm.2013.6732478","title":"StemSearch: RNA search tool based on stem identification and indexing","display_name":"StemSearch: RNA search tool based on stem identification and indexing","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2004368241","doi":"https://doi.org/10.1109/bibm.2013.6732478","mag":"2004368241"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2013.6732478","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732478","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"conference-paper","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/A5031866769","display_name":"Sivan Yogev","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Sivan Yogev","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University of the Negev, Israel","Department of Computer Science, Ben-Gurion University of the Negev, Beer-sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036607839","display_name":"Nimrod Milo","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Nimrod Milo","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University of the Negev, Israel","Department of Computer Science, Ben-Gurion University of the Negev, Beer-sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048383219","display_name":"Michal Ziv-Ukelson","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Michal Ziv-Ukelson","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University of the Negev, Israel","Department of Computer Science, Ben-Gurion University of the Negev, Beer-sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I124227911"],"apc_list":null,"apc_paid":null,"fwci":1.0253,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.77696258,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"32","issue":null,"first_page":"145","last_page":"152"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9987999796867371,"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":0.9868000149726868,"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/identification","display_name":"Identification (biology)","score":0.7162325382232666},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5914112329483032},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5534668564796448},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5494914054870605},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4286547005176544},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25656944513320923},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.24883800745010376},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15942546725273132},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1087416410446167},{"id":"https://openalex.org/keywords/botany","display_name":"Botany","score":0.05306953191757202}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7162325382232666},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5914112329483032},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5534668564796448},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5494914054870605},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4286547005176544},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25656944513320923},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.24883800745010376},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15942546725273132},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1087416410446167},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.05306953191757202}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2013.6732478","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732478","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6800000071525574,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W165772547","https://openalex.org/W1542426682","https://openalex.org/W1554383491","https://openalex.org/W1572817673","https://openalex.org/W1600401233","https://openalex.org/W1950410402","https://openalex.org/W1972708527","https://openalex.org/W1976526581","https://openalex.org/W1984675364","https://openalex.org/W2011368877","https://openalex.org/W2012879790","https://openalex.org/W2020456609","https://openalex.org/W2025763720","https://openalex.org/W2030658020","https://openalex.org/W2036547750","https://openalex.org/W2055043387","https://openalex.org/W2058124910","https://openalex.org/W2095145214","https://openalex.org/W2102017611","https://openalex.org/W2103250001","https://openalex.org/W2105070391","https://openalex.org/W2110957978","https://openalex.org/W2113368761","https://openalex.org/W2116619380","https://openalex.org/W2118702480","https://openalex.org/W2120523244","https://openalex.org/W2122679732","https://openalex.org/W2123157758","https://openalex.org/W2137257434","https://openalex.org/W2138452362","https://openalex.org/W2138662031","https://openalex.org/W2142829010","https://openalex.org/W2143407915","https://openalex.org/W2154085311","https://openalex.org/W2158898099","https://openalex.org/W2161534813","https://openalex.org/W2165639228","https://openalex.org/W2170157200","https://openalex.org/W4230251209","https://openalex.org/W4236236547","https://openalex.org/W4245668478","https://openalex.org/W6677524863"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W3024364549","https://openalex.org/W4206019083","https://openalex.org/W2048865712","https://openalex.org/W1976265003","https://openalex.org/W2370378377","https://openalex.org/W4237510188","https://openalex.org/W2130160813","https://openalex.org/W2054476758"],"abstract_inverted_index":{"The":[0],"discovery":[1],"and":[2,60,118,128,152],"functional":[3,55],"analysis":[4],"of":[5,16,29,76,99,165,183,200,207],"noncoding":[6],"RNA":[7,32,56,101],"(ncRNA)":[8],"systems":[9],"in":[10,35,66,109,114,204],"different":[11],"organisms":[12],"motivates":[13],"the":[14,77,131,138,144,159,201,208],"development":[15],"tools":[17,23],"for":[18,27,43,63,176,198],"aiding":[19],"ncRNA":[20],"research.":[21],"Several":[22],"exist":[24],"that":[25,51],"search":[26],"occurrences":[28],"a":[30,41,49,53,87,96,115],"given":[31],"structural":[33,97],"profile":[34],"genomic":[36,67,110,148],"sequences.":[37],"Yet,":[38],"there":[39],"is":[40,93,125],"need":[42],"an":[44,100],"\u201dRNA":[45],"BLAST\u201d":[46],"tool,":[47,90],"i.e.":[48],"tool":[50],"takes":[52],"putative":[54],"sequence":[57,102,124],"as":[58],"input,":[59],"efficiently":[61],"searches":[62],"similar":[64,136],"sequences":[65,111],"databases,":[68],"taking":[69],"into":[70],"consideration":[71],"potential":[72,105],"secondary":[73],"structure":[74],"features":[75],"input":[78],"query":[79,123,139,160],"sequence.":[80],"This":[81],"work":[82],"aims":[83],"at":[84],"providing":[85],"such":[86],"tool.":[88],"Our":[89],"denoted":[91],"StemSearch,":[92],"based":[94],"on":[95],"representation":[98],"by":[103,195],"its":[104],"stems.":[106],"Potential":[107],"stems":[108,129,140],"are":[112,135,141,150],"identified":[113,151],"preprocessing":[116],"stage,":[117],"indexed.":[119],"A":[120],"user":[121],"provided":[122],"likewise":[126],"processed,":[127],"from":[130,143],"target":[132],"genomes":[133,194],"which":[134],"to":[137,155,158,191],"retrieved":[142],"index.":[145],"Then,":[146],"relevant":[147],"regions":[149],"ranked":[153],"according":[154],"their":[156],"similarity":[157],"stem-set":[161],"while":[162],"enforcing":[163],"conservation":[164],"cross-stem":[166],"topology.":[167],"Experiments":[168],"using":[169],"RFAM":[170],"families":[171],"show":[172],"significantly":[173],"improved":[174],"recall":[175],"StemSearch":[177],"over":[178],"BLAST,":[179],"with":[180],"small":[181],"loss":[182],"precision.":[184],"We":[185],"further":[186],"demonstrate":[187],"our":[188],"system's":[189],"capability":[190],"handle":[192],"eukaryotic":[193],"successfully":[196],"searching":[197],"members":[199],"7SK":[202],"family":[203],"chromosome":[205],"2":[206],"human":[209],"genome.":[210]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
