{"id":"https://openalex.org/W2097424571","doi":"https://doi.org/10.1145/2382936.2383016","title":"Secondary structure predictions for long RNA sequences based on inversion excursions","display_name":"Secondary structure predictions for long RNA sequences based on inversion excursions","publication_year":2012,"publication_date":"2012-10-07","ids":{"openalex":"https://openalex.org/W2097424571","doi":"https://doi.org/10.1145/2382936.2383016","mag":"2097424571"},"language":"en","primary_location":{"id":"doi:10.1145/2382936.2383016","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2383016","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","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/A5016165886","display_name":"Daniel T. Yehdego","orcid":null},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel T. Yehdego","raw_affiliation_strings":["The University of Texas at El Paso","[The University of Texas at El Paso]"],"affiliations":[{"raw_affiliation_string":"The University of Texas at El Paso","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"[The University of Texas at El Paso]","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100714042","display_name":"Boyu Zhang","orcid":"https://orcid.org/0009-0008-5991-2799"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Boyu Zhang","raw_affiliation_strings":["University of Delaware"],"affiliations":[{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078387820","display_name":"Michela Taufer","orcid":"https://orcid.org/0000-0002-0031-6377"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michela Taufer","raw_affiliation_strings":["University of Delaware"],"affiliations":[{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044714154","display_name":"Vikram Kodimala","orcid":null},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vikram Kumar Reddy Kodimala","raw_affiliation_strings":["The University of Texas at El Paso","[The University of Texas at El Paso]"],"affiliations":[{"raw_affiliation_string":"The University of Texas at El Paso","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"[The University of Texas at El Paso]","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061091881","display_name":"Rahulsimham Vegesna","orcid":"https://orcid.org/0000-0001-9829-9765"},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rahulsimham Vegesna","raw_affiliation_strings":["The University of Texas at El Paso","[The University of Texas at El Paso]"],"affiliations":[{"raw_affiliation_string":"The University of Texas at El Paso","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"[The University of Texas at El Paso]","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110749256","display_name":"Sameera Viswakula","orcid":"https://orcid.org/0000-0002-6961-898X"},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sameera Viswakula","raw_affiliation_strings":["The University of Texas at El Paso","[The University of Texas at El Paso]"],"affiliations":[{"raw_affiliation_string":"The University of Texas at El Paso","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"[The University of Texas at El Paso]","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026819884","display_name":"Kyle Johnson","orcid":"https://orcid.org/0000-0001-5126-1399"},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle L. Johnson","raw_affiliation_strings":["The University of Texas at El Paso","[The University of Texas at El Paso]"],"affiliations":[{"raw_affiliation_string":"The University of Texas at El Paso","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"[The University of Texas at El Paso]","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040135909","display_name":"Ming\u2010Ying Leung","orcid":"https://orcid.org/0000-0003-2035-1214"},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming-Ying Leung","raw_affiliation_strings":["The University of Texas at El Paso","[The University of Texas at El Paso]"],"affiliations":[{"raw_affiliation_string":"The University of Texas at El Paso","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"[The University of Texas at El Paso]","institution_ids":["https://openalex.org/I164936912"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5016165886"],"corresponding_institution_ids":["https://openalex.org/I164936912"],"apc_list":null,"apc_paid":null,"fwci":0.1313,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52183163,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"545","last_page":"547"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/computer-science","display_name":"Computer science","score":0.6563214659690857},{"id":"https://openalex.org/keywords/inversion","display_name":"Inversion (geology)","score":0.641998827457428},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5920591354370117},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.576349139213562},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5401586294174194},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.49000993371009827},{"id":"https://openalex.org/keywords/market-segmentation","display_name":"Market segmentation","score":0.43904635310173035},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40827029943466187},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39339005947113037},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37910494208335876},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34315943717956543},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12254953384399414},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07754018902778625}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6563214659690857},{"id":"https://openalex.org/C1893757","wikidata":"https://www.wikidata.org/wiki/Q3653001","display_name":"Inversion (geology)","level":3,"score":0.641998827457428},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5920591354370117},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.576349139213562},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5401586294174194},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.49000993371009827},{"id":"https://openalex.org/C125308379","wikidata":"https://www.wikidata.org/wiki/Q363057","display_name":"Market segmentation","level":2,"score":0.43904635310173035},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40827029943466187},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39339005947113037},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37910494208335876},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34315943717956543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12254953384399414},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07754018902778625},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C109007969","wikidata":"https://www.wikidata.org/wiki/Q749565","display_name":"Structural basin","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2382936.2383016","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2382936.2383016","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:oai:digitalcommons.utep.edu:math_papers-1084","is_oa":false,"landing_page_url":"http://doi.acm.org/10.1145/2382936.2383016","pdf_url":null,"source":{"id":"https://openalex.org/S4377196403","display_name":"scholarworks - UTEP (The University of Texas at El Paso)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I164936912","host_organization_name":"The University of Texas at El Paso","host_organization_lineage":["https://openalex.org/I164936912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Departmental Papers (Math)","raw_type":"text"},{"id":"pmh:oai:scholarworks.utep.edu:math_papers-1084","is_oa":false,"landing_page_url":"https://scholarworks.utep.edu/math_papers/85","pdf_url":null,"source":{"id":"https://openalex.org/S4377196403","display_name":"scholarworks - UTEP (The University of Texas at El Paso)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I164936912","host_organization_name":"The University of Texas at El Paso","host_organization_lineage":["https://openalex.org/I164936912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Departmental Papers (Math)","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2286497907","display_name":null,"funder_award_id":"DMS 0800272/0800266EIA 0080940","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2613127052","display_name":null,"funder_award_id":"DMS 0800272/0800266EIA 0080940","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"},{"id":"https://openalex.org/G7541565603","display_name":null,"funder_award_id":"RCMI 5G12RR008124-18NIMHD 8G12MD007592","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337380","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81"},{"id":"https://openalex.org/F4320337534","display_name":"National Institute on Minority Health and Health Disparities","ror":"https://ror.org/0493hgw16"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2008610661","https://openalex.org/W2019360170","https://openalex.org/W2106293441","https://openalex.org/W2123241418","https://openalex.org/W2163638609","https://openalex.org/W3015238844"],"related_works":["https://openalex.org/W2592395359","https://openalex.org/W2535231171","https://openalex.org/W2045342254","https://openalex.org/W1501331687","https://openalex.org/W2326647871","https://openalex.org/W4205247302","https://openalex.org/W2468652214","https://openalex.org/W2501551404","https://openalex.org/W1504527458","https://openalex.org/W2130144716"],"abstract_inverted_index":{"The":[0,68],"tremendous":[1],"demand":[2],"on":[3,105],"computer":[4],"memory":[5],"and":[6,54,83,96,150,177],"computing":[7],"time":[8],"for":[9,99,141,170],"prediction":[10,23,58,125,172,194],"of":[11,18,50,64,70,77,111,117,173],"complex":[12],"secondary":[13,21,48,136],"structures":[14,49,137],"limits":[15],"the":[16,47,57,62,65,78,94,109,112,121,124,142,148,155,171,179],"applicability":[17],"most":[19],"RNA":[20,28,40,102,175],"structure":[22,63],"programs":[24],"available":[25],"to":[26,32,60],"short":[27],"sequences.":[29],"We":[30],"propose":[31],"approach":[33,169],"this":[34],"problem":[35],"by":[36,183],"segmenting":[37,100],"a":[38,74,115,167],"long":[39,101,174],"sequence":[41,144,185],"into":[42],"shorter":[43],"non-overlapping":[44],"chunks,":[45],"predicting":[46],"each":[51],"chunk":[52],"individually,":[53],"then":[55],"assembling":[56],"results":[59,160],"give":[61],"original":[66],"sequence.":[67],"selection":[69],"cutting":[71,92,131,152,165,180],"points":[72,181],"is":[73,166],"crucial":[75],"component":[76],"approach.":[79],"Noting":[80],"that":[81,164],"stem-loops":[82],"pseudoknots":[84],"always":[85],"contain":[86],"an":[87],"inversion,":[88],"we":[89],"developed":[90],"two":[91],"methods,":[93,98],"centered":[95,149],"optimized":[97,151],"sequences":[103,113],"based":[104],"inversion":[106,189],"excursions.":[107],"For":[108],"majority":[110],"in":[114],"dataset":[116],"50":[118],"RNAs":[119],"from":[120],"RFAM":[122],"database,":[123],"algorithm":[126],"PKnotsRG":[127],"used":[128],"with":[129],"these":[130],"methods":[132,153],"produces":[133],"more":[134],"accurate":[135],"than":[138],"those":[139],"predicted":[140],"whole":[143],"without":[145],"segmentation.":[146,158],"Both":[147],"outperform":[154],"na\u00efve":[156],"regular":[157],"These":[159],"support":[161],"our":[162],"claim":[163],"promising":[168],"sequences,":[176],"choosing":[178],"intelligently":[182],"considering":[184],"features":[186],"such":[187],"as":[188],"excursions":[190],"can":[191],"further":[192],"enhance":[193],"accuracy.":[195]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
