{"id":"https://openalex.org/W2061505337","doi":"https://doi.org/10.1109/bibmw.2012.6470251","title":"A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows","display_name":"A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W2061505337","doi":"https://doi.org/10.1109/bibmw.2012.6470251","mag":"2061505337"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2012.6470251","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470251","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","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/A5100714040","display_name":"Boyu Zhang","orcid":"https://orcid.org/0000-0003-1339-2173"},"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":["Department of Computer and Info. Sciences, University of Delaware, Newark, DE, USA","Department of Computer and Info. Sciences, University of Delaware, Newark, DE 19716"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Info. Sciences, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Info. Sciences, University of Delaware, Newark, DE 19716","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","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":false,"raw_author_name":"Daniel T. Yehdego","raw_affiliation_strings":["Computational Science Program, University of Texas at El Paso, El Paso, TX","Computational Science Program, University of Texas at El Paso, El Paso, TX 79968#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Science Program, University of Texas at El Paso, El Paso, TX","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"Computational Science Program, University of Texas at El Paso, El Paso, TX 79968#TAB#","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":["Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA","Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"middle","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":["Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX, USA","Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX, USA","institution_ids":["https://openalex.org/I164936912"]},{"raw_affiliation_string":"Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"last","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":["Department of Computer and Info. Sciences, University of Delaware, Newark, DE, USA","Department of Computer and Info. Sciences, University of Delaware, Newark, DE 19716"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Info. Sciences, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Info. Sciences, University of Delaware, Newark, DE 19716","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"33 suppl 1","issue":null,"first_page":"86","last_page":"93"},"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":0.9972000122070312,"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":0.9925000071525574,"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":0.7590068578720093},{"id":"https://openalex.org/keywords/chunking","display_name":"Chunking (psychology)","score":0.7016916871070862},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6179922819137573},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5099881887435913},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4792606830596924},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.46714848279953003},{"id":"https://openalex.org/keywords/parametric-statistics","display_name":"Parametric statistics","score":0.42367318272590637},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39697301387786865},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3857605755329132},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.10337749123573303},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07844507694244385}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7590068578720093},{"id":"https://openalex.org/C203357204","wikidata":"https://www.wikidata.org/wiki/Q1089605","display_name":"Chunking (psychology)","level":2,"score":0.7016916871070862},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6179922819137573},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5099881887435913},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4792606830596924},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.46714848279953003},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.42367318272590637},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39697301387786865},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3857605755329132},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.10337749123573303},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07844507694244385},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibmw.2012.6470251","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470251","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1989815251","https://openalex.org/W2011411346","https://openalex.org/W2033677231","https://openalex.org/W2042881722","https://openalex.org/W2106293441","https://openalex.org/W2122465391","https://openalex.org/W2123241418","https://openalex.org/W2147761046","https://openalex.org/W2148317584","https://openalex.org/W2148599336","https://openalex.org/W2165515048","https://openalex.org/W2400250419","https://openalex.org/W3125620659","https://openalex.org/W6653080776"],"related_works":["https://openalex.org/W2384729545","https://openalex.org/W2198395236","https://openalex.org/W2800417007","https://openalex.org/W147604216","https://openalex.org/W2118525872","https://openalex.org/W2279104074","https://openalex.org/W4240300554","https://openalex.org/W2161080928","https://openalex.org/W2041941152","https://openalex.org/W4360764637"],"abstract_inverted_index":{"Ribonucleic":[0],"acid":[1],"(RNA)":[2],"molecules":[3],"play":[4],"important":[5],"roles":[6],"in":[7],"many":[8],"biological":[9],"processes":[10,89],"including":[11],"gene":[12],"expression":[13],"and":[14,25,55,87,94,117,128,173,188,198,219],"regulation.":[15],"Their":[16],"secondary":[17,30,46,59,74],"structures":[18,31,47,65],"are":[19],"crucial":[20],"for":[21],"the":[22,26,29,49,57,62,73,77,140,148,167,170,205],"RNA":[23,79,106],"functionality,":[24],"prediction":[27,121],"of":[28,48,97,126,136,166,169,194],"is":[32],"widely":[33],"studied.":[34],"Previous":[35],"research":[36],"shows":[37,203],"that":[38],"cutting":[39,115],"long":[40],"sequences":[41],"into":[42,111,139],"shorter":[43,137],"chunks,":[44],"predicting":[45,72],"chunks":[50,112],"independently":[51],"using":[52,76,113,153,180],"thermodynamic":[53],"methods,":[54,122],"reconstructing":[56],"entire":[58,78,141],"structure":[60,75],"from":[61],"predicted":[63],"chunk":[64,118],"tend":[66],"to":[67,161,186,210],"yield":[68],"better":[69],"accuracy":[70,127],"than":[71,103],"sequence":[80,107,142],"as":[81],"a":[82,163,177],"whole.":[83],"The":[84,105,134,182],"chunking,":[85,195],"prediction,":[86,196],"reconstruction":[88,135],"can":[90,108,131,143],"use":[91],"different":[92,114,124,214],"methods":[93,116,172],"parameters,":[95,174],"some":[96],"which":[98],"produce":[99],"more":[100,154],"accurate":[101],"predictions":[102,138],"others.":[104],"be":[109,132],"cut":[110],"lengths.":[119],"Several":[120],"with":[123],"degree":[125],"computing":[129],"requirements,":[130],"used.":[133],"rely":[144],"on":[145,152],"simply":[146],"gluing":[147],"parts":[149],"together":[150],"or":[151],"sophisticated":[155],"merging":[156],"algorithms.":[157],"To":[158],"allow":[159],"scientists":[160,185,209],"perform":[162],"systematic":[164],"analysis":[165,199],"impact":[168],"several":[171],"we":[175],"propose":[176],"modularized":[178],"framework":[179,183,207],"MapReduce.":[181],"enables":[184],"automatically":[187],"efficiently":[189],"explore":[190],"large":[191],"parametric":[192],"spaces":[193],"reconstruction,":[197],"methods.":[200],"This":[201],"paper":[202],"how":[204],"MapReduce":[206],"allows":[208],"gain":[211],"insights":[212],"about":[213],"chunking":[215],"strategies":[216],"easily,":[217],"accurately,":[218],"efficiently.":[220]},"counts_by_year":[{"year":2013,"cited_by_count":4}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
