{"id":"https://openalex.org/W2117759335","doi":"https://doi.org/10.1177/109434209500900103","title":"Optimization and Performance Analysis of a Massively Parallel Dynamic Programming Algorithm for Rna Secondary Structure Prediction","display_name":"Optimization and Performance Analysis of a Massively Parallel Dynamic Programming Algorithm for Rna Secondary Structure Prediction","publication_year":1995,"publication_date":"1995-03-01","ids":{"openalex":"https://openalex.org/W2117759335","doi":"https://doi.org/10.1177/109434209500900103","mag":"2117759335"},"language":"en","primary_location":{"id":"doi:10.1177/109434209500900103","is_oa":false,"landing_page_url":"https://doi.org/10.1177/109434209500900103","pdf_url":null,"source":{"id":"https://openalex.org/S4210228336","display_name":"The International Journal of Supercomputer Applications and High Performance Computing","issn_l":"1078-3482","issn":["1078-3482"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of Supercomputer Applications and High Performance Computing","raw_type":"journal-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/A5010562576","display_name":"Bruce A. Shapiro","orcid":null},"institutions":[{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bruce A. Shapiro","raw_affiliation_strings":["Image Processing Section, Laboratory of Mathematical\rBiology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer\rInstitute, Frederick Cancer Research and Development Center, National Institutes\rof Health, Frederick, Maryland 21702","Image Processing Section, Laboratory of Mathematical#R#Biology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer#R#Institute, Frederick Cancer Research and Development Center, National Institutes#R#of Health, Frederick, Maryland 21702"],"affiliations":[{"raw_affiliation_string":"Image Processing Section, Laboratory of Mathematical\rBiology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer\rInstitute, Frederick Cancer Research and Development Center, National Institutes\rof Health, Frederick, Maryland 21702","institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Image Processing Section, Laboratory of Mathematical#R#Biology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer#R#Institute, Frederick Cancer Research and Development Center, National Institutes#R#of Health, Frederick, Maryland 21702","institution_ids":["https://openalex.org/I4210130649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014690923","display_name":"Jih-Hsiang Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I880747138","display_name":"Science Applications International Corporation (United States)","ror":"https://ror.org/00zv91802","country_code":"US","type":"company","lineage":["https://openalex.org/I880747138"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jih-Hsiang Chen","raw_affiliation_strings":["Frederick Biomedical Supercomputer Center, PRI/DYNCORP,\rNCI/FCRDC, Frederick, Maryland 21702","Frederick Biomedical Supercomputer Center, PRI/DYNCORP,#R#NCI/FCRDC, Frederick, Maryland 21702"],"affiliations":[{"raw_affiliation_string":"Frederick Biomedical Supercomputer Center, PRI/DYNCORP,\rNCI/FCRDC, Frederick, Maryland 21702","institution_ids":["https://openalex.org/I880747138"]},{"raw_affiliation_string":"Frederick Biomedical Supercomputer Center, PRI/DYNCORP,#R#NCI/FCRDC, Frederick, Maryland 21702","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007520174","display_name":"Tim Busse","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tim Busse","raw_affiliation_strings":["MASPAR Computer Corporation, Bethesda, Maryland 20817"],"affiliations":[{"raw_affiliation_string":"MASPAR Computer Corporation, Bethesda, Maryland 20817","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039512345","display_name":"Joseph Navetta","orcid":null},"institutions":[{"id":"https://openalex.org/I880747138","display_name":"Science Applications International Corporation (United States)","ror":"https://ror.org/00zv91802","country_code":"US","type":"company","lineage":["https://openalex.org/I880747138"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Navetta","raw_affiliation_strings":["Frederick Biomedical Supercomputer Center, PRI/DYNCORP,\rNCI/FCRDC, Frederick, Maryland 21702","Frederick Biomedical Supercomputer Center, PRI/DYNCORP,#R#NCI/FCRDC, Frederick, Maryland 21702"],"affiliations":[{"raw_affiliation_string":"Frederick Biomedical Supercomputer Center, PRI/DYNCORP,\rNCI/FCRDC, Frederick, Maryland 21702","institution_ids":["https://openalex.org/I880747138"]},{"raw_affiliation_string":"Frederick Biomedical Supercomputer Center, PRI/DYNCORP,#R#NCI/FCRDC, Frederick, Maryland 21702","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035504057","display_name":"Wojciech K. Kasprzak","orcid":null},"institutions":[{"id":"https://openalex.org/I880747138","display_name":"Science Applications International Corporation (United States)","ror":"https://ror.org/00zv91802","country_code":"US","type":"company","lineage":["https://openalex.org/I880747138"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wojciech Kasprzak","raw_affiliation_strings":["Frederick Biomedical Supercomputer Center, PRI/DYNCORP,\rNCI/FCRDC, Frederick, Maryland 21702","Frederick Biomedical Supercomputer Center, PRI/DYNCORP,#R#NCI/FCRDC, Frederick, Maryland 21702"],"affiliations":[{"raw_affiliation_string":"Frederick Biomedical Supercomputer Center, PRI/DYNCORP,\rNCI/FCRDC, Frederick, Maryland 21702","institution_ids":["https://openalex.org/I880747138"]},{"raw_affiliation_string":"Frederick Biomedical Supercomputer Center, PRI/DYNCORP,#R#NCI/FCRDC, Frederick, Maryland 21702","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034987854","display_name":"Jacob V. Maizel","orcid":null},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob V. Maizel","raw_affiliation_strings":["Image Processing Section, Laboratory of Mathematical\rBiology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer\rInstitute, Frederick Cancer Research and Development Center, National Institutes\rof Health, Frederick, Maryland 21702","Image Processing Section, Laboratory of Mathematical#R#Biology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer#R#Institute, Frederick Cancer Research and Development Center, National Institutes#R#of Health, Frederick, Maryland 21702"],"affiliations":[{"raw_affiliation_string":"Image Processing Section, Laboratory of Mathematical\rBiology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer\rInstitute, Frederick Cancer Research and Development Center, National Institutes\rof Health, Frederick, Maryland 21702","institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Image Processing Section, Laboratory of Mathematical#R#Biology, Division of Cancer Biology, Diagnosis, and Centers, National Cancer#R#Institute, Frederick Cancer Research and Development Center, National Institutes#R#of Health, Frederick, Maryland 21702","institution_ids":["https://openalex.org/I4210130649"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010562576"],"corresponding_institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"],"apc_list":null,"apc_paid":null,"fwci":0.7947,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.71599972,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"9","issue":"1","first_page":"29","last_page":"39"},"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":0.9987999796867371,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9975000023841858,"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/dynamic-programming","display_name":"Dynamic programming","score":0.7051156163215637},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6747345924377441},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.671926736831665},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.5400368571281433},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4723062515258789},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.45396173000335693},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.40494516491889954},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17688381671905518}],"concepts":[{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.7051156163215637},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6747345924377441},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.671926736831665},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.5400368571281433},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4723062515258789},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.45396173000335693},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.40494516491889954},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17688381671905518},{"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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/109434209500900103","is_oa":false,"landing_page_url":"https://doi.org/10.1177/109434209500900103","pdf_url":null,"source":{"id":"https://openalex.org/S4210228336","display_name":"The International Journal of Supercomputer Applications and High Performance Computing","issn_l":"1078-3482","issn":["1078-3482"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of Supercomputer Applications and High Performance Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8700000047683716,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1490558618","https://openalex.org/W1522370717","https://openalex.org/W1530482967","https://openalex.org/W1555532796","https://openalex.org/W1964916693","https://openalex.org/W1995403172","https://openalex.org/W2005638772","https://openalex.org/W2017313617","https://openalex.org/W2044326807","https://openalex.org/W2100167293","https://openalex.org/W2124162379","https://openalex.org/W2171582839","https://openalex.org/W2925006810","https://openalex.org/W4245544908"],"related_works":["https://openalex.org/W2117141678","https://openalex.org/W2117014006","https://openalex.org/W4233815414","https://openalex.org/W119040397","https://openalex.org/W1543798151","https://openalex.org/W2022867548","https://openalex.org/W2054028885","https://openalex.org/W2422063225","https://openalex.org/W2183697970","https://openalex.org/W2164202285"],"abstract_inverted_index":{"An":[0],"optimized":[1],"and":[2,15,51,60,75,129],"parallelized":[3],"form":[4],"of":[5,12,24,69,73,112,132],"a":[6,28,121],"dynamic":[7],"pro":[8],"gramming":[9],"algorithm":[10,26,88],"capable":[11],"generating":[13],"optimal":[14],"suboptimal":[16],"RNA":[17,107],"secondary":[18],"structures":[19],"is":[20,34],"pre":[21],"sented.":[22],"Implementation":[23],"this":[25,135],"on":[27],"MasPar":[29,74],"MP-2":[30],"with":[31],"16K":[32],"processors":[33],"shown":[35],"to":[36,94,104,119],"perform":[37],"ex":[38],"tremely":[39],"well":[40],"for":[41],"very":[42],"large":[43,106],"nucleic":[44],"acid":[45],"sequences":[46,56,108],"such":[47],"as":[48],"HIV":[49],"(AIDS)":[50],"Rhinovirus":[52],"(common":[53],"cold).":[54],"These":[55],"are,":[57],"respectively,":[58],"9,128":[59],"7,208":[61],"nu":[62],"cleotides":[63],"in":[64,100,109,124],"length.":[65],"By":[66],"taking":[67],"advantage":[68],"the":[70,78,82,87,126],"parallel":[71],"nature":[72],"also":[76],"optimizing":[77],"communica":[79],"tion":[80],"requirements":[81],"implementation":[83],"essentially":[84],"re":[85],"duced":[86],"from":[89],"order":[90],"O(n":[91],"3":[92],")":[93],"0(n":[95],"2":[96],").":[97],"This":[98,114],"reduction":[99],"complexity":[101],"enables":[102],"us":[103],"fold":[105],"reasonable":[110],"amounts":[111],"time.":[113],"capa":[115],"bility":[116],"has":[117],"proven":[118],"be":[120],"valuable":[122],"tool":[123],"studying":[125],"molecular":[127],"structure":[128],"biological":[130],"function":[131],"mole":[133],"cules":[134],"large.":[136]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}