{"id":"https://openalex.org/W2042844155","doi":"https://doi.org/10.1089/10665270050081441","title":"Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers","display_name":"Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers","publication_year":2000,"publication_date":"2000-02-01","ids":{"openalex":"https://openalex.org/W2042844155","doi":"https://doi.org/10.1089/10665270050081441","mag":"2042844155","pmid":"https://pubmed.ncbi.nlm.nih.gov/10890394"},"language":"en","primary_location":{"id":"doi:10.1089/10665270050081441","is_oa":false,"landing_page_url":"https://doi.org/10.1089/10665270050081441","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of 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/A5071615090","display_name":"Martin Fekete","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Martin Fekete","raw_affiliation_strings":["Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien, A-1090 Wien, Austria"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien, A-1090 Wien, Austria","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011771355","display_name":"Ivo L. Hofacker","orcid":"https://orcid.org/0000-0001-7132-0800"},"institutions":[{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ivo L. Hofacker","raw_affiliation_strings":["The Santa Fe Institute, Santa Fe, NM 87501"],"affiliations":[{"raw_affiliation_string":"The Santa Fe Institute, Santa Fe, NM 87501","institution_ids":["https://openalex.org/I1308548392"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien, A-1090 Wien, Austria and The Santa Fe Institute, Santa Fe, NM 87501"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Theoretische Chemie, Universit\u00e4t Wien, A-1090 Wien, Austria and The Santa Fe Institute, Santa Fe, NM 87501","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071615090"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5975,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.65830948,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"7","issue":"1-2","first_page":"171","last_page":"182"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9984999895095825,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.8592580556869507},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6814748644828796},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6676597595214844},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.6158649325370789},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.5602103471755981},{"id":"https://openalex.org/keywords/massive-parallel-sequencing","display_name":"Massive parallel sequencing","score":0.5481312274932861},{"id":"https://openalex.org/keywords/pairing","display_name":"Pairing","score":0.5133980512619019},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48156240582466125},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.44207826256752014},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4371466636657715},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3707180619239807},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3391255736351013},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2732987105846405},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2002103328704834},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1822732388973236},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16409283876419067}],"concepts":[{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.8592580556869507},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6814748644828796},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6676597595214844},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.6158649325370789},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.5602103471755981},{"id":"https://openalex.org/C192800701","wikidata":"https://www.wikidata.org/wiki/Q6784807","display_name":"Massive parallel sequencing","level":4,"score":0.5481312274932861},{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.5133980512619019},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48156240582466125},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.44207826256752014},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4371466636657715},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3707180619239807},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3391255736351013},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2732987105846405},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2002103328704834},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1822732388973236},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16409283876419067},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C54101563","wikidata":"https://www.wikidata.org/wiki/Q124131","display_name":"Superconductivity","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1089/10665270050081441","is_oa":false,"landing_page_url":"https://doi.org/10.1089/10665270050081441","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:10890394","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/10890394","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 computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312060","display_name":"Francis Crick Institute","ror":"https://ror.org/04tnbqb63"},{"id":"https://openalex.org/F4320332467","display_name":"U.S. Air Force","ror":"https://ror.org/006gmme17"},{"id":"https://openalex.org/F4320334023","display_name":"Arkansas High Performance Computing Center, University of Arkansas","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1490558618","https://openalex.org/W1543796220","https://openalex.org/W1816614902","https://openalex.org/W1964916693","https://openalex.org/W1984675364","https://openalex.org/W1984987205","https://openalex.org/W1999775600","https://openalex.org/W2004982650","https://openalex.org/W2013951307","https://openalex.org/W2017313617","https://openalex.org/W2018603137","https://openalex.org/W2020496613","https://openalex.org/W2025763720","https://openalex.org/W2038224644","https://openalex.org/W2044595289","https://openalex.org/W2061158331","https://openalex.org/W2098607715","https://openalex.org/W2114654749","https://openalex.org/W2117431427","https://openalex.org/W2117759335","https://openalex.org/W2124398596","https://openalex.org/W2170472690","https://openalex.org/W4205373245"],"related_works":["https://openalex.org/W3015473028","https://openalex.org/W3201176751","https://openalex.org/W2057898405","https://openalex.org/W2029180842","https://openalex.org/W2953807518","https://openalex.org/W1993094293","https://openalex.org/W2766795546","https://openalex.org/W2963079118","https://openalex.org/W2596828944","https://openalex.org/W1979242040"],"abstract_inverted_index":{"We":[0],"present":[1],"an":[2,14],"implementation":[3],"of":[4,13,33],"McCaskill's":[5],"algorithm":[6],"for":[7,17],"computing":[8],"the":[9],"base":[10],"pair":[11],"probabilities":[12],"RNA":[15,31],"molecule":[16],"massively":[18],"parallel":[19],"message":[20],"passing":[21],"architectures.":[22],"The":[23],"program":[24],"can":[25],"be":[26],"used":[27],"to":[28,39],"routinely":[29],"fold":[30],"sequences":[32],"more":[34],"than":[35],"10,000":[36],"nucleotides.":[37],"Applications":[38],"complete":[40],"viral":[41],"genomes":[42],"are":[43],"discussed.":[44]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-10-10T00:00:00"}
