{"id":"https://openalex.org/W2100039848","doi":"https://doi.org/10.1371/journal.pcbi.1000124","title":"Efficient Algorithms for Probing the RNA Mutation Landscape","display_name":"Efficient Algorithms for Probing the RNA Mutation Landscape","publication_year":2008,"publication_date":"2008-08-07","ids":{"openalex":"https://openalex.org/W2100039848","doi":"https://doi.org/10.1371/journal.pcbi.1000124","mag":"2100039848","pmid":"https://pubmed.ncbi.nlm.nih.gov/18688270"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000124","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000124","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000124&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000124&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000881484","display_name":"J\u00e9r\u00f4me Waldisp\u00fchl","orcid":"https://orcid.org/0000-0002-2561-7117"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00f4me Waldisp\u00fchl","raw_affiliation_strings":["Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000525449","display_name":"Srinivas Devadas","orcid":"https://orcid.org/0000-0001-8253-7714"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Srinivas Devadas","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044078921","display_name":"Bonnie Berger","orcid":"https://orcid.org/0000-0002-2724-7228"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bonnie Berger","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038186958","display_name":"Peter Clote","orcid":"https://orcid.org/0000-0003-3628-2874"},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter Clote","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America","institution_ids":["https://openalex.org/I103531236"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5038186958"],"corresponding_institution_ids":["https://openalex.org/I103531236"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.7984,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.84509717,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"4","issue":"8","first_page":"e1000124","last_page":"e1000124"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9990000128746033,"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":0.9955000281333923,"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/partition-function","display_name":"Partition function (quantum field theory)","score":0.5587208867073059},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.5471675395965576},{"id":"https://openalex.org/keywords/pointwise","display_name":"Pointwise","score":0.5251390933990479},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5070157051086426},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44354158639907837},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43470993638038635},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4262691140174866},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.420802503824234},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.37184959650039673},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.30624473094940186},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26412880420684814},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24463289976119995},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.20155957341194153}],"concepts":[{"id":"https://openalex.org/C2778401447","wikidata":"https://www.wikidata.org/wiki/Q7140637","display_name":"Partition function (quantum field theory)","level":2,"score":0.5587208867073059},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.5471675395965576},{"id":"https://openalex.org/C2777984123","wikidata":"https://www.wikidata.org/wiki/Q9248237","display_name":"Pointwise","level":2,"score":0.5251390933990479},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5070157051086426},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44354158639907837},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43470993638038635},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4262691140174866},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.420802503824234},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.37184959650039673},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.30624473094940186},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26412880420684814},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24463289976119995},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.20155957341194153},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"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":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"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":"D012093","descriptor_name":"Replicon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012093","descriptor_name":"Replicon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012093","descriptor_name":"Replicon","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016174","descriptor_name":"Hepacivirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1000124","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000124","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000124&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18688270","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18688270","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:b3d904cd5ab84bc4b7fb455bd18e2786","is_oa":true,"landing_page_url":"https://doaj.org/article/b3d904cd5ab84bc4b7fb455bd18e2786","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 8, p e1000124 (2008)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1217865","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2475669","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/150018","is_oa":true,"landing_page_url":"https://figshare.com/articles/Efficient_Algorithms_for_Probing_the_RNA_Mutation_Landscape/150018","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000124","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000124","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000124&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G3172143998","display_name":"RNA-Parafold: Algorithms and Web Server for Parametric Aspects of RNA Secondary Structure","funder_award_id":"0543506","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100039848.pdf","grobid_xml":"https://content.openalex.org/works/W2100039848.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1522740115","https://openalex.org/W1527024319","https://openalex.org/W1543796220","https://openalex.org/W1551334274","https://openalex.org/W1569069879","https://openalex.org/W1585306636","https://openalex.org/W1599612900","https://openalex.org/W1822105579","https://openalex.org/W1969269683","https://openalex.org/W1971013467","https://openalex.org/W1977940795","https://openalex.org/W1979735725","https://openalex.org/W1984675364","https://openalex.org/W1994958179","https://openalex.org/W2000191287","https://openalex.org/W2009818318","https://openalex.org/W2015527441","https://openalex.org/W2018216725","https://openalex.org/W2022916085","https://openalex.org/W2023919813","https://openalex.org/W2025763720","https://openalex.org/W2038815243","https://openalex.org/W2039075777","https://openalex.org/W2042881722","https://openalex.org/W2045864964","https://openalex.org/W2051713039","https://openalex.org/W2060152734","https://openalex.org/W2061930808","https://openalex.org/W2062469063","https://openalex.org/W2067810191","https://openalex.org/W2073774106","https://openalex.org/W2076728538","https://openalex.org/W2097678865","https://openalex.org/W2102304447","https://openalex.org/W2102857384","https://openalex.org/W2103250001","https://openalex.org/W2116155561","https://openalex.org/W2124974356","https://openalex.org/W2125088626","https://openalex.org/W2127979560","https://openalex.org/W2132034333","https://openalex.org/W2133279153","https://openalex.org/W2133876293","https://openalex.org/W2136377885","https://openalex.org/W2137640371","https://openalex.org/W2141157874","https://openalex.org/W2145832146","https://openalex.org/W2150503741","https://openalex.org/W2151994495","https://openalex.org/W2152267201","https://openalex.org/W2155396586","https://openalex.org/W2155761852","https://openalex.org/W2158381555","https://openalex.org/W2158826174","https://openalex.org/W3124837637","https://openalex.org/W4242023031"],"related_works":["https://openalex.org/W2140020064","https://openalex.org/W143502885","https://openalex.org/W42113618","https://openalex.org/W2103468410","https://openalex.org/W1856228368","https://openalex.org/W3197542402","https://openalex.org/W2971527398","https://openalex.org/W4385457841","https://openalex.org/W2581348958","https://openalex.org/W4367048159"],"abstract_inverted_index":{"The":[0],"diversity":[1],"and":[2,13,21,159,184,267,293,298,364],"importance":[3],"of":[4,15,26,55,63,105,131,135,138,168,203,215,222,226,234,241,277,301,326,345,357,379],"the":[5,11,16,53,56,60,88,92,102,111,119,127,139,153,160,174,201,212,223,231,256,260,270,278,323,327,380],"role":[6],"played":[7],"by":[8,110],"RNAs":[9,104],"in":[10,259,359],"regulation":[12],"development":[14],"cell":[17],"are":[18,79,91,386],"now":[19],"well-known":[20],"well-documented.":[22],"This":[23,193,370],"broad":[24],"range":[25],"functions":[27],"is":[28],"achieved":[29],"through":[30,38],"specific":[31,236],"structures":[32,67,134,167],"that":[33,253,322,350],"have":[34,244],"been":[35,333],"(presumably)":[36],"optimized":[37,334],"evolution.":[39],"State-of-the-art":[40],"methods,":[41],"such":[42,100],"as":[43,81,83,101],"McCaskill's":[44],"algorithm,":[45],"use":[46],"a":[47,69,216,218,342],"statistical":[48],"mechanics":[49],"framework":[50],"based":[51],"on":[52,68,274],"computation":[54],"partition":[57,121,161],"function":[58,107,122,162],"over":[59,126,164],"canonical":[61,129],"ensemble":[62,130],"all":[64,132,136,165,169],"possible":[65],"secondary":[66,73,133,166,257],"given":[70,140],"sequence.":[71,141],"Although":[72],"structure":[74,157],"predictions":[75],"from":[76,341],"thermodynamics-based":[77],"algorithms":[78],"not":[80,181],"accurate":[82],"methods":[84,90],"employing":[85],"comparative":[86],"genomics,":[87],"former":[89],"only":[93],"available":[94,387],"tools":[95],"to":[96,124,176,182,188,199,207,248,268,335],"investigate":[97,249],"novel":[98,219],"RNAs,":[99],"many":[103],"unknown":[106],"recently":[108],"reported":[109],"ENCODE":[112],"consortium.":[113],"In":[114,283],"this":[115],"paper,":[116],"we":[117,229,285,319],"generalize":[118],"McCaskill":[120],"algorithm":[123],"sum":[125],"grand":[128],"mutants":[137],"Specifically,":[142],"our":[143,299],"new":[144],"program,":[145],"RNAmutants,":[146],"simultaneously":[147],"computes":[148],"for":[149,376],"each":[150],"integer":[151],"k":[152],"minimum":[154],"free":[155],"energy":[156],"MFE(k)":[158],"Z(k)":[163],"k-point":[170],"mutants,":[171],"even":[172],"allowing":[173],"user":[175],"specify":[177],"certain":[178,185],"positions":[179,186,238],"required":[180,187],"mutate":[183],"base-pair":[189],"or":[190,239],"remain":[191],"unpaired.":[192],"technically":[194],"important":[195],"extension":[196],"allows":[197],"us":[198],"study":[200],"resilience":[202],"an":[204],"RNA":[205,329,362,368,381],"molecule":[206],"pointwise":[208,346],"mutations.":[209,347],"By":[210],"computing":[211],"mutation":[213],"profile":[214],"sequence,":[217],"graphical":[220],"representation":[221],"mutational":[224],"tendency":[225],"nucleotide":[227,237],"positions,":[228],"analyze":[230],"deleterious":[232,250,302,311,343],"nature":[233],"mutating":[235],"groups":[240],"positions.":[242],"We":[243,348],"successfully":[245],"applied":[246,273],"RNAmutants":[247,358],"mutations":[251,303],"(mutations":[252],"radically":[254],"modify":[255],"structure)":[258],"Hepatitis":[261,291],"C":[262,292,331],"virus":[263,330],"cis-acting":[264],"replication":[265],"element":[266],"evaluate":[269],"evolutionary":[271],"pressure":[272],"different":[275],"regions":[276,340],"HIV":[279,294],"trans-activation":[280],"response":[281],"element.":[282],"particular,":[284],"show":[286],"qualitative":[287],"agreement":[288],"between":[289],"published":[290],"experimental":[295],"mutagenesis":[296],"studies":[297],"analysis":[300],"using":[304],"RNAmutants.":[305],"Our":[306],"work":[307,371],"also":[308,372],"predicts":[309],"other":[310],"mutations,":[312],"which":[313],"could":[314],"be":[315,353],"verified":[316],"experimentally.":[317],"Finally,":[318],"provide":[320],"evidence":[321],"3'":[324],"UTR":[325],"GB":[328],"has":[332],"preserve":[336],"evolutionarily":[337],"conserved":[338],"stem":[339],"effect":[344],"hope":[349],"there":[351],"will":[352],"long-term":[354],"potential":[355,374],"applications":[356,375],"de":[360],"novo":[361],"design":[363,366],"drug":[365],"against":[367],"viruses.":[369],"suggests":[373],"large-scale":[377],"exploration":[378],"sequence-structure":[382],"network.":[383],"Binary":[384],"distributions":[385],"at":[388],"http://RNAmutants.csail.mit.edu/.":[389]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-25T08:17:42.794288","created_date":"2025-10-10T00:00:00"}