{"id":"https://openalex.org/W2107728696","doi":"https://doi.org/10.1186/1748-7188-5-22","title":"Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions","display_name":"Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions","publication_year":2010,"publication_date":"2010-05-21","ids":{"openalex":"https://openalex.org/W2107728696","doi":"https://doi.org/10.1186/1748-7188-5-22","mag":"2107728696","pmid":"https://pubmed.ncbi.nlm.nih.gov/20492641"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-5-22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-22","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-22","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-22","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044386095","display_name":"Stefan E. Seemann","orcid":"https://orcid.org/0000-0002-2359-4927"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Stefan E Seemann","raw_affiliation_strings":["Center for non-coding RNA in Technology and Health, IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark","Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, Denmark"],"affiliations":[{"raw_affiliation_string":"Center for non-coding RNA in Technology and Health, IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark","institution_ids":[]},{"raw_affiliation_string":"Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079662525","display_name":"Andreas S. Richter","orcid":"https://orcid.org/0000-0002-4166-0991"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas S Richter","raw_affiliation_strings":["Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany","Bioinformatics Group, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Bioinformatics Group, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004614832","display_name":"Jan Gorodkin","orcid":"https://orcid.org/0000-0001-5823-4000"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jan Gorodkin","raw_affiliation_strings":["Center for non-coding RNA in Technology and Health, IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark","Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, Denmark"],"affiliations":[{"raw_affiliation_string":"Center for non-coding RNA in Technology and Health, IBHV, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, 1870, Denmark","institution_ids":[]},{"raw_affiliation_string":"Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany","Bioinformatics Group, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg, 79110, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Bioinformatics Group, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044386095"],"corresponding_institution_ids":["https://openalex.org/I124055696"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":1.3501,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.79948049,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"5","issue":"1","first_page":"22","last_page":"22"},"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":0.9987000226974487,"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":0.9980000257492065,"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/rna","display_name":"RNA","score":0.6920902729034424},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.634263277053833},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.5997541546821594},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5644143223762512},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5268439054489136},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5232100486755371},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.49707821011543274},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.46617770195007324},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.4633192718029022},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3816932439804077},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3477759063243866},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28654229640960693},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20478865504264832},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12662118673324585}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6920902729034424},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.634263277053833},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.5997541546821594},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5644143223762512},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5268439054489136},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5232100486755371},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.49707821011543274},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.46617770195007324},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.4633192718029022},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3816932439804077},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3477759063243866},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28654229640960693},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20478865504264832},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12662118673324585},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1748-7188-5-22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-22","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-22","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:20492641","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20492641","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:a802b2a275ac4fcc892374d5e332fb96","is_oa":true,"landing_page_url":"https://doaj.org/article/a802b2a275ac4fcc892374d5e332fb96","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 5, Iss 1, p 22 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2903599","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2903599","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-5-22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-22","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-22","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1263940194","display_name":null,"funder_award_id":"SPP 1258","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2386046523","display_name":null,"funder_award_id":"BA 2168/2-1 SPP 1258","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3633743130","display_name":null,"funder_award_id":"SPP 1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5398132153","display_name":null,"funder_award_id":"DFG grant","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7225624288","display_name":null,"funder_award_id":"This work was","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G894356745","display_name":null,"funder_award_id":"0313921","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320321999","display_name":"Lundbeckfonden","ror":"https://ror.org/03hz8wd80"},{"id":"https://openalex.org/F4320327918","display_name":"H. Lundbeck A/S","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2107728696.pdf","grobid_xml":"https://content.openalex.org/works/W2107728696.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W165213868","https://openalex.org/W1501627602","https://openalex.org/W1542565836","https://openalex.org/W1543796220","https://openalex.org/W1577363008","https://openalex.org/W1599141268","https://openalex.org/W1622263187","https://openalex.org/W1873547760","https://openalex.org/W1974736226","https://openalex.org/W1983815263","https://openalex.org/W1984675364","https://openalex.org/W1992361112","https://openalex.org/W1994958179","https://openalex.org/W2009659958","https://openalex.org/W2043653977","https://openalex.org/W2045895660","https://openalex.org/W2053783019","https://openalex.org/W2054931730","https://openalex.org/W2055080756","https://openalex.org/W2075145482","https://openalex.org/W2085534636","https://openalex.org/W2088784401","https://openalex.org/W2099306789","https://openalex.org/W2104442040","https://openalex.org/W2119340328","https://openalex.org/W2120772351","https://openalex.org/W2129706781","https://openalex.org/W2141411594","https://openalex.org/W2150882562","https://openalex.org/W2158826174","https://openalex.org/W2160845145","https://openalex.org/W2161043701","https://openalex.org/W2164700062","https://openalex.org/W2166268906","https://openalex.org/W2170157200","https://openalex.org/W2803927613","https://openalex.org/W4237142329"],"related_works":["https://openalex.org/W2159621058","https://openalex.org/W2591061273","https://openalex.org/W2122204372","https://openalex.org/W2792232401","https://openalex.org/W2472116704","https://openalex.org/W2036643266","https://openalex.org/W1999060916","https://openalex.org/W576226539","https://openalex.org/W2427678045","https://openalex.org/W2338408817"],"abstract_inverted_index":{"We":[0],"derived":[1],"a":[2,38],"rather":[3],"extensive":[4],"algorithm.":[5],"One":[6],"of":[7,10,24,29,40,52],"the":[8,22,48,53],"advantages":[9],"our":[11],"approach":[12],"(in":[13],"contrast":[14],"to":[15],"other":[16],"RNA-RNA":[17],"interaction":[18],"prediction":[19,28],"methods)":[20],"is":[21],"application":[23],"covariance":[25],"detection":[26],"and":[27,33,46,50],"pseudoknots":[30],"between":[31],"intra-":[32],"inter-molecular":[34],"base":[35],"pairs.":[36],"As":[37],"proof":[39],"concept,":[41],"we":[42],"show":[43],"an":[44],"example":[45],"discuss":[47],"strengths":[49],"weaknesses":[51],"approach.":[54]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
