{"id":"https://openalex.org/W2924539322","doi":"https://doi.org/10.1186/s12859-019-2711-y","title":"SSS-test: a novel test for detecting positive selection on RNA secondary structure","display_name":"SSS-test: a novel test for detecting positive selection on RNA secondary structure","publication_year":2019,"publication_date":"2019-03-21","ids":{"openalex":"https://openalex.org/W2924539322","doi":"https://doi.org/10.1186/s12859-019-2711-y","mag":"2924539322","pmid":"https://pubmed.ncbi.nlm.nih.gov/30898084"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2711-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2711-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2711-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2711-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078170872","display_name":"Maria Beatriz Walter Costa","orcid":"https://orcid.org/0000-0002-5143-0858"},"institutions":[{"id":"https://openalex.org/I199691007","display_name":"Brazilian Agricultural Research Corporation","ror":"https://ror.org/0482b5b22","country_code":"BR","type":"government","lineage":["https://openalex.org/I199691007"]},{"id":"https://openalex.org/I40900055","display_name":"Telstra (Australia)","ror":"https://ror.org/04g047260","country_code":"AU","type":"company","lineage":["https://openalex.org/I40900055"]}],"countries":["AU","BR"],"is_corresponding":true,"raw_author_name":"Maria Beatriz Walter Costa","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany. bia.walter@gmail.com","Embrapa Agroenergia, Parque Esta\u00e7\u00e3o Biol\u00f3gica (PqEB), Asa Norte, Bras\u00edlia, DF, 70770-901, Brazil. bia.walter@gmail.com","Embrapa Agroenergia, Parque Esta\u00e7\u00e3o Biol\u00f3gica (PqEB), Asa Norte, Bras\u00edlia, DF, 70770-901, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany. bia.walter@gmail.com","institution_ids":["https://openalex.org/I40900055"]},{"raw_affiliation_string":"Embrapa Agroenergia, Parque Esta\u00e7\u00e3o Biol\u00f3gica (PqEB), Asa Norte, Bras\u00edlia, DF, 70770-901, Brazil. bia.walter@gmail.com","institution_ids":["https://openalex.org/I199691007"]},{"raw_affiliation_string":"Embrapa Agroenergia, Parque Esta\u00e7\u00e3o Biol\u00f3gica (PqEB), Asa Norte, Bras\u00edlia, DF, 70770-901, Brazil","institution_ids":["https://openalex.org/I199691007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005332412","display_name":"Christian H\u00f6ner zu Siederdissen","orcid":"https://orcid.org/0000-0001-9517-5839"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian H\u00f6ner zu Siederdissen","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany","Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, Leipzig, 04107, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9517-5839","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, Leipzig, 04107, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090196426","display_name":"Marko Dunji\u0107","orcid":"https://orcid.org/0000-0002-1050-6027"},"institutions":[{"id":"https://openalex.org/I4068193","display_name":"University of Belgrade","ror":"https://ror.org/02qsmb048","country_code":"RS","type":"education","lineage":["https://openalex.org/I4068193"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE","RS"],"is_corresponding":false,"raw_author_name":"Marko Dunji\u0107","raw_affiliation_strings":["Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, PO box 43, Belgrade, 11000, Serbia","Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, K\u00f6nigin-Luise-Stra\u00dfe 1-3, Berlin, 14195, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, PO box 43, Belgrade, 11000, Serbia","institution_ids":["https://openalex.org/I4068193"]},{"raw_affiliation_string":"Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, K\u00f6nigin-Luise-Stra\u00dfe 1-3, Berlin, 14195, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"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"]},{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"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"]},{"id":"https://openalex.org/I2801030728","display_name":"German Centre for Integrative Biodiversity Research","ror":"https://ror.org/01jty7g66","country_code":"DE","type":"facility","lineage":["https://openalex.org/I2801030728"]},{"id":"https://openalex.org/I36243813","display_name":"Universidad Nacional de Colombia","ror":"https://ror.org/059yx9a68","country_code":"CO","type":"education","lineage":["https://openalex.org/I36243813"]},{"id":"https://openalex.org/I4210091327","display_name":"Max Planck Institute for Mathematics in the Sciences","ror":"https://ror.org/00ez2he07","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210091327"]},{"id":"https://openalex.org/I4210119712","display_name":"Max Planck Institute for Mathematics","ror":"https://ror.org/02dh8ja68","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210119712"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["AT","CO","DE","DK","US"],"is_corresponding":false,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany","Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, DK-1870, Denmark","Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, Vienna, A-1090, Austria","Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogot\u00e1, Ciudad Universitaria, Bogot\u00e1, D.C., COL-111321, Colombia","German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, 04107, Germany","Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, Leipzig, 04103, Germany","Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA","Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, Leipzig, 04107, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, Frederiksberg C, DK-1870, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, Vienna, A-1090, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogot\u00e1, Ciudad Universitaria, Bogot\u00e1, D.C., COL-111321, Colombia","institution_ids":["https://openalex.org/I36243813"]},{"raw_affiliation_string":"German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, 04107, Germany","institution_ids":["https://openalex.org/I2801030728"]},{"raw_affiliation_string":"Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, Leipzig, 04103, Germany","institution_ids":["https://openalex.org/I4210119712","https://openalex.org/I4210091327"]},{"raw_affiliation_string":"Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA","institution_ids":["https://openalex.org/I1308548392"]},{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universit\u00e4t Leipzig, H\u00e4rtelstra\u00dfe 16\u201318, Leipzig, 04107, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078414184","display_name":"Katja Nowick","orcid":"https://orcid.org/0000-0003-3993-4479"},"institutions":[{"id":"https://openalex.org/I110079840","display_name":"University of Hohenheim","ror":"https://ror.org/00b1c9541","country_code":"DE","type":"education","lineage":["https://openalex.org/I110079840"]},{"id":"https://openalex.org/I40900055","display_name":"Telstra (Australia)","ror":"https://ror.org/04g047260","country_code":"AU","type":"company","lineage":["https://openalex.org/I40900055"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["AU","DE"],"is_corresponding":false,"raw_author_name":"Katja Nowick","raw_affiliation_strings":["Bioinformatics, Faculty of Agricultural Sciences, Institute of Animal Science, University of Hohenheim, Garbenstra\u00dfe 13, Stuttgart, 70593, Germany. katja.nowick@fu-berlin.de","Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, K\u00f6nigin-Luise-Stra\u00dfe 1-3, Berlin, 14195, Germany. katja.nowick@fu-berlin.de","Paul-Flechsig-Institute for Brain Research, University of Leipzig, Liebigstra\u00dfe 19. Haus C, Leipzig, 04103, Germany. katja.nowick@fu-berlin.de","TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, Department of Computer Science, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany. katja.nowick@fu-berlin.de","Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, K\u00f6nigin-Luise-Stra\u00dfe 1-3, Berlin, 14195, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics, Faculty of Agricultural Sciences, Institute of Animal Science, University of Hohenheim, Garbenstra\u00dfe 13, Stuttgart, 70593, Germany. katja.nowick@fu-berlin.de","institution_ids":["https://openalex.org/I110079840"]},{"raw_affiliation_string":"Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, K\u00f6nigin-Luise-Stra\u00dfe 1-3, Berlin, 14195, Germany. katja.nowick@fu-berlin.de","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Paul-Flechsig-Institute for Brain Research, University of Leipzig, Liebigstra\u00dfe 19. Haus C, Leipzig, 04103, Germany. katja.nowick@fu-berlin.de","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, Department of Computer Science, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, Leipzig, 04107, Germany. katja.nowick@fu-berlin.de","institution_ids":["https://openalex.org/I40900055"]},{"raw_affiliation_string":"Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, K\u00f6nigin-Luise-Stra\u00dfe 1-3, Berlin, 14195, Germany","institution_ids":["https://openalex.org/I75951250"]}]}],"institutions":[],"countries_distinct_count":8,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5078170872"],"corresponding_institution_ids":["https://openalex.org/I199691007","https://openalex.org/I40900055"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1661,"currency":"EUR","value_usd":1791},"fwci":1.1592,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.7412211,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"151","last_page":"151"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.6880000233650208,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.6880000233650208,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.09009999781847,"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/T12610","display_name":"RNA regulation and disease","score":0.0658000037074089,"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/selection","display_name":"Selection (genetic algorithm)","score":0.667568564414978},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6371141076087952},{"id":"https://openalex.org/keywords/negative-selection","display_name":"Negative selection","score":0.6277613639831543},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5483251214027405},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41953739523887634},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4141232669353485},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3769091069698334},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36979568004608154},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3637329638004303},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.31425315141677856},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2011055052280426},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.19326958060264587}],"concepts":[{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.667568564414978},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6371141076087952},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.6277613639831543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5483251214027405},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41953739523887634},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4141232669353485},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3769091069698334},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36979568004608154},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3637329638004303},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31425315141677856},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2011055052280426},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.19326958060264587}],"mesh":[{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-019-2711-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2711-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2711-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30898084","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30898084","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:refubium.fu-berlin.de:fub188/25089","is_oa":true,"landing_page_url":"https://refubium.fu-berlin.de/handle/fub188/25089","pdf_url":"https://refubium.fu-berlin.de/handle/fub188/25089","source":{"id":"https://openalex.org/S4306402444","display_name":"Refubium (Universit\u00e4tsbibliothek der Freien Universit\u00e4t Berlin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I75951250","host_organization_name":"Freie Universit\u00e4t Berlin","host_organization_lineage":["https://openalex.org/I75951250"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doc-type:article"},{"id":"pmh:oai:doaj.org/article:d093d1a135674950815824fbb782c6ab","is_oa":true,"landing_page_url":"https://doaj.org/article/d093d1a135674950815824fbb782c6ab","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-19 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5433029","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6429701","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:pure.mpg.de:item_3240935","is_oa":false,"landing_page_url":"http://hdl.handle.net/21.11116/0000-0006-A5A2-8","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.17169/refubium-2844","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-2844","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2711-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2711-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2711-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1640067665","display_name":null,"funder_award_id":"57390771","funder_id":"https://openalex.org/F4320320875","funder_display_name":"Deutscher Akademischer Austauschdienst"},{"id":"https://openalex.org/G200089779","display_name":null,"funder_award_id":"SPP 1738","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G581965161","display_name":null,"funder_award_id":"2012-4","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G7380791564","display_name":null,"funder_award_id":"246039/2012-4","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"}],"funders":[{"id":"https://openalex.org/F4320320875","display_name":"Deutscher Akademischer Austauschdienst","ror":"https://ror.org/039djdh30"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320320882","display_name":"Volkswagen Foundation","ror":"https://ror.org/03bsmfz84"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320324521","display_name":"Freie Universit\u00e4t Berlin","ror":null},{"id":"https://openalex.org/F4320325298","display_name":"Universit\u00e4t Leipzig","ror":"https://ror.org/03s7gtk40"},{"id":"https://openalex.org/F4320336557","display_name":"Ci\u00eancia sem Fronteiras","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2924539322.pdf","grobid_xml":"https://content.openalex.org/works/W2924539322.grobid-xml"},"referenced_works_count":117,"referenced_works":["https://openalex.org/W96946988","https://openalex.org/W1235701990","https://openalex.org/W1527024319","https://openalex.org/W1595713348","https://openalex.org/W1602695373","https://openalex.org/W1605441808","https://openalex.org/W1716337982","https://openalex.org/W1822105579","https://openalex.org/W1964666807","https://openalex.org/W1965887164","https://openalex.org/W1968654140","https://openalex.org/W1968876595","https://openalex.org/W1973788996","https://openalex.org/W1974736226","https://openalex.org/W1981311921","https://openalex.org/W1982136814","https://openalex.org/W1986223165","https://openalex.org/W1995724539","https://openalex.org/W1999746344","https://openalex.org/W2006838271","https://openalex.org/W2006936482","https://openalex.org/W2010004816","https://openalex.org/W2011598785","https://openalex.org/W2012206989","https://openalex.org/W2016441739","https://openalex.org/W2022199909","https://openalex.org/W2023691360","https://openalex.org/W2027599886","https://openalex.org/W2038464976","https://openalex.org/W2039925764","https://openalex.org/W2044672052","https://openalex.org/W2048137474","https://openalex.org/W2052918843","https://openalex.org/W2055538302","https://openalex.org/W2069139855","https://openalex.org/W2069511429","https://openalex.org/W2073858449","https://openalex.org/W2074495242","https://openalex.org/W2077327925","https://openalex.org/W2080092700","https://openalex.org/W2081586346","https://openalex.org/W2086433728","https://openalex.org/W2086561953","https://openalex.org/W2088069070","https://openalex.org/W2095258877","https://openalex.org/W2097075232","https://openalex.org/W2100830141","https://openalex.org/W2104143100","https://openalex.org/W2105292164","https://openalex.org/W2106306904","https://openalex.org/W2107894470","https://openalex.org/W2108120430","https://openalex.org/W2108230379","https://openalex.org/W2110065044","https://openalex.org/W2111272410","https://openalex.org/W2112001233","https://openalex.org/W2112388671","https://openalex.org/W2121306035","https://openalex.org/W2122679732","https://openalex.org/W2124397449","https://openalex.org/W2126438612","https://openalex.org/W2126582029","https://openalex.org/W2128291372","https://openalex.org/W2128356721","https://openalex.org/W2128983843","https://openalex.org/W2132926880","https://openalex.org/W2135548188","https://openalex.org/W2136735223","https://openalex.org/W2140302584","https://openalex.org/W2141831115","https://openalex.org/W2142709509","https://openalex.org/W2142735201","https://openalex.org/W2144258405","https://openalex.org/W2145284754","https://openalex.org/W2146120203","https://openalex.org/W2151203827","https://openalex.org/W2156880688","https://openalex.org/W2158826174","https://openalex.org/W2159117141","https://openalex.org/W2160845145","https://openalex.org/W2160973567","https://openalex.org/W2162823258","https://openalex.org/W2163297931","https://openalex.org/W2164918225","https://openalex.org/W2166251028","https://openalex.org/W2167714537","https://openalex.org/W2167807908","https://openalex.org/W2169601480","https://openalex.org/W2179308868","https://openalex.org/W2195626480","https://openalex.org/W2259938310","https://openalex.org/W2284268690","https://openalex.org/W2317812538","https://openalex.org/W2320476296","https://openalex.org/W2336017145","https://openalex.org/W2339745985","https://openalex.org/W2463633368","https://openalex.org/W2472478751","https://openalex.org/W2497832940","https://openalex.org/W2510570670","https://openalex.org/W2551833309","https://openalex.org/W2554065905","https://openalex.org/W2561206768","https://openalex.org/W2595351638","https://openalex.org/W2612916063","https://openalex.org/W2743318930","https://openalex.org/W2766934529","https://openalex.org/W2770660328","https://openalex.org/W2773713082","https://openalex.org/W2777988707","https://openalex.org/W2791055994","https://openalex.org/W2794061717","https://openalex.org/W2804699938","https://openalex.org/W2883348003","https://openalex.org/W2887796563","https://openalex.org/W2904017331","https://openalex.org/W4248924354"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W4205762803","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W3178279768","https://openalex.org/W2535856026","https://openalex.org/W193851735","https://openalex.org/W2773861473","https://openalex.org/W1971903861"],"abstract_inverted_index":{"BACKGROUND:":[0],"Long":[1],"non-coding":[2,74],"RNAs":[3,37,61],"(lncRNAs)":[4],"play":[5],"an":[6],"important":[7,16],"role":[8],"in":[9,25,159,169,191,218,244,260],"regulating":[10],"gene":[11],"expression":[12],"and":[13,38,122,140,234,249],"are":[14,263],"thus":[15,123],"for":[17,99,113,137,230],"determining":[18],"phenotypes.":[19],"Most":[20],"attempts":[21],"to":[22,50,118,164,199],"measure":[23],"selection":[24,58,104,121,168,190,202,217],"lncRNAs":[26,44,173,219],"have":[27,88,175,186],"focused":[28,91],"on":[29,60,70,92,115,204,208],"the":[30,71,110,144,147,192,239],"primary":[31],"sequence.":[32],"The":[33,212,247,257],"majority":[34],"of":[35,43,57,73,84,146,151,188,214,227,241],"small":[36],"at":[39],"least":[40],"some":[41],"parts":[42],"must":[45,63],"fold":[46],"into":[47,238],"specific":[48],"structures":[49,184,207],"perform":[51],"their":[52],"biological":[53,128],"function.":[54],"Comprehensive":[55],"assessments":[56],"acting":[59,69,203],"therefore":[62],"also":[64],"encompass":[65],"structure.":[66],"Selection":[67,114],"pressures":[68],"structure":[72],"genes":[75,229],"can":[76],"be":[77,165],"detected":[78],"within":[79],"multiple":[80],"sequence":[81],"alignments.":[82],"Approaches":[83],"this":[85,261],"type,":[86],"however,":[87],"so":[89],"far":[90],"negative":[93,139],"selection.":[94],"Thus,":[95],"a":[96,152,209,225],"computational":[97],"method":[98],"identifying":[100],"ncRNAs":[101],"under":[102,166],"positive":[103,120,141,167,189,201,216],"is":[105,197,252],"needed.":[106],"RESULTS:":[107],"We":[108],"introduce":[109],"SSS-test":[111,248],"(test":[112],"Secondary":[116],"Structure)":[117],"identify":[119],"adaptive":[124],"evolution.":[125],"Benchmarks":[126],"with":[127,178,221],"as":[129,131],"well":[130],"synthetic":[132],"controls":[133],"yield":[134],"coherent":[135],"signals":[136],"both":[138],"selection,":[142],"demonstrating":[143],"functionality":[145],"test.":[148],"A":[149],"survey":[150],"lncRNA":[153],"collection":[154],"comprising":[155],"15,443":[156],"families":[157],"resulted":[158],"110":[160],"candidates":[161],"that":[162,174,185],"appear":[163],"human.":[170],"In":[171],"26":[172],"been":[176],"associated":[177,220],"psychiatric":[179],"disorders":[180],"we":[181],"identified":[182],"local":[183],"signs":[187],"human":[193],"lineage.":[194],"CONCLUSIONS:":[195],"It":[196],"feasible":[198],"assay":[200],"RNA":[205],"secondary":[206],"genome-wide":[210],"scale.":[211],"detection":[213],"human-specific":[215],"cognitive":[222,242],"disorder":[223],"provides":[224],"set":[226],"candidate":[228],"further":[231],"experimental":[232],"testing":[233],"may":[235],"provide":[236],"insights":[237],"evolution":[240],"abilities":[243],"humans.":[245],"AVAILABILITY:":[246],"related":[250],"software":[251],"available":[253,264],"at:":[254,265],"https://github.com/waltercostamb/SSS-test":[255],".":[256,267],"databases":[258],"used":[259],"work":[262],"http://www.bioinf.uni-leipzig.de/Software/SSS-test/":[266]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
