{"id":"https://openalex.org/W2958013639","doi":"https://doi.org/10.1093/bioinformatics/btz395","title":"ShaKer: RNA SHAPE prediction using graph kernel","display_name":"ShaKer: RNA SHAPE prediction using graph kernel","publication_year":2019,"publication_date":"2019-06-25","ids":{"openalex":"https://openalex.org/W2958013639","doi":"https://doi.org/10.1093/bioinformatics/btz395","mag":"2958013639","pmid":"https://pubmed.ncbi.nlm.nih.gov/31510707"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz395","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz395","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btz395","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003159012","display_name":"Stefan Mautner","orcid":"https://orcid.org/0000-0002-2206-2929"},"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":"Stefan Mautner","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044280010","display_name":"Soheila Montaseri","orcid":null},"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":"Soheila Montaseri","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017381991","display_name":"Milad Miladi","orcid":"https://orcid.org/0000-0002-0173-3009"},"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":"Milad Miladi","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016009812","display_name":"Martin Raden","orcid":"https://orcid.org/0000-0002-7926-5911"},"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":"Martin Raden","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064539521","display_name":"Fabrizio Costa","orcid":"https://orcid.org/0000-0002-4900-995X"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fabrizio Costa","raw_affiliation_strings":["Department Computer Science, University of Exeter, Exeter, UK"],"affiliations":[{"raw_affiliation_string":"Department Computer Science, University of Exeter, Exeter, UK","institution_ids":["https://openalex.org/I23923803"]}]},{"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":true,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5017672883"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6851,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.69002258,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"14","first_page":"i354","last_page":"i359"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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":0.9991999864578247,"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/shaker","display_name":"Shaker","score":0.939815878868103},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6603024005889893},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.6001057624816895},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5894959568977356},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5537996292114258},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4959286153316498},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4654892683029175},{"id":"https://openalex.org/keywords/graph-kernel","display_name":"Graph kernel","score":0.43652892112731934},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3535456657409668},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.24454128742218018},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.15470671653747559},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13970142602920532},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12029722332954407},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.11306518316268921},{"id":"https://openalex.org/keywords/acoustics","display_name":"Acoustics","score":0.10714337229728699},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08497276902198792},{"id":"https://openalex.org/keywords/radial-basis-function-kernel","display_name":"Radial basis function kernel","score":0.08309617638587952},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07116460800170898},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07087904214859009}],"concepts":[{"id":"https://openalex.org/C2779421379","wikidata":"https://www.wikidata.org/wiki/Q898872","display_name":"Shaker","level":3,"score":0.939815878868103},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6603024005889893},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.6001057624816895},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5894959568977356},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5537996292114258},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4959286153316498},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4654892683029175},{"id":"https://openalex.org/C100595998","wikidata":"https://www.wikidata.org/wiki/Q11731931","display_name":"Graph kernel","level":5,"score":0.43652892112731934},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3535456657409668},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.24454128742218018},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.15470671653747559},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13970142602920532},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12029722332954407},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.11306518316268921},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.10714337229728699},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08497276902198792},{"id":"https://openalex.org/C75866337","wikidata":"https://www.wikidata.org/wiki/Q7280263","display_name":"Radial basis function kernel","level":4,"score":0.08309617638587952},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07116460800170898},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07087904214859009},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C198394728","wikidata":"https://www.wikidata.org/wiki/Q3695508","display_name":"Vibration","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz395","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz395","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31510707","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31510707","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5588702","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6612843","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz395","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz395","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2201129563","display_name":null,"funder_award_id":"BA2168/3-3","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4935269520","display_name":null,"funder_award_id":"390939984","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6455713283","display_name":null,"funder_award_id":"CIBSS","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7566894236","display_name":null,"funder_award_id":"BA2168/16-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G762232396","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7942449511","display_name":null,"funder_award_id":"EXC-2189","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8330397625","display_name":null,"funder_award_id":"Funding","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8949437229","display_name":null,"funder_award_id":"68/16-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W2003993220","https://openalex.org/W2011301426","https://openalex.org/W2020077467","https://openalex.org/W2066444035","https://openalex.org/W2071883352","https://openalex.org/W2073858449","https://openalex.org/W2086561953","https://openalex.org/W2100321825","https://openalex.org/W2101234009","https://openalex.org/W2132022337","https://openalex.org/W2134943543","https://openalex.org/W2137476097","https://openalex.org/W2141157874","https://openalex.org/W2142498761","https://openalex.org/W2148725278","https://openalex.org/W2151994495","https://openalex.org/W2159117141","https://openalex.org/W2170157200","https://openalex.org/W2295598076","https://openalex.org/W2486806490","https://openalex.org/W2554920439","https://openalex.org/W2558432341","https://openalex.org/W2582578343","https://openalex.org/W2593813786","https://openalex.org/W2608211995","https://openalex.org/W2610733803","https://openalex.org/W2766137885","https://openalex.org/W2766848373","https://openalex.org/W2793097545","https://openalex.org/W2803927613","https://openalex.org/W2906841844","https://openalex.org/W3102476541","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2110459882","https://openalex.org/W2153211825","https://openalex.org/W4300454542","https://openalex.org/W2189183545","https://openalex.org/W2828181497","https://openalex.org/W2122054752","https://openalex.org/W2103255843","https://openalex.org/W2604913466","https://openalex.org/W2958013639","https://openalex.org/W3008135798"],"abstract_inverted_index":{"ShaKer":[0],"is":[1],"freely":[2],"available":[3],"at":[4],"https://github.com/BackofenLab/ShaKer.":[5]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
