{"id":"https://openalex.org/W3017302601","doi":"https://doi.org/10.1007/978-3-030-45257-5_12","title":"Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification","display_name":"Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3017302601","doi":"https://doi.org/10.1007/978-3-030-45257-5_12","mag":"3017302601"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-030-45257-5_12","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-030-45257-5_12","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072935011","display_name":"Roman Sarrazin\u2010Gendron","orcid":"https://orcid.org/0000-0002-0291-547X"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Roman Sarrazin-Gendron","raw_affiliation_strings":["School of Computer Science, McGill University, Montreal, Canada"],"raw_orcid":"https://orcid.org/0000-0002-0291-547X","affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montreal, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025033338","display_name":"Hua-Ting Yao","orcid":"https://orcid.org/0000-0002-1720-5737"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA","FR"],"is_corresponding":false,"raw_author_name":"Hua-Ting Yao","raw_affiliation_strings":["LIX, CNRS UMR 7161, Ecole Polytechnique, Palaiseau, France","School of Computer Science, McGill University, Montreal, Canada"],"raw_orcid":"https://orcid.org/0000-0002-1720-5737","affiliations":[{"raw_affiliation_string":"LIX, CNRS UMR 7161, Ecole Polytechnique, Palaiseau, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I1294671590","https://openalex.org/I142476485"]},{"raw_affiliation_string":"School of Computer Science, McGill University, Montreal, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089144463","display_name":"Vladimir Reinharz","orcid":"https://orcid.org/0000-0001-8481-1094"},"institutions":[{"id":"https://openalex.org/I159129438","display_name":"Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al","ror":"https://ror.org/002rjbv21","country_code":"CA","type":"education","lineage":["https://openalex.org/I159129438","https://openalex.org/I49663120"]},{"id":"https://openalex.org/I4210104335","display_name":"Institute for Basic Science","ror":"https://ror.org/00y0zf565","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210104335"]}],"countries":["CA","KR"],"is_corresponding":false,"raw_author_name":"Vladimir Reinharz","raw_affiliation_strings":["Center for Soft and Living Matter, Institute for Basic Science, Ulsan, South Korea","D\u00e9partement d\u2019informatique, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, Canada"],"raw_orcid":"https://orcid.org/0000-0001-8481-1094","affiliations":[{"raw_affiliation_string":"Center for Soft and Living Matter, Institute for Basic Science, Ulsan, South Korea","institution_ids":["https://openalex.org/I4210104335"]},{"raw_affiliation_string":"D\u00e9partement d\u2019informatique, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, Canada","institution_ids":["https://openalex.org/I159129438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003324363","display_name":"Carlos Oliver","orcid":"https://orcid.org/0000-0001-8742-8795"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Carlos G. Oliver","raw_affiliation_strings":["School of Computer Science, McGill University, Montreal, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montreal, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076325273","display_name":"Yann Ponty","orcid":"https://orcid.org/0000-0002-7615-3930"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yann Ponty","raw_affiliation_strings":["LIX, CNRS UMR 7161, Ecole Polytechnique, Palaiseau, France"],"raw_orcid":"https://orcid.org/0000-0002-7615-3930","affiliations":[{"raw_affiliation_string":"LIX, CNRS UMR 7161, Ecole Polytechnique, Palaiseau, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I1294671590","https://openalex.org/I142476485"]}]},{"author_position":"last","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/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00f4me Waldisp\u00fchl","raw_affiliation_strings":["School of Computer Science, McGill University, Montreal, Canada"],"raw_orcid":"https://orcid.org/0000-0002-2561-7117","affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montreal, Canada","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":1.9737,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.86925734,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"186","last_page":"201"},"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":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/computer-science","display_name":"Computer science","score":0.7659204006195068},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6403440237045288},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5428855419158936},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4610303044319153},{"id":"https://openalex.org/keywords/scope","display_name":"Scope (computer science)","score":0.43565016984939575},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.43361255526542664},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41331759095191956},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40711355209350586},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3457232713699341},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3404179513454437},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.09208658337593079}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7659204006195068},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6403440237045288},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5428855419158936},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4610303044319153},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.43565016984939575},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.43361255526542664},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41331759095191956},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40711355209350586},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3457232713699341},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3404179513454437},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.09208658337593079},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/978-3-030-45257-5_12","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-030-45257-5_12","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W142718297","https://openalex.org/W1504391652","https://openalex.org/W1685935480","https://openalex.org/W1920564293","https://openalex.org/W1924788487","https://openalex.org/W1970496435","https://openalex.org/W1984675364","https://openalex.org/W1988884185","https://openalex.org/W1993319845","https://openalex.org/W2007615447","https://openalex.org/W2009442732","https://openalex.org/W2023013439","https://openalex.org/W2023209608","https://openalex.org/W2067258168","https://openalex.org/W2086561953","https://openalex.org/W2088784401","https://openalex.org/W2101497394","https://openalex.org/W2106478835","https://openalex.org/W2130479394","https://openalex.org/W2133014975","https://openalex.org/W2142241599","https://openalex.org/W2143406303","https://openalex.org/W2147088328","https://openalex.org/W2147128567","https://openalex.org/W2149250011","https://openalex.org/W2150404344","https://openalex.org/W2153140501","https://openalex.org/W2159117141","https://openalex.org/W2159954944","https://openalex.org/W2225137135","https://openalex.org/W2275580678","https://openalex.org/W2618108760","https://openalex.org/W2766848373","https://openalex.org/W2795053763","https://openalex.org/W2887796563","https://openalex.org/W2919373301","https://openalex.org/W2949965166","https://openalex.org/W2974184992"],"related_works":["https://openalex.org/W4241523039","https://openalex.org/W2360028903","https://openalex.org/W4280543773","https://openalex.org/W178231042","https://openalex.org/W2366083136","https://openalex.org/W2387622493","https://openalex.org/W4385457841","https://openalex.org/W2581348958","https://openalex.org/W4367048159","https://openalex.org/W962838231"],"abstract_inverted_index":null,"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":4}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}