{"id":"https://openalex.org/W2998529923","doi":"https://doi.org/10.1093/bioinformatics/btaa039","title":"<tt>incaRNAfbinv 2.0</tt>: a webserver and software with motif control for fragment-based design of RNAs","display_name":"<tt>incaRNAfbinv 2.0</tt>: a webserver and software with motif control for fragment-based design of RNAs","publication_year":2020,"publication_date":"2020-01-16","ids":{"openalex":"https://openalex.org/W2998529923","doi":"https://doi.org/10.1093/bioinformatics/btaa039","mag":"2998529923","pmid":"https://pubmed.ncbi.nlm.nih.gov/31971575"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa039","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2920/48986446/bioinformatics_36_9_2920.pdf","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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2920/48986446/bioinformatics_36_9_2920.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090841262","display_name":"Matan Drory Retwitzer","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Matan Drory Retwitzer","raw_affiliation_strings":["Department of Computer Science , Ben Gurion University of the Negev, Beer Sheva 84105, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science , Ben Gurion University of the Negev, Beer Sheva 84105, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"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":["Department of Computer Science , Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, H2X 3Y7, Canada","Institute for Basic Science , Daejeon 34126, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science , Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, H2X 3Y7, Canada","institution_ids":["https://openalex.org/I159129438"]},{"raw_affiliation_string":"Institute for Basic Science , Daejeon 34126, South Korea","institution_ids":["https://openalex.org/I4210104335"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028809987","display_name":"Alexander Churkin","orcid":"https://orcid.org/0000-0003-4275-257X"},"institutions":[{"id":"https://openalex.org/I3129975082","display_name":"Sami Shamoon College of Engineering","ror":"https://ror.org/011aa4g29","country_code":"IL","type":"education","lineage":["https://openalex.org/I3129975082"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Alexander Churkin","raw_affiliation_strings":["Software Engineering Department , Sami Shamoon College of Engineering, Beer-Sheva 84100, Israel"],"affiliations":[{"raw_affiliation_string":"Software Engineering Department , Sami Shamoon College of Engineering, Beer-Sheva 84100, Israel","institution_ids":["https://openalex.org/I3129975082"]}]},{"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":["Laboratoire d\u2019Informatique de l\u2019\u00c9cole Polytechnique (LIX CNRS UMR 7161) , Ecole Polytechnique, Palaiseau 91120, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019Informatique de l\u2019\u00c9cole Polytechnique (LIX CNRS UMR 7161) , Ecole Polytechnique, Palaiseau 91120, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]},{"author_position":"middle","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 Montr\u00e9al H3A 0E9, Canada"],"affiliations":[{"raw_affiliation_string":"School of Computer Science , McGill University Montr\u00e9al H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033583960","display_name":"Danny Barash","orcid":"https://orcid.org/0000-0003-4389-5302"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Danny Barash","raw_affiliation_strings":["Department of Computer Science , Ben Gurion University of the Negev, Beer Sheva 84105, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science , Ben Gurion University of the Negev, Beer Sheva 84105, Israel","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5033583960","https://openalex.org/A5090841262"],"corresponding_institution_ids":["https://openalex.org/I124227911"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1672,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.48455827,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"9","first_page":"2920","last_page":"2922"},"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":0.9976999759674072,"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":0.6287473440170288},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5877501368522644},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.5582740902900696},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5413891673088074},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.5041643381118774},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4694459140300751},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.44905686378479004},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3616484999656677},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3122733235359192},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2852098047733307},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.13877969980239868},{"id":"https://openalex.org/keywords/art","display_name":"Art","score":0.07667186856269836}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6287473440170288},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5877501368522644},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.5582740902900696},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5413891673088074},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.5041643381118774},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4694459140300751},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.44905686378479004},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3616484999656677},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3122733235359192},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2852098047733307},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.13877969980239868},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.07667186856269836},{"id":"https://openalex.org/C107038049","wikidata":"https://www.wikidata.org/wiki/Q35986","display_name":"Aesthetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa039","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2920/48986446/bioinformatics_36_9_2920.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31971575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31971575","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:HAL:hal-02423237v1","is_oa":false,"landing_page_url":"https://inria.hal.science/hal-02423237","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2020, 36 (9), pp.2910--2922. &#x27E8;10.1093/bioinformatics/btaa039&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa039","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2920/48986446/bioinformatics_36_9_2920.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5640121800","display_name":null,"funder_award_id":"(CNRS)","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G7758152977","display_name":null,"funder_award_id":"support","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"}],"funders":[{"id":"https://openalex.org/F4320309618","display_name":"Ministry of Science and Technology","ror":"https://ror.org/02b207r52"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"},{"id":"https://openalex.org/F4320333359","display_name":"College of Natural Resources and Sciences, Humboldt State University","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2998529923.pdf"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1669241002","https://openalex.org/W1790782659","https://openalex.org/W1934768785","https://openalex.org/W1969390039","https://openalex.org/W1978036746","https://openalex.org/W2032187763","https://openalex.org/W2086561953","https://openalex.org/W2095258877","https://openalex.org/W2103250001","https://openalex.org/W2111976294","https://openalex.org/W2115434752","https://openalex.org/W2125615424","https://openalex.org/W2140505514","https://openalex.org/W2141157874","https://openalex.org/W2143407915","https://openalex.org/W2407134517","https://openalex.org/W2561599208","https://openalex.org/W2607526881","https://openalex.org/W3012765374","https://openalex.org/W3099817196","https://openalex.org/W6731351848"],"related_works":["https://openalex.org/W1973480752","https://openalex.org/W2805502594","https://openalex.org/W4253208712","https://openalex.org/W3132641048","https://openalex.org/W3170299350","https://openalex.org/W2217679042","https://openalex.org/W1603677234","https://openalex.org/W2368410102","https://openalex.org/W2525971763","https://openalex.org/W2984753899"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2020-01-10T00:00:00"}
