{"id":"https://openalex.org/W2462269547","doi":"https://doi.org/10.1093/bioinformatics/btw401","title":"SwiSpot: modeling riboswitches by spotting out switching sequences","display_name":"SwiSpot: modeling riboswitches by spotting out switching sequences","publication_year":2016,"publication_date":"2016-07-04","ids":{"openalex":"https://openalex.org/W2462269547","doi":"https://doi.org/10.1093/bioinformatics/btw401","mag":"2462269547","pmid":"https://pubmed.ncbi.nlm.nih.gov/27378291"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw401","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3252/7889653/btw401.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/32/21/3252/7889653/btw401.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063324971","display_name":"Marco Barsacchi","orcid":"https://orcid.org/0000-0002-7457-7393"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Barsacchi","raw_affiliation_strings":["1 Department of Information Engineering, University of Pisa, Largo L. Lazzarino, Pisa, IT 56122, Italy"],"affiliations":[{"raw_affiliation_string":"1 Department of Information Engineering, University of Pisa, Largo L. Lazzarino, Pisa, IT 56122, Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057919353","display_name":"Eva Maria Novoa","orcid":"https://orcid.org/0000-0002-9367-6311"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]},{"id":"https://openalex.org/I126820664","display_name":"Vassar College","ror":"https://ror.org/022x6qg61","country_code":"US","type":"education","lineage":["https://openalex.org/I126820664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eva Maria Novoa","raw_affiliation_strings":["2 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA","3 The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA"],"affiliations":[{"raw_affiliation_string":"2 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I126820664","https://openalex.org/I63966007"]},{"raw_affiliation_string":"3 The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089977648","display_name":"Manolis Kellis","orcid":"https://orcid.org/0000-0001-7113-9630"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I126820664","display_name":"Vassar College","ror":"https://ror.org/022x6qg61","country_code":"US","type":"education","lineage":["https://openalex.org/I126820664"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manolis Kellis","raw_affiliation_strings":["2 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA","3 The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA"],"affiliations":[{"raw_affiliation_string":"2 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I126820664","https://openalex.org/I63966007"]},{"raw_affiliation_string":"3 The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007774813","display_name":"Alessio Bechini","orcid":"https://orcid.org/0000-0002-5951-1265"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Alessio Bechini","raw_affiliation_strings":["1 Department of Information Engineering, University of Pisa, Largo L. Lazzarino, Pisa, IT 56122, Italy"],"affiliations":[{"raw_affiliation_string":"1 Department of Information Engineering, University of Pisa, Largo L. Lazzarino, Pisa, IT 56122, Italy","institution_ids":["https://openalex.org/I108290504"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007774813"],"corresponding_institution_ids":["https://openalex.org/I108290504"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6669,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.73059152,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"32","issue":"21","first_page":"3252","last_page":"3259"},"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":0.9944999814033508,"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":0.9944000244140625,"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/riboswitch","display_name":"Riboswitch","score":0.9572645425796509},{"id":"https://openalex.org/keywords/spotting","display_name":"Spotting","score":0.6387835741043091},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6223295331001282},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5638874173164368},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5397520661354065},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41868460178375244},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.39677783846855164},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36004459857940674},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3249828815460205},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31220126152038574},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27748313546180725},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.22282153367996216},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21346056461334229}],"concepts":[{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.9572645425796509},{"id":"https://openalex.org/C2779506182","wikidata":"https://www.wikidata.org/wiki/Q7580141","display_name":"Spotting","level":2,"score":0.6387835741043091},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6223295331001282},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5638874173164368},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5397520661354065},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41868460178375244},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.39677783846855164},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36004459857940674},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3249828815460205},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31220126152038574},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27748313546180725},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.22282153367996216},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21346056461334229}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw401","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3252/7889653/btw401.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:27378291","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27378291","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:arpi.unipi.it:11568/817190","is_oa":true,"landing_page_url":"http://hdl.handle.net/11568/817190","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/21/3252","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/21/3252","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw401","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3252/7889653/btw401.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":[],"funders":[{"id":"https://openalex.org/F4320324499","display_name":"Universit\u00e0 di Pisa","ror":"https://ror.org/03ad39j10"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2462269547.pdf","grobid_xml":"https://content.openalex.org/works/W2462269547.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1984357954","https://openalex.org/W1984675364","https://openalex.org/W1986504247","https://openalex.org/W1987971958","https://openalex.org/W2004945910","https://openalex.org/W2023135381","https://openalex.org/W2027146094","https://openalex.org/W2027685499","https://openalex.org/W2039756922","https://openalex.org/W2064444082","https://openalex.org/W2067258168","https://openalex.org/W2073418519","https://openalex.org/W2086561953","https://openalex.org/W2096647099","https://openalex.org/W2098508116","https://openalex.org/W2108230379","https://openalex.org/W2119582819","https://openalex.org/W2121918723","https://openalex.org/W2125952821","https://openalex.org/W2131462431","https://openalex.org/W2132920850","https://openalex.org/W2146297415","https://openalex.org/W2150147498","https://openalex.org/W2153140501","https://openalex.org/W2158863640","https://openalex.org/W2160378127","https://openalex.org/W2170767438","https://openalex.org/W2491462546"],"related_works":["https://openalex.org/W2419364582","https://openalex.org/W2400719429","https://openalex.org/W3213370823","https://openalex.org/W2304056734","https://openalex.org/W2009133056","https://openalex.org/W3039385523","https://openalex.org/W2898743020","https://openalex.org/W3022554208","https://openalex.org/W2041710960","https://openalex.org/W1988553110"],"abstract_inverted_index":{"a.bechini@ing.unipi.it.":[0]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}