{"id":"https://openalex.org/W2911461034","doi":"https://doi.org/10.1093/bioinformatics/btz093","title":"RiboD: a comprehensive database for prokaryotic riboswitches","display_name":"RiboD: a comprehensive database for prokaryotic riboswitches","publication_year":2019,"publication_date":"2019-02-05","ids":{"openalex":"https://openalex.org/W2911461034","doi":"https://doi.org/10.1093/bioinformatics/btz093","mag":"2911461034","pmid":"https://pubmed.ncbi.nlm.nih.gov/30726866"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz093","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3541/48974980/bioinformatics_35_18_3541.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/35/18/3541/48974980/bioinformatics_35_18_3541.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062476988","display_name":"Sumit Mukherjee","orcid":"https://orcid.org/0000-0001-9807-7994"},"institutions":[{"id":"https://openalex.org/I127439422","display_name":"Indian Institute of Science Education and Research Kolkata","ror":"https://ror.org/00djv2c17","country_code":"IN","type":"education","lineage":["https://openalex.org/I127439422"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Sumit Mukherjee","raw_affiliation_strings":["Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata , Mohanpur-741246, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata , Mohanpur-741246, India","institution_ids":["https://openalex.org/I127439422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078804878","display_name":"Sukhen Das Mandal","orcid":"https://orcid.org/0000-0001-7505-2225"},"institutions":[{"id":"https://openalex.org/I127439422","display_name":"Indian Institute of Science Education and Research Kolkata","ror":"https://ror.org/00djv2c17","country_code":"IN","type":"education","lineage":["https://openalex.org/I127439422"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sukhen Das Mandal","raw_affiliation_strings":["Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata , Mohanpur-741246, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata , Mohanpur-741246, India","institution_ids":["https://openalex.org/I127439422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066933752","display_name":"Nikita Gupta","orcid":"https://orcid.org/0000-0003-3098-6598"},"institutions":[{"id":"https://openalex.org/I56404289","display_name":"Indian Institute of Technology BHU","ror":"https://ror.org/01kh5gc44","country_code":"IN","type":"education","lineage":["https://openalex.org/I56404289"]},{"id":"https://openalex.org/I91357014","display_name":"Banaras Hindu University","ror":"https://ror.org/04cdn2797","country_code":"IN","type":"education","lineage":["https://openalex.org/I91357014"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Nikita Gupta","raw_affiliation_strings":["Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU) Varanasi , Varanasi, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU) Varanasi , Varanasi, India","institution_ids":["https://openalex.org/I56404289","https://openalex.org/I91357014"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059068645","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":false,"raw_author_name":"Matan Drory-Retwitzer","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University , Beer-Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University , Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","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":false,"raw_author_name":"Danny Barash","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University , Beer-Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University , Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045018479","display_name":"Supratim Sengupta","orcid":"https://orcid.org/0000-0001-5294-0561"},"institutions":[{"id":"https://openalex.org/I127439422","display_name":"Indian Institute of Science Education and Research Kolkata","ror":"https://ror.org/00djv2c17","country_code":"IN","type":"education","lineage":["https://openalex.org/I127439422"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Supratim Sengupta","raw_affiliation_strings":["Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata , Mohanpur-741246, India"],"raw_orcid":"https://orcid.org/0000-0001-5294-0561","affiliations":[{"raw_affiliation_string":"Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata , Mohanpur-741246, India","institution_ids":["https://openalex.org/I127439422"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5045018479","https://openalex.org/A5062476988"],"corresponding_institution_ids":["https://openalex.org/I127439422"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1967,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.78215768,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"18","first_page":"3541","last_page":"3543"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9919000267982483,"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":0.9919000267982483,"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":0.002899999963119626,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0013000000035390258,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9758044481277466},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.7577099800109863},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5405157804489136},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.48430100083351135},{"id":"https://openalex.org/keywords/aptamer","display_name":"Aptamer","score":0.4236452579498291},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4219195246696472},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.377238392829895},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.345122754573822},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.2679561376571655},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25966745615005493},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.06310442090034485}],"concepts":[{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.9758044481277466},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.7577099800109863},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5405157804489136},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.48430100083351135},{"id":"https://openalex.org/C128972844","wikidata":"https://www.wikidata.org/wiki/Q418722","display_name":"Aptamer","level":2,"score":0.4236452579498291},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4219195246696472},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.377238392829895},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.345122754573822},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.2679561376571655},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25966745615005493},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.06310442090034485}],"mesh":[{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz093","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3541/48974980/bioinformatics_35_18_3541.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:30726866","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30726866","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz093","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3541/48974980/bioinformatics_35_18_3541.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/F4320320721","display_name":"Council of Scientific and Industrial Research, India","ror":"https://ror.org/021wm7p51"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2911461034.pdf"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1972708527","https://openalex.org/W2031318656","https://openalex.org/W2049912773","https://openalex.org/W2054613021","https://openalex.org/W2086561953","https://openalex.org/W2102619694","https://openalex.org/W2108230379","https://openalex.org/W2120172561","https://openalex.org/W2123732476","https://openalex.org/W2141152740","https://openalex.org/W2141857874","https://openalex.org/W2151957804","https://openalex.org/W2166409098","https://openalex.org/W2176355994","https://openalex.org/W2222032895","https://openalex.org/W2605443933","https://openalex.org/W2753038639","https://openalex.org/W2807561738","https://openalex.org/W4248288579"],"related_works":["https://openalex.org/W2967136651","https://openalex.org/W2033684641","https://openalex.org/W2913646003","https://openalex.org/W3151547568","https://openalex.org/W2918944057","https://openalex.org/W2769114003","https://openalex.org/W21023364","https://openalex.org/W2150147498","https://openalex.org/W2025010701","https://openalex.org/W1986504247"],"abstract_inverted_index":{"SUMMARY:":[0],"Riboswitches":[1],"are":[2],"cis-regulatory":[3],"non-coding":[4],"genomic":[5],"segments":[6],"that":[7,29,55],"control":[8],"the":[9,31,60,80],"expression":[10],"of":[11,26,63],"downstream":[12],"genes":[13],"by":[14],"undergoing":[15],"conformational":[16],"change":[17],"upon":[18],"ligand":[19],"binding.":[20],"We":[21],"present":[22],"a":[23,51],"comprehensive":[24],"database":[25],"prokaryotic":[27],"riboswitches":[28,36],"allows":[30],"user":[32],"to":[33],"search":[34],"for":[35,59],"using":[37],"multiple":[38],"criteria,":[39],"extract":[40],"information":[41],"about":[42],"riboswitch":[43],"location":[44],"and":[45,69],"gene/operon":[46],"it":[47],"regulates.":[48],"RiboD":[49,74],"provides":[50],"very":[52],"useful":[53],"resource":[54],"can":[56,75],"be":[57,76],"utilized":[58],"better":[61],"understanding":[62],"riboswitch-based":[64],"gene":[65],"regulation":[66],"in":[67],"bacteria":[68],"archaea.":[70],"AVAILABILITY":[71],"AND":[72],"IMPLEMENTATION:":[73],"freely":[77],"accessed":[78],"on":[79],"web":[81],"at":[82],"http://ribod.iiserkol.ac.in/.":[83]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4}],"updated_date":"2026-06-20T22:02:38.213706","created_date":"2025-10-10T00:00:00"}
