{"id":"https://openalex.org/W2113221971","doi":"https://doi.org/10.1093/bioinformatics/btu335","title":"RiboMaker: computational design of conformation-based riboregulation","display_name":"RiboMaker: computational design of conformation-based riboregulation","publication_year":2014,"publication_date":"2014-05-09","ids":{"openalex":"https://openalex.org/W2113221971","doi":"https://doi.org/10.1093/bioinformatics/btu335","mag":"2113221971","pmid":"https://pubmed.ncbi.nlm.nih.gov/24833802"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu335","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/17/2508/48927603/bioinformatics_30_17_2508.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/30/17/2508/48927603/bioinformatics_30_17_2508.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024253813","display_name":"Guillermo Rodrigo","orcid":"https://orcid.org/0000-0002-1871-9617"},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]},{"id":"https://openalex.org/I4210101231","display_name":"Institut de Biologie syst\u00e9mique et synth\u00e9tique","ror":"https://ror.org/018r7pa17","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210101231","https://openalex.org/I88467170"]}],"countries":["FR","GB"],"is_corresponding":true,"raw_author_name":"Guillermo Rodrigo","raw_affiliation_strings":["1 \u00a01Institute of Systems and Synthetic Biology, CNRS - Universit\u00e9 d\u2019\u00c9vry Val d\u2019Essonne, F-91000 \u00c9vry, France and 2School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom"],"affiliations":[{"raw_affiliation_string":"1 \u00a01Institute of Systems and Synthetic Biology, CNRS - Universit\u00e9 d\u2019\u00c9vry Val d\u2019Essonne, F-91000 \u00c9vry, France and 2School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362","https://openalex.org/I88467170","https://openalex.org/I4210101231","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040063355","display_name":"Alfonso Jaramillo","orcid":"https://orcid.org/0000-0002-6313-9689"},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]},{"id":"https://openalex.org/I4210101231","display_name":"Institut de Biologie syst\u00e9mique et synth\u00e9tique","ror":"https://ror.org/018r7pa17","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I277688954","https://openalex.org/I4210096427","https://openalex.org/I4210101231","https://openalex.org/I88467170"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR","GB"],"is_corresponding":true,"raw_author_name":"Alfonso Jaramillo","raw_affiliation_strings":["1 \u00a01Institute of Systems and Synthetic Biology, CNRS - Universit\u00e9 d\u2019\u00c9vry Val d\u2019Essonne, F-91000 \u00c9vry, France and 2School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom"],"affiliations":[{"raw_affiliation_string":"1 \u00a01Institute of Systems and Synthetic Biology, CNRS - Universit\u00e9 d\u2019\u00c9vry Val d\u2019Essonne, F-91000 \u00c9vry, France and 2School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom","institution_ids":["https://openalex.org/I39555362","https://openalex.org/I88467170","https://openalex.org/I4210101231","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024253813","https://openalex.org/A5040063355"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I39555362","https://openalex.org/I4210101231","https://openalex.org/I88467170"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.6732,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.83927083,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"17","first_page":"2508","last_page":"2510"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976000189781189,"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":0.9976000189781189,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9918000102043152,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9807999730110168,"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":0.6176738739013672},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41466110944747925},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32956281304359436},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16655674576759338}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6176738739013672},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41466110944747925},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32956281304359436},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16655674576759338}],"mesh":[{"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":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020121","descriptor_name":"5' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu335","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/17/2508/48927603/bioinformatics_30_17_2508.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:24833802","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24833802","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/btu335","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu335","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/17/2508/48927603/bioinformatics_30_17_2508.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/F4320338366","display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113221971.pdf","grobid_xml":"https://content.openalex.org/works/W2113221971.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1988072594","https://openalex.org/W2009818318","https://openalex.org/W2016066165","https://openalex.org/W2020350008","https://openalex.org/W2024060531","https://openalex.org/W2044886350","https://openalex.org/W2045295945","https://openalex.org/W2047360542","https://openalex.org/W2052019888","https://openalex.org/W2059557910","https://openalex.org/W2073936141","https://openalex.org/W2074494141","https://openalex.org/W2074565201","https://openalex.org/W2078791724","https://openalex.org/W2083244446","https://openalex.org/W2087948018","https://openalex.org/W2088482084","https://openalex.org/W2088631531","https://openalex.org/W2096326044","https://openalex.org/W2098508116","https://openalex.org/W2101165625","https://openalex.org/W2102699655","https://openalex.org/W2114099042","https://openalex.org/W2119340328","https://openalex.org/W2125615424","https://openalex.org/W2142008033","https://openalex.org/W2148339059","https://openalex.org/W2150882562","https://openalex.org/W2154952425","https://openalex.org/W2160479378","https://openalex.org/W2162371815","https://openalex.org/W2167117443"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"Web":[0],"server":[1],"is":[2],"available":[3,13],"at":[4,16],"http://ribomaker.jaramillolab.org/.":[5],"Source":[6],"code,":[7],"instructions":[8],"and":[9],"examples":[10],"are":[11],"freely":[12],"for":[14],"download":[15],"http://sourceforge.net/projects/ribomaker/.":[17]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
