{"id":"https://openalex.org/W3013517780","doi":"https://doi.org/10.1093/bioinformatics/btaa221","title":"TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling","display_name":"TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling","publication_year":2020,"publication_date":"2020-03-26","ids":{"openalex":"https://openalex.org/W3013517780","doi":"https://doi.org/10.1093/bioinformatics/btaa221","mag":"3013517780","pmid":"https://pubmed.ncbi.nlm.nih.gov/32232442"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa221","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa221","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019275576","display_name":"Bilal El Houdaigui","orcid":"https://orcid.org/0000-0001-7021-8724"},"institutions":[{"id":"https://openalex.org/I48430043","display_name":"Institut National des Sciences Appliqu\u00e9es de Lyon","ror":"https://ror.org/050jn9y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I203339264","https://openalex.org/I48430043"]},{"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/I4210129159","display_name":"Laboratoire de Microbiologie, Adaptation et Pathog\u00e9nie","ror":"https://ror.org/03p3f6k20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210096427","https://openalex.org/I4210129159","https://openalex.org/I4210166400","https://openalex.org/I48430043","https://openalex.org/I67348948"]},{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Bilal El Houdaigui","raw_affiliation_strings":["Laboratoire de Microbiologie , Adaptation et Pathog\u00e9nie, CNRS UMR5240, Universit\u00e9 de Lyon, INSA Lyon, Universit\u00e9 Claude Bernard Lyon 1, 69621 Villeurbanne, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Microbiologie , Adaptation et Pathog\u00e9nie, CNRS UMR5240, Universit\u00e9 de Lyon, INSA Lyon, Universit\u00e9 Claude Bernard Lyon 1, 69621 Villeurbanne, France","institution_ids":["https://openalex.org/I4210129159","https://openalex.org/I100532134","https://openalex.org/I48430043","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038775097","display_name":"Sam Meyer","orcid":"https://orcid.org/0000-0001-7206-6226"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210129159","display_name":"Laboratoire de Microbiologie, Adaptation et Pathog\u00e9nie","ror":"https://ror.org/03p3f6k20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210096427","https://openalex.org/I4210129159","https://openalex.org/I4210166400","https://openalex.org/I48430043","https://openalex.org/I67348948"]},{"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/I48430043","display_name":"Institut National des Sciences Appliqu\u00e9es de Lyon","ror":"https://ror.org/050jn9y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I203339264","https://openalex.org/I48430043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sam Meyer","raw_affiliation_strings":["Laboratoire de Microbiologie , Adaptation et Pathog\u00e9nie, CNRS UMR5240, Universit\u00e9 de Lyon, INSA Lyon, Universit\u00e9 Claude Bernard Lyon 1, 69621 Villeurbanne, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Microbiologie , Adaptation et Pathog\u00e9nie, CNRS UMR5240, Universit\u00e9 de Lyon, INSA Lyon, Universit\u00e9 Claude Bernard Lyon 1, 69621 Villeurbanne, France","institution_ids":["https://openalex.org/I4210129159","https://openalex.org/I100532134","https://openalex.org/I48430043","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5038775097"],"corresponding_institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210129159","https://openalex.org/I48430043"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.03120843,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"36","issue":"12","first_page":"3899","last_page":"3901"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9997000098228455,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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":0.9986000061035156,"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/dna-supercoil","display_name":"DNA supercoil","score":0.7009849548339844},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.6311894655227661},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5248934030532837},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5111451745033264},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4947211444377899},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.4895687997341156},{"id":"https://openalex.org/keywords/coupling","display_name":"Coupling (piping)","score":0.48829030990600586},{"id":"https://openalex.org/keywords/rna-polymerase","display_name":"RNA polymerase","score":0.47040659189224243},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4672040343284607},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.42248719930648804},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39451438188552856},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3555047810077667},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.34214940667152405},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3402057886123657},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.1864001750946045},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18314874172210693},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08439800143241882},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08047646284103394}],"concepts":[{"id":"https://openalex.org/C158456008","wikidata":"https://www.wikidata.org/wiki/Q412639","display_name":"DNA supercoil","level":4,"score":0.7009849548339844},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.6311894655227661},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5248934030532837},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5111451745033264},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4947211444377899},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.4895687997341156},{"id":"https://openalex.org/C131584629","wikidata":"https://www.wikidata.org/wiki/Q4308705","display_name":"Coupling (piping)","level":2,"score":0.48829030990600586},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.47040659189224243},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4672040343284607},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.42248719930648804},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39451438188552856},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3555047810077667},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.34214940667152405},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3402057886123657},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.1864001750946045},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18314874172210693},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08439800143241882},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08047646284103394},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"mesh":[{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa221","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa221","pdf_url":null,"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:32232442","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32232442","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-03013609v1","is_oa":false,"landing_page_url":"https://hal.science/hal-03013609","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 (12), pp.3899-3901. &#x27E8;10.1093/bioinformatics/btaa221&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5978590546","display_name":null,"funder_award_id":"ANR-18-CE45-0006-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6886915936","display_name":null,"funder_award_id":"BQR 2016","funder_id":"https://openalex.org/F4320325604","funder_display_name":"Institut National des Sciences Appliqu\u00e9es de Lyon"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320325604","display_name":"Institut National des Sciences Appliqu\u00e9es de Lyon","ror":"https://ror.org/050jn9y42"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2003470745","https://openalex.org/W2046892161","https://openalex.org/W2078635599","https://openalex.org/W2146292423","https://openalex.org/W2165350191","https://openalex.org/W2166306420","https://openalex.org/W2407486174","https://openalex.org/W2461066986","https://openalex.org/W2952097502","https://openalex.org/W2953212034","https://openalex.org/W2963646665","https://openalex.org/W2965599833"],"related_works":["https://openalex.org/W2153953146","https://openalex.org/W1974325040","https://openalex.org/W2075284797","https://openalex.org/W4230120984","https://openalex.org/W4242141317","https://openalex.org/W4213252772","https://openalex.org/W2113343277","https://openalex.org/W23947072","https://openalex.org/W2025859988","https://openalex.org/W1515974038"],"abstract_inverted_index":{"TwisTranscripT":[0],"is":[1,7],"freely":[2],"available":[3],"at":[4],"https://github.com/sammeyer2017/TwisTranscripT.":[5],"It":[6],"implemented":[8],"in":[9],"Python3":[10],"and":[11,17],"supported":[12],"on":[13],"MacOS":[14],"X,":[15],"Linux":[16],"Windows.":[18]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
