{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T02:57:33Z","timestamp":1780109853394,"version":"3.54.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,3,31]],"date-time":"2020-03-31T00:00:00Z","timestamp":1585612800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100009081","name":"INSA Lyon","doi-asserted-by":"publisher","award":["BQR 2016"],"award-info":[{"award-number":["BQR 2016"]}],"id":[{"id":"10.13039\/501100009081","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-18-CE45-0006-01"],"award-info":[{"award-number":["ANR-18-CE45-0006-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Transcription and DNA supercoiling are involved in a complex, dynamical and non-linear coupling that results from the basal interaction between DNA and RNA polymerase. We present the first software to simulate this coupling, applicable to a wide range of bacterial organisms. TwisTranscripT allows quantifying its contribution in global transcriptional regulation, and provides a mechanistic basis for the widely observed, evolutionarily conserved and currently unexplained co-regulation of adjacent operons that might play an important role in genome evolution.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TwisTranscripT is freely available at https:\/\/github.com\/sammeyer2017\/TwisTranscripT. It is implemented in Python3 and supported on MacOS X, Linux and Windows.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa221","type":"journal-article","created":{"date-parts":[[2020,3,26]],"date-time":"2020-03-26T12:12:22Z","timestamp":1585224742000},"page":"3899-3901","source":"Crossref","is-referenced-by-count":2,"title":["TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling"],"prefix":"10.1093","volume":"36","author":[{"given":"Bilal","family":"El Houdaigui","sequence":"first","affiliation":[{"name":"Laboratoire de Microbiologie , Adaptation et Pathog\u00e9nie, CNRS UMR5240, Universit\u00e9 de Lyon, INSA Lyon, Universit\u00e9 Claude Bernard Lyon 1, 69621 Villeurbanne, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7206-6226","authenticated-orcid":false,"given":"Sam","family":"Meyer","sequence":"additional","affiliation":[{"name":"Laboratoire de Microbiologie , Adaptation et Pathog\u00e9nie, CNRS UMR5240, Universit\u00e9 de Lyon, INSA Lyon, Universit\u00e9 Claude Bernard Lyon 1, 69621 Villeurbanne, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,3,31]]},"reference":[{"key":"2023063011473480400_btaa221-B1","doi-asserted-by":"crossref","first-page":"018101","DOI":"10.1103\/PhysRevLett.117.018101","article-title":"Stochastic model of supercoiling-dependent transcription","volume":"117","author":"Brackley","year":"2016","journal-title":"Phys. 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