{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:17:43Z","timestamp":1772173063863,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010488","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,9,22]],"date-time":"2022-09-22T00:00:00Z","timestamp":1663804800000}}],"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T00:00:00Z","timestamp":1662940800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["800945"],"award-info":[{"award-number":["800945"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007391","name":"Association pour la Recherche sur le Cancer","doi-asserted-by":"publisher","award":["PGA1 RF20170205342"],"award-info":[{"award-number":["PGA1 RF20170205342"]}],"id":[{"id":"10.13039\/100007391","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004099","name":"Ligue Contre le Cancer","doi-asserted-by":"publisher","award":["Comit\u00e9 Ile-de-France"],"award-info":[{"award-number":["Comit\u00e9 Ile-de-France"]}],"id":[{"id":"10.13039\/501100004099","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    The great advances of sequencing technologies allow the\n                    <jats:italic>in vivo<\/jats:italic>\n                    measurement of nuclear processes\u2014such as DNA repair after UV exposure\u2014over entire cell populations. However, data sets usually contain only a few samples over several hours, missing possibly important information in between time points. We developed a data-driven approach to analyse CPD repair kinetics over time in\n                    <jats:italic>Saccharomyces cerevisiae<\/jats:italic>\n                    . In contrast to other studies that consider sequencing signals as an average behaviour, we understand them as the superposition of signals from independent cells. By motivating repair as a stochastic process, we derive a minimal model for which the parameters can be conveniently estimated. We correlate repair parameters to a variety of genomic features that are assumed to influence repair, including transcription rate and nucleosome density. The clearest link was found for the transcription unit length, which has been unreported for budding yeast to our knowledge. The framework hence allows a comprehensive analysis of nuclear processes on a population scale.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1010488","type":"journal-article","created":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T13:43:14Z","timestamp":1662990194000},"page":"e1010488","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["A quantitative modelling approach for DNA repair on a population scale"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6667-4663","authenticated-orcid":true,"given":"Leo","family":"Zeitler","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3932-5294","authenticated-orcid":true,"given":"Cyril","family":"Denby Wilkes","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4139-247X","authenticated-orcid":true,"given":"Arach","family":"Goldar","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5218-2350","authenticated-orcid":true,"given":"Julie","family":"Soutourina","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,9,12]]},"reference":[{"issue":"3","key":"pcbi.1010488.ref001","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1080\/095530098141429","article-title":"Conservation of eukaryotic DNA repair mechanisms","volume":"74","author":"AR Lehmann","year":"1998","journal-title":"International journal of radiation biology"},{"issue":"10","key":"pcbi.1010488.ref002","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1038\/nsmb1152","article-title":"Rad4\u2013Rad23 interaction with SWI\/SNF links ATP-dependent chromatin remodeling with nucleotide excision 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