{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T11:52:11Z","timestamp":1776858731447,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010138","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000}}],"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2022,5,26]],"date-time":"2022-05-26T00:00:00Z","timestamp":1653523200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["PhD studentship"],"award-info":[{"award-number":["PhD studentship"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000275","name":"Leverhulme Trust","doi-asserted-by":"publisher","award":["RPG-2018-004"],"award-info":[{"award-number":["RPG-2018-004"]}],"id":[{"id":"10.13039\/501100000275","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Darwin Trust"},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/R001359\/1"],"award-info":[{"award-number":["BB\/R001359\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Responding to change is a fundamental property of life, making time-series data invaluable in biology. For microbes, plate readers are a popular, convenient means to measure growth and also gene expression using fluorescent reporters. Nevertheless, the difficulties of analysing the resulting data can be a bottleneck, particularly when combining measurements from different wells and plates. Here we present <jats:monospace>omniplate<\/jats:monospace>, a Python module that corrects and normalises plate-reader data, estimates growth rates and fluorescence per cell as functions of time, calculates errors, exports in different formats, and enables meta-analysis of multiple plates. The software corrects for autofluorescence, the optical density\u2019s non-linear dependence on the number of cells, and the effects of the media. We use <jats:monospace>omniplate<\/jats:monospace> to measure the Monod relationship for the growth of budding yeast in raffinose, showing that raffinose is a convenient carbon source for controlling growth rates. Using fluorescent tagging, we study yeast\u2019s glucose transport. Our results are consistent with the regulation of the hexose transporter (HXT) genes being approximately bipartite: the medium and high affinity transporters are predominately regulated by both the high affinity glucose sensor Snf3 and the kinase complex SNF1 via the repressors Mth1, Mig1, and Mig2; the low affinity transporters are predominately regulated by the low affinity sensor Rgt2 via the co-repressor Std1. We thus demonstrate that <jats:monospace>omniplate<\/jats:monospace> is a powerful tool for exploiting the advantages offered by time-series data in revealing biological regulation.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010138","type":"journal-article","created":{"date-parts":[[2022,5,26]],"date-time":"2022-05-26T17:54:16Z","timestamp":1653587656000},"page":"e1010138","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":19,"title":["Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2383-1483","authenticated-orcid":true,"given":"Luis Fernando","family":"Monta\u00f1o-Gutierrez","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1631-8430","authenticated-orcid":true,"given":"Nahuel Manzanaro","family":"Moreno","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8108-3498","authenticated-orcid":true,"given":"Iseabail L.","family":"Farquhar","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7427-3007","authenticated-orcid":true,"given":"Yu","family":"Huo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8811-4816","authenticated-orcid":true,"given":"Lucia","family":"Bandiera","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7489-8587","authenticated-orcid":true,"given":"Peter S.","family":"Swain","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,5,26]]},"reference":[{"issue":"7203","key":"pcbi.1010138.ref001","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1038\/454424a","article-title":"Life, logic and information","volume":"454","author":"P 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