{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T05:58:31Z","timestamp":1722837511025},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Fluorescent and luminescent reporter gene systems in combination with automated microplate readers allow real-time monitoring of gene expression on the population level at high precision and sampling density. This generates large amounts of data for the analysis of which computer tools are missing to date.<\/jats:p>\n               <jats:p>Results: We have developed WellReader, a MATLAB program for the analysis of fluorescent and luminescent reporter gene data. WellReader allows the user to load the output files of microplate readers, remove outliers, correct for background effects and smooth and fit the data. Moreover, it computes biologically relevant quantities from the measured signals, notably promoter activities and protein concentrations, and compares the resulting expression profiles of different genes under different conditions.<\/jats:p>\n               <jats:p>Availability: WellReader is available under a LGPL licence at http:\/\/prabi1.inrialpes.fr\/trac\/wellreader.<\/jats:p>\n               <jats:p>Contact: \u00a0hidde.de-jong@inria.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq016","type":"journal-article","created":{"date-parts":[[2010,1,24]],"date-time":"2010-01-24T01:24:07Z","timestamp":1264296247000},"page":"1262-1263","source":"Crossref","is-referenced-by-count":13,"title":["WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data"],"prefix":"10.1093","volume":"26","author":[{"given":"Fr\u00e9d\u00e9ric","family":"Boyer","sequence":"first","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]},{"given":"Bruno","family":"Besson","sequence":"additional","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]},{"given":"Guillaume","family":"Baptist","sequence":"additional","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"},{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]},{"given":"J\u00e9r\u00f4me","family":"Izard","sequence":"additional","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"},{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]},{"given":"Corinne","family":"Pinel","sequence":"additional","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"},{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]},{"given":"Delphine","family":"Ropers","sequence":"additional","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]},{"given":"Johannes","family":"Geiselmann","sequence":"additional","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"},{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]},{"given":"Hidde","family":"de Jong","sequence":"additional","affiliation":[{"name":"1 INRIA Grenoble\u2013Rh\u00f4ne-Alpes, 655 avenue de l'Europe, 38334 Saint Ismier Cedex and 2 Laboratoire Adaptation et Pathog\u00e9nie des Microorganismes (CNRS UMR 5163), Universit\u00e9 Joseph Fourier, B\u00e2timent Jean Roget, Domaine de la Merci, 38700 La Tronche, France"}]}],"member":"286","published-online":{"date-parts":[[2010,3,5]]},"reference":[{"key":"2023012508165705500_B1","doi-asserted-by":"crossref","first-page":"4470","DOI":"10.1073\/pnas.0500670102","article-title":"Quantitative kinetic analysis of the bacteriophage \u03bb genetic network","volume":"102","author":"Kobiler","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508165705500_B2","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1002\/bit.10295","article-title":"Differential rates of gene expression monitored by green fluorescent protein","volume":"79","author":"Lu","year":"2002","journal-title":"Biotechnol. Bioengin."},{"key":"2023012508165705500_B3","doi-asserted-by":"crossref","first-page":"4574","DOI":"10.1021\/es803227z","article-title":"Prokaryotic real-time gene expression profiling for toxicity assessment","volume":"43","author":"Onnis-Hayden","year":"2009","journal-title":"Environ. Sci. Technol."},{"key":"2023012508165705500_B4","doi-asserted-by":"crossref","first-page":"10555","DOI":"10.1073\/pnas.152046799","article-title":"Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics","volume":"99","author":"Ronen","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508165705500_B5","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/nmeth895","article-title":"A comprehensive library of fluorescent transcriptional reporters for Escherichia coli","volume":"3","author":"Zaslaver","year":"2006","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/9\/1262\/48854677\/bioinformatics_26_9_1262.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/9\/1262\/48854677\/bioinformatics_26_9_1262.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:17:21Z","timestamp":1674634641000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/9\/1262\/199010"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,3,5]]},"references-count":5,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2010,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq016","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,5,1]]},"published":{"date-parts":[[2010,3,5]]}}}